title: BRCA1-non-mutated_triple_negative_breast_cancer_sample4


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample7

status: Public on Dec 10 2015

type: genomic

city: GOSSELIES

first: SEBASTIEN

last: TOFFOLI

address: AVENUE GEORGES LEMAITRE 25

country: Belgium

institute: IPG

scan_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3. Agilent type C scanner (G2505C - DNA microarray scanner with surescan high-resolution technology) was used with the Agilent Scan Control software (Version A.8.4.1).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used for data extraction.  Agilent Genomic Workbench (Version 7.0) was used to analyse the data (Z-score, threshold 0.2)

molecule: genomic DNA

organism: Homo sapiens

source_name: BRCA1-non-mutated triple negative breast cancer

tag: gender

value: Female

tag: tissue

value: Breast cancer

tag: tumour type

source_name: Pooled gDNA 7 women

tag: reference

value: normal pooled gDNA 7 women

value: Lymphocyte


title: CD4 DC injected mice,rep1

type: RNA

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

country: France

institute: CNRS

description: DC-induced spleen CD4+

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on the Affymetrix® MG-430 PM Array Strip. StripChips were washed and stained on the fluidic station of the Affymetrix GeneAtlas system with HWS kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas scanner.

data_processing: Data were generated with Affymetrix Expression Console v 1.2.1 and GCRMA algorithm

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Spleen DBA/1 DC-injected

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneAtlas IVT Express protocol from 100 ng total RNA (GeneAtlas 3'IVT ExpressTechnical Manual, 2010, P/N702833 Rev4 Affymetrix).

growth_protocol: Mice were repetitively injected intraperitonealy with immature dendritic cells (0.5 x 106), day -7, -5 and -3, before their euthanasia. Splenocytes from DC vaccinated mice were recovered by filtration on cell strainer, washed and CD4+ cells were purified by negative selection using Dynabeads. Cells were stained with anti-CD4, anti-CD49b and anti-CD25 conjugated antibodies and cell sorting was performed on FACSAria

extract_protocol: Rneasy Micro-kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: We determined the differential transcriptional profile associated with DC-vaccination protocol using the comparative analysis of CD4+ cells isolated from non-injected and DC-injected mice. The transcriptional profile of DC-induced CD25+ and CD49b+ include both the transcriptional profile associated with the cell subset and the DC-vaccination induced transcripts.

tag: cell type

value: spleen CD4+

tag: treatment

value: DC-induced


title: CHO-K1-FERM-8-SF-HOST-D1

city: Vienna

first: Gerald

last: Klanert

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Biotechnology

hyb_protocol: Slides were hybridized over night at 56°C in a Tecan HS 400 hybridization station, followed by automated washing and drying with nitrogen (Tecan, Austria).

scan_protocol: Immediately after drying, arrays were scanned using the Roche Nimblegen MS200 scanner (Roche, Germany) at 10 µM resolution and auto-gain settings.

data_processing: Feature extraction from the generated images was performed using GenePix 4.1 (Molecular Devices, Sunnyvale,CA). The resulting GPR-files were processed in R/Bioconductor using the LIMMA package (Ritchie et al., 2015). Raw data of previously published arrays (Gene Expression Omnibus accession number: GSE52994) was compiled with the here generated data for jointly analysis. Global LOESS normalization and Normexp background correction were performed, and the log2-fold changes of the miRNAs were calculated against the common reference pool (LogFC) for each array. To be considered expressed, the average probe intensity had to exceed the average background intensity plus two times the standard deviation. The probe’s validity was reviewed by updating the corresponding miRNA accessions to miRBase v21.

organism: Cricetulus griseus

source_name: Chinese hamster ovary cell line, 24 hours post seeding

label_protocol: End-labeling of 800 ng of total RNA was performed using the Exiqon Power Labeling Kit (Exiqon, Denmark) together with synthetic spike-in controls according to the instructions by the manufacturer.

growth_protocol: All CHO cell lines were cultivated at 37 °C, 7% CO2 and humidified atmosphere. K1-STAT-4-FCS-HOST (CHO-K1, ECACC-CCL61) and DUKXB11-STAT-4-FCS-HOST (CHO-DUKXB11, ATCC CRL-9096) were grown in DMEM/Ham’s F12 media (1:1, Merck KGaA, Darmstadt, Germany) supplied with 5% fetal calf serum (GE Healthcare, Little Chalfont, UK) and 4 mM L-Gln. DUKXB11-STAT-4-FCS-HOST cells were additionally supplied with 1x hypoxanthine/thymidine (HT) supplement (Thermo Fisher Scientific, Waltham, MA). DUKXB11-SHAKE-4-SF-HOST (suspension and serum-free adapted CHO-DUKXB11) cells were cultivated in DMEM/Ham’s F12 (1:1), supplemented with 4 mM L-Gln, 0.25% soy peptone, 0.1% Pluronic F68 (BASF, Germany), 1x protein free supplement (Polymun Scientific, Austria) and 1x HT supplement. K1-SHAKE-8-SF-HOST/K1-FERM-8-SF-HOST (suspension and serum-free adapted CHO-K1), K1-SHAKE-0-SF-HOST/K1-FERM-0-SF-HOST (suspension, serum-free and L-Gln-free adapted CHO-K1), S-SHAKE-8-SF-HOST (CHO-S), DUKXB11-SHAKE-0-SF-PROD/DUKXB11-FERM-0-SF-PROD-M17/DUKXB11-0-SF-FERM-PROD-MNC (recombinant suspension and serum-free adapted CHO-DUKXB11, producing an Erythropoietin-Fc fusion protein) were grown in CD CHO (Thermo Fisher Scientific), supplemented with 1x Anti-Clumping Agent (Thermo Fisher Scientific). K1-SHAKE-8-SF-HOST/K1-FERM-8-SF-HOST and S-SHAKE-8-SF-HOST were additionally supplied with 8 mM L-Gln. DUKXB11-SHAKE-0-SF-PROD, DUKXB11-FERM-0-SF-PROD-M17 and DUKXB11-0-SF-FERM-PROD-MNC cells were supplied with 0.19 µM methotrexate. DUKXB11-FERM-0-SF-PROD-M17 additionally harbours a vector overexpressing miR-17, while DUKXB11-FERM-0-SF-PROD-MNC harbours an empty vector control. DUKXB11-SHAKE-4-SF-HOST, K1-SHAKE-8-SF-HOST, K1-SHAKE-0-SF-HOST, S-SHAKE-8-SF-HOST and DUKXB11-SHAKE-0-SF-PROD were cultivated in shaker flasks at 140 revolutions per minute and a 25 mm shaking diameter. K1-FERM-8-SF-HOST, K1-FERM-0-SF-HOST, DUKXB11-FERM-0-SF-PROD-M17 and DUKXB11-FERM-0-SF-PROD-MNC were cultivated in  DASGIP bioreactor system (DASGIP AG, Jülich, Germany) controlled by DASGIP Control 4.0 software with similar settings as described before (Taschwer et al., 2012). Briefly, advanced spinners vessels used for the cultivation with 800 ml working volume and magnetic drive and pitch blade impellers for constant stirring (80 rpm). Temperature was maintained at 37 °C, constant 30% oxygen concentration was held via probe (Broadley James Oxyprobe) by air saturation and neutral pH (Mettler Toledo) was regulated with 0.5 M NaOH and CO2.

extract_protocol: RNA was extracted using the phenol-chloroform extraction method. Adherent CHO cell lines were washed with PBS and detached using Trypsin. Adherent and suspension cells were collected by centrifugation and lysed using TRI reagent (Sigma- Aldrich, St. Louis, MO). RNA isolation was performed according to the manufacturer’s recommendations. In brief, phase separation was conducted by the addition of chloroform, and the aqueous phase was collected. After centrifugation and washing with 2-Propanol and 70 % Ethanol, RNA pellets were air-dried, and resuspended in nuclease-free water (NFW). For quantity and purity estimation, absorbances at 230, 260 and 280 nm were measured using a NanoDrop ND-1000 UV-Vis Spectrophotometer (Thermo Fisher Scientific). Total RNA quality was assessed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using the RNA 6000 Nano Kit (Agilent Technologies). Only RNA with a RNA integrity number (RIN) > 7 were used for microarray hybridization.

treatment_protocol: No treatments were performed

tag: cho cell line

value: CHO-K1 host suspension, serum-free

tag: cultivation; growth phase

value: Fermenter stirred; exponential

tag: growth rate

source_name: Chinese hamster ovary cell pool

value: DUKXB-11, CHO-K1, CHO-S

tag: growth phase

value: not applicable


title: CTRL 1 Control Tissue

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

country: USA

institute: THE JACKSON LABORATORY

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R, log2 transformed and filtered for probes with bad detection p-values in all samples.

source_name: control tissue

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Tissues were lysed using Tissue Lyser (Qiagen). RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: age

value: 8 weeks

value: Tissue

tag: replicate

value: control


title: CHO-K1-FERM-8-SF-HOST-D8

source_name: Chinese hamster ovary cell line, 192 hours post seeding

value: Fermenter stirred; decline


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample1

hyb_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3


title: CD4 Naive mice,rep1

description: ex-vivo spleen CD4+

source_name: Spleen DBA/1 naive

value: naive


title: CHO-K1-FERM-0-SF-HOST-D8

value: CHO-K1 host suspension, serum-free, L-glutamine-free


title: BRCA1-mutated_triple_negative_breast_cancer_sample23

source_name: BRCA1-mutated triple negative breast cancer

label_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3


title: E12-4 uterine microenvironment at Day 12 after fertilization

description: replicate 4

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: days after fertilization


title: E12-3 uterine microenvironment at Day 12 after fertilization

description: replicate 3


title: BRCA1-mutated_triple_negative_breast_cancer_sample20

extract_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3


title: BRCA1-mutated_triple_negative_breast_cancer_sample18


title: E12-5 uterine microenvironment at Day 12 after fertilization

description: replicate 5


title: E12-2 uterine microenvironment at Day 12 after fertilization

description: replicate 2


title: BRCA1-mutated_triple_negative_breast_cancer_sample16


title: BRCA1-mutated_triple_negative_breast_cancer_sample13


title: BRCA1-mutated_triple_negative_breast_cancer_sample14


title: BRCA1-mutated_triple_negative_breast_cancer_sample12


title: BRCA1-mutated_triple_negative_breast_cancer_sample22


title: CHO-K1-FERM-8-SF-HOST-D7

source_name: Chinese hamster ovary cell line, 168 hours post seeding

value: Fermenter stirred; stationary


title: BRCA1-mutated_triple_negative_breast_cancer_sample15

value: Female


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample2

value: Breast cancer


title: E11-4 uterine microenvironment at Day 11 after fertilization

description: replicate 4


title: E12-1 uterine microenvironment at Day 12 after fertilization

description: replicate 1


title: BRCA1-mutated_triple_negative_breast_cancer_sample19

value: normal pooled gDNA 7 women


title: E11-3 uterine microenvironment at Day 11 after fertilization

description: replicate 3


title: BRCA1-mutated_triple_negative_breast_cancer_sample17

value: Lymphocyte


title: BRCA1-mutated_triple_negative_breast_cancer_sample11


title: CHO-K1-FERM-0-SF-HOST-D4

source_name: Chinese hamster ovary cell line, 96 hours post seeding


title: BRCA1-mutated_triple_negative_breast_cancer_sample21


title: CHO-K1-FERM-0-SF-HOST-D1


title: CHO-K1-FERM-0-SF-HOST-D6

source_name: Chinese hamster ovary cell line, 144 hours post seeding


title: CHO-K1-FERM-8-SF-HOST-D6


title: BRCA1-mutated_triple_negative_breast_cancer_sample10


title: CHO-DUKXB11-FERM-0-SF-PROD-MNC-D5

source_name: Chinese hamster ovary cell line, 120 hours post seeding

value: DUKXB11 recombinant engineered suspension, serum-free, L-glutamine-free


title: E11-2 uterine microenvironment at Day 11 after fertilization

description: replicate 2


title: CHO-K1-FERM-8-SF-HOST-D4


title: E11-1 uterine microenvironment at Day 11 after fertilization

description: replicate 1


title: CHO-DUKXB11-FERM-0-SF-PROD-MNC-D9

source_name: Chinese hamster ovary cell line, 216 hours post seeding


title: CHO-K1-FERM-0-SF-HOST-D7


title: CHO-DUKXB11-FERM-0-SF-PROD-M17-D3

source_name: Chinese hamster ovary cell line, 72 hours post seeding


title: BRCA1-mutated_triple_negative_breast_cancer_sample6


title: BRCA1-mutated_triple_negative_breast_cancer_sample5


title: E10-2 uterine microenvironment at Day 10 after fertilization

description: replicate 2


title: E10-4 uterine microenvironment at Day 10 after fertilization

description: replicate 4


title: BRCA1-mutated_triple_negative_breast_cancer_sample7


title: BRCA1-mutated_triple_negative_breast_cancer_sample8


title: E10-3 uterine microenvironment at Day 10 after fertilization

description: replicate 3


title: BRCA1-mutated_triple_negative_breast_cancer_sample3


title: CHO-DUKXB11-FERM-0-SF-PROD-MNC-D1


title: BRCA1-mutated_triple_negative_breast_cancer_sample4


title: BRCA1-mutated_triple_negative_breast_cancer_sample9


title: E10-1 uterine microenvironment at Day 10 after fertilization

description: replicate 1


title: E8-4 uterine microenvironment at Day 8 after fertilization

description: replicate 4


title: BRCA1-mutated_triple_negative_breast_cancer_sample2


title: BRCA1-mutated_Luminal_A_breast_cancer_sample6

source_name: BRCA1-mutated Luminal A breast cancer

value: Non-triple-negative


title: BRCA1-mutated_Luminal_A_breast_cancer_sample9


title: BRCA1-mutated_Luminal_A_breast_cancer_sample7


title: BRCA1-mutated_HER2-positive_breast_cancer_sample5

source_name: BRCA1-mutated HER2-positive breast cancer


title: BRCA1-mutated_Luminal_A_breast_cancer_sample4


title: BRCA1-mutated_Luminal_A_breast_cancer_sample3


title: E8-3 uterine microenvironment at Day 8 after fertilization

description: replicate 3


title: CHO-DUKXB11-FERM-0-SF-PROD-M17-D5


title: BRCA1-mutated_triple_negative_breast_cancer_sample1


title: CHO-DUKXB11-FERM-0-SF-PROD-M17-D1


title: E8-2 uterine microenvironment at Day 8 after fertilization

description: replicate 2


title: CHO-DUKXB11-FERM-0-SF-PROD-MNC-D3


title: CHO-DUKXB11-FERM-0-SF-PROD-MNC-D7


title: CHO-DUKXB11-FERM-0-SF-PROD-M17-D9


title: BRCA1-mutated_Luminal_A_breast_cancer_sample8


title: CHO-DUKXB11-FERM-0-SF-PROD-M17-D7


title: CHO-DUKXB11-ADH-4-FCS-HOST-D2-R2

source_name: Chinese hamster ovary cell line, 48 hours post seeding

value: DUKXB11 host adherent

value: T-flask static; exponential


title: Luminal_B_breast_cancer_sample21

source_name: Luminal B breast cancer

value: Luminal B

source_name: Pooled gDNA 7 women


title: E6-5 uterine microenvironment at Day 6 after fertilization

description: replicate 5


title: CHO-DUKXB11-ADH-4-FCS-HOST-D2-R1

value: DUKXB-11, CHO-K1, CHO-S

value: not applicable


title: E6-6 uterine microenvironment at Day 6 after fertilization

description: replicate 6

value: 8 weeks

value: Tissue


title: E6-3 uterine microenvironment at Day 6 after fertilization

description: replicate 3


title: BRCA1-mutated_Luminal_A_breast_cancer_sample1


title: Luminal_B_breast_cancer_sample18


title: Luminal_B_breast_cancer_sample22


title: Luminal_B_breast_cancer_sample20


title: BRCA1-mutated_HER2-positive_breast_cancer_sample2


title: E6-4 uterine microenvironment at Day 6 after fertilization

description: replicate 4


title: Luminal_B_breast_cancer_sample19


title: Luminal_B_breast_cancer_sample15


title: Luminal_B_breast_cancer_sample16


title: Luminal_B_breast_cancer_sample17


title: Luminal_B_breast_cancer_sample13


title: E6-2 uterine microenvironment at Day 6 after fertilization

description: replicate 2


title: Luminal_B_breast_cancer_sample11


title: CHO-DUKXB11-SHAKE-4-SF-HOST-D2-R2

value: DUKXB11 host suspension, serum-free

value: Shaker flask shaken; exponential


title: Luminal_B_breast_cancer_sample10


title: Luminal_B_breast_cancer_sample12


title: Luminal_B_breast_cancer_sample14


title: E6-1 uterine microenvironment at Day 6 after fertilization

description: replicate 1


title: CHO-DUKXB11-SHAKE-4-SF-HOST-D2-R1


title: Luminal_B_breast_cancer_sample9


title: CHO-S-SHAKE-8-SF-HOST-D2-R2

value: CHO-S host suspension


title: CHO-DUKXB11-SHAKE-0-SF-PROD-D2-R2

value: DUKXB11 recombinant suspension, serum-free, L-glutamine-free


title: CHO-S-SHAKE-8-SF-HOST-D2-R1


title: Luminal_B_breast_cancer_sample8

value: Female


title: Luminal_B_breast_cancer_sample7

value: Breast cancer


title: CHO-DUKXB11-SHAKE-0-SF-PROD-D2-R1


title: E4-3 uterine microenvironment at Day 4 after fertilization

description: replicate 3


title: E4-4 uterine microenvironment at Day 4 after fertilization

description: replicate 4


title: CHO-K1-ADH-4-FCS-HOST-2-D3-R1-2

value: CHO-K1 host adherent


title: CTRL 6 uterus from non pregnant mice

description: replicate 6

value: non pregnant


title: Luminal_B_breast_cancer_sample1

value: normal pooled gDNA 7 women

value: Lymphocyte


title: Luminal_A_breast_cancer_sample16

source_name: Luminal A breast cancer

value: Luminal A


title: Luminal_A_breast_cancer_sample19


title: CTRL 4 uterus from non pregnant mice

description: replicate 4


title: Luminal_A_breast_cancer_sample18


title: CHO-K1-ADH-4-FCS-HOST-2-D3-R1-1

value: T-flask static; exponential

source_name: Chinese hamster ovary cell pool


title: E4-2 uterine microenvironment at Day 4 after fertilization

description: replicate 2


title: Luminal_B_breast_cancer_sample5

value: Luminal B


title: E4-1 uterine microenvironment at Day 4 after fertilization

description: replicate 1


title: Luminal_B_breast_cancer_sample3


title: Luminal_A_breast_cancer_sample17


title: Luminal_B_breast_cancer_sample2


title: Luminal_B_breast_cancer_sample4


title: Luminal_B_breast_cancer_sample6


title: Luminal_A_breast_cancer_sample14


title: CTRL 3 uterus from non pregnant mice

description: replicate 3


title: Luminal_A_breast_cancer_sample20


title: Luminal_A_breast_cancer_sample15


title: CHO-K1-ADH-4-FCS-HOST-2-D3-R1-3

value: DUKXB-11, CHO-K1, CHO-S


title: CHO-K1-ADH-4-FCS-HOST-2-D3-R2

value: not applicable


title: Luminal_A_breast_cancer_sample13


title: CHO-K1-SHAKE-8-SF-HOST-D2-R2-2

value: CHO-K1 host suspension, serum-free


title: Luminal_A_breast_cancer_sample12


title: CTRL 5 uterus from non pregnant mice

description: replicate 5

value: 8 weeks

value: Tissue


title: CHO-K1-SHAKE-8-SF-HOST-D2-R1-2

value: Shaker flask shaken; exponential


title: CHO-K1-SHAKE-0-SF-HOST-1-D2-R2

value: CHO-K1 host suspension, serum-free, L-glutamine-free


title: CTRL 2 uterus from non pregnant mice

description: replicate 2


title: Luminal_A_breast_cancer_sample10


title: Luminal_A_breast_cancer_sample11


title: CHO-K1-SHAKE-8-SF-HOST-D2-R1-1


title: CTRL 1 uterus from non pregnant mice

description: replicate 1


title: CHO-K1-ADH-4-FCS-HOST-1-D2-R2


title: Luminal_A_breast_cancer_sample8


title: Luminal_A_breast_cancer_sample4


title: Luminal_A_breast_cancer_sample9


title: Luminal_A_breast_cancer_sample7


title: Luminal_A_breast_cancer_sample5


title: E12_PC61-4 uterus from PC61 treated pregnant mice at Day 12 after fertilization

tag: development stage


title: CHO-K1-SHAKE-0-SF-HOST-1-D2-R1


title: Luminal_A_breast_cancer_sample6


title: CHO-K1-SHAKE-0-SF-HOST-4-D2-R2


title: Luminal_A_breast_cancer_sample2


title: Luminal_A_breast_cancer_sample1


title: Luminal_A_breast_cancer_sample3


title: E12_PBS-5 uterus from PBS treated pregnant mice at Day 12 after fertilization


title: E12_PC61-1 uterus from PC61 treated pregnant mice at Day 12 after fertilization


title: CHO-K1-SHAKE-0-SF-HOST-3-D2-R2


title: HER2-positive_breast_cancer_sample21

source_name: HER2-positive breast cancer


title: E12_PC61-3 uterus from PC61 treated pregnant mice at Day 12 after fertilization


title: E12_PC61-2 uterus from PC61 treated pregnant mice at Day 12 after fertilization


title: HER2-positive_breast_cancer_sample19


title: E12_PBS-3 uterus from PBS treated pregnant mice at Day 12 after fertilization


title: HER2-positive_breast_cancer_sample20


title: HER2-positive_breast_cancer_sample17


title: HER2-positive_breast_cancer_sample18


title: HER2-positive_breast_cancer_sample15


title: CHO-K1-SHAKE-0-SF-HOST-2-D2-R1


title: HER2-positive_breast_cancer_sample16


title: E12_PBS-4 uterus from PBS treated pregnant mice at Day 12 after fertilization


title: CHO-K1-SHAKE-0-SF-HOST-2-D2-R2


title: E12_PBS-2 uterus from PBS treated pregnant mice at Day 12 after fertilization


title: CHO-K1-SHAKE-0-SF-HOST-4-D2-R1


title: CHO-K1-SHAKE-0-SF-HOST-3-D2-R1


title: HER2-positive_breast_cancer_sample14


title: HER2-positive_breast_cancer_sample13


title: E12_PBS-1 uterus from PBS treated pregnant mice at Day 12 after fertilization


title: HER2-positive_breast_cancer_sample11


title: HER2-positive_breast_cancer_sample10


title: CHO-K1-SHAKE-8-SF-HOST-D2-R2-1


title: HER2-positive_breast_cancer_sample8


title: CHO-K1-ADH-4-FCS-HOST-1-D2-R1


title: NP4 Uterus from non pregnant mice

source_name: Non pregnant 4

value: non pregnant mice


title: HER2-positive_breast_cancer_sample7

value: Female


title: E8-1 uterine microenvironment at Day 8 after fertilization

description: replicate 1


title: NP3 Uterus from non pregnant mice

source_name: Non pregnant 3


title: HER2-positive_breast_cancer_sample9

value: Breast cancer


title: HER2-positive_breast_cancer_sample12


title: NP2 Uterus from non pregnant mice

source_name: Non pregnant 2


title: HER2-positive_breast_cancer_sample6


title: HER2-positive_breast_cancer_sample5


title: HER2-positive_breast_cancer_sample1


title: shETV4-#2_rep3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Affymetrix Human Genome U133A 2.0 Array following the Affymetrix standard protocol.

scan_protocol: Affymetrix GeneChip Scanner 7G.

data_processing: Expression Console was used to generate the RMA file.

source_name: H1975 cells, shshETV4, 24h hypoxia

label_protocol: Ambion MessageAmp Premier Kit.

growth_protocol: H1975 lung cancer cells with stable knockdown of ACC1, ACLY or ETV4 after 24 hours of serum starvation (0.5% FBS) followed by 24 hours of hypoxia (1% O2).

extract_protocol: RNA was extracted with QIAGEN's RNeasy Mini Kit.

treatment_protocol: Cells in 10cm dishes were serum starved for 24 hours, then transferred to 1% oxygen for an additional 24 hours. Immediately washed with cold PBS, scraped, and frozen at -80C.

tag: cell line

value: lung cancer cells

tag: shRNA

tag: growth condition

value: hypoxia for 24hr


title: NP1 Uterus from non pregnant mice

source_name: Non pregnant 1

tag: tissue


title: HER2-positive_breast_cancer_sample2

tag: gender

tag: tumour type

value: normal pooled gDNA 7 women


title: HER2-positive_breast_cancer_sample4

tag: reference

value: Lymphocyte


title: shETV4-#2_rep2

tag: cell type


title: shETV4-#1_rep3


title: day3 Chaf1a knockdown Rep3

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: Day 3 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Chaf1a knockdown replicate 3

hyb_protocol: Following fragmentation,  3.5 ug of cDNA were hybridized for 16 hr at 45 C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.

molecule: polyA RNA

source_name: OKSM reprogramming intermediates

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA using amplification kit WT PLUS, followed by labeling 5.5 ug cDNA using kit Affymetrix Fragmentation and Labeling kit.

growth_protocol: Reprogrammable MEFs were grown in standard ESC medium (DMEM containing 15% serum and 1,000 U/ml LIF)

extract_protocol: Total RNA was extracted with Qiagen Rneasy mini kit

treatment_protocol: Reprogrammable MEFs were infected with retroviral CAF-1 or Renilla shRNA vectors and induced with doxycycline to induce OKSM expression for 3 or 6 days

value: Mouse Embryonic Fibroblasts

value: E13.5 embryos

tag: genotype

value: Col1a1::tetOP-OKSM ; R26-M2rtTA

tag: time

value: day 3

tag: protocol

value: Chaf1a knockdown


title: day6 renilla control Rep3

description: Day 6 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Renilla control replicate 3

value: day 6

value: Renilla control


title: day6 Chaf1a knockdown Rep3

description: Day 6 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Chaf1a knockdown replicate 3


title: day6 Chaf1a knockdown Rep2

description: Day 6 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Chaf1a knockdown replicate 2


title: shETV4-#2_rep1


title: HER2-positive_breast_cancer_sample3


title: day3 renilla control Rep3

description: Day 3 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Renilla control replicate 3


title: day6 renilla control Rep2

description: Day 6 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Renilla control replicate 2


title: NP5 Uterus from non pregnant mice

source_name: Non pregnant 5

value: 8 weeks

value: Tissue


title: shETV4-#1_rep2


title: shETV4-#1_rep1


title: day3 renilla control Rep2

description: Day 3 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Renilla control replicate 2


title: shScramble_rep4

description: SCR-D

source_name: H1975 cells, shScramble, 24h hypoxia

value: scramble


title: day3 renilla control Rep1

description: Day 3 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Renilla control replicate 1


title: day6 Chaf1a knockdown Rep1

description: Day 6 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Chaf1a knockdownl replicate 1


title: day3 Chaf1a knockdown Rep1

description: Day 3 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Chaf1a knockdown replicate 1


title: day6 renilla control Rep1

description: Day 6 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Renilla control replicate 1


title: shScramble_rep5

description: SCR-E


title: shScramble_rep3

description: SCR-C


title: shACLY-#2_rep3

source_name: H1975 cells, shshACLY, 24h hypoxia

value: shACLY


title: shACLY-#2_rep2


title: shACLY-#2_rep1


title: shACLY-#1_rep2


title: day3 Chaf1a knockdown Rep2

description: Day 3 OKSM reprogramming intermediate derived from Mouse Embryonic Fibroblasts (E13.5 embryos) Chaf1a knockdown replicate 2


title: shACC1-#2_rep3

source_name: H1975 cells, shshACC1, 24h hypoxia


title: shACC1-#1_rep1


title: shACC1-#2_rep1


title: shACC1-#2_rep2


title: shACLY-#1_rep1


title: shACC1-#1_rep2


title: shScramble_rep2

description: SCR-B


title: shACC1-#1_rep3


title: shScramble_rep1

description: SCR-A


title: CTOS_Pre_nondisrupted-rep1

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

department: Clinical Bio-resource Research and Development

country: Japan

institute: Kyoto Univ Graduate School of Medicine

description:
DRCRC_001
Gene expression in non-disrupted cancer tissue-originated spheroids (CTOSs).

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k 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 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Signal intensities were normalized to the 75th percentile (75th percentile shift).

source_name: CTOS, non-disrupted, pre

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: CTOSs were cultured in suspension in StemPro hESC SFM (Life Technologies, Carlsbad, CA).

extract_protocol: Total RNA was extracted from CTOSs with TRIzol reagent (Life Technologies) according to the manufacturer's instructions.

treatment_protocol: We used a 27-gauge needle to shear CTOSs, raising and lowering the plunger several times. We prepared fresh CTOSs from mouse xenografts and cultured them for 7 days in vitro to avoid the possible effects of disruption at the CTOS preparation from the xenograft. The CTOSs were filtered, CTOSs >100 μm were collected, and the CTOS suspension was divided into two groups. In the disrupted group, all of the CTOS were disrupted by needle shearing. In the non-disrupted group, CTOSs were cultured without disruption.

value: cultured spheroids (CTOS)

tag: treatment

tag: time point

value: pre


title: CTOS_6hr_disrupted-rep1

description:
DRCRC_002
Gene expression after 6 hr in mechanically disrupted cancer tissue-originated spheroids (CTOSs).

source_name: CTOS, disrupted, 6 hr

value: mechanical disruption

value: 6 hr


title: Healthy Control Replicate 3

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

hyb_protocol: Each experimental sample was then co-hybridized with the unique human reference on Agilent “SurePrint G3 Human Gene Expression 8x60K Microarray” (Design ID 028004), for 17 hrs, at 65°C under 10 rpm.

scan_protocol: Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 µm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_2Color” protocol. Raw .tif images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE2_1010_Sep10” protocol.

data_processing: Median raw expression values were further normalized by quantile method (B.M Bolstad, R.A. Irizarry, M. Astrand and T.P Speed Bioinformatics, 2003, vol.19, n.2, pp.185-193). Values in the column LogRatio of the raw data files are quantile normalized log10 ratio (reference/test)

source_name: Peripheral Blood Eosinophil Healthy Control

label_protocol: Test samples were linearly amplified and labeled with Cyanine 3, starting from 25 ng of total RNA. In parallel, the “Human Universal Reference Total RNA” (Clonetech, Cat # 636538) was amplified and labeled with Cyanine 5.

extract_protocol: Total RNA was extracted from sorted eosinophils using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions

tag: hypereosinophilic condition

value: healthy control

tag: Sex

value: Male

tag: age (years)

tag: eosinophil blood count (mm3)

source_name: Mixture of total RNAs from a collection of adult human tissues

tag: sample type

value: Human Universal Reference

tag: vendor/catalog#

value: Clonetech, Cat # 636538


title: CTOS_24hr_disrupted-rep1

description:
DRCRC_003
Gene expression after 24 hr in mechanically disrupted cancer tissue-originated spheroids (CTOSs).

source_name: CTOS, disrupted, 24 hr

value: 24 hr


title: Healthy Control Replicate 1

value: Female


title: Dermatologic Disease Replicate 1

source_name: Peripheral Blood Eosinophil Dermatologic disease

value: dermatologic disease


title: Healthy Control Replicate 2


title: Dermatologic Disease Replicate 2


title: Dermatologic Disease Replicate 3


title: Parasitic Disease Replicate 2

source_name: Peripheral Blood Eosinophil Parasitosis

value: parasitosis


title: Parasitic Disease Replicate 1


title: Pulmonary Aspergillosis Replicate 4

source_name: Peripheral Blood Eosinophil Aspergillosis

value: aspergillosis


title: Pulmonary Aspergillosis Replicate 3


title: Parasitic Disease Replicate 3


title: CTOS_4day_disrupted-rep1

description:
DRCRC_004
Gene expression after 4 days in mechanically disrupted cancer tissue-originated spheroids (CTOSs).

source_name: CTOS, disrupted, 4 days

value: 4 days


title: Pulmonary Aspergillosis Replicate 1


title: Pulmonary Aspergillosis Replicate 2


title: Severe Asthma Replicate 4

source_name: Peripheral Blood Eosinophil Asthma

value: asthma


title: Severe Asthma Replicate 2


title: Severe Asthma Replicate 3


title: PG23

city: Aurora

first: Mark

last: Geraci

state: CO

address: Mail Stop C272, 12700 E 19th Ave

department: Division of Pulmonary Sciences and Critical Care Medicine

institute: University of Colorado Anschutz Medical Campus

description:
Blood_PG23
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

hyb_protocol: RA1-resuspended DNA was loaded onto BeadChip arrays. After overnight incubation at 48oC, single-base extension and allele-specific staining was performed in Te-Flow flow-through chambers supplied by Illumina.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 50-55 min and scanned on an iScan Reader (Illumina).

data_processing: Genotyping and probe intensity determinations were performed by GenomeStudio version 2010.3 (Illumina) using an in-house cluster (reference) file, generated from the results of blood samples from a total of 99 male and female controls.

label: C-Bio and A-DNP

source_name: Whole blood

label_protocol: Approximately 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37oC using amplification master mix (MA1) and primer/neutralization mixes (MA2, MSM). After incubation, the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1), then resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed either using proteinase K with ethanol precipitation, or a commercial kit (DNeasy Blood and Tissue Kit, Qiagen).

tag: race/ethnicity

value: Hispanic

value: Blood

tag: disease state

value: Hypoplastic left heart syndrome, other dysmorphia unknown; non-familial


title: Severe Asthma Replicate 1


title: PG10

description:
Blood_PG10
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

tag: gender

value: Caucasian

tag: tissue

value: Coarctation of the aorta, no other dysmorphia; familial


title: PG22

description:
Blood_PG22
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Hypoplastic left heart syndrome, no other dysmorphia; non-familial


title: PG25

description:
Blood_PG25
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: PG20

description:
Blood_PG20
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: PG18

description:
Blood_PG18
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: PG09

description:
Blood_PG09
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: PG12

description:
Blood_PG12
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Aortic valve stenosis, no other dysmorphia; familial


title: PG13

description:
Blood_PG13
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: PG21

description:
Blood_PG21
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: LLC1 3D cell culture replicate 3

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description: Biological replicate 3 of 3. LLC1 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3. For differential gene expression analysis cell grown under 2D conditions served as a control.

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 Control Samples

source_name: LLC1 cell line cultivated in 3D cell culture

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: For 2D cell culture, 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. For 3D cell culture, cells were plated in 0.5 mg/ml laminin rich extracellular matrix (GeltrexTM, Gibco) and cell culture medium upon a layer of agarose ir a 24-well cell culture plates.

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).

value: experimental

tag: cell line

tag: growth condition


title: LLC1 3D cell culture replicate 2

description: Biological replicate 2 of 3. LLC1 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3. For differential gene expression analysis cell grown under 2D conditions served as a control.


title: PG14

description:
Blood_PG14
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Male

value: Hypoplastic left heart syndrome, dysmorphia; non-familial


title: PG15

description:
Blood_PG15
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: LLC1 3D cell culture replicate 1

description: Biological replicate 1 of 3. LLC1 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3. For differential gene expression analysis cell grown under 2D conditions served as a control.


title: PG11

description:
Blood_PG11
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Hypoplastic left heart syndrome, no other dysmorphia; familial


title: PG19

description:
Blood_PG19
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Female


title: PG17

description:
Blood_PG17
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Ventricular septal defect, other dysmorphia unknown; familial


title: LLC1 2D cell culture replicate 1

source_name: LLC1 cell line cultivated in 2D cell culture

value: control


title: LLC1 2D cell culture replicate 3


title: LLC1 2D cell culture replicate 2


title: PG05

description:
Blood_PG05
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Asian (Vietnamese)

value: Hypoplastic left heart syndrome, other dysmorphia unknown; familial


title: PG08

description:
Blood_PG08
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Pulmonary valve atresia, hypoplastic right ventricle, absent coronary artery origins from the aorta, other dysmorphia unknown; familial


title: PG16

description:
Blood_PG16
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Hispanic

value: Shone's complex (multiple left-sided obstruction lesions, small VSD), no other dysmorphia; familial


title: HLHS59

description:
Heart_H59
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

source_name: Heart right ventricle

value: White, non-Hispanic

value: Heart

value: HLHS with aortic stenosis, mitral atresia; double outlet right ventricle


title: PG24

description:
Blood_PG24
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: unknown

value: Blood

value: Hypoplastic left heart syndrome, other dysmorphia unknown; non-familial


title: PG07

description:
Blood_PG07
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Male

value: Pulmonary valve atresia, corrected transposition, no other dysmorphia; familial


title: PG03

description:
Blood_PG03
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Hypoplastic left ventricle, unbalanced atrioventricular canal, no other dysmorphia; familial


title: PG06

description:
Blood_PG06
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Hypoplastic left heart syndrome, no other dysmorphia; non-familial


title: IKK2+SP600125_BCR_Batch2

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

hyb_protocol: Biological replicates were hybridized to Affymetrix HG U133 Plus2.0 GeneChip arrays.

scan_protocol: not provided

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260). Expression values of multiple probeIDs targeting the same gene where summarized into a single representative value by fitting a standard additive model using Tukey’s median polish procedure.

source_name: BL-2 cell line

label_protocol: cDNA was synthesized using 1 μg corresponding RNA and including Poly-A RNA controls with the help of the Affymetrix GeneChip® Poly-A RNA control Kit. Secondly, cRNA synthesis and cleanup was carried out using the Affymetrix GeneChip® IVT Labelling Kit. Subsequently, fragmentation and labeling for microarray hybridization was accomplished with the corresponding kits according to manufacturer’s instructions.

growth_protocol: Burkitt Lymphoma cell lines were cultured in RPMI-1640, 10 % (v/v) FCS, 200 U/m Penicilin, 200 μg/ml Streptomycin, 20 nM BCS, 50 μM α-Thioglycerol, 1 mM Sodium pyruvate. Cells were cultured at 37°C, 5 % CO2 and split daily depending on he observed cell proliferation (cell density: 0.3x106 cells/ml - 1x106 cells/ml). The day before the experiment 0.3x10^6 cells/ml were seeded.

extract_protocol: Samples were frozen at -80°C and RNA was isolated with the RNeasy Kit 30 Material and Methods (Qiagen) for microarray analyses or with the NucleoSpin® RNA II Kit (Macherey-Nagel, Düren Germany).

treatment_protocol: Cells were counted in 0.4 % Trypan blue using a Neubauer counting chamber. To cultivate cells from a frozen aliquot, thawed cells were washed with 10 ml of the respective cell culture medium (centrifugation 250 x g, 7 min at RT). The cell pellet was resuspended in 5-10 ml medium and cells were incubated at 37°C, 5 % CO2. To freeze cells approximately 1x107 cells were sedimented as described above and resuspended in 1 ml freezing medium (90 % FCS, 10 % DMSO). Cells were frozen in cryo boxes containing isopropanol to obtain a constant cooling of approximately 1°C/min and stored immediately at -80°C for 24 hours before permanent storage at -150°C.

tag: cell type

value: Burkitt Lymphoma

tag: inhibitor

value: BCR


title: HLHS60

description:
Heart_H60
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Female

value: HLHS with aortic atresia, mitral atresia; anomalous pulmonary venous return


title: DMSO_BCR_Batch6

value: control


title: HLHS62

description:
Heart_H62
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic atresia, mitral stenosis


title: DMSO_KO_Batch6

value: knockout


title: PG04

description:
Blood_PG04
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Middle Eastern

value: Hypoplastic left heart syndrome, dysmorphia; non-familial


title: HLHS57

description:
Heart_H57
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: White, non-Hispanic

value: Heart

value: HLHS with aortic atresia, mitral stenosis; dysplastic tricuspid valve


title: HLHS58

description:
Heart_H58
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Native American, non-Hispanic


title: 10058F4_KO_Batch6


title: DMSO_BCR_Batch5


title: DMSO_KO_Batch5


title: 10058F4_BCR_Batch5


title: 10058F4_KO_Batch5


title: 10058F4_BCR_Batch6


title: 10058F4_BCR_Batch4


title: DMSO_KO_Batch4


title: HLHS55

description:
Heart_H55
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Male

value: African American, non-Hispanic

value: HLHS with aortic atresia, mitral stenosis; intact atrial septum


title: HLHS44

description:
Heart_H44
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic atresia, mitral atresia


title: 10058F4_KO_Batch4

value: Burkitt Lymphoma


title: HLHS56

description:
Heart_H56
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic stenosis; unbalanced atrioventricular septal defect


title: HLHS53

description:
Heart_H53
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Female

value: White, Hispanic

value: HLHS with aortic stenosis, mitral stenosis; restrictive atrial septum, anomalous pulmonary venous return


title: HLHS51

description:
Heart_H51
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic atresia


title: HLHS48

description:
Heart_H48
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic stenosis, mitral atresia; restrictive atrial septum


title: HLHS41

description:
Heart_H41
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

source_name: Heart left ventricle

value: HLHS with mitral atresia; double outlet right ventricle


title: HLHS40

description:
Heart_H40
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: HLHS39

description:
Heart_H39
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with pulmonary stenosis; dextrocardia


title: Vivit_Ko_Batch1

value: Vivit

value: knockout


title: SB203580+SP600125_Ko_Batch1


title: HLHS42

description:
Heart_H42
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Heart

value: HLHS with aortic atresia, mitral stenosis


title: HLHS47

description:
Heart_H47
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: White, non-Hispanic


title: IKK2+SB203580+SP600125_Ko_Batch1


title: HLHS31

description:
Heart_H31
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Male


title: Ly294002_Ko_Batch1


title: HLHS25

description:
Heart_H25
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic atresia; ventricular septal defect


title: HLHS36

description:
Heart_H36
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: HLHS34

description:
Heart_H34
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic atresia; anomalous pulmonary venous return


title: Vivit_KO_Batch2

value: Burkitt Lymphoma


title: IKK2+SB203580_BCR_Batch1

value: BCR


title: HLHS54

description:
Heart_H54
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: HLHS30

description:
Heart_H30
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Female

value: HLHS with aortic atresia, mitral stenosis; Turner syndrome


title: TAK1_BCR_Batch2


title: HLHS38

description:
Heart_H38
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: not reported


title: HLHS29

description:
Heart_H29
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic stenosis, mitral atresia


title: Vivit_BCR_Batch1


title: SB203580+SP600125_KO_Batch2


title: SB203580+SP600125_BCR_Batch1


title: Ly294002_BCR_Batch1


title: IKK2+SP600125_BCR_Batch1


title: DMSO_BCR_Batch1

value: control


title: HLHS27

description:
Heart_H27
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: IKK2+SB203580_Ko_Batch1


title: HLHS32

description:
Heart_H32
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: White, Hispanic

value: HLHS with aortic atresia, mitral atresia


title: U0126_KO_Batch2


title: DMSO_KO_Batch3


title: HLHS24

description:
Heart_H24
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: DMSO_KO_Batch2


title: DMSO_BCR_Batch4


title: IKK2+SP600125_Ko_Batch1


title: HLHS22

description:
Heart_H22
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: SB203580_BCR_Batch1


title: U0126_BCR_Batch1


title: IKK2_BCR_Batch1


title: HLHS20

description:
Heart_H20
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic stenosis, mitral stenosis


title: HLHS23

description:
Heart_H23
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Asian, non-Hispanic


title: SB203580+SP600125_BCR_Batch2


title: HLHS21

description:
Heart_H21
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

source_name: Heart apex

value: Heart

value: HLHS with mitral atresia; ventricular septal defect


title: DMSO_KO_Batch1

value: knockout


title: U0126_BCR_Batch2


title: SP600125_BCR_Batch2

value: JNK


title: HLHS28

description:
Heart_H28
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Male

value: White, non-Hispanic

value: HLHS with aortic stenosis, mitral stenosis; ventricular septal defect


title: HLHS35

description:
Heart_H35
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: LY294002_KO_Batch2

value: Burkitt Lymphoma


title: SB203580_BCR_Batch2

value: BCR


title: Vivit_BCR_Batch2

value: Vivit


title: LY294002_BCR_Batch2


title: Vivit_KO_Batch


title: TAK1_BCR_Batch3


title: IKK2+SB203580+SP600125_BCR_Batch1


title: Vivit_BCR_Batch3


title: U0126_BCR_Batch3


title: parental cell rep1

city: London

first: Claude

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

country: United Kingdom

institute: Barts & The London School of Medicine (QMUL)

description: parental cell rep1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: O-miner web tool

source_name: cell line, parental

label_protocol: Total RNA quality was assessed using an Agilent 2100 Bioanalyser prior to sample preparation, starting with 100ng of total RNA and 16hrs IVT as per 3’ IVT Express protocol (Affymetrix). Samples were hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays.

growth_protocol: SKOV3 and SKOV3-TR cells in log-growth phase on 10cm diameter plates were trypsinised, centrifuged at 1500rpm for 5min and washed in PBS

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) in combination with the QIAshredder kit (Qiagen) for cell homogenization

treatment_protocol: Paclitaxel-resistant cells were maintained in 300 nM paclitaxel, but released for at least 72h prior to plating onto 10cm plates.

value: parental

value: Ovary


title: U0126_KO_Batch3


title: parental cell rep2

description: parental cell rep2


title: SP600125_BCR_Batch3


title: SB203580+SP600125_BCR_Batch3


title: SB203580+SP600125_KO_Batch3


title: Ly294002_BCR_Batch3


title: HLHS18

description:
Heart_H18
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: paclitaxel-resistant ovarian cancer cell line rep2

source_name: cell line, paclitaxel-resistant

value: paclitaxel-resistant


title: HLHS13

description:
Heart_H13
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Female

value: HLHS with aortic atresia, mitral atresia; anomalous pulmonary venous return


title: IKK2_BCR_Batch2


title: IKK2+SP600125_KO_Batch3


title: IKK2+SP600125_BCR_Batch3


title: IKK2+SB203580+SP600125_BCR_Batch3


title: IKK2+SB203580_KO_Batch3


title: IKK2+SB203580+SP600125_BCR_Batch2


title: HLHS16

description:
Heart_H16
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic atresia, mitral stenosis


title: IKK2+SB203580+SP600125_KO_Batch2


title: Control 1h

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description:
CONTROL 1H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

hyb_protocol: Sample cDNA resolved in hybridization buffer (50% Formamide, 10X SSC, 0.2% SDS) was applied to microarrays, and then enclosed in Corning hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Microarrays were scanned on GenePix 4000B microarray scanner, and signal intensities were extracted by GenePix Pro 6.0.6.0 scanning software.

data_processing: GeneSpring 12.1 (Agilent Technologies, Palo Alto, CA, USA) was used for background subtraction and LOWESS normalization.

organism: Bos taurus

source_name: Embryo, 0.1 MPa, 1h recovery

label_protocol: Aminoallyl-linked cDNA was generated from 10 mcg of the reference and extracted total RNA by reverse transcription, followed by labeling with Cy3 or Cy5.

growth_protocol: In vitro fertilization (Day 0) was performed using abattoir bovine oocytes, and embryos were immediately placed in CR1aa medium supplemented with BSA for Days 1 and 2 of culture. Cleaved embryos were transferred to CR1aa + 10% FBS and cultured at 38.5°C in 5% CO2 in humidified air until Day 7/expanded blastocyst stage.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and treated with DNase I (Invitrogen) to remove any possible genomic DNA contamination.

treatment_protocol: Blastocysts were randomly distributed into the control and HHP treated groups. To apply HHP, groups of embryos were transferred to 0.25 ml straws in embryo holding medium (TCM-199) without air bubbles. Straws were sealed with plastic plugs and were then placed into a pre-warmed stainless steel pressure machine (HHP machine 100; Applied Cell Technology Ltd., Hungary) with distilled water as the pressure medium. The embryos were then vitrified using the Solid Surface Vitrification (SSV) method.

tag: breed

value: Holstein

tag: developmental stage

value: 0.1 MPa

tag: recovery time

source_name: Pooled 5 IVF embryos

value: reference


title: 80 MPa 2h

description:
800 2H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 80 MPa, 2h recovery

tag: treatment

value: 80 MPa


title: Control 2h

description:
CONTROL 2H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 0.1 MPa, 2h recovery


title: Control 0h

description:
CONTROL 0H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 0.1 MPa, 0h recovery


title: SB203580_BCR_Batch3


title: IKK2_BCR_Batch3


title: HLHS04

description:
Heart_H04
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Heart

value: HLHS with aortic atresia, mitral atresia


title: HLHS10

description:
Heart_H10
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Male

value: White, non-Hispanic


title: 80 MPa 1h

description:
800 1H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 80 MPa, 1h recovery


title: HLHS19

description:
Heart_H19
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with pulmonary atresia; complete atrioventricular septal defect, bilateral superior vena cava, 'D' transposition, interrupted inferior vena cava


title: IKK2+SB203580_BCR_Batch3

value: Burkitt Lymphoma

value: BCR


title: HLHS11

description:
Heart_H11
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: African American, non-Hispanic


title: IKK2+SB203580_BCR_Batch2


title: IKK2+SB203580_KO_Batch2

value: knockout


title: HLHS02

description:
Heart_H02
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: White, Hispanic


title: 80 MPa 0h

description:
800 0H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 80 MPa, 0h recovery


title: paclitaxel-resistant ovarian cancer cell line rep1

value: paclitaxel-resistant

value: Ovary


title: HLHS03

description:
Heart_H03
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Double inlet left ventricle with mitral stenosis, second degree AV block; hypoplastic right ventricle


title: HLHS05

description:
Heart_H05
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Female

value: HLHS with aortic atresia; complete atrioventricular septal defect


title: DMSO_BCR_Batch2

value: control


title: HLHS06

description:
Heart_H06
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)


title: HLHS08

description:
Heart_H08
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: HLHS with aortic atresia, mitral stenosis


title: HLHS12

description:
Heart_H12
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

value: Heart

value: HLHS with aortic stenosis


title: PBMC_CTRL_Patient 10

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

hyb_protocol: Labeled cRNA was then hybridized for 17 hours at 65°C on Whole Human Genome Microarray 4x44 K slides, (Agilent Technologies, Santa Clara, CA). After hybridization the slides were washed according to manufacturer’s protocols.

scan_protocol: The slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies).

data_processing:
Data extraction was performed using Agilent Feature Extraction software.
A p-value cut-off of 0.05 and a fold-change cut-off of 2 were applied to identify differentially expressed genes able to discriminate between the study groups.

source_name: PBMC_Transplanted stable recipient

label_protocol: Labeled cRNA was generated using the Low Input Quick Amp Labeling (LIQA) kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: PBMC were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden) gradient (460g for 30 min) and were washed three times with PBS pH 7.4/1 mM EDTA (Sigma, Milan, Italy). Cells were counted and their viability was evaluated by trypan blue exclusion (>90% PBMC were viable).Total RNA was extracted from a minimum of 106 PBMCs using the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). The concentration of total RNA was measured using NANODROP® spectrophotometer ND-1000 (Thermo Scientific, Waltham, MA, US) and RNA integrity was measured using the Agilent 2100 BIOANALYZER® (Agilent Technologies Deutschland GmbH, Waldbronn, Germany) along with the Agilent® RNA 6000 Nano Kit.

value: PBMC

tag: age

value: Tacrolimus


title: PBMC_CTRL_Patient 8


title: PBMC_CTRL_Patient 6

value: Male


title: PBMC_CTRL_Patient 7


title: Ly294002_KO_Batch3

value: Burkitt Lymphoma


title: 40 MPa 1h

description:
400 1H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 40 MPa, 1h recovery

value: Holstein

value: 40 MPa

value: reference


title: SB203580_KO_Batch1

value: knockout


title: PBMC_CAMR_Patient 10

source_name: PBMC_chronic antibody mediated rejection

value: chronic antibody mediated rejection


title: SB203580_KO_Batch2


title: TAK1_KO_Batch3


title: TAK1_BCR_Batch1

value: BCR


title: DMSO_BCR_Batch3


title: 40 MPa 2h

description:
400 2H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 40 MPa, 2h recovery


title: IKK2+SB203580+SP600125_KO_Batch3


title: PBMC_CAMR_Patient 9


title: IKK2+SP600125_KO_Batch2


title: PBMC_CTRL_Patient 3


title: TAK1_KO_Batch2


title: 60 MPa 2h

description:
600 2H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 60 MPa, 2h recovery

value: 60 MPa


title: SP600125_KO_Batch3

source_name: BL-2 cell line

value: JNK


title: 60 MPa 1h

description:
600 1H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 60 MPa, 1h recovery


title: 60 MPa 0h

description:
600 0H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 60 MPa, 0h recovery


title: SP600125_KO_Batch2


title: SP600125_BCR_Batch1


title: SB203580_KO_Batch3


title: IKK2_KO_Batch3


title: TAK1_KO_Batch1


title: 40 MPa 0h

description:
400 0H
This Sample represents multiple replicates. See the 'GSE75559_replicate_information.xls' file for full information about each replicate.

source_name: Embryo, 40 MPa, 0h recovery


title: SP600125_KO_Batch1


title: PBMC_CAMR_Patient 3

value: Female


title: PBMC_CAMR_Patient 8

value: Cyclosporine


title: U0126_Ko_Batch1


title: IKK2_KO_Batch2


title: HLHS01

description:
Heart_H01
Genomic DNA extracted from explanted heart tissue or peripheral blood was genotyped using Infinium HD HumanOmni2.5 BeadChips (Illumina)

source_name: Heart right ventricle

value: White, non-Hispanic

value: HLHS with aortic stenosis, mitral stenosis


title: 561674: HepG2_TBH_24h_repl 3

status: Public on Dec 09 2015

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

country: Netherlands

institute: Maastricht University

description: Immunoprecipitated genomic DNA with antibody against a monoclonal antibody against 5’-methylcytidine

hyb_protocol: The pellet was dissolved in hybridization solution using the NimbleGen Hybridization kit. After denaturing the probe was hybridized overnight on the 2.1M Deluxe Promoter Arrays using the HX1 mixers and the NimbleGen Hybridization system 4.

scan_protocol: Slides were scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner per manufacturer's protocol.

data_processing: Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis. Log2 ratios of the intensities were computed (ratio of MeDIP signal/Input signal) for each array. Detection of differential methylation was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA (Roche NimbleGen) leverages the “neighbor effect” characteristics of Methylation Dependent ImmunoPrecipitation on chip (MeDIP-chip) data from high density oligonucleotide arrays, where enriched fragments sizes far exceed the spacing between probes. In other words, probes within close proximity have a greater likelihood of reporting signals derived from the same enriched fragment during MeDIP procedure. PSW-ANOVA uses a sliding window approach to identify potential sites of differential enrichment and then assigns probability scores (p values) to each probe on the array using a repeated measure ANOVA model. PSW-ANOVA is implemented in the R statistical programming environment as a custom script and was provided by Roche NimbleGen in collaboration.   Briefly, for each probe, a sliding window is determined based on the sliding window size parameter, centering on the probe in question. Within each sliding window, a repeated measures ANOVA is used to assess the difference between the various experimental groups for all probes located within the sliding window, using the probe ID as the reference to reduce the amount of error arising from different probes within a sliding window. It is assumed that the background and non-specific hybridization behavior of adjacent probes within a sliding window can be larger than the changes in intensity difference between the two channels, but within the sliding window, the log ratios will still be proportional to the intensity difference between groups of samples.  PSW-ANOVA (sliding window of 750 bp comprising 7 probes, and a FDR adjusted p- value < 0.05) was used to identify differential methylated regions (DMR) which were statistically significantly different between the different conditions tested in the experiment. Peaks were identified in the DMR by searching for the number of probes (default = 2) above a p-value minimum cutoff (-log10, default = 1.3) within 150 bp distance of each other. Peaks within 500 bp were merged. Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site) and CpG islands of genes using the NimbleScan v2.6 software.

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 24 hours replicate 3

label_protocol: Genomic DNAs were sonicated to obtain fragments ranging from 200 bp to 1000 bp, cleaned up using silica columns (Zymo Research) and eluted in TE buffer. 4.4 µg of each sonicated sample was dissolved in a total volume of 495 µL TE buffer. Ten percent of such prepared mixtures was kept as Input sample (Input) at 4°C, while the remaining was immunoprecipitated with 12 µL of a monoclonal antibody against 5’-methylcytidine (Eurogentec) as described by Weber et al (2005). Immunoprecipitated DNAs (MeDIP) were purified using silica columns (Zymo Research) and eluted in TE buffer. Forty ng of both Input and MeDIP samples were whole genome amplified (WGA) using the WGA2 kit (Sigma Aldrich) following the manufacturer’s instruction, but omitting the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water.     Labeling and hybridization of arrays was performed according to the manufactures’ protocol. In brief, 1 µg of Input DNA and 1 µg of MeDIP DNA were labeled with Cy3 and Cy5 respectively by random priming using the Dual Color DNA labeling kit (Roche NimbleGen). The labeled samples were precipitated using isopropanol and quantified spectrophotometrically using the NanoDrop 1000.

extract_protocol: Cells were washed twice with Hank's Buffered Salt Solution (Invitrogen) and trypsinized. Cell pellets were resuspended in 500 µl digestion buffer (1 mM EDTA; 50 mM Tris–HCl, pH 8.0; 5% SDS) and proteinase K (1 mg/ml) (Ambion) was added. After incubation of 1 hour at 55 °C, the proteinase K was inactivated at 80 °C. RNAse A (400 µg/ml) (Qiagen) treatment was performed for 1 hour at 37 °C. An equal amount of phenol-chloroform-isoamylalcohol (PCI; 25:24:1) (Sigma) was added and shaked manually for 5 min. After centrifugation, the upper phase was again treated with PCI until no protein was visible at the interphase. The upper phase was precipitated with 50 µl 3M NaAc pH 5.6 and 1250 µl cold 100% ethanol. The DNA pellet was washed with cold 70% ETOH, dissolved in 50µl nuclease free water and quantified spectrophotometrically using the NanoDrop 1000 (Thermo Scientific, Waltham, MA). The total amount was at least 10 µg DNA, the 260/280 ratio laid between 1.7-1.9, and the 260/230 was higher than 1.6.

value: HepG2 human hepatoma cells

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 24 hours replicate 3


title: 561729: HepG2_TBH_24h_repl 2

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 24 hours replicate 2

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 24 hours replicate 2


title: 562679: HepG2_Contr_24h_repl 1

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 24 hours replicate 1

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 24 hours replicate 1


title: 562882: HepG2_TBH_8h_repl 2

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 8 hours replicate 2

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 8 hours replicate 2


title: 562783: HepG2_TBH_24h_repl 1

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 24 hours replicate 1

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 24 hours replicate 1


title: 561672: HepG2_TBH_8h_repl 3

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 8 hours replicate 3

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 8 hours replicate 3


title: 561776: HepG2_Contr_24h_repl 3

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 24 hours replicate 3

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 24 hours replicate 3


title: 562699: HepG2_Contr_24h_repl 2

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 24 hours replicate 2

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 24 hours replicate 2


title: 562883: HepG2_Contr_8h_repl 2

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 8 hours replicate 2

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 8 hours replicate 2


title: 562651: HepG2_Contr_8h_repl 1

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 8 hours replicate 1

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 8 hours replicate 1


title: Haploids and DamP collection Biological Replicate 1 (SR7575)

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

description: Biological replicate 1 of 2 (haploid mutant collection)

hyb_protocol: Hybridization was done in Roche RapidHyb buffer at 24°C overnight.

scan_protocol: Genepix 4200AL and GenePix Pro v7

data_processing: The scans were processed using GenePix Pro, v7. The values from the obtained gpr files were filtered to keep only values for spots with an SNR > 10. Next, we performed a loess normalization on groups of probes (UP/DAMP, UP/DELETION, DOWN/DAMP, DOWN/DELETION), followed by aggregation of values for each mutant and a second loess normalization on the aggregated data.

organism: Saccharomyces cerevisiae

source_name: Haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014)

label_protocol: Cy3 and Cy5 5' tagged oligonucleotides were used to amplify the barcode region with universal primers. PCR products were then mixed, precipitated in the presence of linear poly-acrylamide and prepared for hybridization

growth_protocol: Cells were thawed from -80°C aliquots and left to recover for 8 hours in YPD medium. An aliquot of the pool of strains was diluted to a DO of 0.002 in 1 liter of YPD medium with 0.125 µg/ml SR7575 or without (control). Cells were recovered after overnight growth, when reaching a 600 nm OD of 2 (after about 10 generations).

extract_protocol: Genomic DNA was extracted through mechanical lysis (vortexing with glass beads). PCR amplification of the barcode region was followed by a second PCR amplification with Cy3 5' tagged oligonucleotide.

treatment_protocol: Cells in exponential growth were recovered by centrifugation, washed once in cold water and stored at -80°C until RNA or DNA extraction

tag: strain

value: Mix of haploid strains derived from BY4741 (yeast deletion collection)

source_name: Barcoded DNA from haploid, homozygous yeast deletion collection + DamP collection (Decourty et al., Cell Rep. 2014)


title: 562753: HepG2_TBH_8h_repl 1

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 8 hours replicate 1

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 8 hours replicate 1


title: IKK2_KO_Batch1

source_name: BL-2 cell line


title: Diploids collection Biological Replicate 1 (SR7575)

description: Biological replicate 1 of 2 (diploid mutant collection)

source_name: Diploid, heterozygous yeast deletion collection

value: Mix of diploid strains serived from BY4743 (yeast deletion collection)

source_name: Barcoded DNA from diploid, heterozygous yeast deletion collection

value: Mix of diploid strains derived from BY4743


title: 561774: HepG2_Contr_8h_repl 3

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 8 hours replicate 3

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 8 hours replicate 3


title: 561626: HepG2_TBH_1h_repl 3

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 1 hour replicate 3

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 1 hour replicate 3


title: Haploids and DamP collection Biological Replicate 2 (SR7575)

description: Biological replicate 2 of 2 (haploid mutant collection)

value: Mix of haploid strains derived from BY4741


title: S6K2si_c

city: Linköping

first: Patrik

last: Lundström

address: Campus Valla

department: Physics, Chemistry and Biology

country: Sweden

institute: Linköping University

hyb_protocol: Standard hybridization protocol.

scan_protocol: Affymetrix Scanner 3000 7G was used to scan the arrays and generated data were converted to cell intensity files in Affymetrix Genotyping Console

data_processing: Cell intensity data were processed by the software Genespring (Agilent Technologies). Raw data was normalised to the median of the control samples using the Robust Multi-array Average (RMA) summarisation algorithm.

source_name: ZR751 breast cancer cell line

label_protocol: Affymetrix GeneChip Gene 2.0 expression arrays (Affymetrix) were used to profile alterations in global mRNA expression after silencing of S6K1, S6K2 or S6K1+S6K2 in triplicates. The assay was performed according to manufacturer’s protocols with 250 ng total RNA as starting material. Briefly, RNA was reverse transcribed into first and second strand cDNA, thereafter converted to cRNA and finally sscDNA, using Ambion, Life Technologies, WT Expression Kit (Ambion, Life Technologies). The sscDNA was fragmented and labelled with GeneChip WT Terminal labelling and hybridisation kit (Affymetrix), and hybridised to the arrays

growth_protocol: The cells were cultured in phenol-red free Optimem (Gibco), supplemented with 4% Fetal bovine serum (Gibco) until reaching approximately 80% confluence and thereafter seeded into 15 cm2 flasks.

extract_protocol: RNA was isolated with the mirVanaTM miRNA isolation kit (Ambion, Life Technologies) according to instructions provided by the manufacturer

treatment_protocol: The cells were nucleofected using the Amaxa cell line optimisation nucleofector kit, according to manufacturer’s instructions (Lonza). Optimal downregulation of S6K1 and S6K2 were reached 72 h after transfection with S6K1 siRNA 110802 and s12284 (Ambion, Life Technologies) and S6K2 siRNA 471 (Ambion, Life Technologies), respectively. As a control for transfection, scramble siRNA (Ambion, Life Technologies) was used

tag: transfection

value: S6K2 siRNA

value: female


title: S6K1si_c

value: S6K1 siRNA


title: S6K1si_b


title: Diploids collection Biological Replicate 2 (SR7575)

description: Biological replicate 2 of 2 (diploid mutant collection)


title: S6K1+2si_c

value: S6K1 siRNA and S6K2 siRNA


title: S6K1+2si_a


title: Control_c

value: scramble siRNA


title: S6K1si_a


title: S6K2si_a


title: S6K1+2si_b


title: S6K2si_b


title: Control_b


title: 562712: HepG2_TBH_1h_repl 2

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 1 hour replicate 2

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 1 hour replicate 2


title: 561671: HepG2_Contr_1h_repl 2

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 1 hour replicate 2

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 1 hour replicate 2


title: 562642: HepG2_Contr_1h_repl 1

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 1 hour replicate 1

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 1 hour replicate 1


title: 561767: HepG2_Contr_1h_repl 3

source_name: Input DNA from HepG2 cells exposed to zero dose of TBH for 1 hour replicate 3

source_name: Immunoprecipitated DNA from HepG2 cells exposed to zero dose of TBH for 1 hour replicate 3


title: 562716: HepG2_TBH_1h_repl 1

source_name: Input DNA from HepG2 cells exposed to 200µM TBH for 1 hour replicate 1

source_name: Immunoprecipitated DNA from HepG2 cells exposed to 200µM TBH for 1 hour replicate 1


title: SH2D5

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Megakaryocte models

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics suite 6.6 and  in STATA/SE 11.2.

label: Biotin

source_name: ES-cell derived megakaryocyte-erythroid progenitor

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

growth_protocol: All cells were kept in Iscove's modification of DMEM (IMDM) based Tpo containing media to induce megakaryocyte and cultured every other day to maintain 0.5-1.5 x 10^6 cells/mL.

extract_protocol: Rneasy micro kit (Qiagen)

treatment_protocol: Mature megakaryocytes were isolated using two step BSA gradient method on day 4 for GG, day 6 for FL and day 5 for SH of differentiation. GG cells were transduced with MIGR1 retrovirus expressing Gata1 cDNA and GFP on day 0 and GFP+ cells were sorted on day 1 of differentiation.

tag: class genotype

value: G1ME2 (engineered wildtype (WT) murine ES cells to express doxycycline (dox)-regulated Gata1 short hairpin (sh) RNAs)


title: GG1D4

description: Megakaryocte models

value: Gata1– megakaryocyte-erythroid

value: ES-cell derived megakaryocyte-erythroid progenitor


title: FL2

description: Megakaryocte models

source_name: fetal liver

value: fetal liver derived megkaryocytes

value: fetal liver


title: SH3D5

description: Megakaryocte models


title: Control_a


title: SH1D5

description: Megakaryocte models


title: FL3

description: Megakaryocte models


title: FL1

description: Megakaryocte models


title: GG3D4

description: Megakaryocte models


title: GG2D4

description: Megakaryocte models


title: B cell lymphoma 1039 - repeat 2 - mAdbID:128451

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

description: mAdb experiment ID: 128451

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 3 Scan_MicronsPerPixelY: 3 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Data Processing Protocol
Calculation Method: Expression data (Cy5/Cy3 ratios) were extracted using Agilent Technologies Feature Extraction software (v. 9.1). Raw data were normalized with LIMMA package in R.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: Control reference pool

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction
Other: Total RNA was extracted using TRIzol reagent (Invitrogen).

value: spleen

value: Spleenic B-cells

tag: other

value: To allow comparing samples to one another, all samples were compared to a control pool of RNA (including splenic B cells (wild-type (WT) and ATMKO), with or without anti-IgM stimulation, ATMKO.CD3epsilonKO tumors, and ATMWT GC B cells (GCB)).

source_name: B cell lymphoma 1039

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

value: B cell lymphoma

value: lymphoma

tag: genotype/variation

value: gene knock out


title: B cell lymphoma 1001 - repeat 2 - mAdbID:128450

description: mAdb experiment ID: 128450

source_name: B cell lymphoma 1001

tag: disease state


title: ATMKO B cells - IgM Treated 6 hr - repeat 2 - mAdbID:128452

description: mAdb experiment ID: 128452

source_name: ATMKO B cells - IgM Treated 6 hr

treatment_protocol:
Agent: goat-anti-mouse IgM
Treatment dose: 15 ug/ml
Treatment time: 3 hours
In-vitro treatment: Spleenic B cells were stimulated in vitro with 15 ug/ml goat-anti-mouse IgM (Jackson ImmunoResearch) for 6 hours.

value: B cells


title: ATMWT GC B cells - repeat 2 - mAdbID:128447

description: mAdb experiment ID: 128447

source_name: ATMWT GC B cells

treatment_protocol:
Agent: SRBC
In-vivo treatment: GC B cells isolated from SRBC-immunized ATMWT mice.

value: ATMWT

value: GC B cells (germinal center B cells)


title: ATMKO B cells - IgM Treated 24 hr - mAdbID:128229

description: mAdb experiment ID: 128229

source_name: ATMKO B cells - IgM Treated 24 hr

treatment_protocol:
Agent: goat-anti-mouse IgM
Treatment dose: 15 ug/ml
Treatment time: 24 hours
In-vitro treatment: Spleenic B cells were stimulated in vitro with 15 ug/ml goat-anti-mouse IgM (Jackson ImmunoResearch) for 24 hours.


title: ATMKO B cells - Untreated - repeat 3 - mAdbID:128446

description: mAdb experiment ID: 128446

source_name: ATMKO B cells - Untreated


title: B cell lymphoma 1039 - repeat 1 - mAdbID:128228

description: mAdb experiment ID: 128228


title: B cell lymphoma 1010 - repeat 2 - mAdbID:128449

description: mAdb experiment ID: 128449

source_name: B cell lymphoma 1010


title: ATMKO B cells - Untreated - repeat 1 - mAdbID:128226

description: mAdb experiment ID: 128226


title: B cell lymphoma 1016 - mAdbID:128225

description: mAdb experiment ID: 128225

source_name: B cell lymphoma 1016


title: HCT116_Akti1/2 (Antibody Arrays (L-507))

type: protein

first: Ben

middle: S

last: Wittner

address: 185 Cambridge Street

department: Cancer Center

institute: Massachusetts General Hospital

description: Supernatant protein profiling after treatment with Akti-1/2 for 6 days.

hyb_protocol: Place each membrane printed side up into a Plastic Incubation Tray. One membrane per tray. Note: The printed membrane will have a “1” mark (for all L-507 membranes) “2” (for all L-493 membranes) in the upper left corner of the membrane. Add 8 ml of Blocking Buffer to each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 1 hour. Aspirate Blocking Buffer from each tray. Add 8 ml of diluted or undiluted sample onto each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 2 hours. Dilute 20X Wash Buffer 1 with deionized or distilled water to prepare the 1X Wash Buffer 1. Aspirate the samples from each tray and then wash by adding 20 ml of 1X Wash Buffer I at room temperature with gentle shaking (5 min per wash). Repeat the wash 2 more times for a total of 3 washes. Aspirate the 1X Wash Buffer 1 from each tray. Dilute 20X Wash Buffer 2 with deionized or distilled water to prepare the 1X Wash Buffer 2. Wash 3 times with 20 ml of 1X Wash Buffer 2 at room temperature with gentle shaking. Aspirate the 1X Wash Buffer 2 from each tray. Dilute the 500X HRP-Conjugated Streptavidin with Blocking Buffer to prepare the 1X HRP-Conjugated Streptavidin. Add 8 ml of 1X HRPConjugated Streptavidin to each membrane. Incubate at room temperature with gentle shaking for 2 hours. Wash as previously directed.

scan_protocol: For detection of 2 membranes, add 4.2 ml of Detection Buffer C and 4.2 ml of Detection buffer D into a tube and mix both solutions. Drain off excess wash buffer. Place membrane antibody side up (“1” or “2” symbol is marked in the top left corner of each membrane) on a clean plastic plate or its cover. Pipette 4 ml of the mixed Detection Buffers on to each membrane and incubate at room temperature for 2 minutes with gentle shaking. Ensure that the detection mixture is evenly covering the membrane without any air bubbles. Gently place the membrane with forceps (antibody side up) on a plastic sheet (provided) and cover the membrane with another plastic sheet. Gently smooth out any air bubbles. Avoid using pressure on the membrane. Work as quickly as possible. The signal can be detected directly from the membrane using a chemiluminescence imaging system or by exposing the array to x-ray film (we recommend using Kodak X-Omat™ AR film) with subsequent development. Expose the membranes for 40 seconds. Then re-expose the film according to the intensity of signals. If the signals are too strong (background too high), reduce exposure time (eg, 5–30 seconds). If the signals are too weak, increase exposure time (eg, 5–20 min or overnight). Or re-incubate membranes overnight with 1X HRP-Conjugated Streptavidin, and repeat detection on the second day. Save membranes at -20 °C to -80 °C for future reference.

data_processing: The manufacturer provided background-subtracted, positive-control normalized intensities for both L-507 and L-493 antibody arrays. For each one of the subarrays, all samples were mean-centered to a log2 value of 4.5. Data from both subarrays were combined after normalization.

molecule: protein

source_name: HCT116 colon carcinoma cells, Akti-1/2 treated

label_protocol: Immediately before use, prepare 1X Labeling Reagent by briefly centrifuging down the Labeling Reagent vial and add 100 µl 1X PBS (pH=8.0) into the vial. Pipette up and down or vortex briefly to dissolve the powder. Add an appropriate amount of 1X Labeling Reagent into the tube containing the sample and immediately mix the reaction solution. Incubate the reaction solution at room temperature for 30 minutes with gentle shaking. Gently tap the tube to mix the reaction solution every 5 minutes. Add 5 µl Stop Solution (Item D) into the reaction solution and then use the Spin Column to remove any unbound biotin. a). Twist off the bottom closure of the Spin Column and loosen the cap (but keep the cap on). Place the Spin Column into a 50 ml conical collection tube. b). Centrifuge the Spin Column at 1,000 g for 3 minutes to remove storage solution. c). Add 5 ml 1X PBS (pH=8.0) into the Spin Column and centrifuge at 1,000 x g for 3 minutes to remove the 1X PBS. Repeat an additional 2 times to wash the Spin Column. d). Place the Spin Column in a new 50 ml conical collection tube and slowly load 3.5 ml of sample to the center of the compact resin bed. e). Centrifuge the Spin Column at 1,000 x g for 3 minutes. The sample should filter through the resin and deposit into the 50 ml conical collection tube. Store at -80 ºC until needed. Discard the Spin Column after use.

growth_protocol: MCF7 was maintained in DMEM, 10% FCS, 40mM glutamine, 100 U/mL penicillin, and 100µg/mL streptomycin; HCT116 was maintained in McCoy’s 5α medium supplemented with 10% FCS, 100U/mL penicillin, and 100µg/mL streptomycin. All cells were grown at 37ºC and 5% CO2.

extract_protocol: Prepare dialysis buffer (1X PBS) by dissolving 0.6 g KCl, 24 g NaCl, 0.6 g KH2PO4 and 3.45 g Na2HPO4 in 2500 ml de-ionized or distilled water. Adjust to a pH of 8.0 with 1M NaOH and adjust final volume to 3000 ml with de-ionized or distilled water. Load each sample into 2 separate Dialysis Vials, 2.5-3.0 ml of sample per vial, total 5-6 ml per sample) for dialyzing. Carefully place all Dialysis Vials into the Floating Rack. Place the Floating Rack into ≥500 ml dialysis buffer in a large beaker. Place beaker on a stir plate and dialyze for at least 3 hours at 4 °C, occasionally gently stirring the dialysis buffer. Then exchange the dialysis buffer with fresh buffer and repeat dialysis for at least 3 hours at 4 °C. Transfer dialyzed samples into a clean eppendorf tube. Centrifuge dialyzed samples for 5 minutes at 10,000 rpm to remove B24any particulates or precipitates and then transfer and combine each sample into one clean eppendorf tube. Mix well by gently pipetting.

treatment_protocol: MCF7 and HCT116 cells were treated either with DMSO or Akti-1/2 for 6 days and culture supernatant were collected and frozen at -80°C until analysis.

value: colon carcinoma

tag: cell state

value: AKT1 Low


title: HCT116_DMSO (Antibody Arrays (L-507))

description: Supernatant protein profiling after treatment with DMSO for 6 days.

value: AKT1 WT


title: ATMKO B cells - Untreated - repeat 2 - mAdbID:128445

description: mAdb experiment ID: 128445

tag: tissue


title: B cell lymphoma 1007 - mAdbID:128218

description: mAdb experiment ID: 128218

source_name: B cell lymphoma 1007

tag: cell line


title: ATMWT GC B cells - repeat 3 - mAdbID:128448

description: mAdb experiment ID: 128448


title: B cell lymphoma 1013 - mAdbID:128221

description: mAdb experiment ID: 128221

source_name: B cell lymphoma 1013


title: B cell lymphoma 1036 - mAdbID:128227

description: mAdb experiment ID: 128227

source_name: B cell lymphoma 1036


title: ATMWT GC B cells - repeat 1 - mAdbID:128219

description: mAdb experiment ID: 128219


title: B cell lymphoma 1019 - mAdbID:128223

description: mAdb experiment ID: 128223

source_name: B cell lymphoma 1019


title: MCF7_DMSO (Antibody Arrays (L-507))

source_name: MCF7 breast adenocarcinoma cells, Akti-1/2 treated

value: breast adenocarcinoma


title: ATMKO B cells - IgM Treated 6 hr - repeat 1 - mAdbID:128222

description: mAdb experiment ID: 128222


title: ATMKO B cells - IgM Treated 3 hr - mAdbID:128224

description: mAdb experiment ID: 128224

source_name: ATMKO B cells - IgM Treated 3 hr

treatment_protocol:
Agent: goat-anti-mouse IgM
Treatment dose: 15 ug/ml
Treatment time: 3 hours
In-vitro treatment: Spleenic B cells were stimulated in vitro with 15 ug/ml goat-anti-mouse IgM (Jackson ImmunoResearch) for 3 hours.


title: B cell lymphoma 1010 - repeat 1 - mAdbID:128220

description: mAdb experiment ID: 128220


title: ATMWT B cells - IgM Treated 6 hr - mAdbID:128216

description: mAdb experiment ID: 128216

source_name: ATMWT B cells - IgM Treated 6 hr


title: B cell lymphoma 1004 - mAdbID:128217

description: mAdb experiment ID: 128217

source_name: Control reference pool

source_name: B cell lymphoma 1004


title: B cell lymphoma 1001 - repeat 1 - mAdbID:128214

description: mAdb experiment ID: 128214

source_name: B cell lymphoma 1001


title: ATMWT B cells - Untreated - mAdbID:128215

description: mAdb experiment ID: 128215

source_name: ATMWT B cells - Untreated