title: primed NK cells_normoxia_biological rep2


title: GBM.27

status: Public on May 09 2016

type: genomic

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

hyb_protocol: Equal quantity of Cy3- and Cy5-labelled DNA was hybridized into Agilent Human Genome CGH 8 x 60K microarray slide overnight, and washed according to supplier’s default protocol.

scan_protocol: The slides were scanned and decoded by the software Feature Extraction v. 10.7 (Agilent Technologies), using the protocol CGH_107_Sep09.

data_processing: The signal intensities were log2 transformed, and the spots were mapped in the most recent version of the human genome (hg19). The data was Lowess normalized and smoothing corrected. The data was CBS segmented.

molecule: genomic DNA

organism: Homo sapiens

source_name: Central Nervous System tumor

label_protocol: Four hundred nanograms of both tumor and blood DNA was digested by AluI and RsaI restriction enzymes, and incubated with random primers. Blood DNA was labeled with cyanine-3 (Cy3), whereas tumor DNA was labeled with cyanine-5 (Cy5)

extract_protocol: The DNA from patients blood was isolated using QIAmp DNA blood Mini Kit (Qiagen), and DNA from tumor frozen tissue was isolated using DNeasy Blood & Tissue Kit (Qiagen) according to the protocols provided by the supplier.

tag: tumor

value: Glioblastoma

source_name: Matched-patient leucocyte

tag: reference

value: Matched-patient leucocyte


title: prostate_cancer_primary_15

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: CA

address: 10355 Science Center Dr

country: USA

institute: GenomeDx Biosciences

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)

label: biotin

molecule: total RNA

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two [x] 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: pathologic gleason score

tag: age

tag: pathologic stage

tag: preoperative psa


title: resting NK cells_hypoxia_biological rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of HuGene-2_0-st-type from Affymetrix. A Custom CDF Version 17 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: resting NK cells_hypoxia

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

growth_protocol: Freshly isolated NK cells were plated at one million cells per mL RPMI 1640 supplemented with 10% fetal bovine serum and 2 mM L-glutamine in a 3ºC humidified atmosphere of 5% carbon dioxide (normoxia). One percent oxygen (hypoxia) was established in an oxygen controlled carbon dioxide incubator with a nitrogen gas line.

extract_protocol: Total RNA was prepared from NK cells stored in RNAlater using a spin column protocol followed by DNAse treatment according to the manufacturer's instructions.

treatment_protocol: Parallel NK cell cultures were grown under normoxia or hypoxia for 22 hours with or without 45 ng/mL IL-15 present during the final 6 hours.

tag: subject status

value: healthy donor

tag: tissue

value: peripheral blood

tag: cell type

value: Natural killer (NK) cells

tag: cultured under

value: Hypoxia for 22hrs

tag: treated with

value: none (control)


title: E1897B

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Hybridized to SNP5.0

hyb_protocol: fragmentation is confirmed by the presence of a smear between 50 to 200bp, the sample was end labeled with biotin and hybridized onto the array.  The chip was incubated at 49oC for 18 hours in the Affymetrix Genechip system hybridization oven

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing:
Raw GenomeWideSNP_5 CEL files were pre-processed using PennCNV [Wang K, 2007]. This protocol extracts allele-specific signal intensities from genotyping arrays, and then integrates information on SNP spacing and SNP allele frequencies to generate CNV calls by a hidden Markov model (HMM) algorithm.
PennCNV-Affy is a data-preprocessing protocol for Affymetrix genome-wide 5.0. The protocol converts raw CEL files into a signal intensity file that contains Log R Ratio (LRR) and B Allele Frequency (BAF) values.
CNV data can be calculated from LRR (2*2^LRR).

source_name: blood

label_protocol: As per manufacturer protocol (Affymetrix)

extract_protocol: blood DNA was extracted and purified using standard phenol/chloroform method and tumor DNA was extracted using Purification Tissue Kit (Centra System.)

value: blood

tag: disease state

value: control


title: GBM.37


title: GBM.144


title: primed NK cells_hypoxia_biological rep2

source_name: primed NK cells_hypoxia

value: 45 ng/mL IL-15 during the final 6h


title: E1882T

description: Hybridized to SNP5.0

source_name: tumor

value: tumor

value: esophageal cancer


title: resting NK cells_normoxia_biological rep1

source_name: resting NK cells_normoxia

value: Normoxia for 22hrs


title: GBM.51


title: E1880B

description: Hybridized to SNP5.0


title: prostate_cancer_primary_9


title: primed NK cells_normoxia_biological rep1

source_name: primed NK cells_normoxia


title: E1897T

description: Hybridized to SNP5.0


title: prostate_cancer_primary_6


title: E1885B

description: Hybridized to SNP5.0


title: GBM.72


title: GBM.35


title: prostate_cancer_primary_5


title: resting NK cells_hypoxia_biological rep1


title: GBM.12


title: prostate_cancer_primary_12


title: prostate_cancer_primary_8


title: E0410T

description: Hybridized to SNP5.0


title: primed NK cells_hypoxia_biological rep1


title: GBM.31


title: GBM.71


title: GBM.74


title: prostate_cancer_primary_7


title: prostate_cancer_primary_4


title: E1877T

description: Hybridized to SNP5.0


title: E1879T

description: Hybridized to SNP5.0


title: E1879B

description: Hybridized to SNP5.0


title: GBM.58


title: prostate_cancer_primary_3


title: E1877B

description: Hybridized to SNP5.0


title: GBM.67


title: GBM.142


title: GBM.54


title: GBM.32


title: GBM.14


title: GBM.16


title: GBM.139a


title: prostate_cancer_primary_1


title: prostate_cancer_primary_2


title: GBM.44


title: GBM.60


title: GBM.33


title: E1866T

description: Hybridized to SNP5.0


title: GBM.75


title: E1880T

description: Hybridized to SNP5.0


title: E1864T

description: Hybridized to SNP5.0


title: E1793T

description: Hybridized to SNP5.0


title: E1862T

description: Hybridized to SNP5.0


title: E1866B

description: Hybridized to SNP5.0


title: GBM.47


title: E1793B

description: Hybridized to SNP5.0


title: E1864B

description: Hybridized to SNP5.0


title: GBM.15


title: GBM.56


title: GBM.73


title: E1874B

description: Hybridized to SNP5.0


title: E1862B

description: Hybridized to SNP5.0


title: GBM.13


title: GBM.40


title: GBM.59


title: E1627B

description: Hybridized to SNP5.0


title: GBM.63


title: GBM.20


title: E1475T

description: Hybridized to SNP5.0


title: E1451B

description: Hybridized to SNP5.0


title: E1874T

description: Hybridized to SNP5.0


title: E1435B

description: Hybridized to SNP5.0


title: GBM.36


title: E1627T

description: Hybridized to SNP5.0


title: GBM.48b


title: E1451T

description: Hybridized to SNP5.0


title: E1450T

description: Hybridized to SNP5.0


title: E1450B

description: Hybridized to SNP5.0


title: E1475B

description: Hybridized to SNP5.0


title: E1416T

description: Hybridized to SNP5.0


title: E1416B

description: Hybridized to SNP5.0


title: E1400T

description: Hybridized to SNP5.0


title: E1435T

description: Hybridized to SNP5.0


title: E1415B

description: Hybridized to SNP5.0


title: GBM.138b


title: GBM.43


title: GBM.23


title: E1293T

description: Hybridized to SNP5.0


title: GBM.125


title: GBM.68


title: ANA.127

value: Anaplastic astrocytoma


title: GBM.55


title: ANA.121


title: GBM.11


title: E1415T

description: Hybridized to SNP5.0


title: E1242B

description: Hybridized to SNP5.0


title: E1242T

description: Hybridized to SNP5.0


title: E1256B

description: Hybridized to SNP5.0


title: ANA.107


title: ANA.114


title: GBM.25


title: ANA.140


title: ANA.105


title: DIF.106

value: Diffuse astrocytoma


title: E1195B

description: Hybridized to SNP5.0


title: DIF.104


title: ANA.123


title: E1179T

description: Hybridized to SNP5.0


title: E1210T

description: Hybridized to SNP5.0


title: DIF.111a


title: E1195T

description: Hybridized to SNP5.0


title: DIF.143


title: E1293B

description: Hybridized to SNP5.0


title: PIL.8

value: Pilocytic astrocytoma


title: E0742B

description: Hybridized to SNP5.0


title: E1400B

description: Hybridized to SNP5.0


title: E0746T

description: Hybridized to SNP5.0


title: E0822B

description: Hybridized to SNP5.0


title: E0796T

description: Hybridized to SNP5.0


title: DIF.119


title: E0746B

description: Hybridized to SNP5.0


title: E1179B

description: Hybridized to SNP5.0


title: E0822T

description: Hybridized to SNP5.0


title: DIF.110


title: PIL.108


title: E0844B

description: Hybridized to SNP5.0


title: E1256T

description: Hybridized to SNP5.0


title: E1210B

description: Hybridized to SNP5.0


title: E0742T

description: Hybridized to SNP5.0


title: E0381T

description: Hybridized to SNP5.0


title: E0796B

description: Hybridized to SNP5.0


title: E0387B

description: Hybridized to SNP5.0


title: PIL.137c


title: PIL.136


title: PIL.132c


title: PIL.134


title: DIF.112


title: PIL.3


title: E0844T

description: Hybridized to SNP5.0


title: E0381B

description: Hybridized to SNP5.0


title: E0362T

description: Hybridized to SNP5.0


title: EC8413T

description: Hybridized to SNP5.0


title: A375-SM_RMEL3_72h_rep2

status: Public on May 08 2016

city: Ribeirão Preto

first: Enilza

middle: Maria

last: Espreafico

state: São Paulo

address: Av. Bandeirantes, 3900

department: Cell and Molecular Biology

institute: University of São Paulo

description:
Sample name: A.RM3.2
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Background was subtracted and arrays were quantile normalized using GenomeStudio software (Illumina, CA).
GSGX Version: 1.9.0
Group Set: all
Analysis: all_quantile_bkgd
Normalization: quantile

label: Biotin

source_name: A375-SM cell line, RMEL3 sirRNA transfection

label_protocol: Biotinylated cRNA was synthesized by 14-hour amplification with dNTP mix containing biotin-dUTP and T7 RNA polymerase.

growth_protocol: A375-SM human melanoma cell line was grown in RPMI media supplemented with 5% of fetal bovine serum (Life Technologies) and incubated at 37°C and 5% of CO2.

extract_protocol: Three hundred nanograms of total RNA were amplified and purified using Illumina TotalPrep RNA Amplification Kit (Ambion, Cat# IL1791) following kit instructions. Briefly, first strand cDNA was synthesized by incubating RNA with T7 oligo(dT) primer and reverse transcriptase mix at 42 ºC for 2 hours. RNase H and DNA polymerase master mix were immediately added into the reaction mix following reverse transcription and were incubated for 2 hours at 16 ºC to synthesize second strand cDNA. RNA, primers, enzymes and salts that would inhibit in vitro transcription were removed through cDNA filter cartridges (part of the amplification kit).

treatment_protocol: Cells seeded in 6-well plates a day before were transfected with RMEL3 siRNA using Dharmafect 1 (Dharmacon) transfection reagent or control siRNA.

tag: cell line

value: super-metastatic human malignant melanoma cell line

tag: sirna


title: DIF.116


title: A375-SM_RMEL3_72h_rep3

description:
Sample name: A.RM3.3
Replicate 3


title: A375-SM_control_72h_rep3

description:
Sample name: U.NEG.3.3
Replicate 3

source_name: A375-SM cell line, control sirRNA transfection


title: A375-SM_control_72h_rep2

description:
Sample name: U.NEG.3.2
Replicate 2


title: E0387T

description: Hybridized to SNP5.0


title: A375-SM_control_72h_rep1

description:
Sample name: U.NEG.3.1
Replicate 1


title: EC1880T

description: Hybridized to SNP5.0


title: E0362B

description: Hybridized to SNP5.0


title: A375-SM_RMEL3_72h_rep1

description:
Sample name: A.RM3.1
Replicate 1


title: tFL-9

status: Public on May 07 2016

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

institute: UNMC

description: Gene expression data from transformed Follicular Lymphoma tumor

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing: MAS 5.0 Data Processing Protocol

source_name: tumor biopsy

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

extract_protocol: Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

tag: tumor type

value: transformed follicular lymphoma tumor


title: tFL-7


title: tFL-6


title: tFL-60


title: DIF.6

value: Matched-patient leucocyte


title: tFL-8


title: tFL-53


title: EC8413B

description: Hybridized to SNP5.0


title: tFL-54


title: tFL-57


title: EC1877T

description: Hybridized to SNP5.0


title: tFL-59


title: tFL-51


title: EC1415B

description: Hybridized to SNP5.0


title: tFL-4


title: tFL-5


title: tFL-32


title: EC1475B

description: Hybridized to SNP5.0


title: tFL-3


title: tFL-37


title: EC1415T

description: Hybridized to SNP5.0


title: tFL-36


title: tFL-33


title: EC0379B

description: Hybridized to SNP5.0


title: tFL-40


title: EC1475T

description: Hybridized to SNP5.0


title: tFL-224


title: tFL-23


title: tFL-221


title: tFL-218


title: EC0379T

description: Hybridized to SNP5.0


title: tFL-35


title: tFL-223


title: tFL-21


title: tFL-219


title: tFL-39


title: tFL-19


title: tFL-20


title: tFL-62


title: tFL-16


title: tFL-56


title: tFL-34


title: MCF7 cells treated with DMSO, biological rep3, technical rep2

city: Richmond

first: Justin

middle: Michael

last: Craig

state: Virginia

address: 1201 E Marshall St

department: Massey Cancer Center

institute: Virginia Commonwealth University

description: gene expression data from MCF7 cells serum starved for 24 hours prior to treatment with prolactin and/or bufexamac

hyb_protocol: As per the Affymetrix protocol, 10 μg of fragmented cRNA were hybridized on the GeneChip HG U133A 2.0 Arrays (Affymetrix Inc., Santa Clara, CA) for 16 hours at 60 rpm in a 45 °C hybridization oven. The arrays were washed and stained using the GeneChip Hybridization, Wash, and Stain Kit in the Affymetrix fluidics workstation.

scan_protocol: Every chip was scanned at a high resolution, on the Affymetrix GeneChip Scanner 3000 7G according to the GeneChip Expression Analysis Technical Manual procedures (Affymetrix, Santa Barbara, CA). After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the GeneChip Operating Software v1.4 (GCOS) (Affymetrix, Santa Barbara, CA).

data_processing: The 24 resultant .CEL files were analyzed using the R statistical computing language and environment. The data quality of each microarray was assessed by examining the average background, percent of probe sets called present by the MAS5 detection call algorithm, and the 3’:5’ ratio for GAPDH and ACTIN. Additionally, to detect potential spatial artifacts resulting from sub-optimal hybridization conditions, probe level linear models were fit using the R Bioconductor package, “affyPLM”, and plots of the residuals were examined for each microarray. Differential expression was assessed using the “affy” and “limma” Bioconductor packages. Briefly, probesets were quantile normalized and processed by the Robust Multi-Array Average (RMA) algorithm before the manufacturer’s control probesets and probesets considered “absent” in 20 or more arrays by the MAS5 algorithm were filtered from all arrays. Differential expression between treatment conditions was then assessed via moderated t-test adjusted for multiple hypotheses by the Benjamini & Hochberg method.

label_protocol: Each RNA sample was labeled according to the Affymetrix protocol with the following modifications: Starting with 500 ng of total RNA, we performed a single-strand cDNA synthesis primed with a T7-(dT24) oligonucleotide. Second strand cDNA synthesis was performed with E. coli DNA Polymerase I, and biotinylation of the cRNA was achieved by in vitro transcription (IVT) reaction using the GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA). After a 37°C-incubation for 16 hours, the labeled cRNA was purified using the cRNA cleanup reagents from the GeneChip Sample Cleanup Module.

growth_protocol: Prior to RNA isolation, MCF7 cells were plated in DMEM with 10% FBS at 60% confluency in 6 cm plates and incubated for 24 hours followed by an additional 24 hours of serum starvation in DMEM and 1X ITS Liquid Media Supplement.

extract_protocol: RNA was extracted using the MagMAX-96 for Microarrays Total RNA Isolation Kit (Invitrogen, Life Technologies, Carlsbad, CA) in an automated fashion using the magnetic particle processors MagMAX Express. RNA purity was judged by spectrophotometry at 260, 270, and 280 nm. RNA integrity was assessed by running 1 µL of every sample in RNA 6000 Nano LabChips on the 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).

treatment_protocol: Cells were then treated for 4 hours with either DMSO (0.1%) or Bufexamac (100 uM) before stimulation with prolactin (PRL; 250 ng/mL). After 2 hours PRL stimulation, cells were washed with PBS and RNA was extracted.

tag: gender

value: female

value: breast

value: epithelial

tag: cancer type

value: breast adenocarcinoma


title: tFL-15


title: tFL-2


title: MCF7 cells treated with bufexamac, biological rep3, technical rep2


title: EC1877B

description: Hybridized to SNP5.0


title: EC1880B

description: Hybridized to SNP5.0


title: tFL-14


title: tFL-38


title: tFL-17


title: tFL-18


title: tFL-1


title: MCF7 cells treated with bufexamac, biological rep3, technical rep1


title: MCF7 cells treated with prolactin and DMSO, biological rep3, technical rep1


title: MCF7 cells treated with bufexamac, biological rep2, technical rep2


title: MCF7 cells treated with prolactin and bufexamac, biological rep3, technical rep2


title: MCF7 cells treated with DMSO, biological rep2, technical rep1


title: MCF7 cells treated with DMSO, biological rep2, technical rep2


title: MCF7 cells treated with DMSO, biological rep3, technical rep1


title: tFL-10


title: MCF7 cells treated with prolactin and DMSO, biological rep2, technical rep2


title: MCF7 cells treated with bufexamac, biological rep2, technical rep1


title: MCF7 cells treated with prolactin and bufexamac, biological rep3, technical rep1


title: tFL-52


title: MCF7 cells treated with prolactin and DMSO, biological rep3, technical rep2


title: MCF7 cells treated with prolactin and DMSO, biological rep2, technical rep1


title: MCF7 cells treated with DMSO, biological rep1, technical rep2


title: MCF7 cells treated with DMSO, biological rep1, technical rep1


title: MCF7 cells treated with prolactin and bufexamac, biological rep2, technical rep1


title: MCF7 cells treated with prolactin and bufexamac, biological rep1, technical rep1


title: MCF7 cells treated with bufexamac, biological rep1, technical rep2


title: MCF7 cells treated with prolactin and DMSO, biological rep1, technical rep1


title: MCF7 cells treated with prolactin and bufexamac, biological rep2, technical rep2


title: MCF7 cells treated with prolactin and bufexamac, biological rep1, technical rep2


title: MCF7 cells treated with bufexamac, biological rep1, technical rep1


title: MCF7 cells treated with prolactin and DMSO, biological rep1, technical rep2


title: Mice-Medium 12hpi-rep2

city: Shreveport

first: Seong

middle: K

last: Kim

state: Louisiana

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: LSU Health Sciences Center

hyb_protocol: Biotin labeled cRNA are hybridized with Mouse 430 array using Affymetrix Standard Protocol.

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

data_processing: Raw data were processed with the Expression Console (Affymetrix) for MAS5 summarization and Quantile normalization.

organism: Mus musculus

source_name: Mice-Medium 12hpi_lung

label_protocol: Amplified and biotinylated cRNA was generated from total RNA using 3' IVT PLUS kit from (Affymetrix)

growth_protocol: Female CBA mice, 3 to 4 weeks of age, obtained from Harlan Sprague Dawley (Indianapolis, IN), were maintained in filter-topped cages within the Animal Resource Facility of the Louisiana State University Health Sciences Center, Shreveport. The Animal Resource Facility is certified by the Association for Assessment and Accreditation of Laboratory Animal Care International. All procedures were previously approved by the University Animal Care Committee. All mice rested for a period of 5 to 7 days prior to use. All experimental groups consisted of five mice each, and all experiments were repeated a minimum of three times

extract_protocol: Total lung RNA was obtained by grinding the lungs in glass tissue grinders in the presence of TRIzol (Life Technologies, Grand Island, N.Y.). Poly(A)+ RNA was isolated from total RNA using the FastTrack 2.0 kit (Invitrogen, San Diego, CA) according to the manufacturer's instructions.

treatment_protocol: Lungs of the mice infected with 1.5x10^6 pfu of EHV-1 KyA were harvested at 6, 8, and 12 hours post-infection (hpi). Affymetrix microarray analyses were performed with infected mice lung RNA. Mock-infected lung RNAs were used as a control. Lungs of the mice infected with 1.5x106 pfu of EHV-1 RacL11 were harvested at 8 hpi. Affymetrix microarray analyses were performed with infected mice lung RNA. Mock-infected lung RNAs were used as a control. Lungs of the mice were immunized with 2x106 pfu of EHV-1 KyA, challenged with 1.5x106 pfu of RacL11 at 3 days post-immunization, and were harvested at 8 h post-RacL11 challenge infection. Affymetrix microarray analyses were performed with infected mice lung RNA. Mock-infected lung RNAs were used as a control. Lungs of the mice were immunized with 2x106 pfu of heat-inactivated EHV-1 KyA (HI-KyA), challenged with 1.5x106 pfu of RacL11 at 3 days post-immunization, and were harvested at 8 h post-RacL11 challenge infection. Affymetrix microarray analyses were performed with infected mice lung RNA. Mock-infected lung RNAs were used as a control.

tag: strain

value: CBA

value: lung


title: Mice-L11 8hpi-rep1

source_name: Mice-L11 8hpi_lung


title: Mice-L11 8hpi-rep3


title: Mice-KyA 6hpi-rep2

source_name: Mice-KyA 6hpi_lung


title: Mice-KyA 8hpi-rep1

source_name: Mice-KyA 8hpi_lung


title: Mice-L11 8hpi-rep2


title: Mice-KyA→L11 8hpi-rep1

source_name: Mice-KyA→L11 8hpi_lung


title: Mice-KyA→L11 8hpi-rep3


title: Mice-KyA 8hpi-rep4


title: Mice-KyA 12hpi-rep2

source_name: Mice-KyA 12hpi_lung


title: Mice-KyA 12hpi-rep1


title: Mice-KyA 12hpi-rep3


title: Mice-Medium 8hpi-rep1

source_name: Mice-Medium 8hpi_lung


title: Mice-Medium 8hpi-rep3


title: Mice-Medium 8hpi-rep2


title: Mice-KyA 6hpi-rep1


title: Mice-KyA 8hpi-rep3


title: Mice-HI KyA→L11 8hpi-rep3

source_name: Mice-HI KyA→L11 8hpi_lung


title: Mice-KyA→L11 8hpi-rep2


title: Mice-HI KyA→L11 8hpi-rep2


title: Mice-HI KyA→L11 8hpi-rep1


title: Mice-KyA 8hpi-rep2


title: HH panobinostat

city: Akita

first: Akihiro

last: Kitadate

address: Hondo 1-1-1

department: Department of Hematology, Nephrology, and Rheumatology

country: Japan

institute: Akita University Graduate School of Medicine

hyb_protocol: As materials and methods for miRNA mycroarray protocol version 2.4 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent). Normalization was not performed.

source_name: HH panobinostat

growth_protocol: Cells were cultured in Arteimis-1 medium with or 2% inactivated human serum

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: Normal CD4+T-cells, My-La, HH and HUT78 cells were treated with vorinostat (5 µM) or panobinostat (80 nM) for 24 hr

value: CTCL

value: HH

tag: drug

value: panobinostat


title: HUT78 SAHA

source_name: HUT78 SAHA

label_protocol: As materials and methods for miRNA mycroarray protocol version 2.4 (Agilent).

value: SAHA


title: HUT78 panobinostat

source_name: HUT78 panobinostat


title: CD4+ T-cell DMSO

source_name: CD4+ T-cell DMSO

value: healthy control

value: CD4+ T-cell

value: DMSO


title: HUT78 DMSO

source_name: HUT78 DMSO


title: CD4+ T-cell SAHA

source_name: CD4+ T-cell SAHA


title: CD4+ T-cell panobinostat

source_name: CD4+ T-cell panobinostat


title: My-La panobinostat

source_name: My-La panobinostat

value: My-La


title: HH DMSO

source_name: HH DMSO


title: HH SAHA

source_name: HH SAHA


title: Mice-Medium 12hpi-rep1

source_name: Mice-Medium 12hpi_lung


title: My-La SAHA

source_name: My-La SAHA


title: Y955C-Old-3

status: Public on May 06 2016

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

department: Pathology

institute: Emory University

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001)following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol

data_processing: Each sample was processed utilizing NimbleScan software default values, including analysis of the 635/532 ratio utilizing a 500bp sliding window KS test according to manufacturer instructions.

source_name: Methylated Genomic DNA

label_protocol: DNA labeling was completed using NimbleGen Dual-Color DNA labeling Kit (Cat # 06370250001) following their standard operating protocol.

extract_protocol: DNA was extracted  using a MagNAPure DNA Extraction System (Roche), quantiated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA was amplified using whole genome amplification (Sigma-Aldrich).

tag: genotype

value: Y955C-mutated mitochondrial DNA polymerase gamma

tag: tissue type

value: heart

source_name: Total Genomic DNA


title: Y955C-Old-4


title: Wt-Old-3

value: Wild type


title: My-La DMSO

source_name: My-La DMSO


title: Wt-Old-1


title: Y955C-Young-4


title: Y955C-Young-3


title: Wt-Old-4


title: Y955C-Young-1


title: Y955C-Young-2


title: Wt-Old-2


title: WT-Young-1


title: WT-Young-2


title: Y955C-Old-1


title: WT-Young-3


title: Y955C-Old-2


title: hyb6926

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 14 pmol; Cy5 label: 10 pmol) was hybridised on Agilent's 4x44K Whole Mouse Genome Microarrays followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with Surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.1.1.1).

data_processing: The Agilent processed signal values (i.e., features gProcessedSignal and rProcessedSignal from Agilent Feature Extraction v10.1.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3 intensities) were computed and in case of multiple probes for the same Agilent ID, log2-intensities were averaged. Control probes were removed prior to analysis.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Total RNA was prepared using the Absolutely RNA Miniprep Kit (Agilent). All RNA samples were treated with RNase-free DNase I. RNA quality was verified on an Agilent 2100 Bioanalyser using the RNA 6000 Nano LabChip kit (Agilent).

tag: genotype/variation

value: Atg7+/+ SM22α-Cre+

value: Primary aortic smooth muscle cells

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

value: Atg7F/F SM22α-Cre+


title: hyb6927


title: hyb6925


title: hyb6928


title: WT-Young-4


title: none_none_wt (8784129079_F)

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in Partek Genomic Suite

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

value: wt

tag: age

value: 2-5 months

tag: agent

tag: treatment

value: bone marrow derived macrophages


title: none_none_wt (8784129079_E)

tag: cell type


title: none_none_wt (8615616013_D)


title: none_none_wt (8762536005_F)


title: SW480_Treated Rep3

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: 4, Raja S. C. Mullick Road

department: Cancer Biology and Inflammatory Disorder Division

country: India

institute: CSIR-Indian Institute of Chemical Biology

description: Replicate 2

hyb_protocol: Purified biotin labelled cRNAs were hybridised to the Beadchip using Direct hybridisation Whole-Gene Expression assay, according to the manufacturer's protocol (Illumina Inc., San Diego, CA). Subsequently  washing, blocking, and streptavidin-Cy3 staining were done followed by serial nonstringent washing steps to remove unbound conjugate.

scan_protocol: An Illumina iScan Reader was used to read the Illumina bioarrays and the primary intensity data were acquired in standard file format, using Genome  Studio

data_processing: Raw average signal intensity  was background substracted in Genome Studio and imported to bioconductor Lumi Package for data transformation (Log2 transformed). Robust Spline method was used for normalisation. Differential expression was performed in bioconductor package Limma. Up-regulated and down-regulated genes with adjusted p-value < 0.05, and fold change ≥ 1.5 in Floxuridine treated Sw480 cells  were considered for further analysis.

label_protocol: Isolated mRNA was reverse-transcribed to cDNA followed by labelled cRNA preparation using Illumina® TotalPrep™ RNA Amplification Kit

growth_protocol: SW480 cell line was  cultured in DMEM medium (Life Technologies, Thermo Fisher Scientific Inc., MA USA) supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted from Floxuridine treated or untreated SW480 cells using Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the   manufacturer’s protocol. Briefly,  cells were lysed in RLT lysis buffer and subsequently mixed with equal volume of 70% ethanol. The mix was then passed through RNeasy Spin column  followed by on column DNase treatment. The  column was subsequently washed with wash buffer and the column-bound RNA were eluted in RNase free water.The quality of the isolated RNA was checked in Agilent Bioanalyser (Santa Clara).

treatment_protocol: SW480 cells were treated with either 10 µg/ml FUdR (T) or  DMSO (UT)  for 24 hr before harvesting

value: Male

tag: tissue

value: Colon

tag: tumor stage

value: Primary adenocarcinoma of the colon

value: Floxuridine (FUdR)


title: none_crystals_wt (8762536007_F)

value: cholesterol crystals


title: SW480_Untreated Rep2

description: Replicate 1

value: untreated


title: SW480_Untreated Rep3

description: Replicate 1


title: none_crystals_wt (8615616013_F)


title: none_none_wt (8762536031_D)


title: none_crystals_wt (8784129079_C)


title: none_crystals_wt (8762536005_C)


title: CD_crystals_wt (8762536031_F)

value: CD


title: SW480_Treated Rep1

description: Replicate 2


title: SW480_Treated Rep2

description: Replicate 2


title: CD_none_wt (8784129079_B)


title: CD_none_wt (9020366075_F)


title: CD_crystals_wt (9020366075_C)


title: SW480_Untreated Rep1

description: Replicate 1


title: none_crystals_wt (8615616013_E)


title: CD_none_wt (8784129079_A)


title: none_none_DKO-LXR (8762536007_C)

value: LXRa/LXRb dko


title: CD_crystals_wt (8615616013_B)


title: CD_none_wt (8762536007_B)


title: CD_none_wt (8784129079_D)


title: CD_crystals_wt (8615616013_C)


title: none_none_DKO-LXR (8762536007_D)


title: CD_crystals_wt (8615616013_A)


title: none_crystals_DKO-LXR (9020366075_B)


title: pG1300-3, biological rep3

city: Haikou

first: Mengbin

last: Ruan

address: Xueyuan Rd 4#

country: China

institute: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science

description: Gene expression data from pG1300 Arabidopsis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were read by Affymetrix® GeneChip® Command Console® Software and used RMA as normalization method. Diffenet expression genes were identified by SAM method.

organism: Arabidopsis thaliana

source_name: Transgenic Arabidopsis, 45-day-old

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

growth_protocol: Transgenic Arabidopsis plants were grow in 12 hrs light/12 hrs dark at 22 ℃ for 45 days.

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

treatment_protocol: normal conditions

tag: transgenic construct

value: empty vector

value: mature leaves

value: 45 days


title: none_none_DKO-LXR (9020366075_A)


title: none_none_DKO-LXR (8762536005_E)


title: none_crystals_DKO-LXR (8762536005_A)


title: none_crystals_DKO-LXR (8762536031_E)


title: none_crystals_DKO-LXR (8762536005_D)


title: pG1300-1, biological rep1


title: pG1300-2, biological rep2


title: CD_none_DKO-LXR (8762536031_C)


title: MeGRX232-OE-12, biological rep3

description: Gene expression data from MeGRX232-OE Arabidopsis


title: 101036350014_H

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

country: Canada

institute: Université de Montréal

description: replicate 4

data_processing: RMA background adjusted / quantile normalized / log2 transformed

source_name: Transfected with Ypel5-specific siRNA rep2

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

growth_protocol: RAW 264.7 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 units/ml penicillin, 100 µg/ml streptomycin and 2 mM glutamine.

extract_protocol: RNA was extracted with Rneasy microkit with DNase I treatment in accordance with the prescribed protocol  provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with either the Ypel5-specific SASI_Mm01_00066332 siRNA or the scrambled MISSION® siRNA SIC001 (Sigma-Aldrich, St-Louis, MO), using HiPerfect reagents (Qiagen).

value: Balb/c

tag: cell line


title: CD_none_DKO-LXR (8762536031_A)


title: 101036350014_F

description: replicate 3


title: CD_crystals_DKO-LXR (9020366075_D)


title: CD_crystals_DKO-LXR (8762536031_B)


title: 101036350014_D

description: replicate 2


title: MeGRX232-OE-3, biological rep1


title: WT-Ve (9853741046_C)

source_name: WT-Ve

tag: strain of recipient mice

tag: genotype of recipient mice

value: LDLR ko

tag: strain of bone-marrow donor

tag: genotype of bone-marrow donor

value: WT

value: 6 months

value: Ve

value: descending aorta


title: CD_none_DKO-LXR (9020366075_E)

tag: strain

value: 2-5 months

value: bone marrow derived macrophages


title: MeGRX360-OE-20, biological rep3

description: Gene expression data from MeGRX360-OE Arabidopsis


title: CD_none_DKO-LXR (8762536007_E)


title: CD_crystals_DKO-LXR (8762536005_B)


title: MeGRX360-OE-5, biological rep1


title: 101036350014_G

description: replicate 4

source_name: Transfected with scrambled siRNA rep1


title: WT-Ve (9853741051_B)

tag: gender

value: Female


title: 101036350014_C

description: replicate 2

source_name: Transfected with scrambled siRNA rep2


title: MeGRX360-OE-11, biological rep2


title: WT-Ve (9853741045_A)


title: 101036350014_E

description: replicate 3


title: CD_crystals_DKO-LXR (8762536007_A)

tag: genotype


title: 101036350014_A

description: replicate 1


title: 101036350014_B

description: replicate 1

source_name: Transfected with Ypel5-specific siRNA rep1


title: WT-Ve (9853741026_A)

value: Male


title: WT-Ve (9853741026_E)


title: WT-Ve (9853741011_A)


title: replacement_pmys-EBF1ΔC-IRES-GFP-Rep3

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Gene expression after  pmys-EBF1ΔC-IRES-GFP transduction and tamoxifen treatment

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 manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 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 (G2505C) using one color scan setting for 4x44k 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.

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre),2μM 4-hydroxy-tamoxifen (4-OHT) treated, pmys-EBF1ΔC-IRES-GFP,Replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit (One-Color) and RNA Spike-In Kit, according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: A-MuLV transformed cells were cultured without feeder cells in RPMI medium supplemented with 10% FCS, 1% PSG and 50μM β-mercaptoethanol.

extract_protocol: RNA was prepared with the RNeasy Mini Kit following the manufacturer's recommendations.

treatment_protocol: A-MuLV transformed Ebf1fl/fl RERTCre pro-B cells were transfected by pmys-EBF1wt-IRES-GFP or pmys-EBF1ΔC-IRES-GFP and treated with 2μM 4-hydroxy-tamoxifen (4-OHT) 24h after transduction. Five days after treatment, cells were sorted as GFP+. More than two week later, the replacement was validated by IB and the cells were used for downstream analyses. As control, mock-transduced cells were harvested four days after tamoxifen treatment before cell death was observed.

value: A-MuLV transformed pro-B cells

tag: background strain


title: WT-CD (9853741062_E)

source_name: WT-CD


title: replacement_pmys-EBF1wt-IRES-GFP-Rep3

description: Gene expression after pmys-EBF1wt-IRES-GFP transduction and tamoxifen treatment

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), pmys-EBF1wt-IRES-GFP,Replicate3

treatment_protocol: A-MuLV transformed Ebf1fl/fl RERTCre pro-B cells were transfected by pmys-EBF1wt-IRES-GFP or pmys-EBF1DC-IRES-GFP and treated with 2μM 4-hydroxy-tamoxifen (4-OHT) 24h after transduction. Five days after treatment, cells were sorted as GFP+. More than two week later, the replacement was validated by IB and the cells were used for downstream analyses. As control, mock-transduced cells were harvested four days after tamoxifen treatment before cell death was observed.


title: WT-CD (9853741051_E)


title: replacement_Mock-Rep2

description: Gene expression after tamoxifen treatment

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), 2μM 4-hydroxy-tamoxifen (4-OHT) treated ,Replicate2


title: LXR dko-Ve (9853741062_B)

source_name: LXR dko-Ve


title: LXR dko-Ve (9853741062_D)


title: Y955C-Old-3

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

source_name: Total RNA from Y955C-Old Left Ventricle

label_protocol: DNA labeling was completed using NimbleGen labeling Kit following their standard operating protocol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and cDNA was synthesized using Superscript Double-Stranded cDNA Synthesis kit (Invitrogen/Life Technologies).  cDNA quality was determined using a Spectramax 190 plate reader ( ) for A260 and A280 absorbance determination along with gel electrophoresis.

value: Y955C-mutated mitochondrial DNA polymerase gamma

tag: tissue type

value: heart


title: MeGRX232-OE-9,biological rep2

tag: age


title: WT-CD (9853741045_E)

value: CD


title: WT-CD (9853741026_C)


title: WT-CD (9853741011_C)


title: replacement_pmys-EBF1wt-IRES-GFP-Rep2

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), 2μM 4-hydroxy-tamoxifen (4-OHT) treated, pmys-EBF1wt-IRES-GFP,Replicate2


title: pmys-EBF1ΔC-IRES-GFP-Rep2

description: Gene expression after  pmys-EBF1ΔC-IRES-GFP transduction

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 manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°Cin 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.

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1ΔC-IRES-GFP,Replicate2

growth_protocol: Single cell suspensions of freshly isolated Ebf1−/− fetal liver cells were stained with biotinylated c-Kit and c-Kit positive cells were enriched on an AutoMACS separator and subsequently plated on OP9 feeder cells in OptiMEM medium, supplemented with 4% FCS, 1% PSG, 50 μM β-mercaptoethanol, 5 ng/ml interleukin 7 (IL-7), 10 ng/ml Flt3 ligand (Flt3L) and 10 ng/ml stem cell factor (SCF).

treatment_protocol: Retroviral transductions with pMys-EBF1wt-IRES-GFP, pMys-EBF1ΔC-IRES-GFP or pMys-IRES-GFP (vector) retrovirus were performed. 24h after transduction, cells were sorted as GFP+ cells and re-plated on OP9 cells.

value: fetal liver

tag: cell marker

value: c-Kit+


title: pmys-EBF1ΔC-IRES-GFP-Rep3

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1ΔC-IRES-GFP,Replicate3


title: replacement_Mock-Rep3

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), 2μM 4-hydroxy-tamoxifen (4-OHT) treated ,Replicate3


title: replacement_pmys-EBF1ΔC-IRES-GFP-Rep1

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre),2μM 4-hydroxy-tamoxifen (4-OHT) treated, pmys-EBF1ΔC-IRES-GFP,Replicate1


title: pmys-EBF1wt-IRES-GFP-Rep3

description: Gene expression after pmys-EBF1wt-IRES-GFP transduction

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1wt-IRES-GFP,Replicate3


title: replacement_pmys-EBF1wt-IRES-GFP-Rep1

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), 2μM 4-hydroxy-tamoxifen (4-OHT) treated, pmys-EBF1wt-IRES-GFP,Replicate1


title: LXR dko-CD (9853741062_C)

source_name: LXR dko-CD

value: LXRa/LXRb dko

tag: treatment


title: LXR dko-Ve (9853741046_A)


title: WT-CD (9853741046_E)


title: LXR dko-Ve (9853741045_F)


title: WT-Old-2

source_name: Total RNA from WT-Old Left Ventricle

value: Wild type


title: Y955C-Old-2


title: LXR dko-Ve (9853741051_C)

value: LDLR ko


title: WT-Old-3


title: Y955C-Old-1


title: pmys-EBF1ΔC-IRES-GFP-Rep1

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1ΔC-IRES-GFP,Replicate1


title: WT-Old-1


title: replacement_Mock-Rep1

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), 2μM 4-hydroxy-tamoxifen (4-OHT) treated ,Replicate1

tag: cell type


title: ZR-75 - repeat 3

city: Springfield

first: Sophia

last: Ran

state: IL

address: 801 N. Rutledge St.

department: MMICB

institute: Southern Illinois University - School of Medicine

description: Cell Line

data_processing:
Matrix non-normalized i.e. Ct values were obtained from each PCR run using an Eppendorf MasterCycle ep realplex program.
Matrix normalized values show target gene expression normalized to ACTB; 2^-deltaCt*100, where deltaCt = (Ct_Target − Ct_ACTB)
Matrix non-normalized values are Ct values from individual repeats.
Matrix normalized values are deltaCt numbers generated from Ct values normalized to β-actin.

label: SYBR GREEN

label_protocol: Total RNA was reverse transcribed using Revert Aid cDNA synthesis kit (Fermentas, Canada), using 2 µg RNA per 20 µl reaction per manufacturer’s protocol. Primers were designed based on CDS of human targets found in NCBI database and described in Manufacture Protocol section. RT-qPCR was performed using GoTaq Green Master Mix (Promega, WI) with a total reaction volume of 10 µL, including 1 µl cDNA, 5 µl Master Mix, 0.25 µl of each forward and reverse primer, and 3.5 µl DNase water. A MasterCycle realplex PCR machine (Eppendorf, NY) was used and cycling conditions were as follows: 95°C for 2 min followed by 40 cycles of 95°C for 15 s and 65°C for 60 s. A melting curve analysis was performed for each reaction to confirm the absence of nonspecific binding or contamination.

growth_protocol: ZR-75 cell line was cultured in 5% FBS in DMEM at 37ºC in a 10% CO2 incubator.

extract_protocol: Total RNA was isolated by TRI-Reagent.

tag: disease

value: Ductal carcinoma

tag: er

value: Positive

tag: pr


title: ZR-75 - repeat 2

description: Cell Line


title: pmys-EBF1wt-IRES-GFP-Rep2

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1wt-IRES-GFP,Replicate2

tag: tissue


title: ZR-75 - repeat 1

description: Cell Line


title: LXR dko-CD (9853741051_D)

tag: strain of recipient mice

value: 6 months


title: T47D - repeat 3

description: Cell Line

growth_protocol: T47D cell line was cultured in 5% FBS in DMEM at 37ºC in a 10% CO2 incubator.

value: Negative


title: LXR dko-CD (9853741046_D)

tag: genotype of recipient mice

value: descending aorta


title: Y955C-Young-1

source_name: Total RNA from Y955C-Young Left Ventricle


title: LXR dko-CD (9853741026_F)

tag: strain of bone-marrow donor


title: pmys-Empty-IRES-GFP-Rep3

description: Gene expression after pmys-Empty-IRES-GFP transduction

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-Empty-IRES-GFP,Replicate3


title: WT-Young-3

source_name: Total RNA from WT-Young Left Ventricle


title: pmys-EBF1wt-IRES-GFP-Rep1

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1wt-IRES-GFP,Replicate1


title: pmys-Empty-IRES-GFP-Rep1

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-Empty-IRES-GFP,Replicate1


title: Y955C-Young-3


title: pmys-Empty-IRES-GFP-Rep2

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-Empty-IRES-GFP,Replicate2


title: LXR dko-CD (9853741026_B)

tag: genotype of bone-marrow donor


title: T47D - repeat 2

description: Cell Line


title: WT-Young-2

tag: strain


title: LXR dko-CD (9853741011_F)

tag: gender


title: WT-Young-1

tag: genotype


title: T47D - repeat 1

description: Cell Line


title: SUM149 - repeat 3

description: Cell Line

growth_protocol: SUM149 cell line was cultured in 5% FBS in DMEM at 37ºC in a 10% CO2 incubator.


title: Cohort 3 - 7 Month TECs

city: Stanford

first: Kenneth

last: Weinberg

address: 1291 Welch Road, G3040

department: Pediatrics

institute: Stanford University

description: Gene expression data from thymic epithelial cells isolated from7 months old mice.

hyb_protocol: The fragmented and labeled targets were hybridized to GeneChip Mouse 430 2.0 Array (Affymetrix) according to the manufacturer’s protocol, which includes 16hr (overnight) hybridization at 45°C at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics  Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip scanner 3000 7G.

data_processing: Analyses were performed using STATA software, GOCSv.1.4 and Expression Console, the Broad/MIT Molecular Signature Database ( http://www.broad.mit.edu/gsea ), BioCarta ( http://www.biocarta.com ).

source_name: The thymus from 7 months old C57Bl/6 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ng total RNA.

growth_protocol: Thymic epithelial cells (CD45-EpCam+) FACS sorted from the fresh thymus were diretly used for RNA extraction.

extract_protocol: Total RNA extracted from mouse TECs, using PicoPure RNA Isolation Components Kit (Arctrus Technoloies), and its quality was assessed by gel electrophoresis and Agilent 2100 Bioanalyzer. Total RNA (100ng) was reverse transcribed into cDNA followed by in vitro transcription and labeling to produce biotinylated complementary RNA using an IVT labeling kit (Affymetrix, Santa Clara, CA).

treatment_protocol: The fresh thymus was treated with DNaseI (25 μg/ml), collagenase IV (0.2 mg/ml) in 10% FBS/DMEM for 30 min to make single cell suspansion. The cells washed with PBS twice and then incubated with CD90.2 MicroBeads for 15 min on ice. After depleting CD90.2 labeled thymic lymphoid cells with MACS, the cells further incubated with PE-Cy7-anti-CD45 and APC-anti-EpCAm for 30min on ice and washed with PBS twice.

value: 7 months old


title: replacement_pmys-EBF1ΔC-IRES-GFP-Rep2

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre),2μM 4-hydroxy-tamoxifen (4-OHT) treated, pmys-EBF1ΔC-IRES-GFP,Replicate2

tag: background strain


title: Cohort 1 - 15 Month TECs

description: Gene expression data from thymic epithelial cells isolated from 15 months old mice.

source_name: The thymus from 15 months old C57Bl/6 mice

value: 15 months old


title: Cohort 2 - 15 Month TECs


title: Y955C-Young-2

tag: tissue type


title: Cohort 2 - 7 Month TECs

tag: age


title: MDA-MB-231 - repeat 3

description: Cell Line

growth_protocol: MDA-MB-231 cell line was cultured in 5% FBS in DMEM at 37ºC in a 10% CO2 incubator.

value: Adenocarcinoma


title: SUM149 - repeat 2

description: Cell Line


title: Cohort 3 - 15 Month TECs


title: SUM149 - repeat 1

description: Cell Line


title: Cohort 3 - 6 Week TECs

description: Gene expression data from thymic epithelial cells isolated from 6 weeks old mice.

source_name: The thymus from 6 weeks old C57Bl/6 mice

value: 6 weeks old


title: MDA-MB-231 - repeat 2

description: Cell Line


title: Cohort 1 - 7 Month TECs


title: MT-2 Control IgG

city: Tokyo

first: Makoto

last: Yamagishi

address: 4-6-1, Shirokanedai, Minatoku

department: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences

institute: The University of Tokyo

hyb_protocol: Hybridization was performed at 65°C for 40h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with Agilent Oligo aCGH/ChIP-on-chip Wash Buffer 1 for 5min and with Agilent Oligo aCGH/ChIP-on-chip Wash Buffer 2 for 5min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner C using the two color scan setting for 2x400K microarray slides (Scan Area: 61x21.6 mm, Scan resolution: 3 um, Dye channel: red and green, Tiff: 16bit, XDR ratio: NoXDR)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 using default parameters (protocol: ChIP_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Control IgG ChIP DNA from MT-2 cells

label_protocol: Labeled DNA was prepared from 2.6 μg of amplified DNA using SureTag DNA Labeling Kit according to the manufacturer's instructions.

growth_protocol: Cell lines were kept in RPMI1640 with 10% FBS. Tax-cells were kept in RPMI1640 with 10% FBS and 10 ng/ml recombinant human IL-2.

extract_protocol: 1×10E7 cells were cross-linked in fixing solution. After 15 min incubation at room temperature, cross-linking was stopped by adding 1.375 M glycine. The cells were centrifuged for 5 min, 1,400 × g at 4°C. The supernatant was discarded and the pellet was washed two times in PBS. After the washes, cell pellets were resuspended in LB1 (50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100) and incubated for 10 min on ice. After centrifugation for 5 min, 1,400 × g at 4°C, the pellet was resuspended in LB2 (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at room temperature. After centrifugation for 5 min, 1,400 × g at 4°C, the nuclei were resuspended in micrococcal nuclease digestion buffer and incubated in 37°C to digest chromatin to the appropriate size fragments. Digestion was stopped by adding 0.5 M EDTA. After centrifugation, nuclei pellets were resuspended in LB3 (10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-Lauroylsarcosine) and sonicated for 10 min. After sonication and 10 min high-speed centrifugation, sheared chromatin was recovered in the supernatant.

value: MT-2 (HTLV-1 infected cell line)

source_name: Input DNA from MT-2 cells


title: MDA-MB-231 - repeat 1

description: Cell Line


title: shSPS1 F9 3

first: Bradley

middle: A

last: Carlson

address: 9000 Rockville Pike

institute: National Cancer Institute

description: Biological replicate 3 of 3.

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized to Mouse Genome 430 2.0 Array for 16 hours at 45C. Arrays were washed and stained in the Affymetrix Fluidics Station 430.

scan_protocol: The Affymetrix GeneChip scanner 3000 was used to scan the microarrays

data_processing: Affy probe level analysis: bMAS5. Using R version 3.0.1 (2013-05-16) and BioConductor package affy version 1.38.1

source_name: mouse embryonal carcinoma (EC) F9 cell line

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Tissues and cultured cells were harvested and frozen immedieately in liquid nitrogen.

value: embryonal carcinoma; testicular teratoma

tag: Sex

value: male


title: Cohort 1 - 6 Week TECs


title: MCF7 - repeat 2

description: Cell Line

growth_protocol: MCF7 cell line was cultured in 5% FBS in DMEM at 37ºC in a 10% CO2 incubator.


title: MCF7 - repeat 1

description: Cell Line


title: MT-2 Tax

source_name: Tax ChIP DNA from MT-2 cells


title: MCF7 - repeat 3

description: Cell Line


title: LXR dko-Ve (9853741011_E)

source_name: LXR dko-Ve

value: Male

tag: treatment

value: Ve


title: MT-2 EZH2

source_name: EZH2 ChIP DNA from MT-2 cells

tag: cell type


title: shSPS1 F9 1

description: Biological replicate 1 of 3.


title: shSPS1 F9 2

description: Biological replicate 2 of 3.


title: HCC1954 - repeat 2

description: Cell Line

growth_protocol: HCC1954 cell line was cultured in 5% FBS in DMEM at 37ºC in a 10% CO2 incubator.

tag: disease

value: Ductal Carcinoma


title: Control F9 3

description: Biological replicate 3 of 3.


title: TL-Om1 H3K27me3

source_name: H3K27me3 ChIP DNA from TL-Om1 cells

value: TL-Om1 (ATL cell line)

source_name: Input DNA from TL-Om1 cells


title: HCC1954 - repeat 3

description: Cell Line

tag: er


title: TL-Om1 H3K4me3

source_name: H3K4me3 ChIP DNA from TL-Om1 cells


title: MT-2 H3K27me3

source_name: H3K27me3 ChIP DNA from MT-2 cells


title: HCC1806 - repeat 3

description: Cell Line

growth_protocol: HCC1806 cell line was cultured in 5% FBS in DMEM at 37ºC in a 10% CO2 incubator.

value: Primary acantholytic squamous cell carcinoma

tag: pr


title: Cohort 2 - 6 Week TECs


title: Control F9 1

description: Biological replicate 1 of 3.


title: Activated T-cell H3K27me3

source_name: H3K27me3 ChIP DNA from activated CD4 T-cells

value: CD3/CD28 activated CD4 T-cells

source_name: Input DNA from activated CD4 T-cells


title: SPS1 KO Mouse Liver 3

description: Biological replicate 3 of 3.

source_name: Liver

value: Liver


title: Control F9 2

description: Biological replicate 2 of 3.


title: HCC1806 - repeat 2

description: Cell Line

value: Positive


title: Tax-cell H3K27me3

source_name: H3K27me3 ChIP DNA from Tax-cells

value: Tax transduced T-cells

source_name: Input DNA from Tax-cells


title: SPS1 KO Mouse Liver 1

description: Biological replicate 1 of 3.


title: SPS1 KO Mouse Liver 2

description: Biological replicate 2 of 3.


title: wt_vs_MPZ_3u20m_replicate_2

city: Nijmegen

first: Leonie

middle: M

last: Kamminga

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

hyb_protocol: The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit following manufacturer's instructions.  After hybridization, slides were washed with Gene Expression Wash Buffer Kit (Agilent technologies Santa Clara, USA).

scan_protocol: Slides were scanned using Agilent Microarray Scanner with default settings.

data_processing: The arrays were processed using R/Bioconductor and limma single channel experimental design (Smyth 2005). After background correction, within-array normalization (loess) and between-array normalization (Aquantile) was performed. Differential expression was determined using eBayes method. We used the biomaRt package (Durinck 2005; Durinck 2009) to provide the annotation with systematic name and genomic location based on the RefSeq identifiers.

organism: Danio rerio

label_protocol: 100ng of total RNA was amplified and labeled with Cy3-CTP or Cy5-CTP by Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Labeled cRNA were purified by Nucleospin RNA CleanUP kit (MACHEREY-NAGEL).

growth_protocol: Zebrafish were raised and maintained under standard laboratory conditions (Westerfileld M, zebrafish book). Zebrafish embryos were collected within 5 minutes after being produced. Embryos were kept in E3 embryo medium up until the time of RNA isolation.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Zebrafish embryos were maintained under normal growth conditions in E3 embryo medium.

tag: tissue

value: whole embryo

tag: time

tag: developmental stage

value: high

value: wildtype

value: ezh2 nonsense mutant (hu5670, R592STOP)


title: HCC1806 - repeat 1

description: Cell Line

value: Negative


title: Normal - repeat 3

description: Normal Breast Tissue

source_name: Simmons Cancer Instititute Tissue Bank at SIU-SOM

extract_protocol: Normal human breast tissue was procured from the Simmons Cancer Instititute Tissue Bank at Southern Illinois University School of Medicine. The tissue was homogenized in TRI-Reagent and total RNA was extracted


title: ATL#3 H3K27me3

source_name: H3K27me3 ChIP DNA from primary ATL cells

value: primary PBMCs from ATL patient

source_name: Input DNA from primary ATL cells


title: Normal - repeat 2

description: Normal Breast Tissue


title: ATL#3 H3K4me3

source_name: H3K4me3 ChIP DNA from primary ATL cells


title: Normal - repeat 1

description: Normal Breast Tissue


title: NC mimic group

city: Beijing

first: Jie

last: Li

state: HaiDian Qu

address: Taiping Road 27

department: Biochemistry and Molecular Biology

institute: Institute of Basic Medical Sciences

description: human non-small cell lung cancer cell

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Raw data were obtained by using Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by Expression Console.

source_name: Human H1299 cells

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix  WT Amplication Kit(Cat#902224， Affymetrix, Santa Clara, CA, US) and GeneChip  WT Terminal Labeling Kit(Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: H1299 cells were cultured in RPMI-1640 Medium (Sigma-Aldrich, Poole, UK), supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated using the TRIZOL reagent (Invitrogen) according to manufacturer’s protocol

treatment_protocol: Cells at 70% confluence were transfected with miRNA mimics using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s recommendations.

tag: cell line

tag: transfection

value: NC mimics


title: wt_vs_MPZ_zygote_replicate_2


title: miR-138 group

description: human non-small cell lung cancer cell


title: Normal#1 H3K4me3

source_name: H3K4me3 ChIP DNA from normal CD4 T-cells

value: Normal CD4 T-cells isolated from PBMCs

source_name: Input DNA from normal CD4 T-cells


title: MPZ_vs_wt_zygote_replicate_2


title: ATL#2 H3K27me3


title: Control Mouse Liver 2

city: Bethesda

description: Biological replicate 2 of 3.

tag: strain

value: male


title: ATL#2 H3K4me3


title: Control Mouse Liver 1

description: Biological replicate 1 of 3.


title: MPZ_vs_wt_3u20m_replicate_2


title: wt_vs_MPZ_zygote_replicate_1


title: MPZ_vs_wt_3u20m_replicate_1


title: Liver-Treated-96hr-rep10

status: Public on May 05 2016

city: Seattle

first: Kai

last: Lau

address: 1201 Amgen Court West

institute: Amgen Inc.

description: Gene expression data from rat treated with common handling procedures for 4 day

hyb_protocol: For each sample, 10 ug of biotinylated cRNA spiked with hybridization controls (bioB, bioC, bioD and cre) was hybridized to an Affymetrix GeneChip® Rat Genome 230 2.0 array for 16-18 hours at 45ºC.

scan_protocol: Following hybridization, arrays were washed and stained in a GeneChip® Fluidics Station and scanned with a GeneChip® Scanner 3000 (Affymetrix).  Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS).

data_processing: The data were analyzed with Rosetta Resolver using standard processing procedure with background subtraction and batch normalization

organism: Rattus norvegicus

source_name: Liver, Treated, 96hr

label_protocol: Biotinylated cRNA was generated from 100 ng of total RNA using the GeneChip 3’ IVT Express Target Labeling method (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated from ~30 mg pieces of the left liver lobe according to the RNeasy extraction procedure (Qiagen, Valencia, CA).  Snap frozen tissues were transferred to Lysing Matrix D tubes containing RLT lysis buffer supplemented with beta-mercaptoethanol and homogenization was performed using the FastPrep® instrument (MP Biomedicals, Solon, OH).  An on-column DNase digestion was performed to remove any residual genomic DNA contamination.  RNA concentration and yield were measured and quality of the nucleic acid samples was evaluated with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).  All samples were of good quality, as evidenced by distinct ribosomal 18S and 28S peaks, low baseline and high RIN values.

tag: gender

value: Female

value: Liver Left Lobe

value: 10 wk

value: common lab handling procedures

value: 4 d

value: Sprague-Dawley


title: wt_vs_MPZ_3u20m_replicate_1

tag: genotype


title: Liver-Treated-96hr-rep9


title: Liver-Treated-96hr-rep8


title: Normal#1 H3K27me3

source_name: H3K27me3 ChIP DNA from normal CD4 T-cells


title: ATL#1 H3K27me3


title: Liver-Treated-96hr-rep6


title: Liver-Treated-96hr-rep1


title: Liver-Treated-96hr-rep4


title: Normal#2 H3K27me3


title: Liver-Treated-24hr-rep10

description: Gene expression data from rat treated with common handling procedures for 1 day

source_name: Liver, Treated, 24hr

value: 1 d


title: MPZ_vs_wt_zygote_replicate_1


title: Liver-Treated-96hr-rep5


title: Liver-Treated-96hr-rep3


title: Pro-insect vs. Pro-culture (3 replicates)

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

country: Spain

institute: CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

description: 3 biological replicates

hyb_protocol: Dual channel hybridization. Cy5-cDNA was from sand fly promastigotes and Cy3-cDNA from cultured ones. The protocol was performed as described (Alcolea et al., 2009. Genomics 93, 551-564).

scan_protocol: Scanning was performed with the GenePix 4100 instrument following the manufacturers´instructions.

data_processing:
Normalization was performed by the LOWESS per pin method (AlmaZen software) and statistical inference by the Student´s t test with FDR adjustment.
Please note that the AlmaZen software only provides the average of normalized data, the fold changes, the  p-value (Student's t test), z-score, etc., but not the individual  outcome of each array.

organism: Leishmania infantum

label_protocol: First strand cDNA synthesis was performed with 3 ug random hexamer primers and the SuperScript III reverse transcriptase (Invitrogen), incorporating 2/3 dTTP and 1/3 aminoallyl. After purification, Cy5 and Cy3 dyes were coupled. So, the labelling protocol was indirect.

growth_protocol: RPMI plus 10% heat inactivated fetal bovine serum in the presence of ampicillin and penicillin. Incubation at 27 ºC for 7 days (stationary phase). Enrichment in metacyclic promastigotes by negative selection with PNA.

extract_protocol: Total RNA was obtained by the TRIzol method, using glycogen as carrier as specified by the manufacturer for cases of reduced sample amount. Then, RNA from cultured promastigotes and those obtained from the sand fly stomodeal valve was doubly amplified with Message AmpII aRNA Amplification Kit (Ambion).

treatment_protocol: Stationary phase promastigotes were used to infect the U937 myeloid cell line. Infected cultures were used to feed an established colony of the sand fly Phlebotomus perniciosus, which was infected consequently. Promastigotes were extracted from the stomodeal valve by dissection of the midgut.

tag: host

value: Phlebotomus perniciosus

tag: host tissue

value: stomodeal valve

tag: molecule type

value: TotalRNA/aaRNA/cDNA

source_name: MetaPro-Axenic culture

tag: culture type

value: From stationary phase in culture PNA non-agglutinating


title: Liver-Treated-96hr-rep7

tag: age

tag: treatment


title: Liver-Treated-96hr-rep2


title: ATL#1 H3K4me3

tag: cell type


title: Liver-Treated-24hr-rep9


title: Liver-Treated-24hr-rep4


title: Liver-Treated-24hr-rep8


title: Liver-Treated-24hr-rep1


title: Liver-Treated-24hr-rep3


title: Liver-Treated-24hr-rep6


title: Liver-Control-24hr-rep9

description: Gene expression data from control rat

source_name: Liver, Control, 24hr

value: control


title: Liver-Treated-24hr-rep7


title: Liver-Control-24hr-rep8

description: Gene expression data from control rat


title: Liver-Treated-24hr-rep2


title: Liver-Treated-24hr-rep5


title: HCC1954 - repeat 1

description: Cell Line

tag: disease

value: Ductal Carcinoma

tag: er

value: Negative

value: Positive


title: CLBL1

city: Columbus

first: Bonnie

middle: Kate

last: Harrington

state: OH

institute: Ohio State University

description: Canine B cell lymphoma cell line

hyb_protocol: Then, 15 µg of labeled cRNA was fragmented following the manufacturer instructions.  Labeled cRNA targets were hybridized to Affymetrix GeneChip® Canine Genome 2.0 array for 16 hours at 45 °C rotating at 60 rpm.

scan_protocol: Arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000 (Affymetrix). For gene expression analysis, arrays were normalized.

data_processing: For clustering, we downloaded supplementary microarray data (GSE43664) from GEO, then merged the microarray data for CLBL1 and processed the combined data using the robust multiarray averaging (RMA) method in version 3.1.2 of the R statistical programming environment.  We then applied the median polish algorithm to the subset of 1180 canine probe sets found to separate two subtypes of canine B-cell lymphoma (9). Samples were clustered using centroid linkage and a distance metric based on un-centered correlation. To confirm the cluster assignment, we computed distance from CLBL1 to the centers of both the GCB and ABC clusters using three methods: Euclidean, Pearson correlation, and un-centered correlation.

organism: Canis lupus familiaris

source_name: CLBL1 cell line

label_protocol: A 2 µg aliquot of total RNA was linearly amplified and labeled using the BioArray High Yield RNA Transcript labeling kit (Enzo Life Sciences).

growth_protocol: Cells were cultured in RPMI media supplemented with 20% FBS.

extract_protocol: Total RNA was isolated using the Trizol method and DNase treated.  RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: No treatment.


title: Liver-Control-24hr-rep7

description: Gene expression data from control rat

tag: tissue


title: Liver-Control-24hr-rep6

description: Gene expression data from control rat


title: Liver-Control-24hr-rep10

description: Gene expression data from control rat


title: Liver-Control-24hr-rep4

description: Gene expression data from control rat


title: Liver-Control-24hr-rep2

description: Gene expression data from control rat


title: Liver-Control-24hr-rep5

description: Gene expression data from control rat


title: HCT116_ShCDK5_rep3

city: Guangzhou

first: Kangmin

last: Zhuang

address: No.1838, North of Guangzhou Avenue, Guangzhou City, Guangdong Province, China

institute: Nanfang Hospital Southern Medical University

description: gene expression after Scramble in HCT116 cell lines.

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: HCT116 genotype cell line

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: CDK5 knockdown


title: Liver-Control-24hr-rep1

description: Gene expression data from control rat


title: HCT116_Scramble_rep3

description: gene expression after CDK5-knockdown in HCT116 cell lines

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

value: scramble


title: Liver-Control-24hr-rep3

description: Gene expression data from control rat

value: Female


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic co-culture (LGG+B.caccae), rep2

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

description: mRNA expression data from Caco-2 human epithelial colorectal adenocarcinoma cells, anaerobic co-culture (LGG+B.caccae)

hyb_protocol: The cDNA was hybridized onto Affymetrix Human Gene 2.0 ST Arrays and the Affymetrix GeneChip Hybridization, Wash and Stain Kit was used to hybridize and wash the cartridges. Control Oligonucleotide B2 and 20X Eukaryotic Hybridization Controls were added to the hybridization cocktail containing the labeled sample and injected into the cartridge. The Incubation lasted 16 hr at 45°C with a rotation at 60 rpm. Then, the Fluidics Station 450/250 was used to wash and stain the Affymetrix GeneChip Human Gene 2.0 ST probe arrays.

scan_protocol: Whole Transcript (WT) Expression Arrays (P/N 703174 Rev. 2)  were scanned with a GCS3000 Scanner (Affymetrix) for images and intensities.

data_processing: The data was processed using R/bioconductor and RMA with default parameters.

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA was used for fragmentation and labeling.

growth_protocol: Caco-2 human epithelial colorectal adenocarcinoma cells were cultured in the HuMiX device.

extract_protocol: RNA extracts were prepared using the Affymetrix WT PLUS Reagent Kit (Affymetrix). RNA quality and integratiy was checked using a a NanoDrop ND-100 spectrophotometer (Thermo Scientific) and the 2100 Agilent Bioanalyzer (Agilent). For gene expression analysis, 100 ng of total RNA were used in conjunction with the Affymetrix standard protocol for Human Transcriptome Arrays 2.0 (Affymetrix Inc.). For the miRNAs analysis, 1µg of total RNA was analyzed using the FlashTag Biotin HSR RNA labeling kit for the Affymetrix Genechips miRNA 4.0 microarrays (Affymetrix Inc.).

treatment_protocol: Caco-2 human epithelial colorectal adenocarcinoma cells were co-cultured with bacteria (Lactobacillus rhamnosus GG (LGG), and Bacteroides caccae and LGG).

value: co-culture (LGG+B.caccae)


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic co-culture (LGG+B.caccae), rep3


title: AL vs. CR in cardiomyocyte-specific Sirt1knockout murine hearts

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: normalized log2 ratio (S1-KO 41 (CR)/S1-KO 40 (AL))

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

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Six-month-old male mice having the C57BL/6J background

treatment_protocol: cardiomyocyte-specific Sirt1 knockout mice and the corresponding control mice were subjected to either 3-month AL feeding or -40% CR

tag: Sex

value: male

value: Six-month-old

value: murine hearts

tag: diet

value: ad libitium (AL)

tag: genotype/variation

value: cardiomyocye-specific Sirt1 knockout

tag: genotype/variaton

value: caloric restriction (CR)


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic co-culture (LGG), rep1

description: mRNA expression data from Caco-2 human epithelial colorectal adenocarcinoma cells, anaerobic co-culture (LGG)

value: co-culture (LGG)


title: AL vs. CR in the control murine hearts

description: normalized log2 ratio (WT 6M 29 (CR)/WT 6M 31 (AL))

source_name: WT 6M 31 (AL)

tag: strain

source_name: WT 6M 29 (CR)


title: HCT116_Scramble_rep2

tag: cell line


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic co-culture (LGG), rep3


title: OCILY10 PIMASERTIB 8H

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalised using quantile method

source_name: OCI LY10 cell line treated with Pimasertib

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: treatment with Pimasertib

value: OCI LY10

value: PIMASERTIB

tag: time point


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic control, rep3

description: mRNA expression data from Caco-2 human epithelial colorectal adenocarcinoma cells, anaerobic control

value: control


title: HCT116_ShCDK5_rep1


title: HCT116_ShCDK5_rep2


title: HCT116_Scramble_rep1


title: OCILY10 PIMASERTIB 12H


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic co-culture (LGG), rep2


title: H37Rv_0BDQ_48Hr_rep3

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

description:
raw data file: 20150206_SM-D1T1_WT_v_SM-D3_WT.txt
SM-D3_WT

hyb_protocol: Each pair of differentially labeled probes was resuspended in 45μL of hybridization buffer (4.5 μL Agilent 10x blocking agent, 22.5μL Agilent 2x hybridization buffer, Dnase/Rnase-free water) and hybridized to the microarray slide overnight in a 42C incubator.

scan_protocol: Slides were washed in increasingly stringent wash conditions using Agilent Wash Buffers I and II.

data_processing:
Arrays were scanned and spots were quantified using PerkinElmer ScanArray Express scanner.
These data were exported to ArrayStar DNASTAR software (version 4.1.0) for RMA normalization and analysis. Paired samples were processed as though they are single channels (no Cy3/Cy5 ratios calculated). Spots flagged as ‘Not Found’ by the ScanArray software algorithms were excluded from downstream analysis.

organism: Mycobacterium tuberculosis

source_name: H37Rv_0 μM Bedaquiline for 48hr

label_protocol: Up to 3μg of total RNA was used to create cDNA labeled with aminoallyl dUTP (Fermentas). Fluores- cent Cy3 and Cy5 dyes (Amersham) were then covalently attached to the aminoallyl tags.

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol: RNA was isolated and applied to custom tiled Agilent arrays using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen).

treatment_protocol: Bacteria were harvested at 1, 6, 24, 48, 96 hrs after being exposed to concentrations of bedaquiline (no drug, 1.5M, 15M) during a 7-day drug exposure time course experiment (as indicated in each sample title).

tag: bedaquiline dose

value: 0 μM

tag: exposed to

value: 0 μM Bedaquiline for 48hr


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic control, rep1


title: OCILY10 DMSO 8H

source_name: OCI LY10 cell line not treated

value: DMSO


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic co-culture (LGG+B.caccae), rep1


title: Caco-2 human epithelial colorectal adenocarcinoma cells, mRNA, anaerobic control, rep2


title: H37Rv_15BDQ_48Hr_rep3

description:
raw data file: 20150206_SM-D1T1_15_v_SM-D3_15.txt
SM-D3_15

source_name: H37Rv_15 μM Bedaquiline for 48hr

value: 15 μM

value: 15 μM Bedaquiline for 48hr


title: OCILY10 DMSO 4H


title: OCILY10 PIMASERTIB 4H


title: H37Rv_15BDQ_96Hr_rep1

description:
raw data file: 20150206_SM-D1T6_15_v_SM-D5_15.txt
SM-D5_15

source_name: H37Rv_15 μM Bedaquiline for 96hr

value: 15 μM Bedaquiline for 96hr


title: OCILY10 DMSO 12H


title: H37Rv_15BDQ_6Hr_rep1

description:
raw data file: 20150206_SM-D1T6_15_v_SM-D5_15.txt
SM-D1T6_15

source_name: H37Rv_15 μM Bedaquiline for 6hr

value: 15 μM Bedaquiline for 6hr


title: H37Rv_1.5BDQ_48Hr_rep1

description:
raw data file: 20150206_SM-D1T1_1-5_v_SM-D3_1-5.txt
SM-D3_1.5

source_name: H37Rv_1.5 μM Bedaquiline for 48hr

value: 1.5 μM Bedaquiline for 48hr


title: H37Rv_0BDQ_1Hr_rep3

description:
raw data file: 20150206_SM-D1T1_WT_v_SM-D3_WT.txt
SM-D1T1_WT

source_name: H37Rv_0 μM Bedaquiline for 1hr

value: 0 μM Bedaquiline for 1hr


title: H37Rv_1.5BDQ_96Hr_rep2

description:
raw data file: 20150206_EP-D5_1-5_v_MS-D5_1-5.txt
MS-D5_1.5

source_name: H37Rv_1.5 μM Bedaquiline for 96hr

value: 1.5 μM Bedaquiline for 96hr


title: H37Rv_15BDQ_1Hr_rep3

description:
raw data file: 20150206_SM-D1T1_15_v_SM-D3_15.txt
SM-D1T1_15

source_name: H37Rv_15 μM Bedaquiline for 1hr

value: 15 μM Bedaquiline for 1hr


title: H37Rv_0BDQ_24Hr_rep2

description:
raw data file: 20150206_EP-D2_WT_v_MS-D2_WT.txt
MS-D2_WT

source_name: H37Rv_0 μM Bedaquiline for 24hr

value: 0 μM Bedaquiline for 24hr


title: H37Rv_0BDQ_96Hr_rep2

description:
raw data file: 20150206_EP-D5_WT_v_MS-D5_WT.txt
MS-D5_WT

source_name: H37Rv_0 μM Bedaquiline for 96hr

value: 0 μM Bedaquiline for 96hr


title: H37Rv_15BDQ_48Hr_rep2

description:
raw data file: 20150206_EP-D3_15_v_MS-D3_15.txt
MS-D3_15


title: esophagus_Pirb knockout_Dox_rep2

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

address: 3333 Burnet Ave. MLC-7028

department: Allergy

institute: Cincinnati Children's Hospital Medical Center

description: PirB KO2 Dox Eso

hyb_protocol: 3.85ug of fragmented cDNA were hybridized to a Mouse Gene 2.0 ST arrays (Affymetrix).  Probe arrays were incubated at 45C for 17 hours in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm.  Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0002.  The Stain and Antibody solutions are produced by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

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

data_processing: The .cel were created by Common Console (Affymetrix).  The .cel files were analyzed by Expression Console (Affymetrix) to create the .chp files.  The Data were analyzed using Genespring software with a fold-change cutoff of 2 (FC>2) and unpaired Student's t test (P>0.05).  Heat plots and Venn diagrams were generated according to gene lists that were generated by GeneSpring software (Agilent, Santa Clara, CA).

source_name: esophagus, PirB knockout, Dox

label_protocol: The resulting cDNA was fragmented and labeled with the Nugen Encore Biotin Module (cat#4200) per manufacturers instructions.

growth_protocol: Male and females 6-8 week old CC10-IL13Tg/Pirb-/- and littermate control CC10-IL13Tg/Pirb+/+ mice were used.

extract_protocol: The esophagus was removed from the mice and digested with Collagenase to form a single cell suspension.  The bone marrow was also removed from the mice and passed through a needle to form a single cell suspension.  The cells were sorted by flow cytometry, CD45+/SiglecF+/CCR3+, to isolate the eosinophils.  RNA was then extracted from the eosinophils per manufacturers instructions with a Qiagen RNeasy Mini kit (cat#74106).  The RNA was then amplified using Nugen Ovation One-Direct system (cat#3500) per manufacturers instructions.

treatment_protocol: IL13 transgene expression was induced by feeding the CC10-IL13 Tg mice doxycycline-impregnated food (DOX) for two weeks.

value: Esophagus

value: Eosinophils

value: PirB knockout

value: Dox


title: CSB deficient cell line expressing CSB-WT5A, biological replicate2

city: London

first: Yuming

last: Wang

address: South Mimms

department: Mechanisms of Transcription Laboratory

country: United Kingdom

institute: Cancer Research UK

hyb_protocol: Following labelling, 4ug of Cy3-cDNA were hybridized for 16 hr at 42ºC on Nimblegen 12 x 135K human expression array by using Nimblegen hybridization kit. The array was washed using Nimblegen washing buffers followed by drying on a microarray dryer.

scan_protocol: The array was scanned using NimbleGen MS 200 Microarray scanner.

data_processing: Data was analyzed using Biocondutor 2.12 running on R3.0.0. Probe set expression measures were calculated using quantile normalization of log2 transformed data.

label: Cyanine 3

label_protocol: Double-stranded cDNA was synthesized using Nimblegen cDNA synthesis kit from 10-20 μg total RNA, up to 1 μg cDNA was labelled with Cy3 according to the standard Nimblegen protocol by using Nimblegen labeling kit.

growth_protocol: Transformed fibroblast cells were maintained in DMEM + 10% FBS. Cell lines for the tetracycline-inducible systems were cultured in DMEM + 10% Tet-free FBS, 5-10 ng ml-1 doxycycline was added to the cells 48 hr before total RNA isolation.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) as per the manufacturer's instructions.

value: human fibroblast derived from CS patient and transformed with SV40 T-antigen

value: expressing CSB-WT5A


title: esophagus_Pirb knockout_Dox_rep3

description: PirB KO3 Dox Eso


title: H37Rv_0BDQ_1Hr_rep2

description:
raw data file: 20150206_EP-D1T1_WT_v_MS-D1T1_WT.txt
MS-D1T1_WT

value: 0 μM


title: H37Rv_1.5BDQ_1Hr_rep2

description:
raw data file: 20150206_EP-D1T1_1-5_v_MS_D1T1_1-5.txt
MS-D1T1_1.5

source_name: H37Rv_1.5 μM Bedaquiline for 1hr

value: 1.5 μM Bedaquiline for 1hr


title: H37Rv_1.5BDQ_24Hr_rep2

description:
raw data file: 20150206_EP-D2_1-5_v_MS-D2_1-5.txt
MS-D2_1.5

source_name: H37Rv_1.5 μM Bedaquiline for 24hr

value: 1.5 μM Bedaquiline for 24hr


title: CSB deficient cell line expressing CSB-WT5A, biological replicate1


title: H37Rv_0BDQ_0Hr_rep2

description:
raw data file: 20150206_EP-D1T0_WT_v_MS-D1T0_WT.txt
MS-D1T0_WT

source_name: H37Rv_0 μM Bedaquiline for 0hr

value: 0 μM Bedaquiline for 0hr


title: Control Mouse Liver 3

description: Biological replicate 3 of 3.

source_name: Liver

value: Liver

value: male


title: H37Rv_15BDQ_1Hr_rep2

description:
raw data file: 20150206_EP-D1T1_15_v_MS-D1T1_15.txt
MS-D1T1_15

value: 15 μM


title: H37Rv_1.5BDQ_0Hr_rep2

description:
raw data file: 20150206_EP-D1T0_1-5_v_MS-D1T0_1-5.txt
MS-D1T0_1.5

source_name: H37Rv_1.5 μM Bedaquiline for 0hr

value: 1.5 μM Bedaquiline for 0hr


title: esophagus_wildtype_Dox_rep3

description: PirB WT3 Dox Eso

source_name: esophagus, wildtype, Dox

value: wildtype


title: H37Rv_1.5BDQ_1Hr_rep3

description:
raw data file: 20150206_SM-D1T1_1-5_v_SM-D3_1-5.txt
SM-D1T1_1.5


title: H37Rv_0BDQ_48Hr_rep2

description:
raw data file: 20150206_EP-D3_WT_v_MS-D3_WT.txt
MS-D3_WT

source_name: H37Rv_0 μM Bedaquiline for 48hr

value: 0 μM Bedaquiline for 48hr


title: esophagus_Pirb knockout_Dox_rep1

description: PirB KO1 Dox Eso


title: H37Rv_0BDQ_6Hr_rep2

description:
raw data file: 20150206_EP-D1T6_WT_v_MS-D1T6_WT.txt
MS-D1T6_WT

source_name: H37Rv_0 μM Bedaquiline for 6hr

value: 0 μM Bedaquiline for 6hr


title: H37Rv_15BDQ_0Hr_rep1

source_name: H37Rv_15 μM Bedaquiline for 0hr

value: 15 μM Bedaquiline for 0hr


title: H37Rv_0BDQ_96Hr_rep1

description:
raw data file: 20150206_EP-D5_WT_v_MS-D5_WT.txt
EP-D5_WT

value: 0 μM Bedaquiline for 96hr


title: esophagus_wildtype_Dox_rep2

description: PirB WT2 Dox Eso

value: Esophagus

value: Eosinophils


title: CSB deficient cell line expressing CSB-K991R mutant, biological replicate1

value: human fibroblast derived from CS patient and transformed with SV40 T-antigen

value: expressing CSB-K991R


title: CSB deficient cell line derived from CS patient, biological replicate2

value: lacking CSB


title: CSB deficient cell line expressing CSB-UBD mutant, biological replicate1

value: expressing CSB-UBD


title: H37Rv_1.5BDQ_96Hr_rep1

description:
raw data file: 20150206_EP-D5_1-5_v_MS-D5_1-5.txt
EP-D5_1.5

value: 1.5 μM Bedaquiline for 96hr


title: bone marrow_PirB knockout_Dox_rep3

description: PirB KO3 Dox BM

source_name: bone marrow, PirB knockout, Dox

value: Bone marrow

value: PirB knockout

value: Dox


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG+B.caccae), rep2

description: miRNA expression data from Caco-2 human epithelial colorectal adenocarcinoma cells, anaerobic co-culture (LGG+B.caccae)

value: co-culture (LGG+B.caccae)


title: CSB deficient cell line derived from CS patient, biological replicate1


title: CSB deficient cell line expressing CSB-UBD mutant, biological replicate2


title: esophagus_wildtype_Dox_rep1

description: PirB WT1 Dox Eso


title: bone marrow_PirB knockout_Dox_rep2

description: PirB KO2 Dox BM


title: H37Rv_0BDQ_48Hr_rep1

description:
raw data file: 20150206_EP-D3_WT_v_MS-D3_WT.txt
EP-D3_WT

value: 0 μM


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG+B.caccae), rep1


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG+B.caccae), rep3


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG), rep2

description: miRNA expression data from Caco-2 human epithelial colorectal adenocarcinoma cells, anaerobic co-culture (LGG)

value: co-culture (LGG)


title: bone marrow_wildtype_Dox_rep3

description: PirB WT3 Dox BM

source_name: bone marrow, wildtype, Dox

value: wildtype


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic control, rep3

description: miRNA expression data from Caco-2 human epithelial colorectal adenocarcinoma cells, anaerobic control

value: control


title: bone marrow_wildtype_Dox_rep2

description: PirB WT2 Dox BM


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG), rep3


title: H37Rv_1.5BDQ_24Hr_rep1

description:
raw data file: 20150206_EP-D2_1-5_v_MS-D2_1-5.txt
EP-D2_1.5

value: 1.5 μM Bedaquiline for 24hr


title: H37Rv_0BDQ_24Hr_rep1

description:
raw data file: 20150206_EP-D2_WT_v_MS-D2_WT.txt
EP-D2_WT

value: 0 μM Bedaquiline for 24hr


title: bone marrow_PirB knockout_Dox_rep1

description: PirB KO1 Dox BM


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG), rep1


title: H37Rv_0BDQ_1Hr_rep1

description:
raw data file: 20150206_EP-D1T1_WT_v_MS-D1T1_WT.txt
EP-D1T1_WT

source_name: H37Rv_0 μM Bedaquiline for 1hr

value: 0 μM Bedaquiline for 1hr


title: bone marrow_PirB knockout_no Dox_rep3

description: PirB KO3 no Dox BM

source_name: bone marrow, PirB knockout, no Dox

value: Eosinophils

value: no Dox


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic control, rep2


title: Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic control, rep1


title: bone marrow_wildtype_Dox_rep1

description: PirB WT1 Dox BM


title: bone marrow_PirB knockout_no Dox_rep2

description: PirB KO2 no Dox BM


title: H37Rv_1.5BDQ_1Hr_rep1

description:
raw data file: 20150206_EP-D1T1_1-5_v_MS_D1T1_1-5.txt
EP-D1T1_1.5

value: 1.5 μM Bedaquiline for 1hr


title: H37Rv_15BDQ_48Hr_rep1

description:
raw data file: 20150206_EP-D3_15_v_MS-D3_15.txt
EP-D3_15

source_name: H37Rv_15 μM Bedaquiline for 48hr

value: 15 μM

value: 15 μM Bedaquiline for 48hr


title: bone marrow_PirB knockout_no Dox_rep1

description: PirB KO1 no Dox BM


title: H37Rv_15BDQ_1Hr_rep1

description:
raw data file: 20150206_EP-D1T1_15_v_MS-D1T1_15.txt
EP-D1T1_15

source_name: H37Rv_15 μM Bedaquiline for 1hr

value: 15 μM Bedaquiline for 1hr


title: H37Rv_0BDQ_6Hr_rep1

description:
raw data file: 20150206_EP-D1T6_WT_v_MS-D1T6_WT.txt
EP-D1T6_WT

value: 0 μM Bedaquiline for 6hr