title: PAX2 overexpression

city: suzhou

first: Shuyu

last: Zhang

state: jiangsu

address: No.199 Ren’ai Rd

department: Medical  College

institute: Soochow  University

description: The sample is the total RNA of the TE-1 cell which is transfected with PCDNA3.1-PAX2 and seted to be the experiment group.

hyb_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 2 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.
Genes that have values greater than or equal to lower cut-off: 100.0 in at least 1 out of 2 samples (“All Targets Value”) were chosen for data analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: Human esophageal cancer cell line TE-1

growth_protocol: The human esophageal cancer cell line TE-1 was maintained in DMEM supplemented with 10% FBS and antibiotics (100 units/ml penicillin G, 100 units/ml streptomycin sulfate;Gibco, Grand Island, NY). Cells were grown in a 37°C incubator with 5% CO2.

extract_protocol: Total RNA was extracted from cells with Trizol reagent (Invitrogen, Carlsbad, CA ).Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.Results were provided in the RNA_QC.pdf file.

treatment_protocol: TE-1 cells were transfected with PCDNA3.1 or pcDNA3.1-PAX2. 24 h after transfection, RNA was extracted and subjected to microarray analysis.

tag: cell line

tag: transfection


title: H3K9me2_wt_1

status: Public on Dec 12 2014

type: genomic

city: Chestnut Hill

first: Hugh

middle: P

last: Cam

state: MA

address: Higgins Hall Room 355, 140 Commonwealth Avenue

department: Biology

country: USA

institute: Boston College

description: ChIP-chip profiling of H3K9me2 in wildtype cells replicate 1

hyb_protocol: 500 ng of AlexaFluor 555 labeled Input DNA was mixed with 500 ng of AlexaFluro 647 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer. Combined samples were hybridized to Agilent 4x44k array slides in an Agilent SureHyb chamber at 65° C, 20 RPM for 24 hours. Slides were washed once with 6X SSPE. (Invitrogen)/0.005% N-Lauroylsarcosine (Sigma L7414), once with 0.06X SSPE/0.005%  N-Lauroylsarcosine, and once with Agilent Stabilization and Drying solution according to Agilent protocols.

scan_protocol: Slides were scanned using an Agilent G2565CA Scanner.

data_processing: Scanned slides were processed using Agilent Feature Extraction Software (v.10.5.1.1), extraction protocol GE2_105_Jul10. Red and green channel spot and background intensities from Feature Extraction files were processed using the R/Bioconductor Ringo package (v1.3.0) using the read.maimages function (source=agilent). ChIP vs. input ratios (log2) were determined with the preprocess function using the loess normalization method.

label: Alexa Fluor 647

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe cells, H3K9me2 wt ChIP

label_protocol: ChIP and Input DNA were amplified by random priming PCR incorporating amino-allyl dUTP, then covalently coupled with Cy5 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered using Qiagen QIAquick PCR columns.

growth_protocol: Logarithmically growing cultures were grown 18 hours to mid-exponential phase (A595 ~ 0.5) in standard rich media (YEA) shaking at 250 RPM at 30° C.

extract_protocol: Chromatin was extracted from cross-linked cells following bead beater lysis and sonication.  Following immunoprecipitation of ChIP samples, ChIP and input DNA samples were incubated overnight at 65 deg C in TE buffer to reverse cross-links and digested with Rnase A and proteinase K. DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: 50 mL cultures were cross-linked with paraformadehyde at 18 deg C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

tag: genotype

value: wildtype

label: Alexa Fluor 555

source_name: Schizosaccharomyces pombe cells, input


title: H3K4me3_wt_1

description: ChIP-chip profiling of H3K4me3 in wildtype cells replicate 1

source_name: Schizosaccharomyces pombe cells, H3K4me3 wt ChIP


title: Atf1_2

description: ChIP-chip profiling of Atf1 in wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, Atf1 wt ChIP


title: Control

type: RNA

country: China

description: The sample is the total RNA of the TE-1 cell which is transfected with PCDNA3.1 and seted to be the control group.

molecule: total RNA

organism: Homo sapiens

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.


title: Set1_2

description: ChIP-chip profiling of Set1 in wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, Set1 wt ChIP


title: set1FLAG_clr3D_2

description: Gene expression profiling in set1FLAG (H3K4me-), clr3 mutant vs. wildtype cells replicate 2

hyb_protocol: 150 ng each of labeled mutant and wildtype cDNA were combined with 2X Hi-RPM Hybridization Buffer and 10X GE Blocking Reagent from the Agilent Gene Expression Hybridization Kit. Combined samples were hybridized to Agilent 4x44k array slides in an Agilent SureHyb chamber at 65° C, 20 RPM for 24 hours. Slides were washed once with 6X SSPE. (Invitrogen)/0.005% N-Lauroylsarcosine (Sigma L7414), once with 0.06X SSPE/0.005%  N-Lauroylsarcosine, and once with Agilent Stabilization and Drying solution according to Agilent protocols.

data_processing: Scanned slides were processed using Agilent Feature Extraction Software (v.10.5.1.1), extraction protocol GE2_105_Jul10. Red and green channel spot and background intensities from Feature Extraction files were processed using the R/Bioconductor limma package (v.3.10.2) using the read.maimages function (source=agilent). log2 fold-changes of mutant vs. wildtype were determined with the normalizeWithinArrays function using the loess normalization method.

source_name: Schizosaccharomyces pombe cells, set1FLAG (H3K4me-) clr3 deletion

label_protocol: 20 ug of total RNA was reverse transcribed using anchored oligo-dT and labeled with Alexa Fluor 647 (mutant) or Alexa Fluor 555 (wildtype) using the Superscript III Indirect cDNA Labeling Kit (Invitrogen) according to the manufacturer's instructions.

extract_protocol: 10 mL cultures were harvested by centrifuging 2000 RPM for 2 minutes at room temperature, decanted, then snap frozen in liquid nitrogen. RNA was extracted using a hot acid phenol method (Lyne et al., 2003), then purified with Qiagen RNEasy spin columns according to the manufacturer's protocol.

value: set1FLAG (H3K4me-), clr3 mutant

source_name: Schizosaccharomyces pombe cells, wildtype


title: CDR144_sham

city: Montreal

first: Sophie

last: Cardin

state: Qc

address: 110, Pine west

department: Experimental medecine

country: Canada

institute: IRCM

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalisation with package preprocessCore 1.25.3

label: biotin

organism: Mus musculus

source_name: C57Bl/6N_Sham-operated control

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

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

treatment_protocol: Angiotensin II infusion in mini-osmotic pumps implanted sub-cutaneously, treated 48 hours.

tag: strain

tag: gender

value: male

tag: subjected to

value: sham operation (control)

tag: tissue

value: left ventricles


title: H3K4me3_wt_2

description: ChIP-chip profiling of H3K4me3 in wildtype cells replicate 2


title: H3K4me3_atf1D_1

description: ChIP-chip profiling of H3K4me3 in atf1 deletion mutant cells replicate 1

source_name: Schizosaccharomyces pombe cells, H3K4me3 atf1 deletion ChIP

value: atf1 deletion mutant


title: Set1_1

description: ChIP-chip profiling of Set1 in wildtype cells replicate 1


title: H3K9me2_set1D_clr3D_1

description: ChIP-chip profiling of H3K9me2 in set1 clr3 deletion mutant cells replicate 1

source_name: Schizosaccharomyces pombe cells, H3K9me2 set1 clr3 deletion ChIP

value: set1 clr3 deletion mutant


title: set1D_clr3D_1

description: Gene expression profiling in set1, clr3 deletion mutant vs. wildtype cells replicate 1

source_name: Schizosaccharomyces pombe cells, set1 clr3 deletion

value: set1, clr3 deletion mutant


title: Atf1_1

description: ChIP-chip profiling of Atf1 in wildtype cells replicate 1


title: set1FLAG_clr3D_1

description: Gene expression profiling in set1FLAG (H3K4me-), clr3 mutant vs. wildtype cells replicate 1


title: CDR143_angiotensin II

source_name: C57Bl/6N_Angiotensin II treated 48h

value: 48 hrs of angiotensin II infusion


title: set1D_atf1D_1

description: Gene expression profiling in set1, atf1 deletion mutant vs. wildtype cells replicate 1

source_name: Schizosaccharomyces pombe cells, set1 atf1 deletion

value: set1, atf1 deletion mutant


title: set1D_clr3D_2

description: Gene expression profiling in set1, clr3 deletion mutant vs. wildtype cells replicate 2


title: set1D_atf1D_2

description: Gene expression profiling in set1, atf1 deletion mutant vs. wildtype cells replicate 2


title: CDR141_sham

source_name: C57Bl/6J_Sham-operated control


title: clr3D_1

description: Gene expression profiling in clr3 deletion mutant vs. wildtype cells replicate 1

source_name: Schizosaccharomyces pombe cells, clr3 deletion

value: clr3 deletion mutant


title: atf1D_2

description: Gene expression profiling in atf1 deletion mutant vs. wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, atf1 deletion


title: clr3D_2

description: Gene expression profiling in clr3 deletion mutant vs. wildtype cells replicate 2


title: CDR142_angiotensin II

source_name: C57Bl/6J_Angiotensin II treated 48h


title: atf1D_1

description: Gene expression profiling in atf1 deletion mutant vs. wildtype cells replicate 1


title: CDR139_angiotensin II


title: Normal_control_12

city: Baltimore

first: Xinmei

last: Zhao

state: MD

address: 5200 Eastern Avenue

department: Division allergy and clinical immunology

institute: Johns Hopkins U

description: control

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. The expression values for all the probes for each sample were scaled to have median 256 (28) and then log (base 2) transformed. Before performing statistical analysis, we filtered for present/absent genes using a p-value threshold of less than 0.01 and removed 2919 absent genes.

source_name: Colon tissue

label_protocol: Total RNA was labled with the WG-DASL pre 1 MCS4 w/UDG Kit according to manufacturers suggested protocol.

extract_protocol: Total RNA was extracted using the  Allprep RNA/DNA FFPE kit protocol (Qiagen, Gaithersburg, MD, USA).

value: colon

tag: disease state

value: healthy control


title: swd3D_1

description: Gene expression profiling in swd3 deletion mutant vs. wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, swd3 deletion

value: swd3 deletion mutant


title: Normal_control_11

description: control


title: CDR137_angiotensin II


title: Normal_control_9

description: control


title: CDR136_angiotensin II


title: Normal_control_8

description: control


title: Normal_control_10

description: control


title: swd1D_1

description: Gene expression profiling in swd1 deletion mutant vs. wildtype cells replicate 1

source_name: Schizosaccharomyces pombe cells, swd1 deletion

value: swd1 deletion mutant


title: swd1D_2

description: Gene expression profiling in swd1 deletion mutant vs. wildtype cells replicate 2


title: Normal_control_6

description: control


title: CDR135_angiotensin II


title: swd2D_2

description: Gene expression profiling in swd2 deletion mutant vs. wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, swd2 deletion

value: swd2 deletion mutant


title: CDR132_angiotensin II


title: swd3D_2

description: Gene expression profiling in swd3 deletion mutant vs. wildtype cells replicate 1


title: set1FLAG_1

description: Gene expression profiling in set1FLAG (H3K4me-) mutant vs. wildtype cells

source_name: Schizosaccharomyces pombe cells, set1FLAG (H3K4me-) mutant

value: set1FLAG (H3K4me-) mutant


title: swd2D_1

description: Gene expression profiling in swd2 deletion mutant vs. wildtype cells replicate 1

value: wildtype


title: Normal_control_7

description: control


title: spp1D_2

description: Gene expression profiling in spp1 deletion mutant vs. wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, spp1 deletion

value: spp1 deletion mutant


title: H3K4R_1

description: Gene expression profiling in H3K4R mutant vs. wildtype cells

source_name: Schizosaccharomyces pombe cells, H3K4R mutant

value: H3K4R mutant

source_name: Schizosaccharomyces pombe cells, wildtype


title: CDR134_sham

value: male

value: sham operation (control)


title: CDR133_sham

source_name: C57Bl/6N_Sham-operated control

value: left ventricles


title: CDR131_sham


title: Normal_control_4

description: control


title: shg1D_1

description: Gene expression profiling in shg1 deletion mutant vs. wildtype cells replicate 1

source_name: Schizosaccharomyces pombe cells, shg1 deletion

value: shg1 deletion mutant


title: shg1D_2

description: Gene expression profiling in shg1 deletion mutant vs. wildtype cells replicate 2


title: sdc1D_2

description: Gene expression profiling in sdc1 deletion mutant vs. wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, sdc1 deletion

value: sdc1 deletion mutant


title: sdc1D_1

description: Gene expression profiling in sdc1 deletion mutant vs. wildtype cells replicate 1


title: Normal_control_5

description: control


title: spp1D_1

description: Gene expression profiling in spp1 deletion mutant vs. wildtype cells replicate 1


title: Normal_control_3

description: control


title: ash2D_2

description: Gene expression profiling in ash2 deletion mutant vs. wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, ash2 deletion

value: ash2 deletion mutant


title: Normal_control_2

description: control


title: ash2D_1

description: Gene expression profiling in ash2 deletion mutant vs. wildtype cells replicate 1


title: CDR130_angiotensin II

value: 48 hrs of angiotensin II infusion


title: set1D_2

description: Gene expression profiling in set1 deletion mutant vs. wildtype cells replicate 2

source_name: Schizosaccharomyces pombe cells, set1 deletion

value: set1 deletion mutant


title: CDR129_sham

source_name: C57Bl/6J_Sham-operated control


title: UC_inactive_13-2

description: ulcerative colitis inactive

tag: patient

value: UC patient #13 (same site, remission2)

value: ulcerative colitis inactive


title: UC_inactive_11

description: ulcerative colitis inactive

value: UC patient #11 (same site, remission)


title: MIA PaCa-2 cells treated with DMSO (vehicle control) 3

city: Indianapolis

first: shujie

last: cheng

state: IN

address: 1800 N Capitol Ave, E504

department: Methodist Research Institute

institute: Indiana University Health

hyb_protocol: each sample was hybridized to a PrimeView Human array using the standard Affymetrix protocol

scan_protocol: Scanned using the affymetrix GS30007G using Affymetrix GeneChip operating system (GCOS)

data_processing: Cel files were generated by GCOS and imported into Partek Genomics Suite  RMA (robust multi-array average) signals were generated using the RMA background correction, Quantile normalization and summarization by Median Polish. RMA data was log base 2 transformed, only core probesets were generated.

source_name: MIA PaCa-2_DMSO (vehicle control)

label_protocol: 100ng of RNA from each sample was labeled using the Affymetrix 3' IVT Express kit.

growth_protocol: The human pancreatic cancer cell line MIA PaCa-2 was obtained from ATCC (Manassas, VA) and maintained in Dulbecco's modified Eagle's medium containing penicillin (50 U ml−1), streptomycin (50 U ml−1), 10% FBS and 2.5% horse serum (HS). Media came from ATCC. Supplements, FBS and HS were obtained from Gibco BRL (Grand Island, NY).

extract_protocol: Total-RNA from each sample was isolated with RNeasy® Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. The integrity of the isolated RNA was checked on an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: PA was purchased from Shinning-biotech (Chengdu, Sichuan, China) and dissolved in DMSO at a concentration of 50 mM then stored at -20˚C. DMSO was purchased from Sigma (St. Louis, MO). MIA PaCa-2 cells were treated with PA (0 and 30 µM) for 24 h in quadruplicates.

value: MIA PaCa-2

tag: cell type

value: pancreatic cancer cell line

tag: treatment

value: DMSO (control)


title: MIA PaCa-2 cells treated with PA (30 µM) 4

source_name: MIA PaCa-2_PA (30 µM)

value: 30 µM of pachymic acid


title: T.4FP3.TIGIT-.SpLN#1

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Spleen & Lymph Node

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 6 weeks

tag: exclusion markers

value: CD8- CD19- CD11b- CD11c- 7AAD-

tag: genetic background

value: Treg

tag: phenotype markers

value: CD4+ Foxp3+ TIGIT-


title: set1D_1

description: Gene expression profiling in set1 deletion mutant vs. wildtype cells replicate 1

value: wildtype


title: UC_inactive_9

description: ulcerative colitis inactive

source_name: Colon tissue

value: UC patient #9 (same site, remission)


title: MIA PaCa-2 cells treated with PA (30 µM) 3


title: T.4FP3.TIGIT-.SpLN#2

value: male


title: MIA PaCa-2 cells treated with PA (30 µM) 1


title: MIA PaCa-2 cells treated with PA (30 µM) 2


title: UC_inactive_13-1

description: ulcerative colitis inactive

value: UC patient #13 (same site, remission)


title: T.4FP3.TIGIT+.SpLN#2

value: CD4+ Foxp3+ TIGIT+


title: MCF-7-Pit-1 rep 2

city: Santiago de compostela

first: Samuel

last: Seoane

state: A Coruña

address: Avd de Barcelona sn

department: CIMUS-Endocrine

country: Spain

institute: University of Santiago de Compostela

description: 2+ purif encarna

hyb_protocol: The labeled RNA was fragmented and hybridized to human oligonucleotide arrays (HU 1.0 ST Array) using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640 and GeneChip Fluidics Station 450)

scan_protocol: Scanning were performed using GeneChip Scanner 7G).

data_processing: For the microarray data analysis, Affymetrix CEL files from each of the two microarray hybridization experiments for the four conditions (pcDNA3, control, C1 and C2, and  pcDNA3-Pit-1 (+1 and +2) were imported into the dChip software (v.2010.01; Dana Farber Cancer Institute, Boston, MA). Normalization of all arrays was done against the array with median overall intensity.

source_name: MCF-7 Pit-1 overexpression

label_protocol: Double-stranded cDNA and biotinylated cRNA were synthesized using a T7-polyT primer and the BioArray RNA labeling kit (Enzo Life Sciences, Farmingdale, NY), respectively.

growth_protocol: MCF-7 cells were grown in DMEM with 10% of FBS,100 mU/mL penicillin, 100 μg/mL streptomycin, and 2 mM l-glutamine in a 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was extracted and purified using the PureLink Micro-to-Midi kit (Invitrogen).

treatment_protocol: When cells were 80% confluent,  cells were transfected with the pcDNA3 (control) or the pcDNA3-Pit-1 overexpression vector for 48 hours.

value: Breast tumor cell line

tag: transfected with

value: pcDNA3-Pit-1 overexpression vector


title: MCF-7-Pit-1 rep 1

description: 1+ purif encarna


title: T.4FP3.TIGIT+.SpLN#1


title: MIA PaCa-2 cells treated with DMSO (vehicle control) 2


title: MIA PaCa-2 cells treated with DMSO (vehicle control) 4


title: UC_inactive_10

description: ulcerative colitis inactive

value: UC patient #10 (same site, remission)

value: ulcerative colitis inactive


title: Normal_control_1

description: control

value: colon

value: healthy control


title: Pmel_T1

city: Los Angeles

first: Jennifer

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

hyb_protocol: Arrays were washed and stained on a GeneChip Fluidics Station 450

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 7G and image analysis with the Affymetrix GeneChip Command Console Scan Control.

data_processing: Data was RMA normalized in R/Bioconductor using the affy package.

source_name: SM1 tumors mice treated with various drug combinations and pmel-1 adoptive cell transfer

label_protocol: cDNAs were generated, fragmented, biotinylated, and hybridized to the GeneChip Mouse 430 V2 Arrays

extract_protocol: Total RNAs were extracted using the RNeasy MicroKit

value: SM1 tumor

tag: drug

value: trametinib

value: adoptive cell transfer of pmel-1 splenocytes


title: MCF-7 control rep 1

description: C1 purif encarna

source_name: MCF-7 Control

tag: cell line

value: pcDNA3 (control vector)


title: UC_inactive_8

description: ulcerative colitis inactive

value: UC patient #8 (same site, remission)


title: MIA PaCa-2 cells treated with DMSO (vehicle control) 1

value: MIA PaCa-2

value: pancreatic cancer cell line

value: DMSO (control)


title: UC_inactive_6

description: ulcerative colitis inactive

value: UC patient #6 (same site, remission)


title: UC_inactive_7

description: ulcerative colitis inactive

value: UC patient #7 (same site, remission)


title: Pmel_D+T1

value: dabrafenib and trametinib


title: MCF-7 control rep 2

description: C2 purif encarna

value: Breast tumor cell line


title: UC_inactive_5

description: ulcerative colitis inactive

value: UC patient #5 (same site, remission)


title: Huh7 transfected with Mut,biological rep3

city: Beijing

first: Jun

last: Hu

address: No. 1 West Beichen Road, Chaoyang District

department: CAS Key Laboratory of Pathogenic Microbiology and Immunology

institute: Institute of Microbiology, Chinese Academy of Sciences

description:
Gene expression data from Huh7 transfected with Mut
Mut-3

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) andSanta Clara, CA, US).

data_processing: Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by RMA algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

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

growth_protocol: Huh-7 cell line was cultured with DMEM supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and 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).

treatment_protocol: Huh7 cells transfected with pcDNA3.1 plasmid containing HBV mRNA with wild type (WT) or mutant (Mut) miR-122 response elements in its 3’-UTR or the empty pcDNA3.1 vector (3.1) as a mock.

value: hepatoma


title: Pmel_V1

value: vehicle


title: Pmel_V2


title: UC_inactive_4

description: ulcerative colitis inactive

value: UC patient #4 (same site, remission)

value: ulcerative colitis inactive


title: Huh7 transfected with Mut,biological rep2

description:
Gene expression data from Huh7 transfected with Mut
Mut-2


title: Pmel_D1

value: SM1 tumor

value: dabrafenib


title: UC_inactive_1

description: ulcerative colitis inactive

value: UC patient #1 (same site, remission)


title: Huh7 transfected with WT,biological rep3

description:
Gene expression data from Huh7 transfected with WT
WT-3


title: Pmel_T2

value: trametinib

value: adoptive cell transfer of pmel-1 splenocytes


title: Pmel_D2


title: Huh7 transfected with Mut,biological rep1

description:
Gene expression data from Huh7 transfected with Mut
Mut-1


title: UC_active_13-1

description: ulcerative colitis active

value: UC patient #13

value: ulcerative colitis active


title: UC_active_13-2

description: ulcerative colitis active

value: UC patient #13 (same site, post-relapse)


title: UC_active_13-3

description: ulcerative colitis active

value: UC patient #13 (same site, post-relapse2)


title: UC_inactive_2

description: ulcerative colitis inactive

value: UC patient #2 (same site, remission)


title: Huh7 transfected with WT,biological rep2

description:
Gene expression data from Huh7 transfected with WT
WT-2


title: Huh7 transfected with 3.1,biological rep3

description:
Gene expression data from Huh7 transfected with 3.1
3.1-3


title: Pmel_D+T2

value: dabrafenib and trametinib


title: Huh7 transfected with WT,biological rep1

description:
Gene expression data from Huh7 transfected with WT
WT-1


title: Huh7 transfected with 3.1,biological rep1

description:
Gene expression data from Huh7 transfected with 3.1
3.1-1


title: UC_active_12-1

description: ulcerative colitis active

value: UC patient #12


title: Huh7 transfected with 3.1,biological rep2

description:
Gene expression data from Huh7 transfected with 3.1
3.1-2


title: Mock_V1

source_name: SM1 tumors harvested from mice treated with various drug combinations

value: adoptive cell transfer of C57BL/6 splenocytes


title: Pmel_D+T3


title: Mock_V3


title: UC_active_12-2

description: ulcerative colitis active

value: UC patient #12 (same site, post-relapse)


title: UC_active_11-2

description: ulcerative colitis active

value: UC patient #11 (same site, post-relapse)


title: MRP8/14-LPS 3.14

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

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

description:
24h MRP8-14 10µg_LPS 1ng 4h
replicate 3

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite

source_name: human blood monocyte

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

extract_protocol: Extraction of total RNA was performed with chaotropic ions and silica membran according to the manufacturer's instructions (Macherey-Nagel RNA isolation user manual).

value: human blood monocyte

value: 24h MRP8-14 10µg LPS 1ng 4h


title: MRP8/14-LPS 2.14

description:
24h MRP8-14 10µg_LPS 1ng 4h
replicate 2


title: Mock_D+T2

label_protocol: cDNAs were generated, fragmented, biotinylated, and hybridized to the GeneChip Mouse 430 V2 Arrays.

value: SM1 tumor


title: LPS-LPS 3.13

description:
24h LPS 25pg_LPS 1ng 4h
replicate 3

value: 24h LPS 25pg LPS 1ng 4h


title: Mock_D+T3


title: LPS-LPS 2.13

description:
24h LPS 25pg_LPS 1ng 4h
replicate 2


title: UC_active_8

description: ulcerative colitis active

value: UC patient #8


title: UC_active_10

description: ulcerative colitis active

value: UC patient #10


title: MRP8/14-con 3.8

description:
24h MRP8-14 10µg_n 4h
replicate 3


title: UC_active_9

description: ulcerative colitis active

value: UC patient #9


title: LPS-LPS 1.13

description:
24h LPS 25pg_LPS 1ng 4h
replicate 1


title: UC_active_11-1

description: ulcerative colitis active

value: UC patient #11


title: MRP8/14-LPS 1.14

description:
24h MRP8-14 10µg_LPS 1ng 4h
replicate 1


title: MRP8/14-con 2.8

description:
24h MRP8-14 10µg_n 4h
replicate 2


title: 251485013892_3/24262/61

city: Kingston

first: Scott

last: Davey

state: Ontario

address: Botterell Hall, Room 364

institute: Queen's University

description:
test set
US45102857_251485013892_S01_GE2-v5_95_Feb07_1_3.txt

hyb_protocol: 825ng Cy3 labeled control (-IR) and 825 Cy5 labeled experimental samples were mixed and hybridized to to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed with gene expression wash buffer 1 and 2.

scan_protocol: Image acquisition was done using an Agilent Microarray Scanner, Model G2565BA. Imaging analysis was done using Agilent Feature Extraction software v9.1.

data_processing: Although the experiment was done to allow for analysis of radiation-dependent effects (Cy5/Cy3 ratio), the reported results are from unperturbed cells (Cy3 one color data only).  The raw data is  normalized by mean, per chip, using Excel. A total of 43,338 features were used in the analysis. A set of 38 features had gene label values that could not be interpreted by the analysis software, and were eliminated prior to analysis. Each sample was corrected for overall intensity by subtraction of the mean (per array) value from the value for each feature.

source_name: Cell line (-IR)

label_protocol: RNA with an integrity number of at least 7 was amplified and labeled using the Agilent Low RNA Input Linear Amplification kit (Agilent, Santa Clara, CA). Labeling reactions were performed with 250 ng total RNA, along with the Agilent Spike-in RNA mix, using Cy3-CTP and Cy5-CTP for control (-IR) and experimental (+IR) RNA, respectively (Perkin Elmer, MA, USA). Amplified RNA was quantified using the NanoDrop ND-1000 (NanoDrop Technologies, DE, USA) and the concentration of cRNA and the specific dye activity were calculated. Samples with a specific dye activity greater than 8 pmol/l were selected for hybridization to arrays.

growth_protocol: Cells were cultured in RPMI-1640 media (Sigma Aldrich, Oakville, ON) supplemented with non-heat inactivated 15% fetal bovine serum (FBS) (Sigma Aldrich). All cell culture was carried out in 25cm2 flasks (Corning, Nepean, ON) at 37°C in 5% CO2 atmosphere. Cells were split in a 2:1 ratio until the desired cell number of 650,000 cells/ml was reached.

extract_protocol: Total RNA was extracted using TRIZOL® Reagent following the manufacturer’s recommendations (Invitrogen, Burlington,ON). RNA was purified using the RNeasy MinElute Cleanup Kit (Qiagen, Mississauga, ON). RNA quality was assessed by Agilent 2100 Bioanalyzer (Version B.02.02).

treatment_protocol: DNA damage was induced through exposure to 2 Gy ionizing radiation (IR), delivered by a 137Cs Victoreen Electrometer (Atomic Energy of Canada, Mississauga, ON) at a dose rate of 0.52Gy/min. Following treatment, the cells were allowed to recover for a period of 6 hr at 37°C in 5% CO2 atmosphere prior to extraction of total RNA.

value: Non radiated

tag: cell line id

tag: genome/variation

tag: brca1 mutation type

value: c.851ins7  Frameshift

source_name: Cell line (+IR)

value: Radiated


title: UC_active_7

description: ulcerative colitis active

value: UC patient #7

value: ulcerative colitis active


title: UC_active_5

description: ulcerative colitis active

value: UC patient #5


title: 251485014285_4/27636/91

description:
test set
US45102857_251485014285_S01_GE2-v5_95_Feb07_1_4.txt

value: c.3607C>T  Nonsense


title: MRP8/14-con 1.8

description:
24h MRP8-14 10µg_n 4h
replicate 1


title: UC_active_6

description: ulcerative colitis active

value: UC patient #6


title: 251485013896_4/14832/32

description:
test set
US45102857_251485013896_S01_GE2-v5_95_Feb07_1_4.txt

value: c.2475_2467delC  Frameshift


title: UC_active_4

description: ulcerative colitis active

value: UC patient #4


title: HDF68_5HmC_rep1

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: The provided Beta Values are SWAN normalized  Beta values described in the accompanying manuscript.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing:
Standard 450k and TAB-array data were independently normalized using the subset-quantile within array normalization (SWAN) method (Maksimovic, Gordon et al. 2012)
Average Beta Values provided in the processes matrix data are SWAN normalized.  Samples with the extension '*_5mC' are corrected 5mC values as described in detail within the supplementary methods provided with the accompanying manuscript.  Briefly, the corrected 5mC Beta values for each biological replicate by subtraction of the TAB-array generated beta values(5hmC signal) from the standard 450k generated beta values(5mC + 5hmC signal).  Over-corrected 5mC Beta values <=0 were manually reset to a very small value of 0.001.  All raw data exported directly from genome studio are also provided as supplementary data.

label: Cy5 and Cy3

source_name: human dermal fibroblasts

label_protocol: Standard Illumina Protocol

growth_protocol: For differentiation into CVPs, iPSCs were seeded at 125,000 cells per well of a 6 well plate coated with bovine collagen type 1 (BD Bioscience) at 8 μg/cm2.  Cells were cultured for 5 days in CVP medium (Genea Biocells), changing the medium every other day.Neural differentiation of iPSCs was carried out using a previously published protocol (Chen, Coleman, et al. 2014).  Briefly, 1X104 cells per cm2 were seeded on Matrigel (BD Biosciences)-coated 6 well plates in StemPro® medium (Life Technologies) for 24 hours.  The medium was then changed to NPC differentiation medium which contains the following: DMEM/F-12 (Life Technologies), 20% Knockout Serum Replacement (Life Technologies), 1X Glutamax™ (Life Technologies), 0.1 mM 2-mercaptoethanol (Life Technologies), 20 ng/mL midkine (EMD-Millipore), 2 μM dorsomorphin (Sigma-Aldrich), 2 μM A 83-01 (Tocris), and 2 μM PNU-74654 (Sigma-Aldrich).  Cells were Accutase® passaged (1:3) on days 3 and 6 and harvested on day 9.

extract_protocol: DNA was isolated using a DNeasy kit (Qiagen) according to the manufacturer’s recommendations.

value: human dermal fibroblasts

tag: tab-array sample

value: yes


title: LPS-con 2.7

description:
24h LPS 25pg_n 4h
replicate 2

value: human blood monocyte

value: 24h LPS 25pg n 4h


title: UC_active_2

description: ulcerative colitis active

value: UC patient #2


title: NPC_5HmC_rep2

source_name: Neural progenitor cells differentiated from hIPSCs

value: Neural progenitor cells


title: CARDIAC_5HmC_rep1

source_name: Cardiovascular progenitor cells differentiated from hIPSCs

value: Cardiovascular progenitor cells


title: LPS-con 3.7

description:
24h LPS 25pg_n 4h
replicate 3


title: 251485023318_2/13135/17

description:
test set
US45102857_251485023318_S01_GE2-v5_95_Feb07_1_2.txt

value: Non radiated

value: c.66_67delAG  Frameshift


title: 251485023317_3/26950/68

description:
test set
US45102857_251485023317_S01_GE2-v5_95_Feb07_1_3.txt

value: Radiated


title: LPS-con 1.7

description:
24h LPS 25pg_ n 4h
replicate 1

value: 24h LPS 25pg  n 4h


title: HDF68_5HmC_rep2


title: CARDIAC_5HmC_rep2


title: UC_active_1

description: ulcerative colitis active

value: UC patient #1

value: ulcerative colitis active


title: 251485014283_3/20425/48

description:
test set
US45102857_251485014283_S01_GE2-v5_95_Feb07_1_3.txt


title: 251485013775_2/27131/99

description:
test set
US45102857_251485013775_S01_GE2-v5_95_Feb07_1_2.txt

value: c.4484G>T  Missense


title: 251485014282_3/22012/64

description:
test set
US45102857_251485014282_S01_GE2-v5_95_Feb07_1_3.txt


title: HiPSC68_undiff_5HmC_rep2

source_name: Undifferentiated human induced pluripotent stem cells


title: 251485013771_3/14643/19

description:
test set
US45102857_251485013771_S01_GE2-v5_95_Feb07_1_3.txt

value: c.1175_1214del  Frameshift


title: 251485013929_1/19848/16

description:
test set
Scott_251485013929_S01_GE2-v5_95_Feb07_1_1.txt


title: 251485013889_4/20223/63

description:
test set
US45102857_251485013889_S01_GE2-v5_95_Feb07_1_4.txt


title: 251485013889_2/14663/22

description:
test set
US45102857_251485013889_S01_GE2-v5_95_Feb07_1_2.txt

value: c.4327C>T  Nonsense


title: NPC_5HmC_rep1


title: Tsc1-/-_R_3

city: Chengdu

first: Chong

last: Chen

state: Sichuan

address: 17 Renmin S. Road-No. 3

department: State Key Laboratory of Biotherapy

institute: Sichuan University

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4007B (Axon Instruments, Union City, CA)

hyb_protocol: Hybridization of biotin-labeled cDNA was carried out on a miRNA microarray chip (MD Anderson Cancer Center Version 4.0).The labeled targets of first-strand biotin-cDNA are used to hybridize miRNA arrays in 6 X SSPE/30% formamide at 25°C for 18 h.

scan_protocol: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4000B (Axon Instruments, Union City, CA). The images were quantified by GENEPIX 6.0 software (Axon Instruments, Union City, CA).

data_processing: The raw intensity for each probe is the F635 median feature pixel intensity with the median background subtracted, which is normalized to endogenous control GAPDH median. Then, the probe detecting same miRNA in one cohort was averaged.

source_name: mouse embryonic fibroblast

label_protocol: 5 µg of total RNA from each sample was biotin-labeled by reverse transcription using 5’ biotin end-labeled random octamer oligo primer.

growth_protocol: Cells were cultured in DMEM with 10% FBS and 1% Pen/Strep.

extract_protocol: Total RNA isolation was performed with TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Cell were treated with vehicle or rapamycin (5nM) for four days.

tag: strain

value: mouse embryonic fibroblast

tag: genotype


title: HDF68_none_rep2

description: The provided Beta Values are SWAN normalized  Beta values described in the accompanying manuscript, without correction.

value: human dermal fibroblasts

value: no


title: Tsc1-/-_R_2

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4006B (Axon Instruments, Union City, CA)


title: HiPSC68_undiff_5HmC_rep1

value: yes


title: Tsc1-/-_R_4

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4008B (Axon Instruments, Union City, CA)


title: HDF68_none_rep1


title: 251485013773_4/19843/33

description:
test set
US45102857_251485013773_S01_GE2-v5_95_Feb07_1_4.txt


title: 251485013775_1/22029/94

description:
test set
US45102857_251485013775_S01_GE2-v5_95_Feb07_1_1.txt


title: Tsc1-/-_R_5

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4009B (Axon Instruments, Union City, CA)


title: 251485013929_2/19992/43

description:
test set
Scott_251485013929_S01_GE2-v5_95_Feb07_1_2.txt


title: 251485014284_3/13416/3

description:
Training set
US45102857_251485014284_S01_GE2-v5_95_Feb07_1_3.txt

value: c.5263insC  Frameshift


title: 251485013773_2/19633/12

description:
test set
US45102857_251485013773_S01_GE2-v5_95_Feb07_1_2.txt


title: Tsc1-/-_R_1

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4005B (Axon Instruments, Union City, CA)


title: HDF68_5mC_rep1

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from HDF68_5HmC_rep1 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.


title: NPC_5mC_rep2

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from NPC_5HmC_rep2 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.


title: 251485014285_1/21303/77

description:
Training set
US45102857_251485014285_S01_GE2-v5_95_Feb07_1_1.txt


title: HDF68_5mC_rep2

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from HDF68_5HmC_rep2 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.


title: 251485014282_2/18700/73

description:
Training set
US45102857_251485014282_S01_GE2-v5_95_Feb07_1_2.txt

value: IVS9-2A>C  Splicing


title: 251485014282_1/26842/72

description:
Training set
US45102857_251485014282_S01_GE2-v5_95_Feb07_1_1.txt


title: Tsc1-/-_4

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4003B (Axon Instruments, Union City, CA)


title: HiPSC68_undiff_5mC_rep2

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from HiPSC68_undiff_5HmC_rep2 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.


title: 251485014281_2/16236/62

description:
Training set
US45102857_251485014281_S01_GE2-v5_95_Feb07_1_2.txt

value: c.2561insGC  Frameshift


title: NPC_5mC_rep1

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from NPC_5HmC_rep1 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.

value: Neural progenitor cells


title: Tsc1-/-_1

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4000B (Axon Instruments, Union City, CA)


title: Tsc1-/-_2

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4001B (Axon Instruments, Union City, CA)


title: CARDIAC_5mC_rep2

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from CARDIAC_5HmC_rep2 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.

value: Cardiovascular progenitor cells


title: CARDIAC_5mC_rep1

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from CARDIAC_5HmC_rep1 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.


title: Tsc1+/+_5


title: Tsc1-/-_3

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4002B (Axon Instruments, Union City, CA)


title: 251485013929_3/15268/24

description:
Training set
Scott_251485013929_S01_GE2-v5_95_Feb07_1_3.txt

value: Non radiated


title: Burkitt Lymphoma 12

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Array Studio version 5.0 (Omicsoft Corporation)

source_name: tumor DNA

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).  All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Patients diagnosed with BL were biopsied and tumor tissues were frozen.

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

treatment_protocol: Frozen tissue sections were immediately dissolved in Trizol.

tag: gender

value: M

tag: immune status

value: IC

tag: graft

tag: immuno-supression

tag: tx-ptdl interval (months)

tag: stadium

value: IVB

tag: ebv

value: CHOP/RTX

tag: response

value: CR

tag: outcome

tag: cytogenetic and fish findings

value: ND.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[?/200]


title: Tsc1+/+_4

tag: cell type


title: Tsc1-/-_5

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4004B (Axon Instruments, Union City, CA)


title: Burkitt Lymphoma 9

tag: age

value: IIIB

tag: treatment

value: Intensive CT


title: Burkitt Lymphoma 8

value: IA

value: CHOP


title: 251485013892_1/18318/55

description:
Training set
US45102857_251485013892_S01_GE2-v5_95_Feb07_1_1.txt

tag: cell line id

tag: genome/variation

tag: brca1 mutation type

value: c.3756_3759delGTCT  Frameshift

value: Radiated


title: Burkitt Lymphoma 11

value: IIA


title: 251485013898_2/17653/49

description:
Training set
US45102857_251485013898_S01_GE2-v5_95_Feb07_1_2.txt

value: c.5263insC  Frameshift


title: Tsc1+/+_3

tag: strain

value: mouse embryonic fibroblast

tag: genotype


title: Burkitt Lymphoma 10

tag: gender

tag: immune status


title: Tsc1+/+_2


title: Burkitt Lymphoma 7

value: ID

tag: graft

value: kidney

tag: immuno-supression

value: CNI+AM

value: ND.nuc ish(MYCx2)[200]


title: Tsc1+/+_1


title: 251485013891_4/27348/97

description:
Training set
US45102857_251485013891_S01_GE2-v5_95_Feb07_1_4.txt

value: Non radiated

value: c.66_67delAG  Frameshift


title: Burkitt Lymphoma 6

value: M

value: liver

value: CNI

tag: tx-ptdl interval (months)

tag: stadium

value: CHOP/RTX

value: PD


title: 251485013890_3/12928/11

description:
Training set
US45102857_251485013890_S01_GE2-v5_95_Feb07_1_3.txt

value: c.4689C>G  Nonsense


title: HiPSC68_undiff_5mC_rep1

description: The provided Beta Values are the corrected 5mC Beta values described in the accompanying manuscript.  TAB-array generated beta values(5hmC signal) from HiPSC68_undiff_5HmC_rep1 have been subtracted from the SWAN normalized Beta value for this sample, to generate a distinct 5mC signal in this sample.  Over-corrected 5mC Beta values (<=0) were manually reset to a very small value of 0.001.

tag: tab-array sample

value: no


title: 251485013896_2/14834/25

description:
Training set
US45102857_251485013896_S01_GE2-v5_95_Feb07_1_2.txt

value: c.1016insA  Frameshft

value: Radiated


title: 251485013792_4/15285/37

description:
Training set
US45102857_251485013792_S01_GE2-v5_95_Feb07_1_4.txt

value: exon13ins6kb  Other


title: 251485013891_2/15736/51

description:
Training set
US45102857_251485013891_S01_GE2-v5_95_Feb07_1_2.txt

value: c.191G>A  Missense


title: Burkitt Lymphoma 5

value: ID

value: heart

value: IIA

tag: ebv

tag: response

value: CR

tag: outcome


title: Burkitt Lymphoma 3

tag: age

value: kidney

value: CNI+AM+CS

value: IVA

tag: cytogenetic and fish findings

value: NM.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[160/200]


title: Burkitt Lymphoma 4

value: M

value: liver

value: IIIA

tag: treatment

value: Intensive CT

value: NM.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[190/200]


title: Burkitt Lymphoma 2

value: CNI

value: CHOP/RTX


title: 251485013888_3/15737/45

description:
Training set
US45102857_251485013888_S01_GE2-v5_95_Feb07_1_3.txt

value: Non radiated

tag: cell line id

tag: genome/variation

value: IVSI-22A>G  Other

value: Radiated


title: 9231425096_H - 48 hrs - SEA

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

hyb_protocol: cRNA was hybridised to Illumina mouse ref8_V2 expression beadchips according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing: Raw data represent relative signal intensity. Data was analysed using GenomeStudio version 1.1.1 and Genespring GX 12.5. Data were normalised to the median of all samples and are presented in log2 scale.

label_protocol: cRNA was synthesised from total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

extract_protocol:
The liver of female 6 week old C57BL/6 mice (4) were removed and then sectioned at 250um thickness usinga  vibrotome.
Total RNA was extracted from liver tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Sections were cultered at 37oC and 5%CO2 in in William’s Medium E containing 25 mM glucose, 10 mg/ml gentamycin and 10% FBS. SEA was added at 10ug/ml and sections sampled at timepoints 0, 4hr, 24hr and 48hrs.

tag: tissue

value: Liver

tag: strain

tag: Sex

value: Female

value: 6 weeks

tag: timepoint

value: 48 hrs

value: SEA


title: 9231425096_G - 48 hrs - Negative Control

value: Negative Control


title: Burkitt Lymphoma 9

hyb_protocol: DNA was whole-genome amplified, purified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files generated by Affymetrix Command Console and CYCHP files generated byAffymetrix Chromosome Analysis Suite software (ChAS).  DNA copy number and allele analysis were performed using Affymetrix ChAS, which compares all hybridization intensities against a built-in reference data set
Hybridized to Affymetrix Cytogenetics Array

label_protocol: Biotin, affymetrix protocol for the  Cytogenetics array 2.7M

growth_protocol: No culture-just DNA from frozen tissue

extract_protocol: Qiagen kit for DNA extraction

treatment_protocol: no previous treatment

tag: gender

tag: immune status

value: IC

tag: graft

value: IIIB

value: CR

value: ND.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[?/200]


title: Burkitt Lymphoma 1

value: M

value: ID

value: heart

tag: immuno-supression

value: CNI+AM

tag: tx-ptdl interval (months)

tag: stadium

value: IIIA

value: RTX


title: 9231425096_F - 24 hrs - SEA

value: 24 hrs


title: 251485013792_2/27129/95

description:
Training set
US45102857_251485013792_S01_GE2-v5_95_Feb07_1_2.txt

value: Non radiated

tag: brca1 mutation type

value: exon13 dup  Frameshift

value: Radiated


title: Burkitt Lymphoma 10

description: Hybridized to Affymetrix Cytogenetics Array

value: IVB

tag: ebv

value: CHOP/RTX

tag: response

tag: outcome


title: 9231425096_D - 4 hrs - SEA

value: Liver

value: Female

tag: age

value: 6 weeks

value: 4 hrs

tag: treatment

value: SEA


title: 251485013779_3/14703/21

description:
Training set
US45102857_251485013779_S01_GE2-v5_95_Feb07_1_3.txt

tag: cell line id

tag: genome/variation

value: c.2834_2836delGTAinsC  Frameshift


title: 9231425096_C - 4 hrs - Negative Control

tag: tissue

tag: strain

value: Negative Control


title: 251485013778_4/25453/86

description:
Training set
US45102857_251485013778_S01_GE2-v5_95_Feb07_1_4.txt

value: c.2934T>G  Nonsense


title: 9231425096_E - 24 hrs - Negative Control

tag: Sex

tag: timepoint


title: 251485023316_2/33139/101

description:
Training set
US45102857_251485023316_S01_GE2-v5_95_Feb07_1_2.txt

value: c.66_67delA  Frameshift


title: pt. HCL F treated with DMSO for 48h

city: Perugia

first: Enrico

last: Tiacci

address: Santa M. della Misericordia Hospital, San Sisto

department: Department of Medicine

country: Italy

institute: Institute of Hematology

description:
Gene expression data from  primary HCL cell of  patient F treated with DMSO for 48h
ET45

hyb_protocol: Fragmented cRNA was hybridized to HG-U133Plus_2.0 microarrays according to the 3' IVT Express Kit for sample preparation and microarray hybridization (Affymetrix, Santa Clara, CA, USA; catalogue no. 901229). The microarrays were then washed and stained according to the manufacturer's recommendation.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 with G7 update.

data_processing: The data were analyzed by means of the GeneSpring Version 7.3.1 software (Agilent Technologies) with RMA pre-processing of the raw expression data (CEL files).

source_name: primary leukemic cells purified from peripheral blood

label_protocol: High-quality total RNA (50-100 ng) was converted into biotinylated cRNA, purified and fragmented employing the 3' IVT Express Kit for sample preparation and microarray hybridization (Affymetrix, Santa Clara, CA, USA; catalogue no. 901229).

growth_protocol: 7.5x105 primary leukemic cells MACS-purified from the peripheral blood of  HCL patients were seeded in flat-bottom 24-well plates  in complete medium (RPMI 1640 medium supplemented with 10% FBS, 1% Penicillin/Streptomycin and 1% Glutamine) and were then treated with Vemurafenib 1000 nM, or vehicle (DMSO) as control, for 48 hours or 72 hours

extract_protocol: Lysates  (600 μl of Buffer RLT Plus supplemented with β-mercaptoethanol) were  stored at -80°C until total RNA extraction. Total RNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Vemurafenib was dissolved in dimethyl sulfoxide (DMSO) as a 10 mM stock solution. Final drug concentration (1000 nM) was obtained with further serial dilutions in culture medium. Negative controls were represented by cells treated only with DMSO at a concentration of 1:2500 v/v, which is the highest possible DMSO concentration present in cultures of cells treated with the drug (in particular, with 1000 nM drug, the highest drug concentration). After 48 hours to 72 hours, cultures were harvested and lysed.

value: peripheral blood

tag: cell type

value: primary leukemic cells

tag: individual

value: patient F

value: DMSO for 48h


title: 251485013775_4/14023/1

description:
Training set
US45102857_251485013775_S01_GE2-v5_95_Feb07_1_4.txt

value: Non radiated

value: c.2071delA  Frameshift


title: 9231425092_H - 48 hrs - SEA

value: 48 hrs


title: pt. HCL F treated with Vemurafenib 1000 nM for 48h

description:
Gene expression data from  primary HCL cell of  patient F treated with Vemurafenib 1000 nM for 48h
ET46

value: Vemurafenib 1000 nM for 48h


title: 9231425096_B - 0 (before treatment) - Negative Control

value: Liver

value: 0 (before treatment)


title: pt. HCL F treated with DMSO for 72h

description:
Gene expression data from  primary HCL cell of  patient F treated with DMSO for 72h
ET47

value: DMSO for 72h


title: pt. HCL F treated with Vemurafenib 1000 nM for 72h

description:
Gene expression data from  primary HCL cell of  patient F treated with Vemurafenib 1000 nM for 72h
ET48

value: Vemurafenib 1000 nM for 72h


title: 251485013771_4/13537/38

description:
Training set
US45102857_251485013771_S01_GE2-v5_95_Feb07_1_4.txt

value: c.3607C>T  Nonsense

value: Radiated


title: 9231425096_A - Pre-cut whole tissue - Negative Control

value: Female

value: 6 weeks

value: Pre-cut whole tissue

value: Negative Control


title: Burkitt Lymphoma 8

tag: gender

value: M

tag: immune status

value: IC

tag: graft

tag: immuno-supression

value: IA

value: CHOP

value: CR

tag: cytogenetic and fish findings

value: ND.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[?/200]


title: pt. HCL E treated with DMSO for 72h

description:
Gene expression data from  primary HCL cell of  patient E treated with DMSO for 72h
ET43

value: peripheral blood

value: primary leukemic cells

value: patient E


title: Burkitt Lymphoma 12

tag: tx-ptdl interval (months)

tag: stadium

value: IVB

tag: ebv

value: CHOP/RTX

tag: response


title: pt. HCL E treated with Vemurafenib 1000 nM for 72h

description:
Gene expression data from  primary HCL cell of  patient E treated with Vemurafenib 1000 nM for 72h
ET44

tag: treatment

value: Vemurafenib 1000 nM for 72h


title: 251485013774_4/22893/81

description:
Training set
US45102857_251485013774_S01_GE2-v5_95_Feb07_1_4.txt

value: Non radiated

tag: cell line id

tag: genome/variation

tag: brca1 mutation type

value: c.1175_1214del  Frameshift

value: Radiated


title: Burkitt Lymphoma 7

tag: age

value: ID

value: kidney

value: CNI+AM

tag: outcome

value: ND.nuc ish(MYCx2)[200]


title: Burkitt Lymphoma 3

value: M

value: CNI+AM+CS

value: IVA

value: NM.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[160/200]


title: 251485013771_1/17082/89

description:
Training set
US45102857_251485013771_S01_GE2-v5_95_Feb07_1_1.txt

value: c.66_67delAG  Frameshift


title: Burkitt Lymphoma 11

value: IC

value: IIA

value: CR

value: ND.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[?/200]


title: Burkitt Lymphoma 2

value: liver

value: CNI

value: CHOP/RTX


title: 9231425092_G - 48 hrs - Negative Control

tag: tissue

value: Liver

tag: strain

tag: Sex

value: Female

value: 6 weeks

tag: timepoint

value: 48 hrs

value: Negative Control


title: 251485023318_1/19639/15

description:
Training set
US45102857_251485023318_S01_GE2-v5_95_Feb07_1_1.txt

value: Non radiated

value: Radiated


title: 251485013792_1/19018/93

description:
Training set
US45102857_251485013792_S01_GE2-v5_95_Feb07_1_1.txt

value: c.4327C>T Nonsense


title: Burkitt Lymphoma 4

tag: gender

value: M

tag: immune status

value: ID

tag: graft

value: CNI+AM+CS

value: IIIA

value: Intensive CT

value: NM.nuc ish(MYCx2)(5'MYC sep 3'MYCx1)[190/200]


title: pt. HCL E treated with Vemurafenib 1000 nM for 48h

description:
Gene expression data from  primary HCL cell of  patient E treated with Vemurafenib 1000 nM for 48h
ET42

value: peripheral blood

tag: cell type

value: primary leukemic cells

tag: individual

value: patient E

value: Vemurafenib 1000 nM for 48h


title: 9231425092_F - 24 hrs - SEA

value: Liver

value: Female

value: 24 hrs

value: SEA


title: pt. HCL E treated with DMSO for 48h

description:
Gene expression data from  primary HCL cell of  patient E treated with DMSO for 48h
ET41

value: DMSO for 48h


title: 9231425092_D - 4 hrs - SEA

value: 6 weeks

value: 4 hrs


title: 9231425092_E - 24 hrs - Negative Control

value: Negative Control


title: Burkitt Lymphoma 6

description: Hybridized to Affymetrix Cytogenetics Array

value: M

value: ID

value: liver

tag: immuno-supression

value: CNI

tag: tx-ptdl interval (months)

tag: stadium

value: IA

tag: ebv

value: CHOP/RTX

value: PD

tag: cytogenetic and fish findings


title: pt. HCL D treated with DMSO for 72h

description:
Gene expression data from  primary HCL cell of  patient D treated with DMSO for 72h
ET31

value: peripheral blood

value: primary leukemic cells

value: patient D

tag: treatment

value: DMSO for 72h


title: pt. HCL D treated with Vemurafenib 1000 nM for 48h

description:
Gene expression data from  primary HCL cell of  patient D treated with Vemurafenib 1000 nM for 48h
ET30

value: Vemurafenib 1000 nM for 48h


title: 9231425092_C - 4 hrs - Negative Control

value: Liver

value: Female

tag: age


title: 251485014284_1/20664/56

description:
Training set
US45102857_251485014284_S01_GE2-v5_95_Feb07_1_1.txt

value: Non radiated

tag: cell line id

tag: genome/variation

value: Radiated


title: pt. HCL C treated with Vemurafenib 1000 nM for 72h

description:
Gene expression data from  primary HCL cell of  patient C treated with Vemurafenib 1000 nM for 72h
ET28

tag: tissue

value: patient C

value: Vemurafenib 1000 nM for 72h


title: 9231425092_B - 0 (before treatment) - Negative Control

tag: strain

tag: Sex

value: 6 weeks

value: 0 (before treatment)

value: Negative Control


title: 251485014284_4/19487/6

description:
Training set
US45102857_251485014284_S01_GE2-v5_95_Feb07_1_4.txt


title: 251485014282_4/21206/69

description:
Training set
US45102857_251485014282_S01_GE2-v5_95_Feb07_1_4.txt


title: 9231425092_A - Pre-cut whole tissue - Negative Control

tag: timepoint

value: Pre-cut whole tissue


title: 251485014283_2/19641/23

description:
Training set
US45102857_251485014283_S01_GE2-v5_95_Feb07_1_2.txt


title: 9231425085_H - 48 hrs - SEA

value: 48 hrs

value: SEA


title: pt. HCL D treated with DMSO for 48h

description:
Gene expression data from  primary HCL cell of  patient D treated with DMSO for 48h
ET29

value: peripheral blood

value: DMSO for 48h


title: 251485014281_3/21202/65

description:
Training set
US45102857_251485014281_S01_GE2-v5_95_Feb07_1_3.txt


title: Burkitt Lymphoma 5

tag: gender

value: M

tag: immune status

value: ID

value: heart

value: CNI+AM

value: IIA

value: CHOP/RTX

tag: response

value: CR

tag: outcome


title: 251485013898_3/20220/50

description:
Training set
US45102857_251485013898_S01_GE2-v5_95_Feb07_1_3.txt

value: Non radiated

value: Radiated


title: pt. HCL C treated with DMSO for 72h

description:
Gene expression data from  primary HCL cell of  patient C treated with DMSO for 72h
ET27

tag: cell type

value: primary leukemic cells

tag: individual

value: patient C

value: DMSO for 72h


title: Burkitt Lymphoma 1

tag: graft

tag: immuno-supression

tag: tx-ptdl interval (months)

tag: stadium

value: IIIA

value: RTX


title: 9231425085_G - 48 hrs - Negative Control

value: Liver

value: Female

tag: age

value: 6 weeks

value: 48 hrs

tag: treatment

value: Negative Control


title: 251485013898_1/20000/40

description:
Training set
US45102857_251485013898_S01_GE2-v5_95_Feb07_1_1.txt

tag: cell line id

tag: genome/variation


title: 9231425085_E - 24 hrs - Negative Control

tag: tissue

tag: strain

value: 24 hrs


title: pt. HCL B treated with Vemurafenib 1000 nM for 48h

description:
Gene expression data from  primary HCL cell of  patient B treated with Vemurafenib 1000 nM for 48h
ET24

value: peripheral blood

value: patient B

value: Vemurafenib 1000 nM for 48h


title: 9231425085_D - 4 hrs - SEA

tag: Sex

tag: timepoint

value: 4 hrs

value: SEA


title: pt. HCL C treated with DMSO for 48h

description:
Gene expression data from  primary HCL cell of  patient C treated with DMSO for 48h
ET25

value: DMSO for 48h


title: 251485013891_1/19636/14

description:
Training set
US45102857_251485013891_S01_GE2-v5_95_Feb07_1_1.txt

value: Non radiated

value: Radiated


title: 251485013891_3/26214/96

description:
Training set
US45102857_251485013891_S01_GE2-v5_95_Feb07_1_3.txt


title: pt. HCL C treated with Vemurafenib 1000 nM for 48h

description:
Gene expression data from  primary HCL cell of  patient C treated with Vemurafenib 1000 nM for 48h
ET26

value: primary leukemic cells

value: patient C


title: 9231425085_A - Pre-cut whole tissue - Negative Control

value: Pre-cut whole tissue


title: pt. HCL A treated with Vemurafenib 1000 nM for 72h, replicate1

description:
Gene expression data from  primary HCL cell of  patient A treated with Vemurafenib 1000 nM for 72h
ET13

value: patient A

value: Vemurafenib 1000 nM for 72h


title: pt. HCL B treated with DMSO for 48h

description:
Gene expression data from  primary HCL cell of  patient B treated with DMSO for 48h
ET23


title: 251485013892_2/21198/59

description:
Training set
US45102857_251485013892_S01_GE2-v5_95_Feb07_1_2.txt


title: pt. HCL A treated with Vemurafenib 1000 nM for 72h, replicate2

description:
Gene expression data from  primary HCL cell of  patient A treated with Vemurafenib 1000 nM for 72h
ET14


title: 9231425085_C - 4 hrs - Negative Control

value: Liver

value: Female

value: 6 weeks


title: pt. HCL A treated with DMSO for 72h

description:
Gene expression data from  primary HCL cell of  patient A treated with DMSO for 72h
ET12

value: DMSO for 72h


title: 251485013888_4/22027/87

description:
Training set
US45102857_251485013888_S01_GE2-v5_95_Feb07_1_4.txt


title: 251485013890_4/19999/54

description:
Training set
US45102857_251485013890_S01_GE2-v5_95_Feb07_1_4.txt


title: 9231425081_G - 48 hrs - Negative Control

value: 48 hrs

value: Negative Control


title: 9231425081_H - 48 hrs - SEA


title: 9231425085_F - 24 hrs - SEA

value: 24 hrs


title: 9231425085_B - 0 (before treatment) - Negative Control

value: 0 (before treatment)


title: 251485013779_4/20222/53

description:
Training set
US45102857_251485013779_S01_GE2-v5_95_Feb07_1_4.txt


title: 251485013792_3/19997/36

description:
Training set
US45102857_251485013792_S01_GE2-v5_95_Feb07_1_3.txt


title: pt. HCL A treated with Vemurafenib 1000 nM for 48h, replicate1

description:
Gene expression data from  primary HCL cell of  patient A treated with Vemurafenib 1000 nM for 48h
ET10

value: peripheral blood

value: Vemurafenib 1000 nM for 48h


title: pt. HCL A treated with Vemurafenib 1000 nM for 48h, replicate2

description:
Gene expression data from  primary HCL cell of  patient A treated with Vemurafenib 1000 nM for 48h
ET11


title: 9231425081_F - 24 hrs - SEA

value: SEA


title: pt. HCL A treated with DMSO for 48h

description:
Gene expression data from  primary HCL cell of  patient A treated with DMSO for 48h
ET9

value: DMSO for 48h


title: 251485013778_3/21360/82

description:
Training set
US45102857_251485013778_S01_GE2-v5_95_Feb07_1_3.txt

value: Non radiated

value: Radiated


title: MS25_Sample6_TNF_alpha_13.6_20080819

hyb_protocol: hybridization to Affymetrix (Santa Clara, CA) Human Genome 133 Plus 2.0 Gene Chip arrays

scan_protocol: Fluorescent signals  were detected by the Hewlett-Packard G2500A Gene Array Scanner (Affymetrix).

data_processing: Data were imported into Partek Genomics Suite V6.6 (PGS) (Partek) using RMA (Robust Multi-array Average, an algorithm used for background correction, log2-transformation and quantile normalization of Affymetrix expression data) prior to batch-correction.

source_name: human blood monocyte stimulated with TNF for 4h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix Gene Chip Expression 3´Amplification: one-cycle cDNA synthesis and IVT labeling; Expression Analysis Technical Manual, 2001, Affymetrix).

value: human blood monocyte

value: TNF


title: 9231425081_D - 4 hrs - SEA

value: 4 hrs


title: MS25_Sample7_IL1_beta_13.6_20080819

source_name: human blood monocyte stimulated with 1L1b for 4h


title: pt. HCL D treated with Vemurafenib 1000 nM for 72h

description:
Gene expression data from  primary HCL cell of  patient D treated with Vemurafenib 1000 nM for 72h
ET32

value: primary leukemic cells

value: patient D

value: Vemurafenib 1000 nM for 72h


title: 9231425081_C - 4 hrs - Negative Control

value: Liver

value: Female

value: 6 weeks


title: 251485013774_1/20428/46

description:
Training set
US45102857_251485013774_S01_GE2-v5_95_Feb07_1_1.txt


title: 9231425081_E - 24 hrs - Negative Control

value: 24 hrs

value: Negative Control


title: 251485023317_1/19842/30

description:
Training set
US45102857_251485023317_S01_GE2-v5_95_Feb07_1_1.txt


title: 251485013778_2/21535/76

description:
Training set
US45102857_251485013778_S01_GE2-v5_95_Feb07_1_2.txt


title: 251485023316_3/19490/5

description:
Training set
US45102857_251485023316_S01_GE2-v5_95_Feb07_1_3.txt


title: 9231425081_A - Pre-cut whole tissue - Negative Control

value: Pre-cut whole tissue


title: MS25_Sample4_TNF_alpha_30.5_20080819


title: 9231425081_B - 0 (before treatment) - Negative Control

value: 0 (before treatment)


title: 251485023317_2/20666/58

description:
Training set
US45102857_251485023317_S01_GE2-v5_95_Feb07_1_2.txt


title: 251485013774_3/20427/78

description:
Training set
US45102857_251485013774_S01_GE2-v5_95_Feb07_1_3.txt


title: 251485013775_3/20429/104

description:
Training set
US45102857_251485013775_S01_GE2-v5_95_Feb07_1_3.txt


title: 251485023316_1/22026/85

description:
Training set
US45102857_251485023316_S01_GE2-v5_95_Feb07_1_1.txt


title: MS25_Sample3_IL1_beta_5.6_20080819

source_name: human blood monocyte stimulated with IL1b for 4h


title: 251485013774_2/21368/74

description:
Training set
US45102857_251485013774_S01_GE2-v5_95_Feb07_1_2.txt


title: 251485013773_3/19847/29

description:
Training set
US45102857_251485013773_S01_GE2-v5_95_Feb07_1_3.txt


title: 251485023316_4/19850/20

description:
Training set
US45102857_251485023316_S01_GE2-v5_95_Feb07_1_4.txt


title: MS25_Sample5_IL1_beta_30.5_20080819


title: MS25_C_3_S100_A8_12.09_20071214

source_name: human blood monocyte stimulated with MRP8 for 4h


title: MS25_A_1_S100_A8_21.08_20071214


title: MS25_Sample1_KO_5.6_20080819

value: control


title: MS25_B_2_S100_A8_29.08_20071214


title: MS25_Sample2_TNF_alpha_5.6_20080819


title: 251485013772_3/20657/70

description:
Training set
US45102857_251485013772_S01_GE2-v5_95_Feb07_1_3.txt


title: MS25_5_KO_1_091007


title: MS25_3_KO_1_091007


title: JLI_tissue [207_1_1]

status: Public on Dec 11 2014

city: Minneapolis

first: Jong-Hyuk

last: Kim

state: MN

address: 425 East River Rd.

department: Dept of Veterinary Clinical Science

institute: University of Minnesota

description: gene expression in canine hemangiosarcoma tissue

hyb_protocol: Hybridized to Agilent canine 4 x 44,000 feature gene chips according to Agilent’s Protocol Version 6

scan_protocol: Read using an Agilent High Resolution G2500C scanner (Agilent, Santa Clara, CA, USA)

data_processing: Agilent quality control algorithms in Expressionist Refiner Module (v. 7.5; Genedata, Basel, Switzerland,) were used to confirm that data from each chip met the manufacturer’s standards for quality control and quality assurance. Of 45,220 features on each array, 35,676 that had annotation to known genes were used for analysis.

label: Cyanine-3 (Cy3)

organism: Canis lupus familiaris

source_name: canine hemangiosarcoma tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color using Agilent’s Microarray One-Color Quick Amp Labeling kit

growth_protocol: Primary tumor cells or cryopreserved cultured cells. 12 samples for monolayer cells were cultured in conventional HSA medium. 6 samples for sphere cells were cultured in serum-free and non-adherent culture condiotions. Snap Frozen primary tissue used for 24 samples.

extract_protocol: RNA was isolated using the TriPure Isolation Reagent (Roche Applied Science, Indianapolis, IN, USA) and the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Samples determined to be suitable for analysis based on RNA quality (ratio of absorbance at 260 nm over 280 nm between 1.95 and 2.1 and Bioanalyzer RNA Integrity Number > 6.1)

tag: tissue/cell line

value: Tissue

tag: breed

value: Golden Retriever

tag: origin


title: NP_tissue [209_1_1]


title: TS_tissue [205_1_4]

value: Spleen


title: IB_tissue [209_1_3]


title: 251485013771_2/19841/27

description:
Training set
US45102857_251485013771_S01_GE2-v5_95_Feb07_1_2.txt

value: Non radiated

value: Radiated


title: MS25_7_KO_1_091007

tag: cell type

value: human blood monocyte


title: CS_tissue [203_1_1]

value: Border Collie

value: Heart


title: PA_tissue [206_1_4]

value: Portuguese Water Dog


title: GM_tissue [208_1_3]


title: 251485013772_1/19998/44

description:
Training set
US45102857_251485013772_S01_GE2-v5_95_Feb07_1_1.txt


title: SAS_tissue [208_1_4]


title: MH_tissue [207_1_4]


title: FH_tissue [206_1_1]


title: SJ_tissue [207_1_2]


title: SAL_tissue [209_1_2]

value: Liver


title: RG_tissue [208_1_1]

value: German Shepherd


title: TCL_tissue [202_1_4]


title: RC_tissue [205_1_2]


title: JLU_tissue [199_1_3]

value: Lung


title: CB_tissue [199_1_1]

value: Keeshond


title: SH_tissue [208_1_2]


title: OH_tissue [198_1_3]


title: AW_tissue [197_1_4]


title: AH_tissue [198_1_1]


title: SB2_sphere [196_1_3]

description: gene expression in canine hemangiosarcoma sphere cells

source_name: canine hemangiosarcoma sphere

value: Sphere cells

value: Skin


title: MK_tissue [199_1_2]

value: Bernese Mtn Dog


title: SB3_sphere [199_1_4]


title: TCH_tissue [209_1_4]


title: SB1_sphere [196_1_1]


title: EFB_sphere [196_1_4]

value: Brain


title: FH-2_monolayer cell [205_1_3]

description: gene expression in canine hemangiosarcoma monolayer cells

source_name: canine hemangiosarcoma monolayer cells

value: Monolayer cells


title: FH-1_monolayer cell [202_1_3]

value: Golden Retriever


title: JHE-2_monolayer cell [202_1_2]


title: JLU_monolayer cell [200_1_1]


title: SB_monolayer cell [198_1_4]

value: Cutaneous


title: SH_monolayer cell [200_1_2]

value: Spleen


title: FH_sphere [202_1_1]


title: DD1_monolayer cell [197_1_2]

value: GR Mix


title: JLI_monolayer cell [200_1_3]


title: EFB_monolayer cell [203_1_2]


title: JHE_sphere [197_1_1]


title: GM_monolayer cell [197_1_3]


title: JSP_tissue [207_1_3]

value: Tissue


title: EFS_monolayer cell [203_1_3]


title: JHE-1_monolayer cell [200_1_4]


title: WT 2

city: Berkeley

first: Andreas

last: Stahl

address: 119 Morgan Hall, #3104

department: Nutritional Sciences and Toxicology

institute: University of California Berkeley

description: 3 mos old, fasted overnight, WT replicate 2

data_processing: The differential expression analysis was performed using the Linear Models for Microarray Data package (Limma)

source_name: Brown adipose tissue

label_protocol: Labeling was performed using the TotalPrep RNA Amplification Kit # AMIL1791 from Illumina

extract_protocol: RNA was extracted with Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit according to manufacturer's instructions.

treatment_protocol: Mice were placed in clean cages with no food overnight.

tag: genetic background

value: C57BL6J Male BAT

value: brown adipose tissue

tag: gender

value: male

tag: genotype

value: wild type


title: KO 1

description: 3 mos old, fasted overnight, KO replicate 1

value: Cd36 null


title: WT 3

description: 3 mos old, fasted overnight, WT replicate 3


title: KO 3

description: 3 mos old, fasted overnight, KO replicate 3


title: M_met_HFD_wat 3R-1WAT

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

hyb_protocol: Hybridized as recommended by manufacturer

scan_protocol: Scanned as recommended by manufacturer

data_processing:
The data was processed using the R package lumi. The control probe data was added the background subtracted using the lumiB bgAdjust option. The data was then vst transformed and rsn normalized using the lumiT and lumiN functions, respectively
Raw data is as provided by the microarray service facility. Normalized values correspond to variance stabilized robust spline normalized values.

source_name: subcutaneous adipose tissue; postnatal day 4

label_protocol: Labelled as recommended by manufacturer

growth_protocol: Tissues were harvested at postnatal day 4

extract_protocol: RNA was isolated using a RNAeasy Minikit (Qiagen) according to manufacturer's instructions with an additional DNase I digestion (Qiagen) step.

treatment_protocol: Tissues obtained were either snap frozen in liquid nitrogen or stored in RNAlater agent for later RNA extraction. Total RNA was extracted with RNeasy Mini kit (liver, brain) and miRNeasy Micro Kit (adipose tissue) with additional Dnase I treatment.

value: Male

value: adipose tissue

value: metformin

tag: prenatal diet

value: High fat diet

tag: study

value: Study II


title: WT 1

description: 3 mos old, fasted overnight, WT replicate 1


title: M_ctrl_HFD_wat 1T-4WAT

value: control


title: M_met_HFD_wat 3R-6WAT


title: KO 2

description: 3 mos old, fasted overnight, KO replicate 2


title: M_met_HFD_wat 10K-2WAT


title: M_met_HFD_wat 3R-5WAT


title: M_ctrl_HFD_wat 1T-3WAT


title: M_ctrl_HFD_wat 1R-4WAT


title: M_met_HFD_liver 10K-1liver

source_name: liver tissue; postnatal day 4

value: liver


title: M_met_HFD_liver 3R-5liver


title: M_ctrl_HFD_wat 1T-2WAT


title: M_met_HFD_liver 3R-2liver


title: M_met_HFD_liver 3R-6liver


title: M_ctrl_HFD_liver 1T-1liver


title: M_ctrl_HFD_liver 1T-3liver


title: M_met_HFD_liver 3R-1liver


title: M_ctrl_HFD_liver 1R-4liver


title: M_ctrl_HFD_wat 1R-1WAT


title: F_met_RD_liver 4E_Liver

value: Female

value: Regular diet

value: Study I


title: F_met_RD_liver 1F_Liver


title: M_ctrl_HFD_liver 1R-1liver


title: M_ctrl_HFD_liver 1T-4liver


title: F_ctrl_RD_liver 2B_Liver


title: M_ctrl_HFD_wat 1T-1WAT


title: F_ctrl_RD_liver 6C_Liver


title: M_met_HFD_wat 3R-2WAT


title: M_ctrl_RD_brain 5C_Brain

source_name: whole brain; postnatal day 4

value: brain


title: M_ctrl_RD_liver 3B_Liver


title: M_ctrl_RD_liver 5C_Liver


title: M_ctrl_HFD_liver 1T-2liver


title: F_met_RD_liver 4F_Liver


title: M_met_RD_liver 3E_Liver


title: M_met_RD_brain 6F_Brain


title: M_met_RD_liver 1E_Liver


title: M_met_RD_liver 6F_Liver


title: M_met_HFD_liver 10K-2liver


title: M_met_RD_brain 1E_Brain


title: M_ctrl_RD_brain 3B_Brain


title: M_met_RD_brain 3E_Brain


title: F_ctrl_RD_liver 1C_Liver


title: M_ctrl_RD_liver 1B_Liver


title: M_ctrl_RD_brain 1B_Brain


title: Germinating wheat seed at ABAe_biological rep3

first: Yonglong

last: Yu

address: 105 Xisanhuan North Road

institute: College of Life Science, Capital Normal University

description: Wheat seed_ABAe-3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

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

organism: Triticum aestivum

source_name: Wheat seed_endosperm response to ABA

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: The collection of germinative embryo and endosperm which germinated under the untreatment (CK) and under the treatment of ABA/H2O2.

treatment_protocol: Sterile wheat seeds grew in pure water as the contrast check (CK_embryo and CK_endosperm), while seeds were treated with 100 mg/L ABA and 100 μmol H2O2 as experimental groups (ABA_embryo and ABA_endosperm, H2O2_embryo and H2O2_endosperm). When the seeds imbibed water for 16 hour and the radicle just emerged episperm, we harvested embryo and endosperm tissue separately in triplicate as simples. The collected embryo and endosperm of different treatment were placed in -80℃ condition for the subsequent experiments.

value: germinative endosperm

tag: treated with

value: 100 mg/L ABA


title: Germinating wheat seed at H2O2e_biological rep3

description: Wheat seed_H2O2e-3

source_name: Wheat seed_endosperm response to H2O2

value: 100 μmol H2O2


title: Germinating wheat seed at H2O2em_biological rep1

description: Wheat seed_H2O2em-1

source_name: Wheat seed_embryo response to H2O2

value: germinative embryo


title: Germinating wheat seed at H2O2em_biological rep3

description: Wheat seed_H2O2em-3


title: Germinating wheat seed at H2O2em_biological rep2

description: Wheat seed_H2O2em-2


title: Germinating wheat seed at CKe_biological rep3

description: Wheat seed_Cke-3

source_name: Wheat seed_endosperm response to pure water (CK)

value: pure water (control)


title: Germinating wheat seed at ABAem_biological rep2

description: Wheat seed_ABAem-2

source_name: Wheat seed_embryo response to ABA


title: Germinating wheat seed at ABAem_biological rep3

description: Wheat seed_ABAem-3


title: Germinating wheat seed at ABAe_biological rep2

description: Wheat seed_ABAe-2


title: Germinating wheat seed at CKem_biological rep2

description: Wheat seed_CKem-2

source_name: Wheat seed_embryo response to pure water (CK)


title: Germinating wheat seed at H2O2e_biological rep2

description: Wheat seed_H2O2e-2


title: Germinating wheat seed at CKe_biological rep1

description: Wheat seed_Cke-1


title: Germinating wheat seed at H2O2e_biological rep1

description: Wheat seed_H2O2e-1


title: Germinating wheat seed at ABAem_biological rep1

description: Wheat seed_ABAem-1


title: FKC_Jfkidney_Siniae1

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

country: Japan

institute: Tokyo University of Marine Science and Technology

description: Total RNA was extracted from fish kidneys using the RNeasy Mini Kit. The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol. After hybridization cocktails preparation, the Agilent 8x15k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol. Oligo DNA microarray, bound to Cy3-labeled cRNA, were processed using the Genepix pro v6.0 and scanned with a Axon Genepix4000B scanner.

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15k oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent's manuals.

scan_protocol: Oligo DNA microarray, bound to Cy3-labeled cRNA, were processed using the Genepix pro v6.0. and scanned with a Genepix4000B (Axon, USA). Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 025875_D_F_20091023) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.0 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 75th percentile values of the arrays in the experiments.

organism: Paralichthys olivaceus

source_name: Kidney of Paralichthys olivaceus after 6 hours from a injection using formalin killed Streptococcus iniae strain 02

label_protocol: Conversion of double stranded cDNA into Cy3-labeled cRNA was accomplished using the QuickAmp Labeling kit one-color (Agilent, USA) according to the manufacturer’s instructions.

growth_protocol: The fishes were fed with commercial feeds at a one percent of body weight per one day.

extract_protocol: After 6 hours from an intraperitoneal injection of FKC, total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany).

treatment_protocol:
The fishes were kept in an artificial seawater 500 liter tank with a recirculating system at 20°C.
The fishes were administered by an intraperitoneal injection using a 2.58mg of FKC of S. iniae suspended in 100μl of PBS.

tag: injection

value: formalin-killed Streptococcus iniae strain 02

tag: average fish body weight

value: kidney


title: Germinating wheat seed at CKe_biological rep2

description: Wheat seed_Cke-2


title: IgM+IgD+CD27- B cells donor5

city: Essen

first: Marc

last: Seifert

address: Virchowstrasse 173

department: Institute of Cell Biology (Cancer Research)

institute: University of Duisburg Essen

description: Gene expression data from sort-purified PB B cell subsets

hyb_protocol: Following fragmentation, 1 ug of cRNA was hybridized to HG U133 2.0 Plus Arrays.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GeneSpring GX software after vsn normalization and ComBat correction.

source_name: IgM+IgD+CD27- B cells donor5 peripheral blood

label_protocol: Affymetrix enhanced biotinylation protocol

treatment_protocol: sort purification according to surface Ig and CD27 expression patterns

value: peripheral blood

value: caucasian

tag: age


title: FKC_Jfkidney_Siniae2

tag: tissue


title: Germinating wheat seed at CKem_biological rep3

description: Wheat seed_CKem-3


title: IgM+IgD+CD27- B cells donor4

source_name: IgM+IgD+CD27- B cells donor4 peripheral blood


title: IgM+IgD+CD27- B cells donor2

source_name: IgM+IgD+CD27- B cells donor2 peripheral blood


title: FKC_Jfkidney_Vanguillarum1

source_name: Kidney of Paralichthys olivaceus after 6 hours from a injection using formalin killed Vibrio anguillarum strain H775-3

treatment_protocol:
The fishes were kept in an artificial seawater 500 liter tank with a recirculating system at 20°C.
The fishes were administered by an intraperitoneal injection using a 73.4μg (5x10^7 cells) of FKC of V. anguillarum suspended in 100μl of PBS.

value: formalin-killed Vibrio anguillarum strain H775-3


title: Germinating wheat seed at ABAe_biological rep1

description: Wheat seed_ABAe-1


title: FKC_Jfkidney_Vanguillarum2


title: FKC_Jfkidney_Siniae3


title: Germinating wheat seed at CKem_biological rep1

description: Wheat seed_CKem-1


title: FKC_Jfkidney_Vanguillarum3


title: IgM+IgD+CD27- B cells donor3

source_name: IgM+IgD+CD27- B cells donor3 peripheral blood


title: IgM+IgD+CD27- B cells donor1

source_name: IgM+IgD+CD27- B cells donor1 peripheral blood


title: IgM+IgD-CD27+ B cells donor5

source_name: IgM+IgD-CD27+ B cells donor5 peripheral blood


title: FKC_Jfkidney_Lgarviae2

source_name: Kidney of Paralichthys olivaceus after 6 hours from a injection using formalin killed Lactococcus garviae strain EH8706

treatment_protocol:
The fishes were kept in an artificial seawater 500 liter tank with a recirculating system at 20°C.
The fishes were administered by an intraperitoneal injection using a 1.78mg (4.3x10^7 cells) of FKC of L. garviae suspended in 100μl of PBS.

value: formalin-killed Lactococcus garviae strain EH8706


title: FKC_Jfkidney_control1

source_name: Kidney of Japanese flounder, control

extract_protocol: After 6 hours from an intraperitoneal injection of PBS, total RNA was extracted from fish kidney using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Germany).

treatment_protocol:
The fishes were kept in 500 liter tank containing an artificial seawater with a recirculating system at 20°C.
The bacterial cells suspended in 100μl of phosphate buffered-saline were intrapenitoneally injected.

value: control


title: FKC_Jfkidney_Etarda3

source_name: Kidney of Paralichthys olivaceus after 6 hours from a injection using formalin killed Edwardsiella tarda strain 54

treatment_protocol:
The fishes were kept in an artificial seawater 500 liter tank with a recirculating system at 20°C.
The fishes were administered by an intraperitoneal injection using a 0.263mg (6.0 x 10^7 cells) of FKC of E. tarda suspended in 100μl of PBS.

value: formalin-killed Edwardsiella tarda strain 54


title: FKC_Jfkidney_Lgarviae3


title: FKC_Jfkidney_control4


title: FKC_Jfkidney_Lgarviae1


title: FKC_Jfkidney_Etarda1


title: FKC_Jfkidney_Etarda2


title: IgM+IgD-CD27+ B cells donor1

source_name: IgM+IgD-CD27+ B cells donor1 peripheral blood


title: FKC_Jfkidney_control3


title: FKC_Jfkidney_control2


title: IgM+IgD+CD27+ B cells donor2

source_name: IgM+IgD+CD27+ B cells donor2 peripheral blood


title: class switched B cells donor1

source_name: class switched B cells donor1 peripheral blood


title: IgM+IgD+CD27+ B cells donor5

source_name: IgM+IgD+CD27+ B cells donor5 peripheral blood


title: IgM+IgD-CD27+ B cells donor3

source_name: IgM+IgD-CD27+ B cells donor3 peripheral blood


title: IgM+IgD-CD27+ B cells donor2

source_name: IgM+IgD-CD27+ B cells donor2 peripheral blood


title: class switched B cells donor3

source_name: class switched B cells donor3 peripheral blood


title: IgM+IgD+CD27+ B cells donor3

source_name: IgM+IgD+CD27+ B cells donor3 peripheral blood


title: IgM+IgD+CD27+ B cells donor1

source_name: IgM+IgD+CD27+ B cells donor1 peripheral blood


title: class switched B cells donor2

source_name: class switched B cells donor2 peripheral blood


title: 6852.Q3.dosT.wk16.1

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: Sample 23

hyb_protocol: 55 C overnight for no longer than 16 hrs as described in PMID: 25322074

scan_protocol: GenePix 4000B as described in PMID: 25322074

data_processing: DData from stored TIFF files was extracted using GenePix Pro 6.1 and the resulting .gpr files were loaded on to Spotfire DecisionSite for Microarray Analysis. Data was essentially notmalized using locally weighted linear regression based intensity normalization (LOWESS) and statistical significance derived using a one way ANOVA with false discovery rate correction within R, using Log2 fold change values computed by Spotfire.

source_name: dosT infection day 1

label_protocol: Agilent kit as described in PMID: 25322074

growth_protocol: We used euthanized mice to extract RNA (Kramnik, C3HeB/FeJ) obtained from Jackson Laboratories.

extract_protocol: Trizol based extraction followed by on column DNAse treatment as described in Gautam US et al PMID: 25322074

tag: mouse strain

value: Kramnik, C3HeB/FeJ

tag: pathogen

value: M. tuberculosis H37Rv with mutation in dosT

source_name: dosT infection week 16

value: week 16


title: IgM+IgD+CD27+ B cells donor4

source_name: IgM+IgD+CD27+ B cells donor4 peripheral blood


title: 6852.Q4.dosT.wk16.1

description: Sample 24

tag: timepoint


title: class switched B cells donor5

source_name: class switched B cells donor5 peripheral blood


title: class switched B cells donor4

source_name: class switched B cells donor4 peripheral blood


title: 6852.Q2.dosS.wk16.2

description: Sample 22

source_name: dosS infection day 1

value: M. tuberculosis H37Rv with mutation in dosS

source_name: dosS infection week 16


title: 6751.Q2.Mtb.wk16.2

description: Sample 18

source_name: Mtb infection day 1

value: M. tuberculosis H37Rv

source_name: Mtb infection week 16


title: 6751.Q4.dosR.wk16.2

description: Sample 20

source_name: dosR infection day 1

value: M. tuberculosis H37Rv with mutation in dosR

source_name: dosR infection week 16


title: 6750.Q2.dosS.wk8.2

description: Sample 14

source_name: dosS infection week 8

value: week 8


title: 6750.Q1.dosS.wk8.1

description: Sample 13


title: 9312.Q4.dosR.wk4.2

description: Sample 8

source_name: dosR infection week 4

value: week 4


title: 6751.Q3.dosR.wk16.1

description: Sample 19


title: 6749.Q1.Mtb.wk8.1

description: Sample 9

source_name: Mtb infection week 8


title: WT LSK 3

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4000B (Axon Instruments, Union City, CA)

source_name: mouse BM HSPCs

growth_protocol: Mice were maintained in the animal facility at the University of Michigan with standard housing conditions and protocols.  All procedures involving experimental animals were approved by the University Committee on the Use and Care of Animals at the University of Michigan.

treatment_protocol: Mice were treated with 400 µg polyinosinic:polycytidylic acid (pIpC, 2mg/ml in 1xDPBS, Sigma-Aldrich) 7 times every other day by intraperitoneal injection (i.p.) to induce targeted gene deletion.  At 10 days after the last pIpC injection, Lin-cKit+Sca1+ HSPCs were isolated from mouse bone marrow.

value: LSK

tag: strain

value: Female


title: KO LSK 2


title: WT LSK 4


title: KO LSK 3

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4001B (Axon Instruments, Union City, CA)


title: KO LSK 1


title: 9250.Q4.dosT.wk4.2

description: Sample 4

source_name: dosT infection day1

source_name: dosT infection week 4


title: KO LSK 4

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4002B (Axon Instruments, Union City, CA)


title: 6750.Q3.dosT.wk8.1

description: Sample 15

source_name: dosT infection day 1

source_name: dosT infection week 8


title: 6852.Q1.dosS.wk16.1

description: Sample 21


title: 9312.Q3.dosR.wk4.1

description: Sample 7


title: 9250.Q3.dosT.wk4.1

description: Sample 3


title: WT LSK 1


title: WT LSK 2


title: 9250.Q2.dosS.wk4.2

description: Sample 2

source_name: dosS infection day1

source_name: dosS infection week 4


title: 6749.Q4.dosR.wk8.2

description: Sample 12

source_name: dosR infection day1

source_name: dosR infection week 8


title: 9312.Q1.Mtb.wk4.1

description: Sample 5

source_name: Mtb infection week 4


title: Hela-shTSC1kl(2)

city: Washington

first: Yang

last: Liu

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology Research

institute: Childrens' National Medical Center

hyb_protocol: Hybridization of biotin-labeled cDNA was carried out on a miRNA microarray chip (MD Anderson Cancer Center Version 5.0).The labeled targets of first-strand biotin-cDNA are used to hybridize miRNA arrays in 6 X SSPE/30% formamide at 25°C for 18 h.

data_processing: The raw intensity for each probe is the median feature pixel intensity with the median background subtracted. Quantitation of raw intensity is based on global median. First, Median and STDEV are caculated for all blank/buffer banground controls. The threshold value is defined as backgound Median plus 3 times of STDEV. The relative value for each probe is caculated by using the threshold value to divide the F635 median of each probe. The global mdedian is caculated from those have relative values >1. The final output of namalized intensity is caculated by using the global median to divide the relative value of each probe. Signals from probes measuring the same miRNA were averaged.

source_name: Hela cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies, Cat. No. 12430) supplemented with 10% fetal bovine serum (FBS) in a 37 °C humidified incubator with 5% CO2.

treatment_protocol: shRNAs plasmids were co-transfected with the lentiviral packaging plasmids psPAX2 and pMD2.G into HEK293T cells for virus production. HeLa cells were infected with shRNA pseudo-virus and selected with puromycin at 24 hours post-infection.

tag: vector

tag: sequence

tag: open biosystem id#


title: 6749.Q3.dosR.wk8.1

description: Sample 11


title: 9312.Q2.Mtb.wk4.2

description: Sample 6

source_name: Mtb infection day 1


title: 9250.Q1.dosS.wk4.1

description: Sample 1


title: 6750.Q4.dosT.wk8.2

description: Sample 16


title: Hela-shTSC1f(2)

value: AGATATTGCAGCTTCTTCTTT


title: Hela-shTSC1e(1)

value: ATAAAGGCGATGAAAGAGTGC


title: Hela-shTSC1f(1)


title: Hela-control(2)


title: Hela-control(1)


title: Hela-shDROSHA HS(1)

value: pGipz

value: ATCCTTCAAAGATATACTC


title: Hela-shDROSHA HS(3)


title: Hela-shDROSHA HS(2)


title: Hela-shDROSHA-1(1)

value: ATCCTATCAACTTGTCCAG


title: Hela-shDROSHA-1(3)


title: Hela-shDROSHA-1(2)


title: Hela-shTSC1kl(1)


title: Hela-Scr(3)


title: Hela-Scr(1)


title: Hela-Scr(2)


title: Ctrl mouse_3

hyb_protocol: Hybridization of biotin-labeled cDNA was carried out on a miRNA microarray chip (MD Anderson Cancer Center Version 5.0). The labeled targets of first-strand biotin-cDNA are used to hybridize miRNA arrays in 6 X SSPE/30% formamide at 25°C for 18 h.

label_protocol: 5 µg of total RNA from each sample was biotin-labeled by reverse transcription using 5' biotin end-labeled random octamer oligo primer.

treatment_protocol: Mice were treated with 400 µg polyinosinic:polycytidylic acid (pIpC, 2mg/ml in 1xDPBS, Sigma-Aldrich) 7 times every other day by intraperitoneal injection (i.p.) to induce targeted gene deletion.  At 10 days after the last pIpC injection, Lin-cKit+ HSPCs were isolated from mouse bone marrow.

value: Rprtf/f, Mx1-Cre-


title: Ctrl mouse_1


title: Hela-shTSC1e(2)


title: 6751.Q1.Mtb.wk16.1

description: Sample 17

source_name: Mtb infection week 16