title: WB_COPD_PT_353

tag: disease


title: WB_COPD_PT_146

status: Public on May 25 2016

type: RNA

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

hyb_protocol: Affymetrix GeneTitan Hybridization, Wash and Stain Kit for WT Array Plates (Part# 901622)

scan_protocol: Affymetrix GeneChip Command Console (AGCC) version 4.1.2.1567G for scanning, image acquisition and image processing on the Affymetrix GeneTitan Multi-Channel(MC) Instrument.

data_processing: RMA normalization and batch corrected with combat Bioconductor package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PAXgene whole blood mRNA

label_protocol: Affymetrix GeneChip HT WT Terminal Labeling Kit (Part# 901648)

extract_protocol: Qiagen PAXgene Blood miRNA Kit (Cat# 763134), automated processing using the Qiagen QIAcube robotic workstation (Cat# 9001292). Protocol to amplify RNA-Ambion WT Expression RNA Amplification Kit (Part# 4440536)

value: COPD

tag: age

tag: Sex

value: M

tag: prednisone status

tag: cell prop. granulocyte

tag: cell prop. monocyte

tag: cell prop. b lymphocyte

tag: cell prop. cd4 t lymphocyte

tag: cell prop. cd8 t lymphocyte

tag: cell prop. nk lymphocyte


title: WB_COPD_PT_137

value: F


title: WB_COPD_PT_398


title: WB_COPD_PT_024


title: WB_COPD_PT_668


title: WB_COPD_PT_874


title: WB_COPD_PT_306


title: WB_COPD_PT_731


title: WB_COPD_PT_396


title: WB_COPD_PT_223


title: WB_COPD_PT_461


title: WB_COPD_PT_769


title: WB_COPD_PT_209


title: WB_COPD_PT_934


title: Pou2f2 WT, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 2 - mAdbID:128662

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

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

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 128662

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

scan_protocol: Scan_MicronsPerPixelX: 3 Scan_MicronsPerPixelY: 3 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

organism: Mus musculus

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

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was prepared by the TRIzol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).

treatment_protocol:
Treatment time: 3 days
In-vitro treatment: B lymphocytes were purified from spleens of non-deleted mice by magnetic bead technology (B cell isolation kit, mouse, Miltenyi Biotech). Cells were stimulated in vitro with 5 ug/ml anti-IgM (Jackson), 10 ng/ml IL4 (Promega) in the presence of 5-OH-tamoxifen (Sigma). At 48 hours OCT2 was efficiently depleted and 50 ng/ml IL21 (Promega) was added. Cells were harvested 12 hours later.

tag: tissue

value: spleen

tag: cell type

value: B cells

tag: other

value: Wild type Cre-expressing mice were used as controls.

tag: genotype/variation

value: Pou2f2 WT, Ert2-Cre

source_name: Pooled Control

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

value: gene knock out

value: Pou2f2 fl/fl, Ert2-Cre, Pou2f2 WT

value: Sample Pooling Protocol:Pooled RNA from B cells of 4 Pou2/2 flox/flox and 4 Pou2f2 WT mice spleens.


title: WB_COPD_PT_351


title: Pou2f2 WT, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 3 - mAdbID:128663

description: mAdb experiment ID: 128663


title: Pou2f2 WT, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 1 - mAdbID:128661

description: mAdb experiment ID: 128661


title: WB_COPD_PT_992


title: WB_COPD_PT_578


title: WB_COPD_PT_281


title: Pou2f2 flox/flox, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 2 - mAdbID:128666

description: mAdb experiment ID: 128666

value: Homozygous (Pou2f2 fl/fl ), Cre-expressing knock-out mice:We generated conditional Pou2f2 knockout mice from targeted embryonic stem cells created by the European Mouse Knockout Consortium. Pou2f2 fl/fl mice were crossed first to FLPE recombinase mice to excise the neomycin cassette, and then to ERT2-Cre mice in which the Cre recombinase is tamoxifen-inducible. We observed efficient Cre-mediated deletion in germinal center B cells and in splenic B cells. Cre-mediated deletion was associated with persistence of a Pou2f2 transcript and the production of an unstable protein that lacked exons 8-11. Homozygous deletion of Pou2f2 was not associated with any sign of ill health or altered behavior in mice observed for more than two months after deletion.

value: Pou2f2 fl/fl, Ert2-Cre


title: WB_COPD_PT_871


title: Pou2f2 WT, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 4

description: No additional information.

value: Pooling Protocol:Pooled RNA from B cells of 4 Pou2/2 flox/flox and 4 Pou2f2 WT mice spleens.


title: Pou2f2 flox/flox, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 3 - mAdbID:128667

description: mAdb experiment ID: 128667


title: WB_COPD_PT_626


title: WB_COPD_PT_691


title: WB_COPD_PT_640


title: WB_COPD_PT_678


title: WB_COPD_PT_322


title: WB_COPD_PT_042


title: WB_COPD_PT_102


title: WB_COPD_PT_669


title: WB_COPD_PT_995


title: WB_COPD_PT_242


title: WB_COPD_PT_530


title: Pou2f2 flox/flox, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 1 - mAdbID:128665

description: mAdb experiment ID: 128665


title: WB_COPD_PT_143


title: WB_COPD_PT_971


title: WB_COPD_PT_565


title: WB_COPD_PT_448


title: Pou2f2 flox/flox, anti-IgM IL4 5-OH-Tamoxifen IL21 Treated - repeat 4 - mAdbID:128668

description: mAdb experiment ID: 128668


title: WB_COPD_PT_453


title: WB_COPD_PT_547


title: WB_COPD_PT_947


title: 12R0008

type: SRA

city: Los Angeles

first: Harry

middle: Taegyun

last: Yang

state: CA

address: Engineering VI 286

department: Computer Science

institute: University of California, Los Angeles

library_source: transcriptomic

data_processing:
We filtered reads mapped to the human reference genome and transcriptome (tophat v. 2.0.12 with default parameters, ENSEMBL GRCh37 transcriptome and ENSEMBL hg19 build).
unmapped reads were sub-sampled to 0.1 million reads for the taxonomic survey of the microbial communities
we filtered out low-quality and low-complexity reads, that is reads with at least 75% of their base pairs with quality lower then 30 (FASTX, http://hannonlab.cshl.edu/fastx_toolkit/) and reads with sequences of consecutive repetitive nucleotides (SEQCLEAN, http://sourceforge.net/projects/seqclean/), respectively.
Next, the remaining reads were realigned to the reference human genome and transcriptome (ENSEMBL GRCh37 transcripome and ENSEMBL hg19 build) using the Megablast aligner (BLAST+ 2.2.30, edit distance 6) (Camacho et al. 2009) to filter out any remaining potentially human reads.
The following parameters were used for makembindex:  iformat = blastdb.  The following options were used to map the reads using Megablast: for each reference: task = megablast, use_index = true,  perc_identity = 94, outfmt =6, max_target_seqs =1.
Genome_build: GRCh37

organism: human blood metagenome

source_name: Whole Blood RNA-Seq

extract_protocol:
Whole blood was collected in PAXgene Blood RNA tubes and total RNA was isolated using the PAXgene extraction kit (Qiagen). For DNA, whole blood was collected in EDTA tubes and the extraction performed using the Kleargene XL blood DNA extraction kit. HapMap B-lymphoblast cell lines (n=3) were cultured up to 5 days. All cell lines were grown in RPMI 1640 (Sigma-Aldrich) supplemented with 15% fetal bovine serum (Fisher Scientific) and 2mM L-glutamine (Fisher Scientific)  at 37C and 5% (vol/vol) CO2 in a humidified incubator. Cell pellets were lysed with Buffer RLT and RNA was extracted using the RNeasy Mini Kit (Qiagen).
Discovery sample : RNAseq libraries were prepared using Illumina’s TruSeq RNA v2 protocol, including ribo-depletion protocol (Ribo-Zero Gold). Sequencing was performed by UCLA Sequencing Core using the Illumina Hiseq 2000 platform. In total we obtained 6.8 billions 2x100bp paired-end reads (1355 Gbp) of paired-end reads for the primary study(35.3 ± 6.0 million paired-end reads per sample).Replication sample :For the replication sample, RNAseq libraries were prepared using Illumina’s TruSeq RNA v2 protocol, with poly(A) enrichment.  A total of 3.8 billion reads (760 Gbp) were obtained (26.3 ± 12.0 million paired-end reads per sample).RNASeq of B-lymphoblast cell lines :Just as our discovery samples, we used the TruSeq RNA v2 library preparation, including Ribo-Zero Gold rRNA depletion.  Samples were collected from a trio (father, mother, offspring) in duplicate. We obtained 144.6 million 2x69bp paired-end reads (Rapid run).Whole Blood Exome Sequencing : DNAseq libraries were prepared using Illumina’s TruSeq protocol, using the TruSeq Exome enrichment kit. For all samples, RIN values were obtained using Agilent’s RNA 6000 Nano kit and 2100 Bioanalyzer and measures for RNA concentration were obtained using the Quant-iT RiboGreen RNA Assay Kit.

value: blood

value: ALS


title: WB_COPD_PT_936


title: WB_COPD_PT_408


title: WB_CHF_PT_CHF02-010

data_processing: RMA normalization and batch corrected using combat Bioconductor package

value: CHF

tag: cell prop. neutrophil

tag: cell prop. lymphocyte

tag: cell prop. eosinophil

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-250

tag: disease

tag: age


title: WB_CHF_PT_CHF02-005

tag: Sex


title: WB_CHF_PT_CHF02-007


title: 12R0005


title: WB_CHF_PT_CHF02-003


title: WB_COPD_PT_886

tag: prednisone status

tag: cell prop. granulocyte


title: WB_CHF_PT_CHF02-004

tag: cell prop. monocyte


title: WB_CHF_PT_CHF02-006


title: WB_CHF_PT_CHF02-009


title: WB_CHF_PT_CHF01-241


title: WB_CHF_PT_CHF01-246


title: 12R0003


title: WB_COPD_PT_787

tag: cell prop. b lymphocyte

tag: cell prop. cd4 t lymphocyte


title: WB_CHF_PT_CHF01-249


title: WB_COPD_PT_288

tag: cell prop. cd8 t lymphocyte

tag: cell prop. nk lymphocyte


title: WB_COPD_PT_525


title: 12R0007

tag: tissue


title: 12R0001


title: 12R0002


title: WB_COPD_PT_046


title: WB_COPD_PT_880


title: WB_CHF_PT_CHF02-008


title: 11R0872

value: BPD


title: WB_CHF_PT_CHF01-247


title: 11R0871


title: 11R0814


title: 11R0828


title: 11R0812


title: 11R0632


title: 11R0633


title: 11R0629


title: 11R0621


title: 11R0624


title: 11R0619


title: 11R0620


title: 11R0618


title: 11R0590


title: WB_CHF_PT_CHF01-239


title: WB_CHF_PT_CHF01-226


title: WB_CHF_PT_CHF01-227


title: WB_CHF_PT_CHF01-231


title: WB_CHF_PT_CHF01-222


title: WB_CHF_PT_CHF01-240


title: WB_CHF_PT_CHF01-230


title: WB_CHF_PT_CHF01-221


title: WB_CHF_PT_CHF01-234


title: WB_CHF_PT_CHF01-225


title: WB_CHF_PT_CHF01-223


title: WB_CHF_PT_CHF01-229


title: WB_CHF_PT_CHF01-219


title: WB_CHF_PT_CHF01-235


title: WB_CHF_PT_CHF01-218


title: WB_CHF_PT_CHF01-224


title: 11R0401


title: 11R0396


title: WB_CHF_PT_CHF01-232


title: 11R0386


title: 11R0374

value: CSF


title: 11R0407


title: WB_CHF_PT_CHF01-252

value: M


title: WB_CHF_PT_CHF01-216


title: WB_CHF_PT_CHF01-217


title: WB_CHF_PT_CHF01-213

value: F


title: 11R0368


title: WB_CHF_PT_CHF01-211


title: 11R0365


title: WB_CHF_PT_CHF01-215


title: 11R0361


title: WB_CHF_PT_CHF01-214


title: 11R0355


title: 11R0349


title: 11R0341


title: 11R0336


title: 11R0343


title: 11R0333


title: NTUH-K2044 Wild-type

city: Taipei

first: Pei-Fang

last: Hsieh

address: 1, Sec 1, Jen-Ai Rd.

department: Department of Microbiology

country: Taiwan

institute: National Taiwan University College of Medicine

description:
yfgL-induced genes
The genomic library was constructed from a clinical isolate, NTUH-K2044, obtained from a patient with PLA plus meningitis and endophthalmitis for a KP genome shotgun sequencing project. NTUH-K2044 array contains 2,848 cloned sequences, which covering 99.9% of the entire genome sequence of NTUH-K2044.

hyb_protocol: The microarray-carrying membrane was prehybridized in 2 ml of hybridization buffer at 63℃;C for 2 h and hybridized at 63℃ for 16 h. The membrane was washed twice with 2X SSC containing 0.1% SDS at room temperature for 5 min and then washed three times with 0.1X SSC containing 0.1% SDS at 65℃ for 15 min each time. After hybridization and washing, the membrane was blocked with 2 ml of blocking buffer consisting of 7% casein (Sigma, St. Louis, Mo.) in 1X PBST buffer (1X phosphate-buffered saline, 0.05% Tween 20) at room temperature for 1 h and then incubated with 2 ml of a mixture containing 2,500X diluted alkaline phosphatase-conjugated streptavidin (Gibco BRL), 4% polyethylene glycol 8000 (Sigma), and 1% bovine serum albumin in PBST buffer for 1 h. The membrane was then washed with 1X PBST buffer four times for 5 min each and incubated with 2.5 ml nitroblue tetrazolium-5-bromo-4-chloro-3-indolylphosphate substrate buffer (Pierce, Rockford, Ill.) at room temperature for 20 min. Color development was stopped with 1X phosphate-buffered saline containing 20 mM EDTA.

scan_protocol: The signals in the membrane were scanned and converted to gray levels.

data_processing:
Densitometry was performed and analyzed by Image J software.  Expression level of 23S rRNA on each membrane was used as an internal standard for normalization. We used mean of 23S rRNA expression level on each section of membrane to normalize the expression level of whole transcription levels by (2 X 10^5 / mean of 23S rRNA expression level). The formulae used are contained in the file dyfgL_vs_WT_array_results.xls available on the series record.
The file "Non-normalized_data.txt" (available on the series record) also contains the normalized data and the fold change values.

organism: Klebsiella pneumoniae

source_name: The clinical isolate K. pneumoniae NTUH-K2044 was obtained from a patient with community-acquired pyogenic liver abscess plus meningitis and endophthalmitis.

label_protocol: Total RNA (40 μg) was mixed with 12 μM random primers; 1 mM (each) dCTP, dATP, and dGTP; 80 μM dTTP; 80 μM biotin-16-dUTP; RNase inhibitor (0.5 U/μl) (Roche, Mannheim, Germany); 10 mM dithiothreitol; and 600 U of Superscript II reverse transcriptase (Invitrogen/Gibco BRL, Carlsbad, Calif.) in 62.5 μl of solution at 42℃ for 90 min. The reaction was stopped by heating to 94℃ for 5 min, and RNA was degraded in the presence of NaOH and neutralized by addition of acetic acid. The labeled cDNA was precipitated with isopropanol and washed with 70% ethanol. Immediately before use, the probes were resuspended in hybridization buffer containing 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 0.1% N-lauroylsarcosine, 0.1% sodium dodecyl sulfate (SDS), and 1% blocking reagent (Roche).

growth_protocol: Log-phase cultures of the NTUH-K2044 wild-type and yfgL mutant K. pneumoniae strains in LB medium.

extract_protocol: Total RNA was purified with the RNeasy Mini Kit (Qiagen).

treatment_protocol: No treatment.

tag: genotype

value: wildtype

tag: strain


title: 11R0371


title: NTUH-K2044 yfgL mutant

description:
yfgL-repressed genes
The genomic library was constructed from a clinical isolate, NTUH-K2044, obtained from a patient with PLA plus meningitis and endophthalmitis for a KP genome shotgun sequencing project. NTUH-K2044 array contains 2,848 cloned sequences, which covering 99.9% of the entire genome sequence of NTUH-K2044.

source_name: The K. pneumoniae NTUH-K2044 mutated in yfgL was constructed using the unmarked deletion method.

value: yfgL mutant


title: WB_CHF_PT_CHF01-208

tag: cell prop. neutrophil


title: WB_CHF_PT_CHF01-207

tag: cell prop. lymphocyte


title: WB_CHF_PT_CHF01-206

tag: cell prop. eosinophil


title: WB_CHF_PT_CHF01-204

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-205

tag: disease


title: WB_CHF_PT_CHF01-202

tag: age


title: 11R0326


title: WB_CHF_PT_CHF01-203

tag: Sex


title: 11R0312


title: 11R0308


title: 11R0305


title: 11R0298


title: WB_CHF_PT_CHF01-199


title: WB_CHF_PT_CHF01-201


title: 11R0291


title: dysplasia combined with squamous metaplasia_GV

city: Tomsk

first: Aleksei

middle: A

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

description:
Whole Transcriptome Amplification RNA
cancer cells were laser-microdissected from tumor-adjacent lung tissue containing combination of normal cells and lesion.

hyb_protocol: 2 μg of the labeled cDNA were hybridized to SurePrint G3 Human GE v2, 8x60K microarrays (G4851B) for 22 h at 65°C in a rotating Agilent hybridization oven. The cDNA was not fragmented before hybridization. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G….B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%). Images were quantified using Agilent Feature Extraction Software (version v. 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v. 10.7.3.1) was used for background subtraction and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized signal intensity by nec and normalizeBetweenArrays functions from limma package

source_name: gene expression of laser-microdissected dysplasia

label_protocol: 2 μg of cDNA samples was Cy3-labeled using the SureTag DNA labeling kit (Agilent Technologies, Inc., USA), followed by RNAeasy MinElute column purification (Qiagen, USA). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
laser microdissection protocol: Premalignant bronchial lessions were isolated from 5 um hematoxylin&eosin stained sections of tumor-adjacent normal lung tissue of lung cancer patients using PALM MicroBeam laser capture microdissection (Carl Zeiss, Germany). The bronchial epithelium unchanged at sites adjacent to the tumor was used as the control.
Total RNA was extracted by RNeasy Plus Micro Kit (Qiagen, USA). Ribolock RNase inhibitor (Fermentas, Lithuania) was added to the isolated RNA. RNA quality was assessed by RIN using 2200 TapeStation Instrument and High Sensitivity R6K ScreenTape (Agilent Technologies, Inc., Santa Clara, USA). RIN varied from 4.6 to 7.9.
WTA protocol: RNA samples (a total of 8 samples) were amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Inc., USA). Amplified products (cDNA) were purified using QIAquick PCR Purification Kit (Qiagen, USA), had concentration ranging from 60 to 140 ng/ul, and stored at -80°C until gene expression microarray analysis.

tag: subject id

value: GV

value: lung

tag: gender

value: male

tag: histological type of patient tumor

value: squamous cell carcinoma

tag: tnm stage

tag: premalignant lession type

value: squamous metaplasia and dysplasia

tag: therapy

value: without preoperative therapy


title: squamous metaplasia combined with dysplasia_GV

source_name: gene expression of laser-microdissected combined squamous metaplasia


title: WB_CHF_PT_CHF01-195

tag: cell prop. monocyte


title: WB_CHF_PT_CHF01-200


title: WB_CHF_PT_CHF01-198


title: basal cell hyperplasia combined with squamous metaplasia_SM

source_name: gene expression of laser-microdissected combined basal cell hyperplasia

value: SM

tag: tissue

value: lung adenocarcinoma

value: basal cell hyperplasia and squamous metaplasia


title: 11R0288

value: blood

value: ALS


title: squamous metaplasia combined with basal cell hyperplasia_SR

value: SR


title: WB_CHF_PT_CHF01-192

value: CHF


title: WB_CHF_PT_CHF01-191

value: M


title: normal bronchial epithelium_GE

source_name: gene expression of laser-microdissected normal bronchial epithelium

value: GE

value: normal bronchial epithelium


title: isolated basal cell hyperplasia_VO

source_name: gene expression of laser-microdissected isolated basal cell hyperplasia

value: VO

value: basal cell hyperplasia


title: WB_CHF_PT_CHF01-193


title: isolated squamous metaplasia_LI

source_name: gene expression of laser-microdissected isolated squamous metaplasia

value: LI

value: lung

value: squamous metaplasia


title: basal cell hyperplasia combined with squamous metaplasia_SR

value: male

value: squamous cell carcinoma


title: isolated basal cell hyperplasia_DI

value: DI

value: female

value: without preoperative therapy


title: squamous metaplasia combined with basal cell hyperplasia_SM

value: SM

value: lung adenocarcinoma

value: basal cell hyperplasia and squamous metaplasia


title: KGN 20 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_2_2]

city: Montréal

first: Pavine

middle: Lee

last: Lefevre

state: Québec

address: 3655 Promenade Sir-William Osl

department: Pharmacology and Therapeutics

institute: McGill University

description: gene expression following 20 µM of PBDE treatment for 48 h in KGN cells

hyb_protocol: After 17 h of hybridization at 65 degees celsius, the microarray slides were washed as per the recommendations for the Agilent hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (SureScan G2600D) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software Version 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12). Normalized by shift to 75.0 percentile .

source_name: KGN 20 µM PBDEs

label_protocol: Sample input was 100 ng of total RNA to generate fluorescent cRNA using the Agilent's low input Quick Amp labeling kit and 600 ng of Cy3 labeled cDNA was used for the single-color microarray.

growth_protocol: KGN cells were seeded at 3.105 cells per ml of DMEM:HamF12 for 24h before treatements.

extract_protocol: Total RNA was extracted using theRNeasy Plus minikit (Qiagen)

treatment_protocol: KGN cells were treated with 0, 1, 5 or 20 µM of PBDEs for 48h.

tag: cell line

value: KGN

tag: cell type

value: immortalized human granulosa cells

value: ovary


title: WB_CHF_PT_CHF01-187

value: CHF

value: M

tag: cell prop. neutrophil


title: 11R0286

value: blood

value: ALS


title: 11R0283


title: KGN 20 µM PBDEs [SG11514161_253949420150_S001_GE1_1105_Oct12_1_4]


title: KGN 20 µM PBDEs  [SG11514161_253949420150_S001_GE1_1105_Oct12_2_2]


title: 11R0275


title: 11R0259


title: 11R0243


title: KGN 5 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_2_1]

description: gene expression following 5 µM of PBDE treatment for 48 h in KGN cells

source_name: KGN 5 µM PBDEs


title: KGN 20 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_1_4]


title: WB_CHF_PT_CHF01-184

tag: cell prop. lymphocyte


title: KGN 20 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_2_2]


title: WB_CHF_PT_CHF01-186

tag: cell prop. eosinophil


title: KGN 5 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_1_3]


title: 11R0231


title: KGN 5 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_1_3]


title: KGN 5 µM PBDEs [SG11514161_253949420150_S001_GE1_1105_Oct12_1_3]


title: WB_CHF_PT_CHF01-183

tag: cell prop. basophil


title: KGN 1 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_2_3]

description: gene expression following 1 µM of PBDE treatment for 48 h in KGN cells

source_name: KGN 1 µM PBDEs


title: 11R0229

tag: disease


title: WB_CHF_PT_CHF01-182

tag: age


title: KGN 1 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_1_2]


title: KGN 1 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_2_3]


title: KGN 5 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_2_1]


title: KGN 1 µM PBDEs [SG11514161_253949420150_S001_GE1_1105_Oct12_1_2]


title: 11R0226


title: WB_CHF_PT_CHF01-180

tag: Sex


title: KGN 1 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_1_2]


title: WB_CHF_PT_CHF01-177

value: F


title: WB_CHF_PT_CHF01-181


title: 11R0217


title: KGN 20 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_1_4]


title: 11R0216


title: KGN 1 µM PBDEs  [SG11514161_253949420150_S001_GE1_1105_Oct12_2_3]


title: KGN 0 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_1_1]

description: gene expression following 0 µM of PBDE treatment for 48 h in KGN cells

source_name: KGN 0 µM PBDEs


title: WB_CHF_PT_CHF01-176


title: KGN 0 µM PBDEs [SG11514161_253949420150_S001_GE1_1105_Oct12_1_1]


title: KGN 0 µM PBDEs [SG11514161_253949420151_S001_GE1_1105_Oct12_2_4]


title: 11R0215


title: 11R0170

value: BPD


title: KGN 0 µM PBDEs [SG11514161_253949420150_S001_GE1_1105_Oct12_2_4]


title: 11R0219


title: 11R0165


title: WB_CHF_PT_CHF01-175


title: 11R0164


title: 22-as2-1 rh10-1

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

country: Japan

institute: Kanazawa University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip ATH1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with MSA5.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

organism: Arabidopsis thaliana

source_name: 22-as2-1 rh10-1 shoot apex

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

growth_protocol: Plants were grown on soil under long day condition (16 hours light and 8 hours dark) for 15 days at 22, 26°C.

extract_protocol: Total RNAs were extracted using RNeasy (QIAGEN).

treatment_protocol: Shoot apices were collected.

value: shoot apex

tag: cultivar

tag: genotype

value: as2; rh10

tag: growth temperature

value: 22 °C


title: KGN 0 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_1_1]


title: KGN 0 µM PBDEs [SG11514161_253949420149_S001_GE1_1105_Oct12_2_4]


title: 11R0158


title: WB_CHF_PT_CHF01-172


title: WB_CHF_PT_CHF01-174


title: WB_CHF_PT_CHF01-173


title: 11R0157


title: 11R0156


title: whole_blood_medip_adultSEP_low_childSEP_high_20080229_S40_rep3

type: genomic

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

description: childhood SEP was assessed at birth, adulthood SEP was assessed at 42 and 45 years old

hyb_protocol: All the steps of hybridization and washing were performed following the Agilent protocol for chip-on-chip analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The value is background subtracted and log2R quantile normalized.

molecule: genomic DNA

label_protocol: 2ug of each of the input and bound fractions were labeled for the microarray hybridization. Cy3-dUTP and Cy5-dUTP (Perkin Elmer) were used to label the input and the bound fractions respectively. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive element. The anti-5 methylcytosine antibody used was from Calbiochem, Cat. # NA81, Lot: D00048001

extract_protocol: DNA was extracted from whole blood collected in EDTA at 45y using an in-house, manual guanidine hydrochloride and ethanol precipitation method. DNA (2.g) was sonicated on ice for a total of 3 min, using 5 sec pulses with 15 sec resting times to fragment the DNA to between 200 bp and 700 bp, as verified subsequently on a 1.5% agarose gel. After denaturing, 1/10th of the each sample was removed as input DNA. The remainder of the sample was then precleared with sepharose beads, bound to anti-5 methylcytosine antibody (Calbiochem), washed, and eluted. Samples were PCR purified (Genescript), quantified by nanodrop, and for each sample 100ng of input and immunoprecipitated DNA were subject to whole genome amplification (Sigma). Samples were again quantified to assess the results of WGA, and then labeled with Cy3 (Input) or Cy5 (mDIP) prior to hybridization to the microarray.

tag: gender

value: male

value: adult (45yr)

tag: socio-economic position (sep)

value: low adulthood and high childhood SEP

tag: chip antibody

value: anti-5 methylcytosine

tag: chip antibody vendor

value: Calbiochem

tag: chip antibody catalog #

tag: chip antibody lot #

tag: sample type

value: input DNA


title: WB_CHF_PT_CHF01-166

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: 22-Col-0

source_name: 22-Col-0 shoot apex

tag: tissue

value: wildtype


title: 11R0159


title: whole_blood_medip_adultSEP_low_childSEP_high_20080229_S40_rep2


title: 11R0155


title: 26-Col-0

source_name: 26-Col-0 shoot apex

value: 26 °C


title: WB_CHF_PT_CHF01-170

source_name: PAXgene whole blood mRNA

value: CHF

tag: cell prop. lymphocyte

tag: cell prop. eosinophil

tag: cell prop. basophil


title: 11R0154

source_name: Whole Blood RNA-Seq

tag: disease


title: whole_blood_medip_adultSEP_low_childSEP_high_20081217_S40_rep1

tag: age


title: 22-rh10-1

source_name: 22-rh10-1 shoot apex

tag: cultivar

tag: genotype


title: 26-rh10-1

source_name: 26-rh10-1 shoot apex

tag: growth temperature


title: 22-as2-1

source_name: 22-as2-1 shoot apex


title: 26-as2-1

source_name: 26-as2-1 shoot apex


title: whole_blood_medip_adultSEP_high_childSEP_high_20080314_S39_rep4

tag: gender

tag: socio-economic position (sep)

value: high adulthood and high childhood SEP


title: WB_CHF_PT_CHF01-159

tag: Sex

value: M


title: WB_CHF_PT_CHF01-162


title: OCI-Ly10 shOCT2_3410 DOX Treated - 2 days - repeat 2 - mAdbID:128685

description: mAdb experiment ID: 128685

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_3410. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

tag: cell line

tag: cell type

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: OCI-Ly10 shControl DOX Treated - 2 days

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: 11R0152

value: blood

value: BPD


title: whole_blood_medip_adultSEP_high_childSEP_high_20081217_S39_rep2

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody catalog #

tag: chip antibody lot #

tag: sample type


title: 11R0151

tag: tissue


title: WB_CHF_PT_CHF01-151

tag: disease

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte

tag: cell prop. eosinophil

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-155

tag: age


title: 26-as2-1 rh10-1

source_name: 26-as2-1 rh10-1 shoot apex

value: shoot apex

tag: cultivar

tag: genotype

value: as2; rh10

tag: growth temperature


title: WB_CHF_PT_CHF01-153

tag: Sex


title: OCI-Ly10 shOCT2_1196 DOX Treated - 1 day - mAdbID:128682

description: mAdb experiment ID: 128682

source_name: OCI-Ly10 shControl DOX Treated - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

tag: cell line

tag: cell type

tag: disease state

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: whole_blood_medip_adultSEP_high_childSEP_high_20081217_S39_rep1

tag: gender

value: male

tag: socio-economic position (sep)

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody catalog #

tag: chip antibody lot #


title: WB_CHF_PT_CHF01-149

tag: disease

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte


title: 11R0150

tag: tissue


title: whole_blood_medip_adultSEP_low_childSEP_high_20080923_S38_rep7

tag: age

value: adult (45yr)

tag: sample type


title: 11R0149


title: WB_CHF_PT_CHF01-158

tag: Sex

tag: cell prop. eosinophil

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-147

value: F


title: WB_CHF_PT_CHF01-148


title: OCI-Ly10 shOCT2_3410 DOX Treated - 1 day - repeat 2 - mAdbID:128684

description: mAdb experiment ID: 128684

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_3410. shRNA expression was induced with 50 ng/mL doxycycline for 1 day.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).

tag: cell line

tag: cell type

tag: disease state


title: OCI-Ly10 shOCT2_1196 DOX Treated - 2 days - repeat 2 - mAdbID:128683

description: mAdb experiment ID: 128683

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shOCT2_1196. shRNA expression was induced with 50 ng/mL doxycycline for 2 days.
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).


title: whole_blood_medip_adultSEP_low_childSEP_high_20081016_S38_rep6

tag: gender

tag: socio-economic position (sep)

value: low adulthood and high childhood SEP

tag: chip antibody

value: anti-5 methylcytosine


title: TMD8 shOCT2_3410 DOX Treated - 2 days - mAdbID:128681

description: mAdb experiment ID: 128681

source_name: TMD8 shOCT2_3410 DOX Treated - 2 days

source_name: TMD8 shControl DOX Treated - 2 days


title: WB_CHF_PT_CHF01-146


title: TMD8 shOCT2_3410 DOX Treated - 1 day - mAdbID:128680

description: mAdb experiment ID: 128680

source_name: TMD8 shOCT2_3410 DOX Treated - 1 day

source_name: TMD8 shControl DOX Treated - 1 day


title: TMD8 shOCT2_1196 DOX Treated - 2 days - mAdbID:128679

description: mAdb experiment ID: 128679

source_name: TMD8 shOCT2_1196 DOX Treated - 2 days


title: whole_blood_medip_adultSEP_low_childSEP_high_20081016_S38_rep2

tag: chip antibody vendor

value: Calbiochem

tag: chip antibody catalog #

tag: chip antibody lot #

value: input DNA


title: TMD8 shOCT2_1196 DOX Treated - 1 day - mAdbID:128678

description: mAdb experiment ID: 128678

source_name: TMD8 shOCT2_1196 DOX Treated - 1 day


title: HBL1 shOCT2_3410 DOX Treated, OCT2 T223A vs WT - mAdbID:125537

description: mAdb experiment ID: 125537

source_name: HBL1 shOCT2_3410 DOX Treated, OCT2 T223A - 14 days

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 14 days
In-vitro treatment: Cells were depleted of OCT2 by shOCT2_3410 and rescued with OCT2 T223A rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 14 days.

source_name: HBL1 shOCT2_3410 DOX Treated, OCT2 WT - 14 days

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 14 days
In-vitro treatment: Cells were depleted of OCT2 by shOCT2_3410 and rescued with OCT2 WT rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 14 days.


title: 11R0147

tag: disease


title: WB_CHF_PT_CHF01-144

source_name: PAXgene whole blood mRNA

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte


title: whole_blood_medip_adultSEP_high_childSEP_low_20080208_S37_rep3

tag: age

value: high adulthood and low childhood SEP

tag: sample type


title: whole_blood_medip_adultSEP_high_childSEP_low_20080208_S37_rep2


title: 11R0146

source_name: Whole Blood RNA-Seq

tag: tissue


title: 11R0148


title: whole_blood_medip_adultSEP_high_childSEP_low_20080208_S37_rep1


title: 11R0145


title: WB_CHF_PT_CHF01-143

value: CHF

tag: Sex

tag: cell prop. eosinophil

tag: cell prop. basophil


title: 11R0144


title: 11R0143


title: whole_blood_medip_adultSEP_low_childSEP_low_20081217_S36_rep5

value: low adulthood and low childhood SEP


title: whole_blood_medip_adultSEP_low_childSEP_low_20080919_S36_rep4


title: WB_CHF_PT_CHF01-142


title: WB_CHF_PT_CHF01-141

value: M


title: HBL1 shOCT2_1196 DOX Treated, OCT2 T223A vs WT - mAdbID:125536

description: mAdb experiment ID: 125536

source_name: HBL1 shOCT2_1196 DOX Treated, OCT2 T223A - 14 days

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 14 days
In-vitro treatment: Cells were depleted of OCT2 by shOCT2_1196 and rescued with OCT2 T223A rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 14 days.

tag: cell line

tag: cell type

value: ABC DLBCL cells

tag: disease state

source_name: HBL1 shOCT2_1196 DOX Treated, OCT2 WT - 14 days

treatment_protocol:
Other: Plasmids: OCT2 was cloned from cDNA from BJAB and OCA-B cDNA purchased from Origene. Both were cloned into the vectors pCMV-TOP and pFlagBiopCMV-TOP(30). Site directed mutations were introduced using the QuikChange Lightning kit from Agilent. shRNAs targeting OCT2 or OCA-B were designed and cloned as double stranded oligonucleotides into a retroviral vector (pRSMX_PuroGFP) for doxycycline-inducible shRNA expression. RNAi sequences used are as follows: OCT2 shRNA#1_1196 5'-GCACAACAGTTACTACCTTAT-3', OCT2 shRNA#2_3410 5'-GGATGCTTCTTTCTCTTCACA-3', OCA-B shRNA_3017 5'-CAGCCAGAAGTACCATTAGG-3'. Because OCT2 shRNA#1 targeted the coding region of OCT2, silent mutations were introduced into the recognition site to allow the shRNA to be rescued by OCT2 constructs. Vectors: The pRSMX-PG vector coexpressing GFP and shRNA was introduced into cells and where required selection was carried out with puromycin. Expression of shRNA was induced by addition of doxycycline (50 ng/mL).
Treatment type: shRNA transduction
Treatment dose: 50 ng/mL
Treatment time: 14 days
In-vitro treatment: Cells were depleted of OCT2 by shOCT2_1196 and rescued with OCT2 WT rescue construct. shRNA expression was induced with 50 ng/mL doxycycline for 14 days.


title: WB_CHF_PT_CHF01-140


title: WB_CHF_PT_CHF01-139


title: WB_CHF_PT_CHF01-138


title: SUDHL4 shOCT2_3410 DOX Treated, OCT2 T223A vs WT - repeat 2 - mAdbID:125440

description: mAdb experiment ID: 125440

source_name: SUDHL4 shOCT2_3410 DOX Treated, OCT2 T223A - 14 days

value: GCB DLBCL cells

value: germinal center B cell-restricted (GCB) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: SUDHL4 shOCT2_3410 DOX Treated, OCT2 WT - 14 days


title: 11R0142

value: blood

value: BPD


title: SUDHL4 shOCT2_1196 DOX Treated, OCT2 T223A vs WT - repeat 1 - mAdbID:125437

description: mAdb experiment ID: 125437

source_name: SUDHL4 shOCT2_1196 DOX Treated, OCT2 T223A - 14 days

source_name: SUDHL4 shOCT2_1196 DOX Treated, OCT2 WT - 14 days


title: SUDHL4 shOCT2_1196 DOX Treated, OCT2 T223A vs WT - repeat 2 - mAdbID:125438

description: mAdb experiment ID: 125438


title: whole_blood_medip_adultSEP_low_childSEP_low_20080130_S36_rep2

tag: gender

tag: socio-economic position (sep)

tag: chip antibody


title: 11R0141


title: SUDHL4 shOCT2_3410 DOX Treated, OCT2 T223A vs WT - repeat 1 - mAdbID:125439

description: mAdb experiment ID: 125439


title: whole_blood_medip_adultSEP_low_childSEP_low_20080130_S36_rep1

tag: chip antibody vendor

tag: chip antibody catalog #

tag: chip antibody lot #


title: whole_blood_medip_adultSEP_low_childSEP_low_20080125_S35_rep4


title: 11R0139

tag: disease


title: BJAB shOCT2_3410 DOX Treated, OCT2 T223A vs WT - repeat 2 - mAdbID:125436

description: mAdb experiment ID: 125436

source_name: BJAB shOCT2_3410 DOX Treated, OCT2 T223A - 14 days

value: BJAB

source_name: BJAB shOCT2_3410 DOX Treated, OCT2 WT - 14 days


title: whole_blood_medip_adultSEP_low_childSEP_low_20080619_S35_rep2

value: male


title: BJAB shOCT2_3410 DOX Treated, OCT2 T223A vs WT - repeat 1 - mAdbID:125435

description: mAdb experiment ID: 125435


title: whole_blood_medip_adultSEP_low_childSEP_low_20080612_S35_rep1

value: adult (45yr)


title: WB_CHF_PT_CHF01-136

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte


title: WB_CHF_PT_CHF01-134

tag: age

value: F


title: WB_CHF_PT_CHF01-133

tag: Sex


title: WB_CHF_PT_CHF01-137

tag: cell prop. eosinophil


title: whole_blood_medip_adultSEP_low_childSEP_high_20071107_S34_rep3

value: low adulthood and high childhood SEP

tag: sample type


title: WB_CHF_PT_CHF01-135

tag: cell prop. basophil


title: WT2_SirpaDC

city: Saint Louis

first: Carlos

middle: Gustavo

last: Briseno

state: Missouri

address: 660 S Euclid

institute: Washington University School of Medicine

hyb_protocol: Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Standard Affymetrix protocol

data_processing: Data was processed using RMA summarization and quartile normalization using Arraystar ver. 5

source_name: WT C57Bl/6

label_protocol: Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

growth_protocol: Splenocytes were prepared by digestion with Collagase B and Dnase I

extract_protocol: WT and IRF4-/- Sirp-a+ DCs were sorted as: B220–MHCII+CD11c+CD24–Sirp-a+

treatment_protocol: Mice were analyzed at steady state

tag: strain

value: Female

tag: genotype

value: WT

tag: cell type

value: Splenic CD172a+ DC

tag: treatment


title: WB_CHF_PT_CHF01-132


title: BJAB shOCT2_1196 DOX Treated, OCT2 T223A vs WT - repeat 2 - mAdbID:125434

description: mAdb experiment ID: 125434

source_name: BJAB shOCT2_1196 DOX Treated, OCT2 T223A - 14 days

tag: cell line

tag: disease state

source_name: BJAB shOCT2_1196 DOX Treated, OCT2 WT - 14 days


title: BJAB shOCT2_1196 DOX Treated, OCT2 T223A vs WT - repeat 1 - mAdbID:125432

description: mAdb experiment ID: 125432


title: WB_CHF_PT_CHF01-131


title: 11R0136

tag: tissue


title: Irf4KO2_SirpaDC

source_name: IRF4 KO C57Bl/6

tag: gender

value: IRF4 KO


title: 11R0138

tag: disease


title: 11R0135


title: 11R0137


title: whole_blood_medip_adultSEP_low_childSEP_high_20071107_S34_rep1

tag: socio-economic position (sep)

tag: chip antibody

value: anti-5 methylcytosine

tag: chip antibody vendor

value: Calbiochem

tag: chip antibody catalog #

tag: chip antibody lot #

value: input DNA


title: 11R0132


title: whole_blood_medip_adultSEP_low_childSEP_high_20071107_S33_rep3

tag: age


title: WB_CHF_PT_CHF01-129

value: CHF

tag: Sex

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: whole_blood_medip_adultSEP_low_childSEP_high_20071107_S34_rep2

tag: sample type


title: WT1_SirpaDC

tag: strain

tag: genotype

tag: cell type

tag: treatment


title: WB_CHF_PT_CHF01-130

tag: disease

value: M

tag: cell prop. basophil


title: 11R0130

tag: tissue


title: Ly-6Clo TremL4+ mono

growth_protocol: Primary peripheral blood leukocytes were collected from 10 WT C57Bl/6 females

extract_protocol: Monocytes were sorted as: Ter-119– CD45.2+ MHC-IIlo Ly-6G– CD115+. Monocyte subsets were defined as Ly-6ChiTremL4–, Ly-6ChiTremL4+ and Ly-6Clo TremL4+

tag: gender

value: Ly-6Clo TremL4+ monocyte


title: Irf4KO1_SirpaDC


title: whole_blood_medip_adultSEP_low_childSEP_high_20071107_S33_rep2

tag: socio-economic position (sep)

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody catalog #


title: whole_blood_medip_adultSEP_low_childSEP_high_20071107_S33_rep1

tag: age

tag: chip antibody lot #


title: 11R0128

value: blood


title: Ly-6Chi TremL4+ mono

value: Ly-6Chi TremL4+ monocyte


title: 11R0134

value: BPD


title: whole_blood_medip_adultSEP_high_childSEP_low_20080229_S32_rep4

value: male

value: high adulthood and low childhood SEP


title: 11R0127


title: Ly-6Chi TremL4– mono

value: Ly-6Chi TremL4– monocyte


title: WB_CHF_PT_CHF01-128

tag: Sex

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte


title: 11R0126


title: WB_CHF_PT_CHF01-127

value: F

tag: cell prop. eosinophil


title: whole_blood_medip_adultSEP_high_childSEP_low_20081217_S32_rep2

value: adult (45yr)

tag: sample type


title: WT_CD24_DCs

growth_protocol: WT Ly6Chi BM monocytes were differentiated into Mo-DCs by culturing in GM-CSF alone or GM-CSF and IL-4 for 72 hours. IRF4KO Ly6Chi BM monocytes were differentiated into Mo-DCs by culturing in GM-CSF and IL-4 for 72 hours. Splenocytes were harvested by digestion with Collagenase B and Dnase I. BM marrow cells were harvested by crushing of femurs and tibias.

extract_protocol: WT and IRF4KO Mo-DCs were sorted as Ly-6Clo CD11c+, WT BM monocytes were gated as Ter-119– CD45.2+ MHC-IIlo Ly-6G– CD115+. Monocyte subsets were sorted as Ly-6ChiTremL4– and Ly-6Clo TremL4+. WT CD24+ DCs were sorted as B220– CD11c+ MHCII+ Sirp-a– CD24+

tag: strain

value: female

tag: genotype

value: WT

tag: treatment

tag: cell type

value: Splenic CD24+ DC


title: WB_CHF_PT_CHF01-124

tag: disease

tag: cell prop. basophil


title: WT_Ly6CloTremL4pos_BMMono

tag: gender

value: BM Ly-6Chi TremL4+ monocyte


title: WT_Ly6ChiTremL4neg_BMMono

value: BM Ly-6Chi TremL4- monocyte


title: 11R0125

tag: tissue


title: WB_CHF_PT_CHF01-123


title: 11R0101

value: ALS


title: whole_blood_medip_adultSEP_low_childSEP_low_20081127_S31_rep3

tag: socio-economic position (sep)

value: low adulthood and low childhood SEP

tag: chip antibody

value: anti-5 methylcytosine

tag: chip antibody vendor

value: Calbiochem

tag: chip antibody catalog #

value: input DNA


title: whole_blood_medip_adultSEP_low_childSEP_low_20080215_S31_rep2

tag: age

tag: chip antibody lot #


title: 11R0100

value: blood


title: WT_GMOnly_MoDC

tag: cell type (before treatment)

value: BM Ly-6Chi monocyte

value: Ly6ChiTremL4- bone marrow monocytes GM-CSF for 72 hours

value: Mo-DC


title: 11R0098


title: whole_blood_medip_adultSEP_low_childSEP_high_20080919_S30_rep8

value: male

value: low adulthood and high childhood SEP


title: 11R0096


title: WB_CHF_PT_CHF01-121

value: CHF

tag: Sex

value: M

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: WB_CHF_PT_CHF01-116

value: F


title: whole_blood_medip_adultSEP_high_childSEP_low_20081217_S32_rep1

value: adult (45yr)

value: high adulthood and low childhood SEP

tag: sample type


title: WB_CHF_PT_CHF01-117

tag: disease


title: whole_blood_medip_adultSEP_low_childSEP_high_20081217_S30_rep6


title: 11R0095


title: WB_CHF_PT_CHF01-122

tag: cell prop. basophil


title: GRDC VS GRC 2

first: Hsing-Yu

last: Chen

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

institute: National Taiwan University

description: Biological replicate 2 of 2. 35S:ORA47-GR treated with 50 μM CYC as control, normal condition.

hyb_protocol: Following manufacturer's instructions of Agilent Two-color Microarray Based Gene Exppression Analysis v4, Agilent microarray hybridization chamber were used.

scan_protocol: Scanned on an Agilent Microarray scanner.

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: 35S:ORA47-GR +CYC + Dex

label_protocol: Following manufacturer's instructions of Agilent Quick Amp Labeling Kit

growth_protocol: Arabidopsis seeds of each genotype were sterilized with 0.5% bleach and 0.1% Triton X-100, and then plated on the 1/2 Murashige and Skoog (MS) medium with 1% sucrose and agar. Seeds were treated with vernalization in the darkness for 3 days and then transferred to a walk-in growth chamber of 22℃ under a 16 h light / 8 h dark photoperiod.

extract_protocol: Total RNA extracted using REzol C&T (PROTECH) following manufacturer's instructions

treatment_protocol: P35S:ORA47-GR transgenic plants treated with CYC for 1 h followed by DEX treatment for 2 h.

value: seedling

tag: genotype

tag: ecotype

value: Columbia

value: 7 days

source_name: 35S:ORA47-GR +CYC

value: seedlings


title: WB_CHF_PT_CHF01-115


title: whole_blood_medip_adultSEP_low_childSEP_high_20081127_S30_rep5

tag: gender

tag: socio-economic position (sep)

value: anti-5 methylcytosine

value: Calbiochem


title: GRDC VS WTDC 2

description: Biological replicate 2 of 2. WT treated with 50 μM CYC and 20 μM DEX as control, normal condition.

tag: tissue

source_name: WT +CYC +Dex

value: wild type


title: whole_blood_medip_adultSEP_low_childSEP_high_20080619_S30_rep4

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody catalog #

value: input DNA


title: GRDC VS GRC 1

description: Biological replicate 1 of 2. 35S:ORA47-GR treated with 50 μM CYC as control, normal condition.

tag: age


title: 11R0093

value: blood

value: ALS


title: WB_CHF_PT_CHF01-111

source_name: PAXgene whole blood mRNA

tag: Sex


title: 11R0088

source_name: Whole Blood RNA-Seq


title: whole_blood_medip_adultSEP_low_childSEP_low_20080215_S31_rep1

value: male

value: low adulthood and low childhood SEP

tag: chip antibody lot #


title: WT_GM_IL4_MoDC

tag: strain

value: female

value: WT

tag: cell type (before treatment)

value: BM Ly-6Chi monocyte

tag: treatment

value: Ly6ChiTremL4- bone marrow monocytes GM-CSF + IL-4 for 72 hours

tag: cell type

value: Mo-DC


title: WB_CHF_PT_CHF01-110

tag: disease

value: CHF

value: F

tag: cell prop. neutrophil

tag: cell prop. monocyte

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: WB_CHF_PT_CHF01-109

value: M

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-108


title: whole_blood_medip_adultSEP_low_childSEP_low_20080227_S29_rep2

tag: gender

value: adult (45yr)

tag: socio-economic position (sep)

tag: sample type


title: GRDC VS WTDC 1

description: Biological replicate 1 of 2. WT treated with 50 μM CYC and 20 μM DEX as control, normal condition.

tag: tissue

value: seedling

tag: genotype

tag: ecotype

value: Columbia

value: 7 days

value: seedlings


title: 118172B

value: blood

value: SCZ


title: WB_CHF_PT_CHF01-112

tag: age

tag: Sex


title: WB_CHF_PT_CHF01-107


title: 109667A

value: CSF


title: whole_blood_medip_adultSEP_high_childSEP_low_20080424_S28_rep3

value: male

value: high adulthood and low childhood SEP

tag: chip antibody

value: anti-5 methylcytosine

tag: chip antibody vendor

value: Calbiochem

tag: chip antibody catalog #

tag: chip antibody lot #

value: input DNA


title: whole_blood_medip_adultSEP_high_childSEP_low_20080424_S28_rep1


title: WB_CHF_PT_CHF01-105

tag: disease

tag: cell prop. neutrophil


title: 109666A


title: 11R0092

value: ALS


title: whole_blood_medip_adultSEP_low_childSEP_low_20080201_S29_rep3

value: low adulthood and low childhood SEP


title: 109648A


title: 109647A


title: whole_blood_medip_adultSEP_high_childSEP_low_20080612_S27_rep1


title: WB_CHF_PT_CHF01-103

value: CHF

tag: cell prop. monocyte

tag: cell prop. lymphocyte


title: whole_blood_medip_adultSEP_high_childSEP_high_20080605_S26_rep6

value: high adulthood and high childhood SEP


title: 109646A


title: whole_blood_medip_adultSEP_low_childSEP_low_20080201_S29_rep1

value: adult (45yr)


title: whole_blood_medip_adultSEP_high_childSEP_high_20080605_S26_rep3


title: WB_CHF_PT_CHF01-099

value: M

tag: cell prop. eosinophil

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-100


title: WB_CHF_PT_CHF01-104


title: 118125B


title: whole_blood_medip_adultSEP_high_childSEP_high_20080605_S26_rep1

tag: gender

tag: socio-economic position (sep)


title: whole_blood_medip_adultSEP_high_childSEP_low_20081217_S27_rep6

tag: sample type


title: 109630A

tag: tissue


title: whole_blood_medip_adultSEP_high_childSEP_low_20080612_S27_rep5


title: 109597A


title: 109645A


title: 109596A


title: 109665A


title: WB_CHF_PT_CHF01-095


title: whole_blood_medip_adultSEP_low_childSEP_high_20080605_S25_rep2

value: low adulthood and high childhood SEP


title: whole_blood_medip_adultSEP_low_childSEP_high_20071116_S25_rep3


title: WB_CHF_PT_CHF01-097

value: F


title: 109581A


title: whole_blood_medip_adultSEP_low_childSEP_high_20071116_S25_rep1


title: whole_blood_medip_adultSEP_low_childSEP_low_20080227_S24_rep3


title: WB_CHF_PT_CHF01-102


title: WB_CHF_PT_CHF01-094


title: WB_CHF_PT_CHF01-096


title: 109571A


title: WB_CHF_PT_CHF01-092


title: whole_blood_medip_adultSEP_low_childSEP_low_20080227_S24_rep2


title: WB_CHF_PT_CHF01-091


title: 108773A


title: WB_CHF_PT_CHF01-093


title: whole_blood_medip_adultSEP_low_childSEP_low_20081016_S23_rep6


title: whole_blood_medip_adultSEP_low_childSEP_low_20080227_S24_rep1


title: whole_blood_medip_adultSEP_low_childSEP_low_20081016_S23_rep5


title: 108747B


title: whole_blood_medip_adultSEP_low_childSEP_low_20081016_S23_rep2


title: WB_CHF_PT_CHF01-089


title: 108765A


title: WB_CHF_PT_CHF01-088


title: whole_blood_medip_adultSEP_high_childSEP_low_20080402_S22_rep3


title: 108740B


title: 109580A


title: whole_blood_medip_adultSEP_high_childSEP_low_20080402_S22_rep2


title: 108671A


title: whole_blood_medip_adultSEP_high_childSEP_low_20080402_S22_rep1


title: 11R0140

value: BPD


title: whole_blood_medip_adultSEP_low_childSEP_low_20080201_S21_rep3


title: 108669A

value: blood


title: 108648A

value: SCZ


title: WB_CHF_PT_CHF01-087


title: 108741B

value: CSF


title: WB_CHF_PT_CHF01-086


title: RSV_24

city: London

first: Myrsini

last: Kaforou

address: Norfolk Place

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using RSN, after background subtraction

source_name: Whole Blood from patient with RSV

label_protocol: Standard Illumina TotalPrep RNA Amplification kits (Applied Biosystems).

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

tag: category

value: RSV

tag: dataset

value: Discovery

value: Female


title: RSV_26


title: WB_CHF_PT_CHF01-090

tag: age

tag: Sex


title: WB_CHF_PT_CHF01-083


title: 108618A


title: WB_CHF_PT_CHF01-084


title: WB_CHF_PT_CHF01-081


title: RSV_27


title: RSV_25

value: Male


title: RSV_22


title: whole_blood_medip_adultSEP_low_childSEP_low_20080201_S21_rep1

value: male

tag: chip antibody

value: anti-5 methylcytosine

tag: chip antibody vendor

value: Calbiochem

value: input DNA


title: 108611A


title: whole_blood_medip_adultSEP_high_childSEP_high_20080130_S20_rep3

value: high adulthood and high childhood SEP

tag: chip antibody catalog #

tag: chip antibody lot #


title: RSV_23


title: 108610A

tag: disease


title: 108582A


title: RSV_21


title: whole_blood_medip_adultSEP_high_childSEP_high_20080130_S20_rep2

value: adult (45yr)


title: whole_blood_medip_adultSEP_low_childSEP_low_20080227_S21_rep2

value: low adulthood and low childhood SEP


title: RSV_20


title: WB_CHF_PT_CHF01-079

value: CHF

value: M

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: whole_blood_medip_adultSEP_high_childSEP_high_20080130_S20_rep1


title: RSV_19


title: 108581A


title: whole_blood_medip_adultSEP_high_childSEP_high_20080116_S19_rep3


title: 108552A


title: WB_CHF_PT_CHF01-077

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: whole_blood_medip_adultSEP_high_childSEP_high_20080116_S19_rep2

tag: gender


title: RSV_18


title: WB_CHF_PT_CHF01-080

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-076

value: F


title: WB_CHF_PT_CHF01-078


title: 108264

value: blood


title: RSV_17


title: RSV_16


title: whole_blood_medip_adultSEP_high_childSEP_high_20080116_S19_rep1

tag: socio-economic position (sep)

tag: sample type


title: 108220A

tag: tissue


title: whole_blood_medip_adultSEP_low_childSEP_high_20080605_S18_rep2

value: low adulthood and high childhood SEP


title: 108219A

value: CSF


title: 108209A


title: whole_blood_medip_adultSEP_low_childSEP_high_20080114_S18_rep1


title: WB_CHF_PT_CHF01-075


title: RSV_15

tag: category

value: RSV

tag: dataset


title: 108208A


title: WB_CHF_PT_CHF01-085

tag: age

tag: Sex


title: RSV_14

value: Discovery


title: WB_CHF_PT_CHF01-073


title: whole_blood_medip_adultSEP_low_childSEP_high_20081217_S17_rep5

tag: chip antibody

tag: chip antibody vendor


title: WB_CHF_PT_CHF01-074


title: whole_blood_medip_adultSEP_low_childSEP_high_20070927_S17_rep4

tag: chip antibody catalog #

tag: chip antibody lot #


title: WB_CHF_PT_CHF01-072

tag: disease

tag: cell prop. neutrophil


title: WB_CHF_PT_CHF01-071

tag: cell prop. monocyte

tag: cell prop. lymphocyte


title: 108180


title: 108176


title: WB_CHF_PT_CHF01-070

tag: cell prop. eosinophil


title: RSV_12

tag: gender


title: whole_blood_medip_adultSEP_low_childSEP_high_20080114_S18_rep3

tag: socio-economic position (sep)


title: RSV_11


title: RSV_13


title: 108174

value: SCZ


title: whole_blood_medip_adultSEP_high_childSEP_low_20080227_S16_rep3

value: high adulthood and low childhood SEP

tag: sample type


title: 108130

tag: tissue


title: WB_CHF_PT_CHF01-068

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-069


title: RSV_08

tag: category

tag: dataset

value: Male


title: RSV_09


title: whole_blood_medip_adultSEP_high_childSEP_low_20080227_S16_rep2

value: male

tag: age

value: anti-5 methylcytosine


title: WB_CHF_PT_CHF01-066

tag: Sex


title: WB_CHF_PT_CHF01-067


title: 108129


title: RSV_07


title: RSV_10


title: whole_blood_medip_adultSEP_high_childSEP_low_20080227_S16_rep1

tag: chip antibody

tag: chip antibody vendor

value: Calbiochem

value: input DNA


title: whole_blood_medip_adultSEP_low_childSEP_high_20070927_S17_rep2

value: adult (45yr)

tag: chip antibody catalog #

tag: chip antibody lot #


title: whole_blood_medip_adultSEP_high_childSEP_low_20081016_S15_rep4


title: whole_blood_medip_adultSEP_high_childSEP_low_20081016_S15_rep2


title: 108094

tag: disease


title: whole_blood_medip_adultSEP_low_childSEP_low_20081010_S14_rep6

value: low adulthood and low childhood SEP


title: 108087


title: RSV_06


title: whole_blood_medip_adultSEP_low_childSEP_low_20080619_S14_rep3


title: WB_CHF_PT_CHF01-065

value: CHF

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: 108086


title: RSV_05

value: Female


title: 108099A


title: WB_CHF_PT_CHF01-064

value: M

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: 108085

value: blood


title: WB_CHF_PT_CHF01-063

value: F


title: 108095

value: CSF


title: WB_CHF_PT_CHF01-062


title: WB_CHF_PT_CHF01-060


title: whole_blood_medip_adultSEP_low_childSEP_low_20080619_S14_rep1

tag: gender

tag: socio-economic position (sep)


title: RSV_04

value: RSV


title: WB_CHF_PT_CHF01-061


title: RSV_02

value: Discovery


title: whole_blood_medip_adultSEP_low_childSEP_low_20080201_S13_rep3

tag: sample type


title: RSV_03


title: RSV_01


title: 108084

tag: tissue


title: 108082


title: WB_CHF_PT_CHF01-059

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-058


title: whole_blood_medip_adultSEP_low_childSEP_low_20080201_S13_rep1


title: 108077


title: Control_51

source_name: Whole Blood from healthy control

tag: category

value: Control

tag: dataset


title: Control_52


title: whole_blood_medip_adultSEP_low_childSEP_low_20080227_S13_rep2

tag: age


title: Control_50


title: WB_CHF_PT_CHF01-057

tag: Sex


title: Control_49


title: whole_blood_medip_adultSEP_high_childSEP_low_20080130_S12_rep2

value: high adulthood and low childhood SEP

tag: chip antibody

tag: chip antibody vendor


title: whole_blood_medip_adultSEP_high_childSEP_low_20080130_S12_rep1

tag: chip antibody catalog #

tag: chip antibody lot #


title: whole_blood_medip_adultSEP_high_childSEP_high_20080116_S11_rep3

value: high adulthood and high childhood SEP


title: 108040B

tag: disease


title: 108034B


title: whole_blood_medip_adultSEP_high_childSEP_high_20080116_S11_rep2

value: male


title: whole_blood_medip_adultSEP_high_childSEP_low_20080130_S12_rep3

value: anti-5 methylcytosine


title: 108000B


title: WB_CHF_PT_CHF01-056

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: WB_CHF_PT_CHF01-053

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: 108067


title: Control_48

tag: gender


title: whole_blood_medip_adultSEP_high_childSEP_high_20080116_S11_rep1

tag: socio-economic position (sep)

value: Calbiochem

tag: sample type


title: Control_46

value: Male


title: WB_CHF_PT_CHF01-049

tag: cell prop. basophil


title: Control_47

tag: category


title: Control_45

tag: dataset


title: WB_CHF_PT_CHF01-051

tag: age


title: WB_CHF_PT_CHF01-047

tag: Sex


title: whole_blood_medip_adultSEP_low_childSEP_high_20081127_S10_rep3

value: adult (45yr)

value: low adulthood and high childhood SEP

tag: chip antibody

value: input DNA


title: WB_CHF_PT_CHF01-045

value: CHF


title: 099418A

tag: tissue

value: SCZ


title: Control_43

value: Female


title: whole_blood_medip_adultSEP_low_childSEP_high_20080314_S10_rep2

tag: chip antibody vendor

tag: chip antibody catalog #


title: Control_44


title: Control_42


title: 099355A

value: blood

tag: disease


title: whole_blood_medip_adultSEP_low_childSEP_high_20080314_S10_rep1

tag: chip antibody lot #


title: 099244A


title: whole_blood_medip_adultSEP_high_childSEP_high_20080313_S9_rep3


title: 099194A


title: WB_CHF_PT_CHF01-043

value: M

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: WB_CHF_PT_CHF01-042

value: F

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: whole_blood_medip_adultSEP_high_childSEP_high_20081217_S9_rep2

tag: gender

tag: socio-economic position (sep)


title: 099103B


title: whole_blood_medip_adultSEP_high_childSEP_high_20080313_S9_rep1

tag: sample type


title: WB_CHF_PT_CHF01-041

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-040


title: WB_CHF_PT_CHF01-039


title: Control_40

tag: category

tag: dataset

value: Discovery


title: Control_41

value: Control


title: 099101A


title: Control_39


title: whole_blood_medip_adultSEP_high_childSEP_high_20080313_S8_rep3

tag: age


title: 089776A


title: 99548


title: 99032


title: 089746B


title: whole_blood_medip_adultSEP_high_childSEP_low_20081010_S7_rep3

value: high adulthood and low childhood SEP

tag: chip antibody


title: Control_38


title: whole_blood_medip_adultSEP_high_childSEP_high_20080313_S8_rep2

value: high adulthood and high childhood SEP


title: whole_blood_medip_adultSEP_high_childSEP_high_20080313_S8_rep1

value: male


title: WB_CHF_PT_CHF01-038

tag: Sex


title: WB_CHF_PT_CHF01-035


title: 089688A

tag: tissue


title: Control_36


title: Control_37


title: Control_35


title: whole_blood_medip_adultSEP_high_childSEP_low_20081010_S7_rep2

value: anti-5 methylcytosine

tag: chip antibody vendor

tag: chip antibody catalog #


title: Control_34


title: WB_CHF_PT_CHF01-034

tag: disease


title: 089606A


title: Control_33


title: 089596A


title: whole_blood_medip_adultSEP_high_childSEP_low_20080208_S6_rep3

value: Calbiochem

tag: chip antibody lot #


title: 089585A


title: WB_CHF_PT_CHF01-037

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: WB_CHF_PT_CHF01-036

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: 089574A


title: whole_blood_medip_adultSEP_high_childSEP_low_20080208_S6_rep2

tag: gender

tag: socio-economic position (sep)


title: Control_32

value: Male


title: whole_blood_medip_adultSEP_high_childSEP_low_20081010_S7_rep1

value: adult (45yr)

tag: sample type


title: WB_CHF_PT_CHF01-032

tag: cell prop. basophil


title: whole_blood_medip_adultSEP_high_childSEP_low_20080208_S6_rep1


title: 089533A


title: 089524A


title: WB_CHF_PT_CHF01-031


title: 089495A


title: Control_30

tag: category

tag: dataset


title: Control_29


title: Control_31


title: WB_CHF_PT_CHF01-030

tag: age


title: 089483A


title: WB_CHF_PT_CHF01-029

tag: Sex


title: WB_CHF_PT_CHF01-028


title: whole_blood_medip_adultSEP_low_childSEP_high_20080201_S5_rep1

value: low adulthood and high childhood SEP

tag: chip antibody


title: Control_28


title: whole_blood_medip_adultSEP_high_childSEP_low_20081217_S4_rep5

tag: chip antibody vendor

value: input DNA


title: 089471A

tag: tissue


title: WB_CHF_PT_CHF01-027

tag: disease

value: CHF


title: WB_CHF_PT_CHF01-026


title: Control_27


title: whole_blood_medip_adultSEP_high_childSEP_low_20080125_S4_rep3

tag: chip antibody catalog #

tag: chip antibody lot #


title: Control_26


title: WB_CHF_PT_CHF01-025

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: whole_blood_medip_adultSEP_low_childSEP_high_20080201_S5_rep3


title: 089461B

value: SCZ


title: Control_25

value: Female


title: whole_blood_medip_adultSEP_low_childSEP_high_20080201_S5_rep2


title: WB_CHF_PT_CHF01-024

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: whole_blood_medip_adultSEP_high_childSEP_low_20081127_S4_rep1

tag: gender

tag: socio-economic position (sep)


title: Control_24


title: 089458A

value: blood


title: whole_blood_medip_adultSEP_low_childSEP_high_20080116_S3_rep3

tag: sample type


title: Control_23

tag: category


title: whole_blood_medip_adultSEP_low_childSEP_high_20080116_S3_rep2


title: 089338A


title: WB_CHF_PT_CHF01-020

tag: cell prop. basophil


title: whole_blood_medip_adultSEP_low_childSEP_high_20080116_S3_rep1

tag: age


title: Control_22

tag: dataset


title: 089310A


title: WB_CHF_PT_CHF01-023

tag: Sex

value: M


title: 089210A


title: WB_CHF_PT_CHF01-018


title: WB_CHF_PT_CHF01-015

value: F


title: 089170B


title: whole_blood_medip_adultSEP_high_childSEP_high_20071107_S2_rep3

tag: chip antibody

tag: chip antibody vendor


title: 089193B

tag: tissue

tag: disease


title: Control_20

value: Discovery


title: Control_21

value: Control


title: 088984A


title: whole_blood_medip_adultSEP_high_childSEP_high_20071107_S2_rep1

tag: chip antibody catalog #

tag: chip antibody lot #


title: Control_19


title: 088971A


title: Control_18


title: 108046


title: whole_blood_medip_adultSEP_high_childSEP_high_20071107_S2_rep2


title: WB_CHF_PT_CHF01-013

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: 088964A


title: Control_17


title: WB_CHF_PT_CHF01-017

tag: cell prop. lymphocyte

tag: cell prop. eosinophil


title: Control_15

tag: gender


title: whole_blood_medip_adultSEP_low_childSEP_low_20070927_S1_rep1

tag: socio-economic position (sep)

value: low adulthood and low childhood SEP

tag: sample type


title: WB_CHF_PT_CHF01-011

tag: cell prop. basophil


title: WB_CHF_PT_CHF01-014

tag: age


title: Control_16

tag: category

tag: dataset


title: 088791B


title: Control_14


title: whole_blood_medip_adultSEP_low_childSEP_low_20070927_S1_rep5

tag: chip antibody


title: whole_blood_medip_adultSEP_low_childSEP_low_20081127_S1_rep3

tag: chip antibody vendor


title: WB_CHF_PT_CHF01-007

tag: Sex


title: WB_CHF_PT_CHF01-010

tag: disease


title: 088774B

tag: tissue


title: 088962A


title: WB_CHF_PT_CHF01-006


title: WB_CHF_PT_CHF01-008


title: Control_11


title: Control_13


title: 088758A


title: 088746B


title: 088839B


title: Control_12


title: 088706A


title: Control_09


title: WB_CHF_PT_CHF01-009


title: WB_CHF_PT_CHF01-003


title: Control_10


title: 88720


title: Control_06


title: 088526B


title: 088527A


title: 88503


title: WB_CHF_PT_CHF01-001


title: Control_07


title: 088006A


title: WB_CHF_PT_CHF01-002


title: 088478B


title: B. subtilis gdpP pgpH mutant_exponential growth_rep3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

hyb_protocol: 100 ng of Cy5-labeled cDNA and 100 ng of Cy3-labeled cDNAwere hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).
The normalization/ dye bias correction method as defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol GE2_105_Dec08) is: Linear and Lowess.  The normalization/ dye bias correction method is: Linear and Lowess.

organism: Bacillus subtilis

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol:
For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D
(final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye,
GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: B. subtilis 168 wild type and gdpP pgpH double mutant cells were grown under vigorous agitation at 37 °C in Spizizen minimal medium supplemented with glutamate..

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

treatment_protocol: Samples were taken at OD600 of 0.5.

tag: strain

value: Bacillus subtilis subsp. subtilis str. 168

tag: genotype/variation

value: gdpP pgpH mutant


title: Control_05


title: WB_CHF_PT_CHF01-012

tag: cell prop. neutrophil

tag: cell prop. monocyte


title: B. subtilis wild type_exponential growth_rep3

value: wild type


title: B. subtilis gdpP pgpH mutant_exponential growth_rep1


title: Control_02


title: B. subtilis wild type_exponential growth_rep2


title: B. subtilis gdpP pgpH mutant_exponential growth_rep2


title: B. subtilis wild type_exponential growth_rep1


title: Control_04


title: Control_03


title: Control_08


title: Control_01


title: wt_isotype_ozone_1

status: Public on May 24 2016

city: Boston

first: Stephanie

last: Shore

state: MA

address: 665 Huntigton Av Bld1 room 307

department: Environmental Health

institute: Harvard School of Public Health

hyb_protocol: After fragmentation at 95°C for 5 min in hybridization master mix and then at 45°C for 5 min.  The mixture of labelled cRNA was then added to plates (mouse 1.0 ST arrays) and allowed to at 45°C for 16h.

scan_protocol: Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 450, and scanned in the Affymetrix 3000 7G scanner

data_processing: Arrays were processed using the oligo Bioconductor package, quality-controlled with arrayQualityMetrics and RMA normalization. Differentially expressed genes (as defined by a minimum 2 fold change in expression and a Benjamini-Hochberg FDR adjusted p value of less than 0.1) were identified using limma.

source_name: wt, isotype, ozone exposed

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Female mice (db/db, C57B/6 background) were bought from Jackson laboratory at 6 weeks of age and then allowed to continue to grow for four weeks.

extract_protocol: The left lungs were homogenized and total RNA was purified using an RNAeasy column kit (Qiagen, Valenica, CA) according to the manufactures specifications.

treatment_protocol: Mice were exposed for 3 hours to 2 ppm ozone without access to food or water.  Mice were then transferred back to cages with free access to food and water and then studied 24 hours later.

value: lung

value: female

tag: genetic background

tag: genotype

value: wt

tag: exposure

value: ozone

tag: treatment

value: isotype


title: db_isotype_air_2

source_name: db/db, isotype, air exposed

tag: gender

value: db/db

value: air


title: db_isotype_air_4


title: db_isotype_ozone_2

source_name: db/db, isotype, ozone exposed


title: db_isotype_ozone_4


title: db_IL17_ozone_4

source_name: db/db, anti IL-17, ozone exposed


title: db_isotype_ozone_1


title: WB_CHF_PT_CHF01-050

value: CHF

tag: age

tag: cell prop. lymphocyte

tag: cell prop. eosinophil

tag: cell prop. basophil


title: db_IL17_ozone_1


title: BK06_3

first: JIN

last: ZHANG

state: Massachusetts

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School/Boston Children's Hospital

hyb_protocol: standard for Mouse WG6 Expression BeadChip

data_processing: Genomestudio software computated normalized (or unnormalized) signal intensity

source_name: lin28b loss of function

growth_protocol: Cells were cultured in mES media – KnockOut DMEM (Gibco 10829-018) containing 15% of FBS, 100 uM MEM-NEAA (Invitrogen 11140-050) and 1000 U/ml mLif (Millipore ESG1107) with 50 uM 2-Mercaptoethanol (Sigma M7522-100ML).

extract_protocol: Total RNA was extracted with Trizol reagent and cleaned up with Qiagen RNA clean up kit

tag: sample phenotype

value: lin28b loss of function

value: embryonic stem cells


title: BK06_1

scan_protocol: standard for Mouse WG6 Expression BeadChip


title: DK05_2

source_name: lin28a and b loss of function

label_protocol: standard for Mouse WG6 Expression BeadChip

value: lin28a and b loss of function


title: AK01_3

source_name: lin28a loss of function

value: lin28a loss of function


title: DK05_1


title: db_IL17_ozone_2


title: db_isotype_air_3


title: db_isotype_ozone_3


title: BK06_2


title: wt2_2

source_name: control


title: db_isotype_air_1


title: wt2_3


title: AK01_2


title: AK01_1


title: DK05_3


title: proB.FrBC.FL#2

first: Liang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

hyb_protocol: Affymetrix WT Sense Target Labeling Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were 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: liver

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 15 days

tag: exclusion markers

value: Ly6c, Ter119, CD3, GR1, CD11b

tag: phenotype markers

tag: separation method

value: dissection/trimming

tag: Sex

value: pooled male and female


title: proB.FrBC.FL#3

value: Ly6c, Ter119, CD3, CD11b, GR1


title: wt2_1

value: wild type

tag: tissue


title: LEC.SLN.OT#1

source_name: lymph node (subcutaneous)

value: 6 weeks

value: B6 (stroma) received B6 OT-I Rag1-/- T cells

value: MACS negative selection for CD45 followed by FACS

value: male


title: LEC.SLN.OT#2


title: FRC.SLN.OT#3


title: BEC.SLN.OT#1


title: LEC.SLN.OT#3


title: proB.FrBC.FL#1

value: Ter119, Ly6c, CD11b, GR1, CD3


title: BEC.SLN.OT#2


title: UC_R_210_2

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Colonic mucosal gene expression data

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 17h at 45°C on Affymetrix human Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

source_name: Colonic mucosal biopsy from UC patient in remission after placebo intake

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

treatment_protocol: Endoscopically-derived biopsies were immersed in RNAlater® (Applied Biosystems, Lennik, Belgium) and stored at -80°C for RNA isolation

value: colonic mucosa

tag: time point

value: after placebo intake


title: FRC.SLN.OT#1


title: UC_R_208

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from UC patient in remission before probiotics intake

value: before probiotics intake


title: FRC.SLN.OT#2


title: UC_R_211_2

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from UC patient in remission after probiotics intake

value: after probiotics intake


title: UC_R_209_2

description: Colonic mucosal gene expression data


title: UC_R_209

description: Colonic mucosal gene expression data


title: UC_R_208_2

description: Colonic mucosal gene expression data


title: BEC.SLN.OT#3


title: UC_R_207_2

description: Colonic mucosal gene expression data


title: UC_R_210

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from UC patient in remission before placebo intake

value: before placebo intake


title: UC_R_211

description: Colonic mucosal gene expression data


title: UC_R_207

description: Colonic mucosal gene expression data


title: UC_R_205

description: Colonic mucosal gene expression data


title: UC_R_205_2

description: Colonic mucosal gene expression data


title: Li-fraumeni Off vs Ref rep 1

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description: Li-Fraumeni Off vs Ref replicate 3

hyb_protocol: Tumors and reference samples were combined and hybridized onto the arrays according to manufacturer's (Agilent) instructions. After hybridization, arrays were washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned using a laser scanner from Agilent Technologies

data_processing: Agilent Feature Extraction Software was used for spot quality filtering and normalization

source_name: Li-fraumeni Off vs Ref

label_protocol: standard Agilent protocol

growth_protocol: All cell lines were maintained in DMEM (Invitrogen) with 10% FCS (Invitrogen), 2mM l-glutamine (Invitrogen), and 100μg/ml penicillin and streptomycin (Invitrogen) at 37°C and 5% CO2

extract_protocol: Genomic DNA was extracted using TRIzol and purified by chloroform extraction and subsequent ethanol precipitation.

treatment_protocol: Tet-ON inducible cell lines were treated with 1μg/ml Doxycycline (Applichem)

tag: cell line

value: LI-Fraumeni

tag: sample type

value: Tet OFF cells

value: Reference HG


title: UC_R_206_2

description: Colonic mucosal gene expression data


title: UC_R_204_2

description: Colonic mucosal gene expression data


title: UC_R_203_2

description: Colonic mucosal gene expression data


title: Li-fraumeni Off vs Ref rep 2

description: Li-Fraumeni Off vs Ref replicate 4


title: Li-fraumeni Escape vs Ref rep 2

description: Li-Fraumeni Esc vs Ref replicate 4

source_name: Li-fraumeni Escape vs Ref

value: Tet ON cells


title: Saos2_Off vs ref_m1

description: Saos2_Off vs ref_m1

source_name: Saos2 Off vs Ref


title: UC_R_204

description: Colonic mucosal gene expression data


title: UC_R_203

description: Colonic mucosal gene expression data


title: Li-fraumeni Escape vs Ref rep 1

description: Li-Fraumeni Esc vs Ref replicate 3


title: UC_R_201

description: Colonic mucosal gene expression data


title: Saos2_Esc vs ref_m1

description: Saos2_Esc vs ref_m1

source_name: Saos2 Escape vs Ref


title: UC_R_202_2

description: Colonic mucosal gene expression data


title: UC_R_201_2

description: Colonic mucosal gene expression data


title: UC_R_206

description: Colonic mucosal gene expression data


title: UC_R_202

description: Colonic mucosal gene expression data


title: UC_R_108_2

description: Colonic mucosal gene expression data


title: UC_R_108

description: Colonic mucosal gene expression data


title: UC_R_107_2

description: Colonic mucosal gene expression data


title: UC_R_105_2

description: Colonic mucosal gene expression data


title: UC_R_104_2

description: Colonic mucosal gene expression data


title: UC_R_107

description: Colonic mucosal gene expression data


title: UC_R_106_2

description: Colonic mucosal gene expression data


title: UC_R_106

description: Colonic mucosal gene expression data


title: UC_R_105

description: Colonic mucosal gene expression data


title: UC_R_101

description: Colonic mucosal gene expression data


title: UC_R_101_2

description: Colonic mucosal gene expression data


title: UC_8_2

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient after probiotics intake


title: UC_8

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient before probiotics intake


title: UC_6

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient before placebo intake


title: UC_2

description: Colonic mucosal gene expression data


title: UC_2_2

description: Colonic mucosal gene expression data


title: UC_18_2

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient after placebo intake


title: Reactive Hyperplasia Patient No.7, lymph node sample

city: Shanghai

first: Fan

last: YANG

address: 197, Rui Jin Er Road

country: China

institute: Shanghai Institute of Hematology

description: Genomic DNA extracted from lymph node tissue was genotyped using Human610W-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Regions were determined based on the Log R Ratio (LRR) of the signal intensity and B allele frequency (BAF) of genotyping call using platform of GenomeStudio V2011.1 with CnvPartition 3.1.6 (Illumina).

label: C-Bio and A-DNP

source_name: lymph node 52, at diagnosis

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted using Wizard Genomic DNA Purificaiton Kit (Promega, WI, USA) according to the manufacturer's protocol.

tag: tumor

value: Reactive hyperplasia

value: Female


title: Reactive Hyperplasia Patient No.5, lymph node sample

source_name: lymph node 50, at diagnosis


title: UC_18

description: Colonic mucosal gene expression data


title: Reactive Hyperplasia Patient No.6, lymph node sample

source_name: lymph node 51, at diagnosis


title: TCL Patient No.9, lymph node sample

source_name: lymph node 34, at diagnosis

value: T cell lymphoma

value: Male


title: TCL Patient No.11, lymph node sample

source_name: lymph node 36, at diagnosis


title: Reactive Hyperplasia Patient No.3, lymph node sample

source_name: lymph node 48, at diagnosis


title: Reactive Hyperplasia Patient No.1, lymph node sample

source_name: lymph node 46, at diagnosis


title: UC_16

description: Colonic mucosal gene expression data


title: Reactive Hyperplasia Patient No.4, lymph node sample

source_name: lymph node 49, at diagnosis


title: Reactive Hyperplasia Patient No.2, lymph node sample

source_name: lymph node 47, at diagnosis


title: TCL Patient No.7, lymph node sample

source_name: lymph node 32, at diagnosis


title: DLBCL Patient No.25, lymph node sample

source_name: lymph node 25, at diagnosis

value: Diffuse large B cell lymphoma


title: UC_14_2

description: Colonic mucosal gene expression data


title: UC_16_2

description: Colonic mucosal gene expression data


title: TCL Patient No.10, lymph node sample

source_name: lymph node 35, at diagnosis


title: UC_17

description: Colonic mucosal gene expression data


title: UC_13

description: Colonic mucosal gene expression data


title: UC_14

description: Colonic mucosal gene expression data


title: TCL Patient No.3, lymph node sample

source_name: lymph node 28, at diagnosis


title: TCL Patient No.5, lymph node sample

source_name: lymph node 30, at diagnosis


title: TCL Patient No.1, lymph node sample

source_name: lymph node 26, at diagnosis


title: UC_12

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient before probiotics intake


title: UC_15

description: Colonic mucosal gene expression data


title: TCL Patient No.2, lymph node sample

source_name: lymph node 27, at diagnosis


title: DLBCL Patient No.19, lymph node sample

source_name: lymph node 19, at diagnosis


title: DLBCL Patient No.18, lymph node sample

source_name: lymph node 18, at diagnosis


title: DLBCL Patient No.24, lymph node sample

source_name: lymph node 24, at diagnosis


title: DLBCL Patient No.23, lymph node sample

source_name: lymph node 23, at diagnosis


title: DLBCL Patient No.22, lymph node sample

source_name: lymph node 22, at diagnosis


title: TCL Patient No.8, lymph node sample

source_name: lymph node 33, at diagnosis


title: DLBCL Patient No.21, lymph node sample

source_name: lymph node 21, at diagnosis


title: TCL Patient No.4, lymph node sample

source_name: lymph node 29, at diagnosis


title: PLZF-deficient Luxoid Valpha14 tg stage 1 NKT, biological replicate 3

city: Chicago

first: Aiping

last: Mao

state: IL

address: 929 East 57th street

institute: University of Chicago

description:
LuxNKT st1 3
thymic stage 1 NKT from pooled PLZF-deficient Luxoid Valpha14 TCR tg mice

hyb_protocol: Affymetrix GeneChip Hybridization, Wash and Stain Kit was used to hybridize the labeled DNA to Mouse Genome 430 2.0 arrays

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: RMA normalization was performed using Expression Console

label_protocol: The WT-Ovation Pico RNA Amplification System (NuGEN Technologies) was used to generate amplified single-stranded cDNA that was fragmented and labeled using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies)

growth_protocol: Mouse thymus from C57BL/6J background

extract_protocol: RNA was extracted from FACS-sorted lymphocytes using TRIzol (Thermo Fisher Scientific) followed by Rneasy Mini Kit (Qiagen) column purification

treatment_protocol: Not applicable

tag: strain background

value: 4-6 weeks

tag: genotype/variation

value: Luxoid Valpha14 tg

value: thymus

tag: cell type

value: FACS-sorted stage 1 NKT (CD1d tetramer+ CD24low CD44- NK1.1-)


title: WT CD4SP, biological replicate 1

description:
CD4SP 1
thymic CD4SP from pooled wildtype mice

source_name: WT CD4SP

tag: age

value: wild type


title: UC_10_2

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient after placebo intake

value: colonic mucosa

value: after placebo intake


title: TCL Patient No.6, lymph node sample

source_name: lymph node 31, at diagnosis


title: PLZF-deficient Luxoid Valpha14 tg stage 1 NKT, biological replicate 2

description:
LuxNKT st1 2
thymic stage 1 NKT from pooled PLZF-deficient Luxoid Valpha14 TCR tg mice


title: UC_11_2

description: Colonic mucosal gene expression data


title: WT CD4SP, biological replicate 2

description:
CD4SP 2
thymic CD4SP from pooled wildtype mice


title: UC_1_2

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient after probiotics intake

value: after probiotics intake


title: UC_10

description: Colonic mucosal gene expression data

source_name: Colonic mucosal biopsy from active UC patient before placebo intake

value: before placebo intake


title: UC_11

description: Colonic mucosal gene expression data


title: DLBCL Patient No.20, lymph node sample

source_name: lymph node 20, at diagnosis