title: TKCBV5-6s15

value: human induced pluripotent stem cell line TKCBV5-6 subclone


title: Untreated Animal #24, Tumor

status: Public on Aug 04 2014

type: RNA

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX software (Agilent Technologies, Santa Clara, CA).

molecule: total RNA

organism: Rattus norvegicus

source_name: 4-NQO induced tongue lesion

label_protocol: First and second strand cDNA was prepared from the total RNA samples. Labeled cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Male F344 rats were received at six to seven weeks of age from virus-free barrier colonies that are maintained under contract to the National Cancer Institute, Frederick, MD. Rats were held in quarantine for a minimum of one week prior to study initiation; prior to randomization into a study, each rat underwent a hand-held physical examination to ensure its suitability for use as a test subject.  Animals were housed on hardwood bedding in polycarbonate shoebox cages (two to three per cage) in a windowless room that was illuminated for 12 hours each day and maintained at 22 ± 1°C and within the range of 30% to 70% relative humidity. Throughout all studies, rats were permitted free access to Purina 5001 Laboratory Diet (PMI Feeds, Brentwood, MO) and City of Chicago drinking water (provided in water bottles). All food cups and water bottles were replaced a minimum of twice weekly.

extract_protocol: Paired sets of normal and neoplastic oral tissues were harvested from rats at 23 to 26 weeks after their first exposure to 4-NQO.  At necropsy, gross lesions were collected from the tongue of 4-NQO-treated rats and bisected longitudinally. Half of each lesion was flash-frozen in liquid nitrogen for analysis of gene expression/promoter methylation. The other half of each lesion was fixed in formalin, processed using routine histologic methods, stained with H&E, and evaluated microscopically to confirm malignancy. Phenotypically normal tissue was collected from adjacent areas of the tongue of the same 4-NQO-treated rats, and was flash-frozen or fixed in a manner identical to that used for tumor tissues.  Total RNA was isolated from histologically confirmed squamous cell carcinomas and adjacent phenotypically normal tissues using Qiagen’s RNeasy Mini kit by following the manufacturer’s instructions.  Total RNA was used for microarray or RT-PCR analysis.

treatment_protocol: NQO was purchased from Sigma-Aldrich, St. Louis, MO, and was stored in the dark at −20°C until used. NQO was administered in the drinking water at 20 ppm for a period of 10 weeks. After dose preparation, all formulations of NQO were stored in the dark at 4°C until used. Bottles containing NQO-supplemented drinking water were wrapped with foil to preclude possible photodegradation of the carcinogen, and were changed at two- to three-day intervals throughout the study. Rats received their first exposure to NQO at seven to nine weeks of age.

tag: tissue

value: 4-NQO induced tongue lesion

tag: strain

value: F344 Rat

tag: gender

value: Male

tag: histology

value: Squamous cell carcinoma

tag: age

value: approximately 33 weeks

tag: treatment

value: 4-NQO at 20ppm in drinking water for 10 weeks.


title: Untreated Animal #21, Tumor


title: Untreated Animal #22, Tumor


title: TIG118-4F1s5

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

description: human induced pluripotent stem cell line TIG118-4F1 subclone

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the Gene Spring GX 11.5.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm.

organism: Homo sapiens

label_protocol: Agilent standard protocol

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

tag: cell type


title: primary colorectal carcinoma S54-Frozen-rep1

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

country: France

institute: Ligue Nationale contre le Cancer

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45°C, 60 rpm on Human GeneChip HG-U133 Plus 2.0 arrays (Affymetrix).  The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v5_450.

scan_protocol: Scanner GeneChip 3000 7G ; Wavelenght : 570 nm, size pixel: 1.56 µm ; each chip is scanned once; Http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: RMA signal intensity generated using Bioconductor R affy package

label: biotin

source_name: Frozen tissue of primary colorectal carcinoma

label_protocol: Biotinylated cRNA targets were prepared from 3.0 mg of total RNA, according to the GeneChip Expression Analysis Technical Manual : One-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: samples stored at -80 C

extract_protocol: total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA)

treatment_protocol: total RNA was performed according to the manufacturer's instructions.

value: M

tag: lastnews or death.date

tag: death

tag: relapse

value: right colon

tag: tnm

tag: msi.status [mismatch repair status]

value: High

value: WT

tag: group

value: primary colorectal carcinoma

tag: organism part

value: colorectal


title: TIG118-4F1s6

source_name: human induced pluripotent stem cell line TIG118-4F1 subclone


title: Untreated Animal #16, Tumor


title: Untreated Animal #17, Tumor


title: primary colorectal carcinoma S52-Frozen-rep1


title: primary colorectal carcinoma S51-Frozen-rep1

value: F


title: TIG118-4F1s3

value: human induced pluripotent stem cell line TIG118-4F1 subclone


title: TIG108-4F3s41

description: human induced pluripotent stem cell line TIG108-4F3 subclone


title: TIG108-4F3s26

source_name: human induced pluripotent stem cell line TIG108-4F3 subclone


title: TIG118-4F1s2


title: primary colorectal carcinoma S43-Frozen-rep1

value: left colon

value: Low


title: primary colorectal carcinoma S49-Frozen-rep1


title: Untreated Animal #11, Tumor


title: TIG108-4F3s25

value: human induced pluripotent stem cell line TIG108-4F3 subclone


title: TIG108-4F3s30


title: Untreated Animal #13, Tumor

value: 4-NQO induced tongue lesion


title: TIG118-4F1s1


title: TIG118-4F1s4


title: TIG108-4F3s22


title: TIG108-4F3s24


title: primary colorectal carcinoma S47-Frozen-rep1


title: TIG108-4F3s20


title: Untreated Animal #4, Tumor

value: F344 Rat


title: Untreated Animal #26, Normal

source_name: Normal tongue tissue

value: Normal tongue tissue

value: Male

value: Normal


title: TIG108-4F3s23


title: TIG108-4f3s16


title: TIG108-4f3s17


title: Untreated Animal #25, Normal

value: approximately 33 weeks


title: TIG108-4f3s2


title: TIG108-4F3s19


title: Untreated Animal #9, Tumor

value: Squamous cell carcinoma

value: 4-NQO at 20ppm in drinking water for 10 weeks.


title: primary colorectal carcinoma S37-Frozen-rep1

value: M

value: No


title: TIG118-4F1s12


title: primary colorectal carcinoma S38-Frozen-rep1

value: WT

value: primary colorectal carcinoma


title: primary colorectal carcinoma S41-Frozen-rep1

value: F

value: colorectal


title: Untreated Animal #24, Normal


title: primary colorectal carcinoma S36-Frozen-rep1

value: left colon

value: High


title: 451F3s12

description: human induced pluripotent stem cell line 451F3 subclone


title: 451F3s15

source_name: human induced pluripotent stem cell line 451F3 subclone


title: Untreated Animal #17, Normal


title: 451F3s17

value: human induced pluripotent stem cell line 451F3 subclone


title: 451F3s9


title: primary colorectal carcinoma S35-Frozen-rep1

value: right colon


title: TIG108-4f3s1

value: human induced pluripotent stem cell line TIG108-4F3 subclone


title: 451F3s10


title: 451F3s14


title: 451F3s13


title: Untreated Animal #22, Normal

value: Normal tongue tissue

value: F344 Rat


title: Untreated Animal #21, Normal

value: Male

value: Normal


title: 451F3s11


title: primary colorectal carcinoma S30-Frozen-rep1


title: primary colorectal carcinoma S33-Frozen-rep1


title: 451F3s5


title: Untreated Animal #16, Normal

value: approximately 33 weeks


title: 451F3s6


title: Untreated Animal #13, Normal


title: 451F3s7


title: 451F3s3


title: primary colorectal carcinoma S27-Frozen-rep1

value: low rectum


title: primary colorectal carcinoma S34-Frozen-rep1

value: M


title: 451F3s4


title: Untreated Animal #11, Normal


title: primary colorectal carcinoma S25-Frozen-rep1

value: tumor

value: No


title: primary colorectal carcinoma S20-Frozen-rep1

value: WT

value: primary colorectal carcinoma


title: primary colorectal carcinoma S8-Frozen-rep1

value: F

value: multiple location

value: colorectal


title: primary colorectal carcinoma S22-Frozen-rep1

value: left colon


title: primary colorectal carcinoma S7-Frozen-rep1


title: primary colorectal carcinoma S101-Frozen-rep1

value: right colon

value: High


title: primary colorectal carcinoma S14-Frozen-rep1


title: primary colorectal carcinoma S21-Frozen-rep1


title: primary colorectal carcinoma S6-Frozen-rep1


title: primary colorectal carcinoma S9-Frozen-rep1


title: primary colorectal carcinoma S23-Frozen-rep1

value: Low


title: 451F3s2

value: human induced pluripotent stem cell line 451F3 subclone


title: primary colorectal carcinoma S4-Frozen-rep1


title: 451F3s1


title: primary colorectal carcinoma S3-Frozen-rep1


title: Untreated Animal #9, Normal

value: Normal tongue tissue

value: F344 Rat

value: Male


title: primary colorectal carcinoma S18-Frozen-rep1

value: low rectum


title: primary colorectal carcinoma S100-Frozen-rep1

value: M


title: TIG108-4F3s37

value: human induced pluripotent stem cell line TIG108-4F3 subclone


title: primary colorectal carcinoma S5-Frozen-rep1

value: No


title: Untreated Animal #4, Normal

value: Normal

value: approximately 33 weeks


title: P5 BMPR2 Mutant_2

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: Inducible pluripotent stem cells from a BMPR2 mutant, in endothelial-like differentiation, passage 5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome 1.1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-1_1-st-v1
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: iPS cells

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

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

tag: genotype/variation

value: BMPR2 2504DELC mutation

tag: differentiation state

value: Passage 5 endothelial-like differentiation

value: iPS cells


title: P4 BMPR2 Mutant_1

description: Inducible pluripotent stem cells from a BMPR2 mutant, in endothelial-like differentiation, passage 4

value: Passage 4 endothelial-like differentiation


title: P5 BMPR2 Mutant_1


title: Early BMPR2 Mutant_2

description: Inducible pluripotent stem cells from a BMPR2 mutant in early mesenchymal differentiation

value: Early mesenchymal differentiation


title: P4 BMPR2 Mutant_2


title: Early BMPR2 Mutant_1


title: Late BMPR2 Mutant_2

description: Inducible pluripotent stem cells from a BMPR2 mutant, in late mesenchymal differentiation

value: Late mesenchymal differentiation


title: Late BMPR2 Mutant_1


title: H9_2

type: genomic

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard recommended Illumina scanner setting protocol using BeadArray Reader

data_processing: Illumina GenomeStudio software  Unmethylated(Signal_A) and methylated(Signal_B) signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: human Embryonic stem cells

label_protocol: Standard Illumina Protocol

extract_protocol: GenomicDNA lysates were extracted with DNeasy(R) blood and tissue kit (QIAgen) in accordance with manufacture's protocol.

value: human Embryonic stem cells


title: H9_1


title: 201B7

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells


title: p2_1

source_name: Intermediate reprogrammed cells

value: induced pluripotent stem cells 7 days after 2nd passage


title: p3_3

value: induced pluripotent stem cells 7 days after 3rd passage


title: p1_2

value: induced pluripotent stem cells 7 days after TRA-1-60(+) cell sorting on day 28


title: p3_1


title: p3_2


title: p2_3


title: p1_3


title: Day15_2

value: TRA-1-60(+) cells on day 15


title: Day28_3

value: TRA-1-60(+) cells on day 28


title: Day28_1


title: p1_1


title: Day28_2


title: Day20_1

value: TRA-1-60(+) cells on day 20


title: Day20_2


title: Day11_2

value: TRA-1-60(+) cells on day 11


title: Day11_3


title: p2_2


title: P5 WT_2

description: Inducible pluripotent stem cells from a healthy control, in endothelial-like differentiation, passage 5

value: WT for BMPR2


title: Chipseq-Pit1

status: Public on Aug 03 2014

type: SRA

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description: Pit1 ChIP-seq in rat GC pituitary cells

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the rn4 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

source_name: rat GC pituitary cells

growth_protocol: GC cells are grown in Untraculture medium containing 5% FBS

extract_protocol:
For ChIP-seq, fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C overnight. For samples fixed with glutaraldehyde, proteinase K (0.3mg/ml) (Ambion) was added during de-crosslinking. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) ;
the libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: siRNA and overexpression experiments in GC cells were performed using Neon system (Invitrogen). Conditions of 2 pulses of 1150 V with 30ms spacing were used. 100 nM siRNA and 3ug of DNA were used per 3x106 cells. Knockdown was repeated after 48h to obtain optimal depletion of the protein, verified by Western blotting.

value: rat GC pituitary cells

tag: chip antibody

tag: chip antibody vendor

value: Rosenfeld Lab


title: Day15_1


title: P5 WT_1

value: Passage 5 endothelial-like differentiation


title: P4 WT_2

description: Inducible pluripotent stem cells from a healthy control, in endothelial-like differentiation, passage 4

value: iPS cells


title: Day11_1


title: TTHB8 wild type at 5h, rep2

city: Bunkyo-ku, Tokyo

first: Naoki

last: IWANAGA

address: 1-1, Yayoi

institute: The university of Tokyo

description: Gene expression data from wild-type strain at 5h.

hyb_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50°C in a solution comprising 100 mM MES, pH 6.6, 20 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 0.1 mg/ml of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm and normalized by global scaling method using GeneChip Operating Software, version 1.4 (Affymetrix, Santa Clara, CA). The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Thermus thermophilus HB8

source_name: TTHB8 wild type at 5h, rep2

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.35 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer's instructions (Affymetrix).

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C until the optical density at 600 nm reached 1.0 in 10 ml of TM medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2. The cells (0.1 ml) were inoculated into 10 ml of the same medium and then cultivated at 70°C for 5 h.

extract_protocol: Cells were collected from 10 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 0.25% SDS, and 50% of TE buffer containing 10 mM Tris-HCl, pH 7.5, 1mM EDTA-saturated phenol. This mixture was incubated at 60°C for 5 min, chilled on ice for 3.5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.03 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: Cells were collected from 10 ml of the culture with centrifugation.

tag: genotype

value: wild-type

tag: time point


title: TTHB8 DTTHA1559 at 5h, rep3

description: Gene expression data from TTHA1559 disrupted strain at 5h.

source_name: T. thermophilus

growth_protocol: The T. thermophilus HB8 TTHA1559 disrupted strain was pre-cultured at 70°C until the optical density at 600 nm reached 1.0 in 10 ml of TM medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2. The cells (0.1 ml) were inoculated into 10 ml of the same medium and then cultivated at 70°C for 5 h.

value: TTHA1559 disrupted


title: TTHB8 wild type at 5h, rep1

source_name: TTHB8 wild type at 5h, rep1


title: TTHB8 wild type at 5h, rep3

source_name: TTHB8 wild type at 5h, rep3


title: Late Wild-Type_1

description: Inducible pluripotent stem cells from a healthy control, in late mesenchymal differentiation

value: Late mesenchymal differentiation


title: TTHB8 DTTHA1559 at 5h, rep1


title: TTHB8 DTTHA1559 at 5h, rep2


title: Early Wild-Type_1

description: Inducible pluripotent stem cells from a healthy control, in early mesenchymal differentiation

value: Early mesenchymal differentiation


title: P4 WT_1

value: Passage 4 endothelial-like differentiation


title: Late Wild-Type_2


title: Group C_Experiment_30 days_rep4

status: Public on Aug 02 2014

city: chongqing

first: guo

middle: zhen

last: zhao

address: Cancer Institute of PLA, Xinqiao Hospital, Third Military Medical University, Chongqing, China

country: China

hyb_protocol: The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data=(Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

organism: Mus musculus

source_name: primary lung adenocarcinoma

label_protocol: After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.11.0).

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

tag: strain

value: Lox-stop-lox Kras G12D mice

tag: infected with

value: adenovirus CRE (Ad-Cre)

tag: tissue

value: lung

tag: tissue type

value: primary lung adenocarcinoma

value: Sca-1+CD34+ cells


title: Group B_Experiment_15 days_rep4

institute: Cancer Institute of PLA, Xinqiao Hospital, Third Military Medical University,

tag: cell type


title: Group A_Experiment_0 days_rep4


title: Day7_2

value: TRA-1-60(+) cells on day 7


title: Day7_3


title: Early Wild-Type_2


title: KB/TP

city: Suita

first: Sho

last: Tabata

state: Osaka

address: 3-2 Yamadaoka

department: Institute for Protein Research,ces

institute: Osaka University

description: Gene expression of KB/TP cells after 12hr in serum free condition.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: KB/TP, 12h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: KB cells (4 × 10^5) in 5 ml of culture media were cultured for 24 hours, then the growth medium was replaced with serum-free medium.  These cells were maintained at 37 ˚C in a humidified atmosphere of 5% CO2 for 12 hours.

extract_protocol: Total RNA was extracted using theTRIzol .

tag: cell-type

value: epidermoid carcinoma KB cells

tag: condition

value: carcinoma


title: chip#109

city: New York

first: Joel

middle: M

last: Correa da Rosa

state: New York

address: 1230 York Avenue

department: CTSA

institute: Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

source_name: skin

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Qiagen RNeasy Kit protocol

tag: gender

value: F

tag: allergen

value: Nickel


title: chip#89

value: Petrolatum

tag: group


title: Day7_1


title: Day3_1

value: SOX2-EGFP (+) cells on day 3


title: KB/CV

description: Gene expression of KB/CV cells after 12hr in serum free condition.

source_name: KB/CV, 12h


title: chip#92


title: chip#100


title: chip#90


title: chip#107


title: Day0_1

source_name: Human dermal fibroblast

value: Human dermal fibroblast


title: chip#102


title: chip#82


title: Day0_3


title: chip#81

value: K Dichromate

value: Other Metals


title: chip#86


title: chip#85

value: Cobalt


title: chip#78

value: M


title: chip#93


title: chip#77

value: Carba Mix

value: Rubber


title: Day3_2


title: Patient3 MCL-non-ICs

city: Houston

first: Rohit

last: Mathur

state: Texas

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma and Myeloma

institute: M.D. Anderson cancer center

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

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1  (Agilent) using default parameters (Protocol: GE1_1100_Jul11 and Grid: 039809_D_F_20120327) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The 'Gene expression comparision between MCL-ICs MCL-non-ICs and B-cells.xls' contains statistical analysis results with venn diagram and p values.

source_name: Primary Mantle cell lymphoma

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

growth_protocol: Directly isolated cells from buffy coats primary patient samples or healthy donor were used for microarray experiment

extract_protocol: Total RNA isolated using RNAaquoes kit was used for further experiment

treatment_protocol: No treatment to isolated primary cells was given. However primary cells from chemotherapy naïve and treated patients were isolated as described above in patient charecteristics

tag: subject status

value: mantle cell lymphoma primary patient

tag: age (yrs)

tag: cell/tissue type

value: Primary Mantle cell lymphoma

tag: cell subtype

value: mantle cell lymphoma-non-initiating cells (MCL-non-ICs)

tag: prior chemotherapy

value: R-hyperCVAD


title: chip#71


title: Day0_2


title: Patient3 MCL-ICs

value: mantle cell lymphoma-initiating cells (MCL-ICs)


title: chip#70

value: Thiuram Mix


title: chip#73

value: F


title: Slide2.1

city: Leiden

first: Jeroen

last: Corver

address: Albinusdreef 2

department: Medical Microbiology

country: Netherlands

institute: LUMC

hyb_protocol: 300 ng labeled cDNA (1:1 RATIO) were hybridized (2xgex Hi-RPM hybridisation buffer) for 17hr at 65 C and 10 rpm.

scan_protocol: Scanned on a GenePix scanner. Images were quantified using GenePix 6.1 software program.

data_processing: LiimaR package via Genome2D (http://genome 2d.molgenrug.nl), LOESS normalized, followed by quantile normalization between the slides

organism: Clostridioides difficile

label_protocol: 6 µg of total RNA were primed with 2 µl (1.6 µg/µl) random nanomers at 70°C for 5 min, then reversed transcribed at 42°C for 16 h in the presence SuperScript III RTase (life technologies), and 25X AA-dUTP/nucleotide mix. Synthesized cDNA was labeled with DyLight550 or DyLight650

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

value: wild type

tag: wild type


title: Slide2.3

tag: time point


title: chip#68

value: Petrolatum


title: chip#61


title: chip#63

value: BOP

value: Fragrance


title: Slide1.6

tag: strain


title: chip#67


title: chip#60


title: chip#46


title: Slide1.1


title: Slide1.2


title: Slide1.5


title: Patient1 MCL-ICs


title: chip#74


title: chip#55


title: Healthy donor 1 (CD19+ Bcells)

source_name: Buffy coats from Healthy donor

value: healthy donor

value: Buffy coats from Healthy donor


title: Patient2 MCL-ICs


title: Patient1 MCL-non-ICs


title: chip#64


title: chip#45

value: Nickel


title: chip#56

value: M


title: Patient2 MCL-non-ICs


title: chip#42


title: Healthy donor 2 (CD19+ Bcells)


title: chip#35


title: E2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file: E12_US83300186_251487921018_3.txt
Gene expression in dentate gyrus of EB-treated OVX adult female rat

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

source_name: EB treated

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: 150-200g adult female Sprague-Dawley rats purchased from Taconic Farms were kept on a 12-h light/dark cycle (lights on at 0700) and housed in groups of four with food and water ad libitum. Rats were ovariectomized (OVX) under ketamine/xylazine anesthesia one week prior to hormonal replacement

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Rats were injected with 17-estradiol benzoate (EB; Sigma Chemical) or with just oil for control

value: Sprague-Dawley

tag: Sex

value: female

tag: developmental stage

value: adult

tag: status

value: ovaryectomized

tag: injected with

value: 17-estradiol benzoate (EB)

value: dentate gyrus


title: chip#43


title: chip#31


title: chip#34


title: E3

description:
raw data file: E34_US83300186_251487921018_4.txt
Gene expression in dentate gyrus of EB-treated OVX adult female rat

tag: tissue


title: E1


title: chip#16


title: O3

description:
raw data file: O34_US83300186_251487921018_2.txt
Gene expression in dentate gyrus of oil-treated OVX adult female rat

source_name: Oil treated

value: oil (control)


title: O4


title: chip#24


title: chip#30

value: Thiuram Mix

value: Rubber


title: chip#23

value: Carba Mix


title: chip#12

value: F

value: Petrolatum


title: chip#11


title: chip#9


title: chip#6


title: chip#5


title: chip#8


title: chip#15

value: Frangrance

value: Fragrance


title: chip#3


title: O2

description:
raw data file: O12_US83300186_251487921018_1.txt
Gene expression in dentate gyrus of oil-treated OVX adult female rat


title: chip#2


title: chip#26


title: Eight weeks AJ strain mouse liver sample 7

city: Chicago

first: Richard

last: Green

address: 675 N Saint Clair

institute: Northwestern University

description: Male eight weeks AJ strain mouse High Fat High Calorie

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing:
Raw signal intensities of each probe were obtained using data analysis software(Beadstudio; Illumina) and imported to the Lumi package of Bioconductor fordata transformation and normalization [1-3]. A/P call detection was performed based on detection p value. The probes with less than 0.01 were considered as valid signals. The data for these probes were normalized by quantile method. Differentially expressed genes were identified using an Analysis of Variance (ANOVA) model with empirical Bayesian variance estimation [4]. The problem of multiple comparisons was corrected using the false discovery rate (FDR). Initially, genes were identified as being differentially expressed on the basis of a statistically significant (raw p-value < 0.01 and fdr < 0.05 and 1.5-fold change (up or down) in expression level in different treatment samples.
[1] Du, P, Kibbe, W. A, and Lin, S. M. (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics. 24(13):1547-8.
[2] Lin, S. M., Du, P, Huber, W, and Kibbe, W. A. (2008) Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 36(2):e11
[3] Du, P, Kibbe, W. A., and Lin, S. M. (2007) nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, andother microarrays. Biol Direct. 2:16.
[4] Wettenhall, J. M., and Smyth, G. K. (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705-3706.

label: Biotin

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: male

tag: age

value: eight weeks

value: AJ

tag: diet

value: High Fat High Calorie

value: liver


title: O1

value: Sprague-Dawley

value: female

value: adult


title: Eight weeks C57BL6J strain mouse liver sample 4

description: Male Eight weeks C57BL6J strain mouse High Fat High Calorie

tag: gender


title: Eight weeks C57BL6J strain mouse liver sample 8

source_name: Male Eight weeks C57BL6J strain mouse High Fat High Calorie


title: ShSuz12 IEC-6 cells rep.3

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

country: Canada

institute: Agriculture and AgriFood Canada

description: gene expression data in Suz12 depleted IEC-6 cells

hyb_protocol: Hybridized target cRNA is stained with streptavidin phycoerythrin

scan_protocol: arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

data_processing: Data analysis, normalization average difference and expression measurements were subsequently completed with Flexarray software version 1.6.1.  Background correction and normalization were assessed with a multi-array average (RMA) algorithm. Significant statistical differences were calculated with the Student’s t test, with the cut-off for statistical significance set to a p value of 0.05 or below.

source_name: RNA from ShSuz12 rat intestinal epithelial cells no.3

label_protocol: Target RNA is reversed transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization

growth_protocol: Cells were grown in Dulbecco’s modified Eagle medium (DMEM) with 5% fetal bovine serum (FBS).

treatment_protocol: Multiple shRNA lentiviral constructs were tested in IEC-6 cells for their ability to down-regulate Suz12 expression (MISSION shRNA lentiviral transduction particles, Sigma–Aldrich Canada, Oakville, ON). Forty percent confluent cells were infected in medium supplemented with 4 mg/ml polybrene (Sigma–Aldrich Canada) for 6 h. Two days after infection, cell populations were selected with 2 mg/ml puromycin (Sigma–Aldrich Canada). The clone TRCN0000038728 was selected: the shRNA against Suz12 (GCTGACAATCAAATGAATCAT) is conserved in rat (accession number FM084383), murine (accession number NM_199196) and human (accession number NM_015355.2) Suz12 sequences. Efficiency of infection was estimated at 25%. Control or ShSuz12 IEC-6 cell total RNAs were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada), according to the manufacturer’s instructions. RNA samples from three independent experiments were used for microarray analysis.

tag: cell line

value: IEC-6 cultured cells


title: Eight weeks C57BL6J strain mouse liver sample 5


title: control IEC-6 cells rep.3

description: gene expression data in IEC-6 control cells

source_name: RNA from control rat intestinal epithelial cells no.3

extract_protocol: Control or ShSuz12 IEC-6 cell total RNAs were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada), according to the manufacturer’s instructions.


title: Eight weeks AJ strain mouse liver sample 6

source_name: Male eight weeks AJ strain mouse High Fat High Calorie


title: Eight weeks C57BL6J strain mouse liver sample 2


title: Eight weeks AJ strain mouse liver sample 8


title: ShSuz12 IEC-6 cells rep.2

source_name: RNA from ShSuz12 rat intestinal epithelial cells no.2


title: Eight weeks C57BL6J strain mouse liver sample 6


title: Eight weeks C57BL6J strain mouse liver sample 3


title: Eight weeks AJ strain mouse liver sample 5


title: Eight weeks AJ strain mouse liver sample 3


title: Eight weeks C57BL6J strain mouse liver sample 7


title: Eight weeks AJ strain mouse liver sample 4


title: J2-YJ-M

city: Ya'an

first: long

last: jin

state: Sichuan

address: Ya’an, Xinkang Road #46 Sichuan

institute: Sichuan Agricultural University

description: Genome-wide gene expression profile

hyb_protocol: Fragmentation was carried out by incubation at 60 °C for 30 min in a fragmentation buffer (Agilent Technologies), and the process was stopped by the addition of an equal volume of hybridization buffer (Agilent Technologies).Hybridization was carried out at 60 °C for 17 h in a  hybridization oven (Robbins Scientific).

scan_protocol: The hybridized single channel array was scanned with an Agilent microarray scanner (G2565BA).

data_processing: The TIFF image generated was loaded into Feature Extraction Software (Agilent Technologies) for feature data extraction, and data analysis was performed with MultiExperiment Viewer (MeV). The quantile normalization was performed using GeneSpring 11.5 software.

organism: Sus scrofa

source_name: LDM: longissimus dorsi muscle

label_protocol: The labeling procedure was carried out using an RNA Fluorescent Linear Amplification Kit (Agilent Technologies). The sample was labeled with Cy-3 dye only.

growth_protocol: pigs aged 0.5 years and 7 years

extract_protocol: The total RNA (10 μg) of the six samples was extracted using TRIzol (Invitrogen) and further purified using an RNeasy column (Qiagen). The integrity of total RNA were also analyzed with the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent Technologies).

treatment_protocol: longissimus dorsi muscle were sampled rapidly from each carcass, and immediately frozen in liquid nitrogen. All tissue samples were stored at − 80 °C until total RNA extraction.

tag: breed

value: Jinhua

value: 0.5 years


title: Eight weeks C57BL6J strain mouse liver sample 1


title: E4

value: ovaryectomized

value: 17-estradiol benzoate (EB)

value: dentate gyrus


title: J3-YJ-M

description: Genome-wide gene expression profile


title: ShSuz12 IEC-6 cells rep.1

source_name: RNA from ShSuz12 rat intestinal epithelial cells no.1


title: control IEC-6 cells rep.2

source_name: RNA from control rat intestinal epithelial cells no.2


title: A3-YJ-M

description: Genome-wide gene expression profile

value: 7 years


title: J1-YJ-M

description: Genome-wide gene expression profile


title: Primary colon tumor GIM-14A

status: Public on Aug 01 2014

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

hyb_protocol: Expression analysis was performed according to the written protocol provided by NanoString Technologies (Seattle, WA). Briefly, a 5 µl aliquot containing 100 ng of denatured total RNA was added to 20 µl of master mix consisting of equal amounts of Reporter CodeSet solution and hybridization buffer. Five µl of Capture ProbeSet were added to the mix the hybridization was performed overnight at 65°C.

scan_protocol: Post-hybridization processing and scanning was performed using the nCounter analysis system at the NCI CCR DNA Sequencing and Digital Gene Expression Core Facility.

data_processing: Probe level background subtraction was applied for the 13 probes which had background hybridizations levels as indicated by the manufacturer.  microRNAs are listed with their background coefficient for correction in parentheses.   hsa-miR-27b (0.08) hsa-miR-133a (0.05), hsa-miR-544 (0.03), hsa-miR-320c (0.03), hsa-miR-590-5p (0.01), hsa-miR-16 (0.01), hsa-miR-494 (0.01), hsa-miR-579 (0.01), hsa-miR-193a-3p (0.005), hsa-miR-196a (0.005), hsa-miR-485-3p (0.005), hsa-miR-1283 (0.005).  Data was then normalized to the geometric mean of the 75 highest expressed microRNAs.  These are the first 75 microRNAs listed the normalized data.

source_name: Primary colon tumor

label_protocol: Nanostring Human MicroRNA assays v1

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.

value: Primary colon tumor

tag: case id


title: colon tumor metastasis to the liver GIM09B

source_name: colon tumor metastasis to the liver

value: colon tumor metastasis to the liver


title: colon tumor metastasis to the liver GIM-01B


title: Primary colon tumor GIM09A


title: Primary colon tumor GIM-01A


title: colon tumor metastasis to the liver 14129


title: Primary colon tumor 10697


title: control IEC-6 cells rep.1

source_name: RNA from control rat intestinal epithelial cells no.1


title: colon tumor metastasis to the liver GIM04B


title: Primary colon tumor 14716


title: colon tumor metastasis to the liver GIM-14B


title: colon tumor metastasis to the liver GIM-13B


title: Eight weeks AJ strain mouse liver sample 1

value: male


title: Primary colon tumor GIM-13A


title: Eight weeks AJ strain mouse liver sample 2

value: eight weeks


title: A2-YJ-M

description: Genome-wide gene expression profile


title: A1-YJ-M

description: Genome-wide gene expression profile


title: colon tumor metastasis to the liver GIM10B


title: Primary colon tumor GIM10A


title: Primary colon tumor GIM12A


title: colon tumor metastasis to the liver 27296


title: colon tumor metastasis to the liver GIM12B


title: GEK51

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Brassica napus

source_name: mature seed

growth_protocol: B. napus (cultivar PFB-2, Embrapa) plants were grown in an open environment (30°S 51°W) from May to October 2010. Flowers were tagged upon opening and developing siliques from different plants were collected in the middle of a light cycle at 7, 14, 21, 28, 42 and 50 days after flower opening (DAF). The seeds were dissected from the siliques, immediately frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. Two sRNA libraries were constructed, one from mature seeds (50 DAF) and one from an equivalent mixture of RNA from immature seeds at DAF stages 7-42, and they were sequenced by Illumina HiSeq2000. Briefly, the construction of the small RNA libraries consisted of the following successive steps: acrylamide gel purification of the RNA bands corresponding to the size range 20-30 nt, ligation of the 3p and 5p adapters to the RNA in two separate subsequent steps, each followed by acrylamide gel purification, cDNA synthesis followed by acrylamide gel purification, and a final step of PCR amplification to generate a cDNA colony template library for Illumina sequencing.

tag: cultivar

value: PFB-2, Embrapa

tag: sample type

value: single

tag: days after flower opening (daf)

value: seeds

tag: rna type

value: small RNA


title: GEK52

source_name: developing seed

value: pooled


title: Control CD8_vs_TGF b CD8

city: Würzburg

first: Anoop

last: Chandran P

address: Josef-schneiderstrasse

country: Germany

institute: University of Würzburg

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays CTID 878 using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore ™ microarrays was done with the Agilent's Microarray Scanner System (Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Hy5/Hy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using LOWESS.

source_name: CD8+ T cells, untreated

label_protocol: 1.5 µg of the respective total RNA were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labeled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The corresponding total RNA samples were hybridized in a dual colour approach to microarrays.

growth_protocol: Cells were cultured in X-VIVO15 medium (Lonza).

extract_protocol: RNA was isolated using Trizol.

treatment_protocol: Cells were activated using T cell activation beads (Miltenyi) overnight and then treated for 24 h with 5ng/ml TGF-b , with 1µM SD-208 or left untreated.

tag: cell type

value: CD8+ T cells

value: peripheral blood

tag: disease status

value: healthy

tag: treatment

source_name: CD8+ T cells, TGF-b

value: TGF-b


title: SD 208 CD8_vs_TGF b CD8

source_name: CD8+ T cells, SD-208


title: PBMo-derived macrophages stimulated with TE-9CM

city: Kobe

last: Urakawa

address: 7-5-1, Kusunoki-cho, Chuo-ku

department: Pathology

institute: Kobe University Graduate School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral Blood Monocytes stimulated with 25 ng/ml M-CSF plus 50% conditioned media of TE9 human ESCC cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from healthy volunteer donors with written informed consents. CD14+ PBMo were purified from PBMC by positive selection using auto MACS® Pro Separator (Miltenyi Biotec, Bergisch Gladbach, Germany). PBMo were plated in 1 × 105 cells/mL per well, and cultured with macrophage-colony stimulating factor (M-CSF) (25 ng/mL; R&D Systems, Minneapolis, MN) for 6 days to induce macrophages differentiation. 50% TECM was added for 2 days to induce M2-like polarization.

extract_protocol: Total mRNA was extracted from each cell using RNeasy Kit (Qiagen, Hilden, Germany).

value: whole blood


title: HBL1 shBRD4 - 24 hours - mAdbID:124453

first: Louis

middle: M.

last: Staudt

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

department: Lymphoid Malignancies Branch

description: mAdb experiment ID: 124453

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

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

data_processing:
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)

source_name: HBL1 shControl - 24 hours

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 type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 24 hours.

value: ABC DLBCL cells

tag: disease state

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

source_name: HBL1 shBRD4 - 24 hours

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).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shBRD4. shRNA expression was induced with doxycycline for 24 hours.


title: PBMo-derived macrophages

source_name: Peripheral Blood Monocytes stimulated with 25 ng/ml M-CSF


title: Keratinocyte differentiating RA 4 h rep3

city: Uppsala

first: Hans

last: Törmä

address: Dag Hammarskjölds väg 20

department: Dept of Medical Sciences

country: Sweden

institute: Uppsala University

hyb_protocol: GeneChip® Human Gene 2.1 ST Arrays were hybridized for 16 hours in a 45°C incubator, followed by washing and staining

scan_protocol: The GeneChip® Array-plates were scanned with GeneTitan® Multi-Channel (MC) Instrument

data_processing: The raw data was normalized in Expression Console provided by Affymetrix, using the robust multi-array average (RMA) method.

source_name: keratinocyte

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual ( P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA)

growth_protocol: Proliferating keratinocytes were grown in EpiLife medium containing HKGS+GA and used at 30-40% confluency. Cells induced to differentiate was at 80% confluency when switched to EpiLife medium (without rhEGF) supplemented with 1.5 mM CaCl2 for 4 days.

extract_protocol: Total RNA was isolated using TriReagent (Ambion).

treatment_protocol: Vehicle (ethanol), RA in ethanol or ddRA in ethanol was added to the cells (the final concentration of ethanol being 0.001%).

tag: primary cells

value: Keratinocytes

value: RA 4h


title: PBMo-derived macrophages stimulated with TE-8CM

source_name: Peripheral Blood Monocytes stimulated with 25 ng/ml M-CSF plus 50% conditioned media of TE8 human ESCC cell line


title: Primary colon tumor GIM04A

value: Primary colon tumor


title: HBL1 shBRD2 - 48 hours - mAdbID:124452

description: mAdb experiment ID: 124452

source_name: HBL1 shControl - 48 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 48 hours.

source_name: HBL1 shBRD2 - 48 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shBRD2. shRNA expression was induced with doxycycline for 48 hours.


title: HBL1 shBRD4 - 48 hours - mAdbID:124454

description: mAdb experiment ID: 124454

source_name: HBL1 shBRD4 - 48 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shBRD4. shRNA expression was induced with doxycycline for 48 hours.


title: PBMo-derived macrophages stimulated with TE-15CM

source_name: Peripheral Blood Monocytes stimulated with 25 ng/ml M-CSF plus 50% conditioned media of TE15 human ESCC cell line

value: male


title: Keratinocyte differentiating ddRA 24 h rep3

value: ddRA 24h


title: Keratinocyte differentiating vehicle 24 h rep3

value: vehicle 24h


title: Keratinocyte differentiating vehicle 24 h rep2


title: Keratinocyte proliferating ddRA 24 h rep3


title: Keratinocyte differentiating vehicle 4 h rep2

value: vehicle 4h


title: Keratinocyte differentiating ddRA 4 h rep3

value: ddRA 4h


title: Keratinocyte differentiating vehicle 4 h rep3


title: Keratinocyte differentiating RA 24 h rep1

value: RA 24h


title: Keratinocyte differentiating ddRA 4 h rep1


title: Keratinocyte differentiating RA 24 h rep2


title: Keratinocyte differentiating RA 24 h rep3


title: Keratinocyte differentiating ddRA 24 h rep2


title: Keratinocyte differentiating RA 4 h rep1


title: Keratinocyte differentiating ddRA 24 h rep1


title: Keratinocyte differentiating RA 4 h rep2


title: HBL1 shBRD2 - 24 hours - mAdbID:124451

description: mAdb experiment ID: 124451

source_name: HBL1 shBRD2 - 24 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shBRD2. shRNA expression was induced with doxycycline for 24 hours.


title: Keratinocyte differentiating vehicle 24 h rep1


title: Keratinocyte proliferating vehicle 24 h rep3


title: Keratinocyte differentiating vehicle 4 h rep1


title: Keratinocyte proliferating ddRA 24 h rep2


title: Keratinocyte proliferating vehicle 24 h rep2


title: Keratinocyte proliferating ddRA 4 h rep3


title: Keratinocyte proliferating RA 4 h rep3


title: Keratinocyte proliferating ddRA 4 h rep2


title: Keratinocyte proliferating RA 24 h rep1


title: Keratinocyte proliferating RA 4 h rep2


title: Keratinocyte proliferating vehicle 24 h rep1


title: Keratinocyte proliferating vehicle 4 h rep3


title: Keratinocyte proliferating RA 24 h rep2


title: Keratinocyte proliferating ddRA 4 h rep1


title: pTH9457_ME_8mer_7826

type: protein

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

label_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector, in most cases.  See paper supplemental web site (http://hugheslab.ccbr.utoronto.ca/supplementary-data/CisBP/) for exceptions.

tag: dbd

value: CXC

tag: platform_id_id design

value: ME

tag: dbd source organism


title: pTH9470_ME_8mer_7930

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.


title: Keratinocyte proliferating RA 24 h rep3


title: Keratinocyte proliferating vehicle 4 h rep2


title: pTH9450_HK_8mer_7855

value: HK


title: pTH9457_HK_8mer_7848


title: Keratinocyte proliferating RA 4 h rep1


title: pTH9450_ME_8mer_7810


title: pTH9449_HK_8mer_7854

value: WRKY


title: Keratinocyte proliferating vehicle 4 h rep1


title: pTH9470_HK_8mer_7959


title: pTH9449_ME_8mer_7655


title: pTH9447_HK_8mer_7790


title: pTH9447_ME_8mer_7584


title: pTH9446_HK_8mer_7853

source_name: DMRT1_HK design

value: DM


title: pTH9441_ME_8mer_7579


title: pTH9441_HK_8mer_7852


title: pTH9446_ME_8mer_7647

source_name: DMRT1_ME design


title: pTH9431_ME_8mer_7801

value: zf-Dof


title: pTH9439_HK_8mer_7791


title: pTH9420_ME_8mer_7561


title: pTH9439_ME_8mer_7577


title: pTH9430_HK_8mer_7850

value: GATA


title: pTH9432_HK_8mer_7851


title: pTH9430_ME_8mer_7571


title: pTH9419_HK_8mer_7634


title: pTH9419_ME_8mer_7560


title: pTH9424_ME_8mer_7565


title: pTH9420_HK_8mer_7635


title: pTH9431_HK_8mer_7701


title: pTH9410_ME_8mer_7547


title: pTH9410_HK_8mer_7633


title: pTH9424_HK_8mer_7636


title: pTH9432_ME_8mer_7573


title: pTH9393_ME_8mer_7824

source_name: CBG08311_ME design


title: Keratinocyte proliferating ddRA 24 h rep1


title: pTH9387_ME_8mer_6838

source_name: DMRTC2_ME design


title: pTH9383_HK_8mer_6940

source_name: PRKRIR_HK design

value: THAP


title: pTH9384_ME_8mer_6835

source_name: ARID3A_ME design

value: ARID


title: pTH9393_HK_8mer_7849

source_name: CBG08311_HK design


title: pTH9392_ME_8mer_7645

source_name: SPL11_ME design

value: SBP


title: pTH9382_HK_8mer_6939

source_name: ENSOANG00000014967_HK design


title: pTH9386_HK_8mer_6943

source_name: GCM1_HK design

value: GCM


title: pTH9384_HK_8mer_7958

source_name: ARID3A_HK design


title: pTH9392_HK_8mer_7856

source_name: SPL11_HK design


title: pTH9386_ME_8mer_6837

source_name: GCM1_ME design


title: pTH9382_ME_8mer_6833

source_name: ENSOANG00000014967_ME design


title: pTH9367_ME_8mer_6829

source_name: AAH82862_ME design

value: IRF


title: pTH9387_HK_8mer_6944

source_name: DMRTC2_HK design


title: pTH9385_ME_8mer_6836

source_name: RFX1_ME design


title: pTH9367_HK_8mer_6935

source_name: AAH82862_HK design


title: pTH9365_ME_8mer_6827

source_name: POU3F2_ME design

value: Pou,Homeobox


title: pTH9369_ME_8mer_6819

source_name: BRADI3G55950_ME design


title: pTH9380_ME_8mer_6831

source_name: estExt_fgeneshNG_pg.C_820014_ME design


title: pTH9381_HK_8mer_6938

source_name: nasonia_NCBI_hmm302924_HK design


title: pTH9383_ME_8mer_6963

source_name: PRKRIR_ME design


title: pTH9366_HK_8mer_6977

source_name: LIN54_HK design


title: pTH9357_ME_8mer_6742

source_name: ENSTRUG00000003586_ME design


title: pTH9381_ME_8mer_6832

source_name: nasonia_NCBI_hmm302924_ME design


title: pTH9346_ME_8mer_6882

source_name: HCAG_07413_ME design

value: KilA-N


title: pTH9369_HK_8mer_6859

source_name: BRADI3G55950_HK design


title: pTH9356_ME_8mer_6626

source_name: ENSCING00000003435_ME design

value: SAND


title: Keratinocyte differentiating ddRA 4 h rep2

source_name: keratinocyte

value: Keratinocytes

value: ddRA 4h


title: pTH9345_HK_8mer_6856

source_name: PASA_GEN_2600044_HK design

value: zf-CXXC


title: pTH9356_HK_8mer_6816

source_name: ENSCING00000003435_HK design


title: pTH9366_ME_8mer_6828

source_name: LIN54_ME design

value: CXC

value: ME


title: pTH9346_HK_8mer_6975

source_name: HCAG_07413_HK design

value: HK


title: pTH9385_HK_8mer_6942

source_name: RFX1_HK design


title: pTH9342_ME_8mer_6880

source_name: WUBG_18372T0_ME design


title: pTH9344_ME_8mer_6738

source_name: CJA05633_ME design

value: DM


title: pTH9341_ME_8mer_6736

source_name: GCM2_ME design


title: pTH9345_ME_8mer_6881

source_name: PASA_GEN_2600044_ME design


title: pTH9344_HK_8mer_6855

source_name: CJA05633_HK design


title: pTH9342_HK_8mer_6815

source_name: WUBG_18372T0_HK design


title: pTH9365_HK_8mer_6933

source_name: POU3F2_HK design


title: pTH9340_HK_8mer_6852

value: T-box


title: pTH9340_ME_8mer_6735


title: pTH9339_HK_8mer_6814


title: pTH9338_HK_8mer_6813

source_name: LOC_Os04g40930_HK design


title: pTH9335_ME_8mer_6732

source_name: PHF21A_ME design


title: pTH9311_HK_8mer_6946

source_name: NCU00392_HK design


title: pTH9341_HK_8mer_6853

source_name: GCM2_HK design


title: pTH9357_HK_8mer_6858

source_name: ENSTRUG00000003586_HK design


title: pTH9310_HK_8mer_6974

source_name: C11orf9_HK design


title: pTH9313_ME_8mer_6878

source_name: scaffold_301743.1_ME design

value: TCP


title: pTH9380_HK_8mer_6979

source_name: estExt_fgeneshNG_pg.C_820014_HK design


title: pTH9310_ME_8mer_7042

source_name: C11orf9_ME design


title: pTH9335_HK_8mer_6849

source_name: PHF21A_HK design


title: pTH9339_ME_8mer_6617


title: pTH9337_ME_8mer_6734

source_name: IRF9_ME design


title: pTH9338_ME_8mer_6879

source_name: LOC_Os04g40930_ME design


title: pTH9311_ME_8mer_6747

source_name: NCU00392_ME design


title: pTH9302_HK_8mer_6848

source_name: irf6.2_HK design


title: pTH9300_HK_8mer_7699

source_name: dmrta2_HK design


title: pTH9299_HK_8mer_6811

source_name: AAI23253_HK design


title: pTH9302_ME_8mer_6731

source_name: irf6.2_ME design


title: pTH9337_HK_8mer_6851

source_name: IRF9_HK design


title: pTH9300_ME_8mer_6876

source_name: dmrta2_ME design


title: pTH9299_ME_8mer_6723

source_name: AAI23253_ME design


title: pTH9298_HK_8mer_6810

source_name: AAH72195_HK design


title: pTH9313_HK_8mer_6812

source_name: scaffold_301743.1_HK design


title: pTH9298_ME_8mer_6611

source_name: AAH72195_ME design


title: pTH9297_ME_8mer_6722

source_name: AAH72060_ME design


title: pTH9297_HK_8mer_6809

source_name: AAH72060_HK design


title: pTH9296_ME_8mer_6721

source_name: WUBG_11979T0_ME design


title: pTH9296_HK_8mer_6846

source_name: WUBG_11979T0_HK design


title: pTH9291_ME_8mer_6718

source_name: E2F2_ME design


title: pTH9289_ME_8mer_6717

source_name: TBX2_ME design


title: pTH9289_HK_8mer_6802

source_name: TBX2_HK design


title: pTH9293_HK_8mer_6805

source_name: GSVIVG00007522001_HK design


title: pTH9295_HK_8mer_6807

source_name: GSVIVG00033765001_HK design


title: pTH9293_ME_8mer_6606

source_name: GSVIVG00007522001_ME design


title: pTH9290_HK_8mer_6803

source_name: POU2F3_HK design


title: pTH9295_ME_8mer_6720

source_name: GSVIVG00033765001_ME design


title: pTH9294_ME_8mer_6875

source_name: GSVIVG00027588001_ME design


title: pTH9294_HK_8mer_6806

source_name: GSVIVG00027588001_HK design


title: pTH9287_ME_8mer_6716

source_name: IRF9_ME design


title: pTH9288_HK_8mer_6801

source_name: E2F3_HK design


title: pTH9291_HK_8mer_6973

source_name: E2F2_HK design


title: pTH9285_HK_8mer_6798

source_name: CPRT0000009601_HK design


title: pTH9286_ME_8mer_6715


title: pTH9288_ME_8mer_6601

source_name: E2F3_ME design


title: pTH9287_HK_8mer_6800

source_name: IRF9_HK design


title: pTH9283_HK_8mer_6797

source_name: Gcm1_HK design


title: pTH9290_ME_8mer_6957

source_name: POU2F3_ME design


title: pTH9286_HK_8mer_6799


title: pTH9283_ME_8mer_6874

source_name: Gcm1_ME design


title: pTH9281_ME_8mer_6584

source_name: ppa000682m_ME design


title: pTH9285_ME_8mer_6714

source_name: CPRT0000009601_ME design


title: pTH9282_HK_8mer_6796

source_name: GMEB1_HK design


title: pTH9281_HK_8mer_6795

source_name: ppa000682m_HK design


title: pTH9280_ME_8mer_6583

source_name: B9GPL8_POPTR_ME design


title: pTH9282_ME_8mer_6585

source_name: GMEB1_ME design


title: pTH9280_HK_8mer_6794

source_name: B9GPL8_POPTR_HK design


title: pTH9279_HK_8mer_6793

source_name: ENSPPYG00000004736_HK design


title: pTH9279_ME_8mer_6712

source_name: ENSPPYG00000004736_ME design


title: pTH9277_HK_8mer_6791

source_name: ENSORLG00000007805_HK design


title: pTH9273_ME_8mer_6873

source_name: LOC_Os02g01380_ME design


title: pTH9277_ME_8mer_6580

source_name: ENSORLG00000007805_ME design


title: pTH9278_HK_8mer_6792

source_name: PHUM046580_HK design


title: pTH9278_ME_8mer_6581

source_name: PHUM046580_ME design


title: pTH9273_HK_8mer_6788

source_name: LOC_Os02g01380_HK design


title: pTH9274_ME_8mer_6577

source_name: OsI_08196_ME design


title: pTH9275_ME_8mer_6578

source_name: LCOR_ME design


title: pTH9275_HK_8mer_6790

source_name: LCOR_HK design


title: pTH9272_ME_8mer_6575

source_name: IRF5_ME design


title: pTH9271_ME_8mer_6574

source_name: ENSOANG00000013938_ME design


title: pTH9271_HK_8mer_6786

source_name: ENSOANG00000013938_HK design


title: pTH9274_HK_8mer_6789

source_name: OsI_08196_HK design


title: pTH9272_HK_8mer_6787

source_name: IRF5_HK design


title: pTH9269_ME_8mer_6572

source_name: RFX2_ME design


title: pTH9266_HK_8mer_6783

source_name: nasonia_NCBI_hmm1312624_HK design


title: pTH9267_ME_8mer_6708

source_name: e_gw1.5.76.1_ME design


title: pTH9262_ME_8mer_6565

source_name: GE12548_ME design


title: pTH9261_HK_8mer_6780

source_name: dmrt99B_HK design


title: pTH9261_ME_8mer_6704

source_name: dmrt99B_ME design


title: pTH9263_HK_8mer_6782

source_name: B5BV17_CHICK_HK design

value: RHD


title: pTH9267_HK_8mer_6972

source_name: e_gw1.5.76.1_HK design


title: pTH9269_HK_8mer_6785

source_name: RFX2_HK design


title: pTH9266_ME_8mer_6872

source_name: nasonia_NCBI_hmm1312624_ME design


title: pTH9260_ME_8mer_6703

source_name: Xrp1_ME design


title: pTH9263_ME_8mer_6705

source_name: B5BV17_CHICK_ME design


title: pTH9262_HK_8mer_6781

source_name: GE12548_HK design


title: pTH9259_ME_8mer_6562

source_name: GCM1_ME design


title: pTH9260_HK_8mer_6779

source_name: Xrp1_HK design


title: pTH9257_ME_8mer_6898

source_name: FBXL19_ME design


title: pTH9257_HK_8mer_6931

source_name: FBXL19_HK design


title: pTH9256_HK_8mer_6777

source_name: ENSDARG00000044872_HK design


title: pTH9256_ME_8mer_6700

source_name: ENSDARG00000044872_ME design


title: pTH9253_ME_8mer_6556

source_name: LCORL_ME design


title: pTH9254_HK_8mer_6776

source_name: phf21a_HK design


title: pTH9259_HK_8mer_6778

source_name: GCM1_HK design


title: pTH9253_HK_8mer_6869

source_name: LCORL_HK design


title: pTH9252_ME_8mer_6697


title: pTH9252_HK_8mer_6775


title: pTH9250_ME_8mer_6695

source_name: DMRTC2_ME design


title: pTH9250_HK_8mer_6774

source_name: DMRTC2_HK design


title: pTH9254_ME_8mer_6698

source_name: phf21a_ME design


title: pTH9249_HK_8mer_6868

source_name: RFX4_HK design


title: pTH9249_ME_8mer_6552

source_name: RFX4_ME design


title: pTH9247_ME_8mer_6693

source_name: CBN06605_ME design


title: pTH9246_HK_8mer_6772

source_name: Bm1_12445_HK design


title: pTH9247_HK_8mer_6773

source_name: CBN06605_HK design


title: pTH9245_HK_8mer_6867

source_name: estExt_fgenesh2_pg.C_80253_HK design


title: pTH9239_ME_8mer_6892

source_name: BGIBMGA012843_ME design


title: pTH9246_ME_8mer_6692

source_name: Bm1_12445_ME design


title: pTH9245_ME_8mer_6548

source_name: estExt_fgenesh2_pg.C_80253_ME design


title: pTH9239_HK_8mer_6928

source_name: BGIBMGA012843_HK design


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source_name: BRADI5G22430_HK design


title: pTH9241_HK_8mer_6643

source_name: BRADI1G55710_HK design


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source_name: BRADI1G55710_ME design


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source_name: BRADI5G22430_ME design


title: pTH9236_ME_8mer_6685

source_name: stuA_ME design


title: pTH9237_HK_8mer_6770

source_name: CADATEAP00000246_HK design


title: pTH9238_HK_8mer_6970

source_name: BGIBMGA008956_HK design


title: pTH9235_ME_8mer_6538


title: pTH9236_HK_8mer_6769

source_name: stuA_HK design


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source_name: CADATEAP00000246_ME design


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source_name: BGIBMGA008956_ME design


title: pTH9233_HK_8mer_6767


title: pTH9235_HK_8mer_6642


title: pTH9232_ME_8mer_6535


title: pTH9234_ME_8mer_6537

value: NAM


title: pTH9234_HK_8mer_6768


title: pTH9232_HK_8mer_6639


title: pTH9233_ME_8mer_6536


title: pTH9231_HK_8mer_6638


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title: pTH9230_ME_8mer_6870


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title: pTH9222_HK_8mer_6763

source_name: PHF21A_HK design


title: pTH9225_ME_8mer_6528

source_name: amel4_ncbi_hmm42917_ME design


title: pTH9228_HK_8mer_6635


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source_name: amel4_ncbi_hmm7004_ME design


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title: pTH9227_ME_8mer_6530


title: pTH9223_ME_8mer_6526

source_name: RFX1_ME design


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source_name: PHF21A_ME design


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source_name: RFX1_HK design


title: pTH9226_HK_8mer_6765

source_name: amel4_ncbi_hmm7004_HK design


title: pTH9221_HK_8mer_7698

source_name: E2F2_HK design


title: pTH9213_HK_8mer_7697

source_name: Minc10479_HK design


title: pTH9214_HK_8mer_6656

source_name: ARID3A_HK design

value: ARID


title: pTH9220_HK_8mer_6628

source_name: LCOR_HK design


title: pTH9219_ME_8mer_6522

source_name: GMEB2_ME design


title: pTH9215_HK_8mer_6762


title: pTH9220_ME_8mer_6523

source_name: LCOR_ME design


title: pTH9225_HK_8mer_6633

source_name: amel4_ncbi_hmm42917_HK design


title: pTH9214_ME_8mer_6517

source_name: ARID3A_ME design


title: pTH9216_HK_8mer_6658

source_name: Ame_R001268_HK design


title: pTH9212_ME_8mer_6887

source_name: KDM2A_ME design


title: pTH9215_ME_8mer_6518


title: pTH9221_ME_8mer_6524

source_name: E2F2_ME design


title: pTH9213_ME_8mer_6516

source_name: Minc10479_ME design


title: pTH9219_HK_8mer_6659

source_name: GMEB2_HK design


title: pTH9216_ME_8mer_6519

source_name: Ame_R001268_ME design


title: pTH9212_HK_8mer_6926

source_name: KDM2A_HK design


title: pTH9211_ME_8mer_6514


title: pTH9211_HK_8mer_6654


title: pTH9229_HK_8mer_6636


title: pTH9210_HK_8mer_6653

source_name: IRF6_HK design


title: pTH9209_ME_8mer_6512

source_name: Medtr8g106590.1_ME design


title: pTH9210_ME_8mer_6513

source_name: IRF6_ME design


title: pTH9208_ME_8mer_6511

source_name: Medtr3g103160.1_ME design


title: pTH9208_HK_8mer_6651

source_name: Medtr3g103160.1_HK design


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