title: KSL_Pz

city: Tsu

first: Tetsuya

last: Nosaka

address: 2-174 Edobashi

department: Department of Microbiology and Molecular Genetics

institute: Mie University Graduate School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Plzf/GFP-transduced KSL cells

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Culture in alpha MEM supplemented with 20% FBS, SCF, TPO, IL-6, and FLT3 ligand

extract_protocol: Total RNA was extracted from the sorted cells with Tri Reagent LS (Molecular Research Center), followed by purification using RNeasy Mini Kit (QIAGEN).

value: Bone marrow

tag: cell type

value: hematopoietic stem-progenitor cells (HSPCs)


title: MP_Pz

status: Public on Apr 26 2017

type: RNA

country: Japan

molecule: total RNA

organism: Mus musculus

source_name: Plzf/GFP-transduced MP cells

treatment_protocol: not applicable

tag: strain

tag: tissue


title: Patient_OSCC_OC2118

city: Navi Mumbai

first: Manoj

middle: Balkrishna

last: Mahimkar

state: Maharashtra

address: Sector-22, Owe Village, Kharghar Node

country: India

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

description: Oral Tumor Tissue

hyb_protocol: 1.65 µg of labeled cRNA sample were fragmented at 60ºC and hybridized on to microarray slides. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies; 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Scanned using an Agilent Scanner (Agilent Technologies, G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

organism: Homo sapiens

source_name: Oral Tumor Tissue

label_protocol: 500ng of samples were labeled with fluorochromes Cy3 using Agilent Quick-Amp labeling Kit (Agilent Technologies, 5190-0442). Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000

extract_protocol: RNA was extracted using AllPrep® DNA/RNA/miRNA Universal kit, QIAGEN. RNA quantification was performed on Nanodrop-1000 spectrophotometer (Thermo Scientific: 1000). The RNA integrity was evaluated using Agilent RNA 6000 Nano Chip, Bioanalyzer (Agilent: 2100)

treatment_protocol: Freshly collected oral tissues from oral leukoplakia, oral cancer patients and healty indivduals were kept at -80°C till RNA was extracted.

tag: age

tag: gender

value: Male

tag: site

value: Gingivobuccal complex

tag: Stage


title: Genomic DNA from patient 570 [570N]

type: genomic

city: Dunedin

first: Parry

last: Guilford

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: Colon biopsy

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray reader using standard recommended Illumina scanner setting

data_processing: Beadstudio software v1.8

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Colon biopsy sample 570

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from fresh frozen tissue using Quick-gDNA miniPrep kit (Zymo Research) according to standard instructions

value: M

tag: disease state

value: Normal

tag: colon subdivision

value: Ascending


title: Patient_OSCC_OC2112

description: Oral Tumor Tissue


title: Patient_OSCC_OC2052

description: Oral Tumor Tissue


title: Patient_OSCC_OC2122

description: Oral Tumor Tissue

value: Female


title: Patient_OSCC_OC 2213

description: Oral Tumor Tissue


title: Genomic DNA from patient 535 [535N]

description: Colon biopsy

source_name: Colon biopsy sample 535

value: F

value: Hepatic flexure


title: Patient_OSCC_OC 1869

description: Oral Tumor Tissue


title: Patient_OSCC_OC2102

description: Oral Tumor Tissue


title: Patient_OSCC_OC2048

description: Oral Tumor Tissue


title: Patient_OSCC_OC 2214

description: Oral Tumor Tissue


title: Patient_OSCC_OC 1823

description: Oral Tumor Tissue


title: Patient_OSCC_OC 1646

description: Oral Tumor Tissue


title: Patient_OSCC_OC 1629

description: Oral Tumor Tissue


title: MP_G

source_name: GFP-transduced MP cells


title: Genomic DNA from patient 539 [539N]

description: Colon biopsy

source_name: Colon biopsy sample 539


title: KSL_G

source_name: GFP-transduced KSL cells


title: Genomic DNA from patient 370 [370N]

description: Colon biopsy

source_name: Colon biopsy sample 370


title: Patient_OSCC_OC 1716

description: Oral Tumor Tissue


title: Genomic DNA from patient 429 [429N]

description: Colon biopsy

source_name: Colon biopsy sample 429

value: Transverse


title: Genomic DNA from patient 543 [543N]

description: Colon biopsy

source_name: Colon biopsy sample 543

value: Caecum


title: Genomic DNA from patient 436 [436N]

description: Colon biopsy

source_name: Colon biopsy sample 436

value: Sigmoid


title: Genomic DNA from patient 517 [517N]

description: Colon biopsy

source_name: Colon biopsy sample 517


title: Patient_OSCC_OC 2176

description: Oral Tumor Tissue


title: Genomic DNA from patient 617 [617N]

description: Colon biopsy

source_name: Colon biopsy sample 617


title: Patient_OSCC_OC2112

description: Biological replicate

hyb_protocol: 4.5 µg of purified labelled samples was mixed with human Cot-1 DNA, and denatured at 95°C (Oligo aCGH hybridization kit, Agilent Technologies, 5188-5380). The mixture was applied to Agilent microarrays slides and hybridization was performed at 65°C for 40 hours. After hybridization, the microarrays were washed with Oligo aCGH wash buffer followed by drying of slides.

data_processing: Image Analysis was performed using Agilent feature extraction software version 11.5 and Linear Normalization

source_name: Male_Pooled_Cy3 control

label_protocol: 1.5µg of tumor and pooled gender-matched reference DNA were labeled with fluorochromes Cy3 and Cy5, respectively using Agilent Sure tag DNA labeling kit (Agilent Technologies, 5190-3400). Labeled samples were purified using the genomic DNA purification module (Agilent Technologies).

extract_protocol: DNA was extracted using AllPrep® DNA/RNA/miRNA Universal kit, QIAGEN. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.

treatment_protocol: Freshly collected oral tissues from oral leukoplakia and oral cancer patients were kept at -80°C till DNA was extracted.  Peripheral blood lymhocytes from healthy donors were processed immediately for DNA extraction.

value: Peripheral Blood

value: Lymphocytes

tag: diagnosis

value: Oral Squamous Cell Carcinoma (OSCC)

value: Oral


title: Patient_OSCC_OC2118

description: Biological replicate


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep2 [Primed-CB-hPSC#1P9]

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

label: biotin

growth_protocol: Human induced pluripotent stem cells were cultured on Matrigel [BD Biosciences] in MEF conditioned medium (MEF-CM) supplemented with 8 ng/ml bFGF [Invitrogen] or maintained on irradiated feeder MEFs (iMEFs) with hPSC medium (DMEM/F12 [Gibco] with 20% Knockout Serum Replacement [Gibco], 100 mM b-mercaptoethanol, 100 mM nonessential amino acid [Gibco], 1 mM L-glutamine [Gibco], and 10 ng/ml bFGF, as previously described (Werbowetski-Ogilvie et al., 2009). Cells were routinely passaged every 5-7 days by mechanical transfer using 1 mg/ml Collagenase IV [Invitrogen]. For the derivation of naïve hPSCs, cells in primed pluripotent states were switched into hPSC medium supplemented with 1 mM MEK inhibitor PD0325901, 3 mM GSK3 inhibitor CHIR99021, and 10 ng/ml LIF (abbreviated LIF/2i) as previously reported (Buecker et al., 2010; Hanna et al., 2010; Li et al., 2009) or de novo reprogramming of somatic cells in naïve conditions. We also established naïve hPSCs using 10 ng/ml LIF and a combination of inhibitors for MEK/ERK (1 mM PD0325901), GSK3 (0.3 mM CHIR99021), LCF/SRC (1 mM WH-4-023), BRAF (0.5 mM SB590885) and ROCK (10 mM Y-27632) (5i)(Theunissen et al., 2014). Emerging colonies with a mESC-like morphology (appeared after 10-20 days of culture) were individually picked and subcultured by trypsinization or mechanical passaging onto feeder-free Matrigel or iMEFs with LIF/2i

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.


title: iPSCs derived from human adult dermal fibroblasts, biological rep3 [Primed-Fib-hPSC#3P11]

source_name: iPSCs derived from human adult fibroblasts

label_protocol: In accordance with manufacturer's protocols


title: Patient_OSCC_OC1716

description: Biological replicate


title: Patient_OSCC_OC 1760

description: Oral Tumor Tissue


title: Genomic DNA from patient 458 [458N]

description: Colon biopsy

source_name: Colon biopsy sample 458


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep3 [Primed-CB-hPSC#1P11]


title: Patient_OSCC_OC2213

description: Biological replicate


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep3 [Primed-CB-hPSC#2P11]


title: Patient_OSCC_OC1823

description: Biological replicate


title: Patient_OSCC_OC2102

description: Biological replicate


title: Patient_OSCC_OC2192

description: Biological replicate


title: iPSCs derived from human adult dermal fibroblasts, biological rep3 [Naive-Fib-hPSC#3 P4/8]

value: iPSCs derived from human adult fibroblasts


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep2 [Primed-CB-hPSC#2P9]


title: Patient_OSCC_OC 2215

description: Oral Tumor Tissue


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep1 [Primed-CB-hPSC#1P10]


title: Patient_OSCC_OC2214

description: Biological replicate

source_name: Female_Pooled_Cy3 control


title: iPSCs derived from human adult dermal fibroblasts, biological rep2 [Primed-Fib-hPSC#3P9]


title: iPSCs derived from human adult dermal fibroblasts, biological rep1 [Primed-Fib-hPSC#3P10]


title: Patient_OSCC_OC1760

description: Biological replicate


title: Patient_OSCC_OC1869

description: Biological replicate


title: Patient_OSCC_OC 2192

description: Oral Tumor Tissue


title: Patient_OSCC_OC2215

description: Biological replicate


title: iPSCs derived from human adult dermal fibroblasts, biological rep2 [Naive-Fib-hPSC#3 P4/7]


title: Patient_OSCC_OC2184

description: Biological replicate


title: Patient_OSCC_OC1646

description: Biological replicate


title: Patient_OSCC_OC2176

description: Biological replicate


title: Patient_OSCC_OC2048

description: Biological replicate


title: Patient_OSCC_OC2109

description: Biological replicate


title: Patient_OSCC_OC2052

description: Biological replicate


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep3 [Naive-CB-hPSC#1 P4/8]


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep1 [Naive-CB-hPSC#2 P7/6]


title: iPSCs derived from human adult dermal fibroblasts, biological rep1 [Naive-Fib-hPSC#3 P4/6]


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep2 [Naive-CB-hPSC#1 P4/7]


title: Patient_OSCC_OC1891

description: Biological replicate


title: Patient_OSCC_OC1986

description: Biological replicate


title: Patient_OSCC_OC1910

description: Biological replicate


title: Patient_OSCC_OC1896

description: Biological replicate


title: Patient_OSCC_OC1947

description: Biological replicate


title: Patient_OSCC_OC2185

description: Biological replicate


title: Patient_OSCC_OC1984

description: Biological replicate


title: iPSCs derived from mouse adult dermal fibroblasts, biological rep2

source_name: iPSCs derived from mouse embryonic fibroblasts

growth_protocol: Mouse PSC were cultured in primed conditions using MEF-CM + 8ng/ml bFGF on feeders or matrigel and were also cultured I naïve conditions using DMEM %15FBS 1xNEAA 1xL-Glu 1xNa-Pyr 55uMB-Merc and 1000U/ml ESGRO LIF

value: Primed-mPSC


title: Patient_OSCC_OC1983

description: Biological replicate

value: Male


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep1 [Primed-CB-hPSC#2P10]


title: Patient_OSCC_OC1844

description: Biological replicate

value: Gingivobuccal complex


title: Patient_OSCC_OC1965

description: Biological replicate


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep2 [Naive-CB-hPSC#2 P7/7]


title: Patient_OSCC_OC2122

description: Biological replicate


title: Patient_OSCC_OC1914

description: Biological replicate


title: Patient_OSCC_OC1845

description: Biological replicate


title: Patient_OSCC_OC1846

description: Biological replicate


title: Patient_OSCC_OC1932

description: Biological replicate


title: Patient_OSCC_OC1843

description: Biological replicate


title: iPSCs derived from mouse adult dermal fibroblasts, biological rep1


title: iPSCs derived from mouse adult dermal fibroblasts, biological rep3


title: Patient_OSCC_OC1587

description: Biological replicate


title: iPSCs derived from mouse embryonic fibroblasts in naïve culture condition, biological rep3

value: Naive-mPSC


title: Patient_OSCC_OC1698

description: Biological replicate


title: iPSCs derived from mouse embryonic fibroblasts in naïve culture condition, biological rep2


title: iPSCs derived from mouse embryonic fibroblasts in naïve culture condition, biological rep1


title: Patient_OSCC_OC1313

description: Biological replicate


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep3 [Naive-CB-hPSC#2 P7/8]


title: Patient_OPL_OC1884

description: Biological replicate

value: Oral leukoplakia

value: Oral Precancer


title: Patient_OSCC_OC1791

description: Biological replicate


title: Patient_OPL_OC1952

description: Biological replicate


title: Patient_OPL_OC1435

description: Biological replicate


title: Patient_OPL_OC1377

description: Biological replicate

source_name: Female_pool_Cy3 control

value: Female


title: Patient_OPL_OC1445

description: Biological replicate


title: Sample 32_YJ_mbd7-5_MBD7-3xHA

type: SRA

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

country: USA

institute: The Salk Institute for Biological Studies

description: please note that 'ABI 3730XL DNA Analyzer' is the actual model (not the AB 5500 Genetic Analyzer)

library_source: genomic

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: Illumina sequence reads were filtered to remove duplicate reads either with prinseq [71], using the remove exact duplicates option (-derep 1), or the BSseeker2[72] filterReads.py script, using default conditions.  The reads were then mapped to the YJ or LUCH transgene sequences (LUC_transgene6.fa or LUC_transgene7.fa) using bsmap-2.74 [73] with the default parameters, allowing 2 mismatches (-v 2) and allowing uniquely mapping reads and multi-mapping reads with the maximum number of equal best hits set to 2 (-w 2). In addition, the reads were also mapped to the tair10 genome using the BSseeker2 bs_seeker2-align.py script, using the bowtie1 aligner (version bowtie-1.0.0)[74] and allowing for 2 mismatches (-m 2).
Methylation levels: The percent methylation level at each cytosine was calculated using the BSseeker2 bs_seeker2-call_methylation.py script requiring a minimum coverage of 4 reads (-r 4) for mapping to the Tair10 genome or the bsmap methratio.py script, reporting loci with zero methylation ratios (-z) for the YJ and LUCH transgenes. In house scripts were used to convert the resulting .CGmap or .txt files, respectively, into wiggle files containing the percent methylation levels of cytosines covered by at least 4 reads in the CG, CHG, and CHH contexts individually.
DMR calling: DMRs were identified using parameters outlined in Stroud et al. [54] using in house scripts. Briefly, the genome was split into 100bp, non-overlapping bins and the methylation level across each bin in the CG, CHG, or CHH context was calculated independently using the percent methylation values in the wiggle files. The methylation values in each bin were then compared between two samples to call DMRs with the following requirements: (1) To account for 100bp regions of the genome with low numbers of cytosines and for regions that display lower than average coverage, only bins with at least 4 cytosines in the given context that are covered by at least 4 reads in both samples being compared were included in the DMR analysis.  (2) Only bins with an absolute change in methylation of 0.4, 0.2, and 0.1 for the CG, CHG, and CHH contexts, respectively, and with an adjusted p-value of ≤0.01 were identified as DMRs.
Genome_build: TAIR10; LUC_Transgene6.fa; LUC_Transgene7.fa
Supplementary_files_format_and_content: wiggle (.wig) file, header with Chromosome, and two columns: position, % methylation
Supplementary_files_format_and_content: bed file, which has 3 columns:Chr#, start position, end position

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis seeds were surface-sterilized and then planted on either half-strength Murashige and Skoog (MS) media supplemented with 8% agar and 1% sucrose or Linsmaier and Skoog (LS) media (Caissen, LSP03) supplemented with 8% agar. Seed were then stratified at 4°C for three days. Plants were grown in a growth incubator at 23°C under either continuous light or short day conditions (8 hrs light, 16 hrs dark). 10-day-old seedlings were used for all of the experiments.

extract_protocol:
For the MethylC-seq libraries corresponding to the “_r2, _r5, and_B” series (Table S4), genomic DNA was extracted using the DNeasy Plant Mini  Kit (Qiagen, Cat# 69104). One microgram of genomic DNA was sonicated into  fragments 150 to 300 bp in length using a Diagenode Bioruptor, followed by purification with the PureLink PCR Purification Kit (Invitrogen, Cat#  K3100-01). For all the remaining MethylC-seq libraries (Table S4), genomic  DNA was extracted from 10-day-old seedlings using the DNeasy Plant Mini Kit  (Qiagen, Cat# 69104). 2 ug of genomic DNA was sonicated into 200 bp fragments using a Covaris S2 Sonicator, followed by purification with Sera-Mag Magnetic SpeedBeads (ThermoScientific, Cat# 65152105050250)."
For the MethylC-seq libraries corresponding to the '_r2, _r5, and_B' series  (Table S4), the sonicated and purified genomic DNA fragments were repaired using the End-It DNA End-Repair Kit (Epicentre, Cat# ER0720), and the DNA fragments were purified using the Agencourt AMPure XP-PCR Purification system (Beckman Coulter, Cat# A63880). The purified DNAs were adenylated at the 3? end using the polymerase activity of Klenow Fragment (3?"5? exo-) (New England Biolabs, Cat# M0212), followed by purification using the Agencourt AMPure XP-PCR Purification system. The methylated adapters in the TruSeq DNA Sample Preparation Kit (Illumina, Cat# FC-121-2001) were ligated to the DNA fragments using T4 DNA Ligase (New England Biolabs, Cat# M0202). After purification using AMPure XP beads, less than 400 ng DNA was subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, Cat# MECOV-50). PfuTurbo Cx Hotstart DNA polymerase (Agilent, Cat# 600414) and the following PCR conditions were used for amplification: 95°C for 2 minutes; 9 cycles of 98°C for 15 seconds, 60°C for 30 seconds and 72°C for 4 minutes; and 72°C for 10 minutes. The resulting libraries were quantified, pooled and sequenced using HiSeq 2000 with the 101-cycle single-end sequencing mode (Illumina). For all the remaining MethylC-seq libraries (Table S4), the sonicated and purified genomic DNA fragments were repaired using the End-It DNA End-It DNA End-Repair Kit (Epicentre, Cat# ER81050), and the DNA fragments were purified using Sera-Mag Magnetic SpeedBeads. The purified DNAs were adenylated at the 3? end using the polymerase activity of Klenow Fragment (3?"5? exo-) (New England Biolabs, Cat# M0212), followed by purification using Sera-Mag Magnetic SpeedBeads. The methylated adapters in the NEXTflex Bisulfite-Seq Barcodes Kit (BIOO Scientific, Cat# 511911) were ligated to the DNA fragments using T4 DNA Ligase (New England Biolabs, Cat# M0202). After purification using Sera-Mag Magnetic SpeedBeads, the DNA was subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, Cat# MECOV-50). KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (KAPA Biosystems, Cat# KK2801) and the following PCR conditions were used for amplification: 95°C for 2 minutes; 98°C for 30 seconds; 4 cycles of 98°C for 15 seconds, 60°C for 30 seconds and 72°C for 4 minutes; and 72°C for 10 minutes. After purification using Sera-Mag Magnetic SpeedBeads, the libraries were quantified, pooled and sequenced at single-end 50 base-pair using the Illumina HiSeq 2500 v4 at the Salk NGS Core. Raw sequencing data was de-multiplexed and converted into FASTQ files using CASAVA (v1.8.2)

tag: ecotype

value: Columbia

value: ten-day-old seedlings

tag: genotype/variation

value: YJ_rdr6-11_mbd7-5 + MBD7-3xHA


title: Sample 24_colYJ_rep_2


title: Patient_OPL_OC1358

description: Biological replicate


title: Sample 29_YJ_rdd


title: Patient_OPL_OC2299

description: Biological replicate


title: Patient_OPL_OC1669

description: Biological replicate


title: Patient_OPL_OC2300

description: Biological replicate


title: Patient_OPL_OC2201

description: Biological replicate


title: Patient_OPL_OC1348

description: Biological replicate


title: Sample 31_YJ_mbd7-5


title: Patient_OPL_OC2209

description: Biological replicate


title: Patient_OPL_OC2202

description: Biological replicate


title: Patient_OPL_OC2061

description: Biological replicate

source_name: Male_pooled_Cy3 control


title: Patient_OPL_OC1560

description: Biological replicate


title: Patient_OPL_OC2303

description: Biological replicate


title: Patient_OPL_OC1565

description: Biological replicate


title: Patient_OPL_OC2203

description: Biological replicate


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep1 [Naive-CB-hPSC#1 P4/6]


title: Sample 26_YJ_mbd7-4


title: Patient_OPL_OC2293

description: Biological replicate


title: Sample 28_YJ_nrpe1


title: Patient_OPL_OC2204

description: Biological replicate


title: Patient_OPL_OC2067

description: Biological replicate


title: Sample 27_YJ_ago4


title: Patient_OPL_OC1566

description: Biological replicate


title: Follicular_Fluid_rep6

status: Public on Apr 25 2017

city: Catania

first: Cinzia

last: Di Pietro

address: via S.Sofia 87

department: Department of Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

description: Test

data_processing:
MiRNA expression profiles were analyzed using real-time RQ Manager software v1.2 (Applied Biosystems).  Statistically significant miRNA differences were identified by Significance of Microarrays Analysis (SAM). MiRNA expression changes were calculated by applying the 2−ΔΔCT method and using the average Ct of each plate as endogenous controls.
DCt means of FF and oocytes were used to determine DDCt; oocytes were chosen as Calibrator. miRNA expression levels are reported as the natural logarithm of RQ values

label: FAM

source_name: Human Follicular Fluid

extract_protocol: Total RNA was isolated from fluids using the Qiagen miRNeasy Mini Kit (Qiagen GmbH). For RNA isolation from single oocyte see previous published protocols (PMID: 18765004)

value: Human Follicular Fluid

tag: maturation stage

value: Follicular Fluid sample containing nuclear mature oocytes (metaphase II)

tag: patients

value: Women undergone to ovarian stimulation for ICSI


title: Follicular_Fluid_rep2

description: Test


title: Oocyte_rep1

description: Control

source_name: Human MII Oocyte

value: Human MII Oocyte

value: Metaphase II


title: Oocyte_rep2

description: Control


title: Follicular_Fluid_rep5

description: Test


title: Follicular_Fluid_rep4

description: Test


title: Oocyte_rep4

description: Control


title: Oocyte_rep6

description: Control


title: Oocyte_rep5

description: Control


title: Follicular_Fluid_rep1

description: Test


title: Oocyte_rep3

description: Control


title: Sample 30_LerYJ

source_name: LerYJ


title: 500 mGy: PN1: MB-22

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

institute: National Institute of Radiological Sciences

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 40 hours at 65°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 (Protocol v.7.1) in an ozone-depleted hood.

scan_protocol: The slides were scanned in an Agilent DNA Microarray scanner (G2565CA)

data_processing: Agilent Feature Extraction Software (10.7.3.1) was used for computing ratios

source_name: Medulloblastoma

label_protocol: 300 ng of RNase-treated DNA (test or reference) was labelled using the Agilent SureTag DNA labeling kit (Protocol v.7.1), following all instructions for a 8x60K array.

extract_protocol: DNA was extracted from frozen medulloblastoma tissue and ear skin tissue using a Maxwell 16 Tissue DNA Purification Kit on a Maxwell 16 Instrument (Promega)

treatment_protocol: A portion of each medulloblastoma tumour mass taken at autopsy, and normal ear tissue were snap-frozen in liquid nitrogen before long-term storage at -80°C.

tag: developmental stage

value: Medulloblastoma

value: C3H/HeNcrlCrlj x B6.129-Ptch1tm1Zim/Cnrm (F1)

tag: Sex

source_name: Ear

value: Ear


title: 500 mGy: PN1-4: MB-19


title: 500 mGy: PN1: MB-17


title: Spontaneous: MB-28


title: 500 mGy: PN1: MB-19

value: Male


title: Patient_OPL_OC1555

description: Biological replicate

value: Peripheral Blood

value: Lymphocytes

value: Oral

value: Gingivobuccal complex


title: Patient_OSCC_OC1629

description: Biological replicate

value: Oral Squamous Cell Carcinoma (OSCC)

value: Female


title: Sample 25_YJ_lil-1_rep_2

value: Columbia

value: ten-day-old seedlings


title: Follicular_Fluid_rep3

description: Test

value: Human Follicular Fluid


title: Patient_OPL_OC2199

description: Biological replicate

value: Oral leukoplakia

value: Oral Precancer


title: TC71 treated with MG-262 rep 1

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

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

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
affymetrix-progid = GeneChip.CallGEBaseCall.1
program-name = Expression Console
program-id = 1.4.1.46

source_name: TC71 treated with MG-262

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

growth_protocol: Cells were grown in RPMI + 10% FBS

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

treatment_protocol: Cells were treated with drug for 6 hours.  Performed in triplicate.

tag: cell line

value: EWSR1 fusion positive Ewing sarcoma cell line

tag: treated with


title: TC71 treated with DMSO

source_name: TC71 treated with DMSO

tag: cell type

value: DMSO


title: TC71 treated with Bortezomib rep 3

source_name: TC71 treated with Bortezomib

value: Bortezomib


title: TC71 treated with MG-262 rep 3


title: TC71 treated with Bortezomib rep 2


title: TC71 treated with Bortezomib rep 1


title: TC71 treated with MG-262 rep 2


title: TC71 treated with EWS-W rep 3

source_name: TC71 treated with EWS-W

value: EWS-W


title: TC71 treated with EWS-W rep 1


title: CHP100 treated with DMSO

source_name: CHP100 treated with DMSO


title: TC71 treated with EWS-W rep 2


title: TC71 treated with EWS-P rep 2

source_name: TC71 treated with EWS-P

value: EWS-P


title: CHP100 treated with MG-262 rep 1

source_name: CHP100 treated with MG-262


title: CHP100 treated with MG-262 rep 3


title: CHP100 treated with MG-262 rep 2


title: TC71 treated with EWS-P rep 1


title: CHP100 treated with Bortezomib rep 3

source_name: CHP100 treated with Bortezomib


title: TC71 treated with EWS-P rep 3


title: CHP100 treated with Bortezomib rep 2


title: CHP100 treated with Bortezomib rep 1


title: CHP100 treated with EWS-W rep 1

source_name: CHP100 treated with EWS-W


title: CHP100 treated with EWS-W rep 3


title: CHP100 treated with EWS-W rep 2


title: CHP100 treated with EWS-P rep 2

source_name: CHP100 treated with EWS-P


title: MS2 B

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
Replicate 2
9286492017_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalization GenomeStudio V2011.1, Gene Expression version 1.9.0.

source_name: HCT116 cells

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

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

tag: shRNA

value: shCtrl


title: CHP100 treated with EWS-P rep 3


title: MUT_h3.3kd/+_1

city: Singapore

first: Heike

last: Wollmann

address: 61 Biopolis Drive

country: Singapore

institute: IMCB

hyb_protocol: According to Affymetrix GeneChip protocol.

data_processing: Affymetrix® Expression Console™ Software, default settings.

label: Biotin

source_name: 10 day seedlings, h3.3kd/+

growth_protocol: Sterilized seeds were grown on 1 x MS medium with glucose at long day conditions in a Percival incubator for 10 days.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen).

value: h3.3kd/+ (htr4;htr8;amiRHTR5-II/+)

tag: tissue

value: seedling

tag: age

value: 10 days


title: MS2 C

description:
Replicate 3
9286492017_F


title: MS4 C

description:
Replicate 3
9286492017_L


title: MUT_h3.3kd_1

scan_protocol: According to Affymetrix GeneChip protocol.

source_name: 10 day seedlings, h3.3kd

value: h3.3kd (htr4;htr8;amiRHTR5-II)


title: MUT_h3.3kd/+_2

label_protocol: According to Affymetrix GeneChip protocol.


title: WT_Col-0_2

source_name: 10 day seedlings, WT

value: wildtype


title: MUT_h3.3kd_2


title: MS4 A

description:
Replicate 1
9286492017_J


title: WT_Col-0_1


title: 141 persistent atrial fibrillation

city: Yufu

first: Masaki

last: Morishima

state: Oita

address: 1-1 Idaigaoka Hasama

department: Pathophysiology

institute: Oita University School of Medicine

description: MicroRNA expression in human atrial cardiomyocytes with persistent atrial fibrillation

hyb_protocol: MicroRNA expression were hybridized with a miRNA labelling and hybridization kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with a laser confocal scanner (g2565BA, Agilent Technologies) according to the manufecturer's instructions. The intensity of fluorescence were calculated by use of Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The further processed data on the Series record is explained as: We used a miRNA microarray platform, covering a total of 1205 human miRNAs, to compare the expression profiles of miRNAs in atrial myocardia from 9 individuals with persistent atrial fibrillation with those from 11 normal sinus rhythm individuals. The microarray data for miRNA profiles were processed and analyzed with GeneSpring GX software, version 11.5 (Agilent Technologies). Raw data were transformed by setting values <1.0.  Of the total 1205 miRNAs studied, 355 were selected after filtering with an algorithm based on raw signal intensity (>20.0), finally yielding 39 miRNAs that were filtered by Welch's t-test (P<0.05).

source_name: atrial cardiomyocytes

label_protocol: Total RNA was labeled with Cy3 with a miRNA and hybridization kit (Agilent Technologies, Santa Clara, CA, USA) followed by procedures with the Human miRNA Microarray (8x60K, ID31181, miRBase release 16.0, Agilent Technologies).

extract_protocol: Total RNA was prepared using the Trizol reagent (Life technology) following the manufacturer's recommendations. Briefly, after homogenizing the sample with TRIzol® Reagent, chloroform is added, and the homogenate is allowed to separate into a clear upper aqueous layer (containing RNA), an interphase, and a red lower organic layer (containing the DNA and proteins). RNA is precipitated from the aqueous layer with isopropanol. The precipitated RNA is washed to remove impurities, and then resuspended for use in downstream applications.

treatment_protocol: Human right atrial appendage were obtained from patients undergoing open-heart surgery at Oita University Hospital. Tissue samples were immediately frozen in liquid nitrogen, and then stored in a deep freezer at -80°C.  The use of tissue samples for all experiments was approved by all the patients in documents and by Oita University Ethics Committee.

value: right atrial appendage

tag: gender

value: male

tag: histroy of atrial fibrillation

value: patients with documented record of sustained AF for 6 months or longer


title: MS4 B

description:
Replicate 2
9286492017_K


title: 129 persistent atrial fibrillation


title: 260 persistent atrial fibrillation


title: 226 persistent atrial fibrillation


title: 82 persistent atrial fibrillation


title: 231 persistent atrial fibrillation


title: 194 persistent atrial fibrillation


title: 106 persistent atrial fibrillation


title: 221 persistent atrial fibrillation


title: 38 persistent atrial fibrillation


title: 174 normal sinus ryhthm

description: MicroRNA expression in human atrial cardiomyocytes with normal sinus rhythm

value: patients with no documented history of AF.


title: BG2 Young 1

status: Public on Apr 24 2017

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Candida_glabrata reference build Ensemble_R31 (ASM254v2.31) with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.  All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR  and TMM normalized to adjust for differences in library size.  Genes or transcripts not expressed in any sample were excluded from further analysis.
Genome_build: Candida_glabrata reference build Ensemble_R31 (ASM254v2.31)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each or all samples.

organism: Nakaseomyces glabratus

source_name: BG2_young_whole cell

growth_protocol: Comparable number of young or old yeast cells (background strain BG2) were grown in yeast extract peptone with 2% for 16 hours at 37degCelsius with agitation at 150rpm

extract_protocol:
Total RNA was extracted using a QIAGEN RNeasy kit (mechanical disruption) per manufacturer's instructions
The library preparation protocol was oligo-d(T)-priming based Clontech SMARTer Ultra Low RNA Kit for Illumina® Sequencing from Clontech (a Takara Bio Company, hereafter labeled as “ClonTech”).  A starting amount of 10 ng RNAs was processed in ClonTech assays, amplified cDNA was sheared using a Covaris E210 instrument. cDNA was then end repaired, A tailed, and standard Illumina adapters were ligated on. Libraries were then amplified with primers to incorporate a unique index to each sample.  In pooling of multiple libraries for running on 2 lanes of 50bp single reads, equal amount of library mass was determined by Qubit reading and Bioanalyzer for the 24 RNA libraries.  Lastly, pooled libraries were amplified with Illumina® TruSeq™ Cluster kits and sequenced with Illumina® sequencing primers on Illumina® HiSeq2500™ next-generation sequencing system as a high output single read 50 cycle run.

tag: strain

value: 0-2 generation-old cell grown in 2% YPD

value: GAGGCGT


title: BG2 Old 3

source_name: BG2_old_whole cell

value: 12-14 generation-old cell grown in 2% YPD

value: GCAGGGG


title: BG2 Young 3

value: TTTTGTC


title: BG2 Old 2

value: CAAGCCG


title: BG2 Old 1

value: GTCTGAT


title: 122 normal sinus ryhthm


title: 144 normal sinus ryhthm


title: 116 normal sinus ryhthm


title: 98 normal sinus ryhthm


title: 44 normal sinus ryhthm


title: 187 normal sinus ryhthm


title: 128 normal sinus ryhthm


title: 21 normal sinus ryhthm


title: 58 normal sinus ryhthm


title: colorectal cancer sample AUS2_550

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: SST RMA expression values at the gene-level derived using Expression Console software

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

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

data_processing: Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software.

source_name: Colorectal cancer patient

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from CRC biopsies using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer biopsy


title: colorectal cancer sample AUS2_553


title: colorectal cancer sample AUS2_448


title: colorectal cancer sample AUS2_548


title: colorectal cancer sample AUS2_496


title: colorectal cancer sample AUS2_473


title: colorectal cancer sample AUS2_488


title: colorectal cancer sample AUS2_491


title: colorectal cancer sample AUS2_446


title: 59 normal sinus ryhthm


title: colorectal cancer sample AUS2_444


title: colorectal cancer sample AUS2_546


title: MS2 A

description:
Replicate 1
9286492017_D

value: shCtrl


title: MtbΔwhiB4_CHP_2

city: Bangalore

first: Amit

last: Singh

address: C V Raman Avenue

department: MCBL

institute: Indian Institute of Science

description:
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS medium, treated with 0.25 mM CHP for 2 h
MtbΔwhiB4 0.25 mM CHP 2

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040).  The purified cRNA (600ng) was fragmented with fragmentation blocking mix by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into thehybridization chamber, samples were placed in thehybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µm using Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer's instructions (G2505-90020). Settings included Agilent HD_GX_1colour (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and baseline transformation was done with respect to the control sample using GeneSpring GX  v12.0 from Agilent Technologies

organism: Mycobacterium tuberculosis H37Rv

source_name: MtbΔwhiB4_2hrs_0.25 mM CHP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Quick Amplification Labelling kit (Agilent Technologies, G4140-90040) 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: Mtb H37Rv and MtbΔwhiB4 were seeded at 0.05 OD600 in 7H9-ADS medium and grown till early log phase of ~0.4.

extract_protocol: Gene expression from Treated cultures were fixed using Guanidine thiocyanate, pelleted and total RNA was isolated using FastRNA PRO blue kit (according to manufacturer's instructions). RNA was purified using Qiagen RNeasy plus kit according to manufacturer's instructions. DNAse treatment was done using Ambion TURBO DNA-free kit according to manufacturer's instructions. RNA quality was measured using Agilent Bioanalyzer.

treatment_protocol: Early log phase culture cells were taken. Mtb H37Rv and MtbΔwhiB4 were treated with 0.25 mM CHP for 2 h. Control Mtb H37Rv and MtbΔwhiB4 cultures were left untreated.

tag: strain background

value: Mtb H37Rv

value: WhiB4 mutant

tag: growth phase

value: early log phase

tag: exposed to

value: 0.25 mM CHP for 2hrs


title: colorectal cancer sample AUS2_318


title: colorectal cancer sample AUS2_327


title: colorectal cancer sample AUS2_338


title: colorectal cancer sample AUS2_344


title: MtbΔwhiB4_CHP_1

description:
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS medium, treated with 0.25 mM CHP for 2 h
MtbΔwhiB4 0.25 mM CHP 1

tag: genotype/variation


title: MtbΔwhiB4_UT_5

description:
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS
MtbΔwhiB4 UT 5

value: none (untreated control)


title: colorectal cancer sample AUS2_322


title: MtbΔwhiB4_UT_4

description:
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS
MtbΔwhiB4 UT 4


title: colorectal cancer sample AUS2_354


title: colorectal cancer sample AUS2_315


title: colorectal cancer sample AUS2_400


title: colorectal cancer sample AUS2_375


title: colorectal cancer sample AUS2_385


title: colorectal cancer sample AUS2_388


title: colorectal cancer sample AUS2_366


title: MtbΔwhiB4_UT_1

description:
Gene expression of MtbΔwhiB4 early log phase cultures in 7H9-ADS
MtbΔwhiB4 UT 1


title: colorectal cancer sample AUS2_291


title: colorectal cancer sample AUS2_422


title: colorectal cancer sample AUS2_374


title: colorectal cancer sample AUS2_434


title: colorectal cancer sample AUS2_421


title: colorectal cancer sample AUS2_439


title: colorectal cancer sample AUS2_362


title: Mtb_CHP_4

description:
Gene expression of Mtb early log phase cultures in 7H9-ADS medium, treated with 0.25 mM CHP for 2 h
Mtb H37Rv 0.25mM CHP 4

source_name: Mtb H37Rv_2hrs_0.25 mM CHP

value: wild type


title: colorectal cancer sample AUS2_299


title: colorectal cancer sample AUS2_410


title: CHP100 treated with EWS-P rep 1

value: EWSR1 fusion positive Ewing sarcoma cell line

value: EWS-P


title: Mtb_UT_1

description:
Gene expression of Mtb early log phase cultures in 7H9-ADS medium
Mtb H37Rv UT 1

source_name: Mtb H37Rv_2hrs_untreated


title: Mtb_CHP_1

description:
Gene expression of Mtb early log phase cultures in 7H9-ADS medium, treated with 0.25 mM CHP for 2 h
Mtb H37Rv 0.25mM CHP 1


title: 20073368 Muscle 2 High Gain

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

hyb_protocol: Following fragmentation, cRNA was hybridized for 20 hr at 45C on Bovine 1.1ST Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix GeneAtlas Imager.

data_processing: The data were transformed by Affymetrix and analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console using the one-way between-Subject ANOVA (Unpaired) algorithm was (Linear Fold Change cutoff of 2 and ANOVA p-value (Condition pair) <0.05).

organism: Bos taurus

source_name: Gluteus medius muscle tissue was biopsied

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Cows (n=121) were placed on a diet to provide 120 kcal ME/kg BW0.75 for 112 days. Gluteus medius muscle was sampled using a U. C. H. skeletal muscle biopsy needle on the 105th day of this trial. Cows were then offered feed ad libitum for 112 days. Muscle tissue was sampled at day 49.

extract_protocol: TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform.

treatment_protocol: Animals most divergent for gain (6 highes gaining animals, and 6 lowest gaining animals) calculated using data from the ad libitum study, were selected and muscle tissue samples were collected. The muscle transcriptome was evaluated by microarray.

value: High Gain

value: Muscle


title: colorectal cancer sample AUS2_427


title: colorectal cancer sample AUS2_436


title: Mtb_UT_4

description:
Gene expression of Mtb early log phase cultures in 7H9-ADS medium
Mtb H37Rv UT 4


title: Mtb_CHP_2

description:
Gene expression of Mtb early log phase cultures in 7H9-ADS medium, treated with 0.25 mM CHP for 2 h
Mtb H37Rv 0.25mM CHP 2


title: 20073368 Muscle 1 High Gain


title: Mtb_CHP_3

description:
Gene expression of Mtb early log phase cultures in 7H9-ADS medium, treated with 0.25 mM CHP for 2 h
Mtb H37Rv 0.25mM CHP 3


title: 20073292 Muscle 2 Low Gain

value: Low Gain


title: 20073228 Muscle 2 Low Gain


title: 20073271 Muscle 1 High Gain


title: 20073240 Muscle 1 Low Gain


title: 20073228 Muscle 1 Low Gain


title: 20073240 Muscle 2 Low Gain


title: 20073271 Muscle 2 High Gain


title: 20073292 Muscle 1 Low Gain


title: 20073070 Muscle 1 High Gain


title: 20073093 Muscle 1 High Gain


title: 20073093 Muscle 2 High Gain


title: 20073070 Muscle 2 High Gain


title: 20073167 Muscle 2 Low Gain


title: 20073167 Muscle 1 Low Gain


title: 20073048 Muscle 2 High Gain


title: 20073011 Muscle 2 Low Gain


title: 20073007 Muscle 2 High Gain


title: 20073007 Muscle 1 High Gain


title: 20073017 Muscle 1 Low Gain


title: 20073011 Muscle 1 Low Gain


title: cells treated by fluconazole + osthole vs  fluconazole replication-3

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

country: China

institute: PLA General Hospital

hyb_protocol: Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42°C and washed in a Capitalbio SlideWasher TM (CapitalBio) with two consecutive solutions (0.2% SDS, 2× SSC at 42°C for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K (CapitalBio) Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. There was no reversal fluorescent strategy used. All test samples was labeled with Cy5 and all control samples was labeled with Cy3.

organism: Candida albicans

source_name: cells treated by fluconazole + osthole

label_protocol: 2 µg amplified RNA was mixed with 4 µg random nanomer, denatured at 65°C for 5min, and cooled on ice. Then, 5 μl of 4 × first-strand buffer, 2 μl of 0.1 M DTT, and 1.5 μl CbcScript II reverse transcriptase were added. The mixtures were incubated at 25°C for 10 min, then at 37°C for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μl. The cDNA was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice for 5 min. Then, 5 μl Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μl Klenow enzyme was then added, and the reaction was performed at 37°C for 90 min.

growth_protocol: Candida albicans cells were propagated in RPMI 1640 medium.

extract_protocol: Total RNA was isolated by the hot phenol method.

treatment_protocol: 0304103 cells were cultured to 1.5×106 cells/ml in YPD, then divided into two parts: one was exposed to fluconazole  (8 μg/ml) and osthole (16 μg/ml) whereas the other was exposed to fluconazole  (8 μg/ml) and grown an additional 6 h, at which point they were pelleted by centrifugation for 5 min at room temperature and frozen in liquid nitrogen.

tag: passage

tag: agent

value: fluconazole and osthole

source_name: Control Candida albicans, treated with fluconazole for 6 h.

tag: time point

value: 6 h

value: fluconazole


title: 20073048 Muscle 1 High Gain


title: 20073017 Muscle 2 Low Gain


title: cells treated by fluconazole + osthole vs  fluconazole replication-1


title: cells treated by fluconazole + osthole vs  fluconazole replication-2


title: leaf_w+os_24h_rep4

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

country: Germany

institute: Freie Universität Berlin

description:
ws_24h_m
Solanum dulcamara L.

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer's protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Data were analyzed using the limma software packages from Bioconductor in R (R Core Team; Ritchie et al. 2015). The uploaded data were background-corrected using the normexp method and normalized between microarrays using the quantile method and log2-transformed. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, twice the fluorescence value of the 90% percentile of non-labelled hairpin DNA probes (dark-corner spots) was set as limit of detection on each microarray. About 40% of the probes showed fluorescence values below this threshold in at least one microarray within each treatment group. These probes were considered non-expressed and removed from further analysis in the paper. Background-correction and normalization across arrays was then performed after removal of the non-expressed genes.

organism: Solanum dulcamara

source_name: leaf, w+os, 24h

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacturer's protocol.

growth_protocol: Solanum dulcamara plants were grown from stem cuttings in a greenhouse at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol/ m s.

extract_protocol: For each microarray sample, leaf material from six independent biological replicates was pooled. Leaf material was ground under liquid nitrogen and RNA was extracted with the NucleoSpin® RNA Plant kit (Macherey-Nagel GmbH & Co. KG) according to the manufacturer's instructions using double the amount of RAP lysis buffer. RNA was DNase digested using TURBO DNA-free™ (AmbionTM) according to the manufacturer's instructions.

treatment_protocol: The third leaf from the top was subjected to either feeding by 2 3rd instar Spodoptera exigua larvae or to mechanical wounding with a pattern wheel (four rows in parallel to the mid-vein) and application of 20µL of S. exigua oral secretions (w+os). Plants of one w+os treatment group and half of the untreated control plants were harvested 1 h after treatment application, whereas all other plants were harvested 24 hrs after treatment application.

tag: genotype location

value: Mehrow

value: leaf

tag: treatment

value: damaged, then treated with S. exigua oral secretions (w+os)

tag: time


title: leaf_w+os_24h_rep3

description:
ws_24h_g
Solanum dulcamara L.

value: Grunewald


title: Input

first: Sagar

last: Chhangawala

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

description:
CL1_(MoGene-1_0-st-v1)
Adult C57-BL6 mice intestines were harvested and RNA was isolated and combined from two independent experiments

hyb_protocol: Samples were prepared for hybridization using 5 µg fragmented biotinylated cDNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using GeneChip Expression Console.

data_processing: CEL files proccessed using affy package in R. Probes with no expression were discarded.

source_name: intestinal epithelium

label_protocol: Biotinylated cDNA was generated from 100ng RNA according to the Whole Transcriptome Affymetrix protocol.

extract_protocol: RNA was isolated using QIAzol and RNeasy according to manufacturer's protocols.

tag: developmental stage

value: adult

value: intestinal epithelium

tag: ip antibody

value: none (input)


title: leaf_w+os_1h_rep3

description:
ws_1h_g
Solanum dulcamara L.

source_name: leaf, w+os, 1h

tag: tissue


title: leaf_w+os_24h_rep2

description:
ws_24h_e
Solanum dulcamara L.

value: Erkner


title: leaf_S.exigua_rep4

description:
spodo_m
Solanum dulcamara L.

source_name: leaf, S. exigua fed

value: fed upon by S. exigua (spodo) caterpillars


title: leaf_w+os_1h_rep1

description:
ws_1h_s
Solanum dulcamara L.

value: Siethen


title: leaf_S.exigua_rep1

description:
spodo_s
Solanum dulcamara L.


title: hnRNP

description:
CL4_(MoGene-1_0-st-v1)
Adult C57-BL6 mice intestines were harvested and RNA was isolated and combined from two independent experiments

value: hnRNP


title: leaf_w+os_1h_rep4

description:
ws_1h_m
Solanum dulcamara L.


title: leaf_w+os_24h_rep1

description:
ws_24h_s
Solanum dulcamara L.


title: leaf_w+os_1h_rep2

description:
ws_1h_e
Solanum dulcamara L.


title: Msi1

description:
CL3_(MoGene-1_0-st-v1)
Adult C57-BL6 mice intestines were harvested and RNA was isolated and combined from two independent experiments

value: Msi1 (Millipore AB5977)


title: leaf_S.exigua_rep2

description:
spodo_e
Solanum dulcamara L.


title: leaf_control_rep4

description:
control_m
Solanum dulcamara L.

source_name: leaf, undamaged control

value: undamaged


title: IgG

description:
CL2_(MoGene-1_0-st-v1)
Adult C57-BL6 mice intestines were harvested and RNA was isolated and combined from two independent experiments

value: IgG


title: leaf_control_rep3

description:
control_g
Solanum dulcamara L.


title: leaf_control_rep2

description:
control_e
Solanum dulcamara L.


title: High-fat diet endometriotic lesion HFD-1

status: Public on Apr 23 2017

city: Little Rock

first: Rosalia

middle: CM

last: Simmen

state: AR

address: 4301 West Markham  Mail Slot 750

department: Physiology and Biophysics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Fifteen microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Mouse Genome 430 2.0 Array (N = 2/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing:
Cel files were generated using GCOS and utilized for analysis using GeneSpring GX v 11
Summarization Algorithm: RMA
Technology: Affymetrix.GeneChip.Mouse430_2
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: Mouse endometriotic lesion

label_protocol: First- and second- strand cDNA synthesis (from 0.1 ug total RNA), biotin-labeled aRNA synthesis, and fragmentation of cRNA  reactions were performed following protocols described by Affymetrix. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated using the Arcturus PicoPure RNA isolation kit (Life Technologies Corporation, Carlsbad, CA)

value: Endometriotic lesion

tag: protocol

value: HFD


title: Casein diet endometriotic lesion CAS-1

value: control


title: 256685310004_b4 - Ppmax2+GR24_2 vs Ppmax2+ac_2

status: Public on Apr 22 2017

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: How does the Ppmax2 moss mutant respond to Strigolactone (GR24)?

hyb_protocol: Ppmax2+ac_2 Cy5 / Ppmax2+GR24_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Physcomitrium patens

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media: PpNO3 medium (moss minimal medium) Hygrometry: Growth chamber 60% Temperatire: 24°C during the day-22°C during the night Light: White light 16h ( day)/8h dark (night)

extract_protocol: Ppmax2+ac_2:50mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Acetone - compound based treatment - compound addition,acetone:time 6hour . Acetone was plated on medium containing- Petri dishes prior transfer of the moss (transfer of cellophane disks on which the moss have grown).

tag: physcomitrella patens  mutant (mutant) - age

extract_protocol: Ppmax2+GR24_2:50mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:GR24 - compound based treatment - compound addition,gr24:quantity 1uM time 6hour . GR24 1microM in acetone was plated on medium containing- Petri dishes prior transfer of the moss (transfer of cellophane disks on which the moss have grown).


title: High-fat diet endometriotic lesion HFD-2


title: leaf_S.exigua_rep3

description:
spodo_g
Solanum dulcamara L.


title: 256685310004_b3 - Ppmax2+ac_2 vs Ppmax2+GR24_2

hyb_protocol: Ppmax2+GR24_2 Cy5 / Ppmax2+ac_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Casein diet endometriotic lesion CAS-2


title: 256685310004_b1 - Ppmax2+ac_1 vs Ppmax2+GR24_1

hyb_protocol: Ppmax2+GR24_1 Cy5 / Ppmax2+ac_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ppmax2+GR24_1:50mg. (Qiagen_RNeasy.pdf)

extract_protocol: Ppmax2+ac_1:50mg. (Qiagen_RNeasy.pdf)


title: 256685310003_b4 - Ppmax2+ac_2 vs WT+ac_2

hyb_protocol: WT+ac_2 Cy5 / Ppmax2+ac_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: WT+ac_2:50mg. (Qiagen_RNeasy.pdf)

tag: physcomitrella patens  - age


title: 256685310003_b3 - WT+ac_2 vs Ppmax2+ac_2

hyb_protocol: Ppmax2+ac_2 Cy5 / WT+ac_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256685310004_b2 - Ppmax2+GR24_1 vs Ppmax2+ac_1

hyb_protocol: Ppmax2+ac_1 Cy5 / Ppmax2+GR24_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256685310003_b1 - WT+ac_1 vs Ppmax2+ac_1

hyb_protocol: Ppmax2+ac_1 Cy5 / WT+ac_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: WT+ac_1:50mg. (Qiagen_RNeasy.pdf)


title: 256685310003_b2 - Ppmax2+ac_1 vs WT+ac_1

hyb_protocol: WT+ac_1 Cy5 / Ppmax2+ac_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Empty_2

city: Ribeirao Preto

first: Mariana

middle: Tomazini

last: Pinto

state: Sao Paulo

address: Tenente Catao Roxo 2501

country: Brazil

institute: Fundacao Hemocentro de Ribeirao Preto

description: Endothelial cell containing Empty vector

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) (Agilent Technologies) was done according to the manufacturer’s instructions.

scan_protocol: The microarray was scanned with an Agilent Microarray Scanner (Agilent Technologies) and data were processed using Feature Extraction software version 10.7.3 (Agilent Technologies).

data_processing: Data analysis was performed with R packages from the Bioconductor project (www.bioconductor.org).

label_protocol: Briefly, 1µg total RNA from each studied sample was spiked with a control RNA and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

extract_protocol: Total RNA was extracted with TRIZOL® (Life Technologies, US) according to manufactures’ guidelines

treatment_protocol: Human coronary artery endothelial cells were induced under three distinct conditions: I) ectopic expression of Snail; II) ectopic expression of Snail associated with TGF-β2 treatment; III) TGF-β2 treatment

tag: cell type

value: Human coronary artery endothelial cells


title: SNAIL_2

description: Endothelial cell containing SNAIL vector


title: TGF-B2_2

description: Endothelial cell treated with TGF-β2

source_name: Endothelial cell treated with TGF-β2


title: CT_1

description: Endothelial cell control

source_name: Endothelial cell control


title: TGF-B2_3

description: Endothelial cell treated with TGF-β2


title: Empty_1

source_name: Endothelial cell containing Empty vector


title: SNAIL_1

source_name: Endothelial cell containing SNAIL vector


title: SNAIL+TGF-B2_2

description: Endothelial cell containing SNAIL vector and treated with TGF-β2


title: SNAIL+TGF-B2_1

source_name: Endothelial cell containing SNAIL vector and treated with TGF-β2


title: SNAIL+TGF-B2_3


title: CT_2

description: Endothelial cell control


title: Mock, biological rep2

status: Public on Apr 21 2017

city: Horsholm

first: Peter

middle: H

last: Hagedorn

state: Danmark

address: Fremtidsvej 3

department: Research

country: Denmark

institute: Roche Innovation Center Copenhagen A/S

hyb_protocol: Following fragmentation, 5 ug of cDNA were prepared and hybridized using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Robust Multiarray Averaging (Bioconductor package Affy) with summarization method using Brainarray cdf annotations.

source_name: HuH7 cells transfected with mock and measured after 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: HuH7 cells were seeded in 6 well plates with 2,5x10^5 cells/ml in 2ml

extract_protocol: Cells were homogenized in Trizol and RNA was extracted according to standard protocols.

treatment_protocol: 24h after seeding (50%-70% confluence) HuH7 cells were transfected with 10nM antisense oligonucleotide or mock in 6 well plates using lipofectamine (5 ug/ml). After 4 hours media was changed and cells incubated for 20h without antisense oligonucleotide or mock.

value: mock


title: Mock, biological rep1


title: SPC3833, biological rep1

source_name: HuH7 cells transfected with SPC3833 and measured after 24h


title: Mock, biological rep3


title: TGF-B2_1

description: Endothelial cell treated with TGF-β2


title: SNAIL_3


title: SPC3833, biological rep3


title: SPC3302, biological rep3

source_name: HuH7 cells transfected with SPC3302 and measured after 24h


title: SPC3833, biological rep2


title: SPC3302, biological rep2


title: leaf_control_rep1

description:
control_s
Solanum dulcamara L.

value: leaf


title: CD123NEG_D7_S256_S42

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street

institute: Broad Institute

description:
paired-end RNA-seq data
processed data file:
raw.expMatrix_deeper.characterization.set.submission.txt

data_processing:
Read were aligned to the UCSC hg19 transcriptomee using Bowtie v0.12.7
Expression levels were quantified using RSEM v1.2.1 (TPM values)
UCSC genome table browser was used to map UCSC gene ID (kgID) and the gene name (geneSymbol) for all genes in hg19
If multiple UCSC gene IDs are assigned to the same geneSymbol, the TPM values of all kgIDs that share the same geneSymbol are summed
Genome_build: hg19
Supplementary_files_format_and_content: Text file with tab delimiters

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Enriched immune cell fractions isolated from healthy blood PBMCs were FACS sorted in 96-well plates (single cell sorted) containing lysis buffer (TCL together with 1% of 2-Mercaptoethanol).
Smart-seq2 (Picelli et al., Nature Methods, 2014)
Full-length RNA-sequencing


title: CD123NEG_D7_S258_S38


title: CD123NEG_D7_S97_S383


title: CD123NEG_D7_S253_S48


title: CD123NEG_D7_S252_S74


title: CD123NEG_D7_S261_S32


title: CD123NEG_D7_S257_S40


title: CD123NEG_D7_S259_S36


title: CD123NEG_D7_S99_S379


title: CD123NEG_D7_S98_S381


title: CD123NEG_D7_S264_S26


title: CD123NEG_D7_S262_S30


title: CD123NEG_D7_S255_S44


title: CD123NEG_D7_S250_S78


title: SPC3302, biological rep1


title: CD123NEG_D7_S260_S34


title: CD123NEG_D7_S251_S76


title: CD123NEG_D7_S244_S90


title: CD123NEG_D7_S249_S80


title: CD123NEG_D7_S248_S82


title: CD123NEG_D7_S263_S28


title: CD123NEG_D7_S247_S84


title: CD123NEG_D7_S241_S96


title: CD123NEG_D7_S254_S46


title: CD123NEG_D7_S246_S86


title: CD123NEG_D7_S243_S92


title: CD123NEG_D7_S245_S88


title: CD123NEG_D7_S239_S124


title: CD123NEG_D7_S240_S122


title: CD123NEG_D7_S238_S126


title: CD123NEG_D7_S236_S130


title: CD123NEG_D7_S233_S136


title: CD123NEG_D7_S242_S94


title: CD123NEG_D7_S232_S138


title: CD123NEG_D7_S229_S144


title: CD123NEG_D7_S226_S174


title: CD123NEG_D7_S225_S176


title: CD123NEG_D7_S228_S170


title: CD123NEG_D7_S237_S128


title: CD123NEG_D7_S231_S140


title: CD123NEG_D7_S223_S180


title: CD123NEG_D7_S234_S134


title: CD123NEG_D7_S235_S132


title: CD123NEG_D7_S218_S97


title: CD123NEG_D7_S220_S186


title: CD123NEG_D7_S219_S188


title: CD123NEG_D7_S217_S9


title: CD123NEG_D7_S230_S142


title: CD123NEG_D7_S217_S192


title: CD123NEG_D7_S227_S172


title: CD123NEG_D7_S218_S190


title: CD123NEG_D7_S224_S178


title: CD123NEG_D7_S222_S182


title: CD123NEG_D7_S221_S184


title: CD123NEG_D7_S215_S292


title: CD123NEG_D7_S216_S290


title: CD123NEG_D7_S216_S218


title: CD123NEG_D7_S215_S220


title: CD123NEG_D7_S214_S294


title: CD123NEG_D7_S213_S296


title: CD123NEG_D7_S212_S298


title: CD123NEG_D7_S212_S226


title: CD123NEG_D7_S211_S300


title: CD123NEG_D7_S210_S230


title: CD123NEG_D7_S211_S228


title: CD123NEG_D7_S208_S306


title: CD123NEG_D7_S214_S222


title: CD123NEG_D7_S207_S236


title: CD123NEG_D7_S206_S310


title: CD123NEG_D7_S204_S338


title: CD123NEG_D7_S205_S312


title: CD123NEG_D7_S203_S340


title: CD123NEG_D7_S203_S268


title: CD123NEG_D7_S201_S344


title: CD123NEG_D7_S213_S224


title: CD123NEG_D7_S201_S272


title: CD123NEG_D7_S200_S346


title: CD123NEG_D7_S210_S302


title: CD123NEG_D7_S199_S276


title: CD123NEG_D7_S209_S304


title: CD123NEG_D7_S209_S232


title: CD123NEG_D7_S208_S234


title: CD123NEG_D7_S207_S308


title: CD123NEG_D7_S206_S238


title: CD123NEG_D7_S205_S240


title: CD123NEG_D7_S204_S266


title: CD123NEG_D7_S202_S342


title: CD123NEG_D7_S202_S270


title: CD123NEG_D7_S197_S280


title: CD123NEG_D7_S196_S354


title: CD123NEG_D7_S196_S282


title: CD123NEG_D7_S195_S356


title: CD123NEG_D7_S194_S358


title: CD123NEG_D7_S200_S274


title: CD123NEG_D7_S193_S288


title: CD123NEG_D7_S192_S314


title: CD123NEG_D7_S199_S348


title: CD123NEG_D7_S191_S316


title: CD123NEG_D7_S190_S318


title: CD123NEG_D7_S189_S320


title: CD123NEG_D7_S188_S322


title: CD123NEG_D7_S198_S278


title: CD123NEG_D7_S198_S350


title: CD123NEG_D7_S197_S352


title: CD123NEG_D7_S187_S324


title: CD123NEG_D7_S186_S37


title: CD123NEG_D7_S186_S326


title: CD123NEG_D7_S185_S39


title: CD123NEG_D7_S194_S286


title: CD123NEG_D7_S195_S284


title: CD123NEG_D7_S192_S25


title: CD123NEG_D7_S193_S360


title: CD123NEG_D7_S191_S27


title: CD123NEG_D7_S183_S332


title: CD123NEG_D7_S182_S45


title: CD123NEG_D7_S189_S31


title: CD123NEG_D7_S190_S29


title: CD123NEG_D7_S188_S33


title: CD123NEG_D7_S181_S47


title: CD123NEG_D7_S181_S336


title: CD123NEG_D7_S187_S35


title: CD123NEG_D7_S185_S328


title: CD123NEG_D7_S184_S41


title: CD123NEG_D7_S180_S362


title: CD123NEG_D7_S183_S43


title: CD123NEG_D7_S184_S330


title: CD123NEG_D7_S179_S75


title: CD123NEG_D7_S182_S334


title: CD123NEG_D7_S179_S364


title: CD123NEG_D7_S180_S73


title: CD123NEG_D7_S178_S77


title: CD123NEG_D7_S177_S79


title: CD123NEG_D7_S176_S81


title: CD123NEG_D7_S178_S366


title: CD123NEG_D7_S177_S368


title: CD123NEG_D7_S176_S370


title: CD123NEG_D7_S175_S83


title: CD123NEG_D7_S175_S372


title: CD123NEG_D7_S174_S85


title: CD123NEG_D7_S174_S374


title: CD123NEG_D7_S170_S93


title: CD123NEG_D7_S171_S380


title: CD123NEG_D7_S173_S376


title: CD123NEG_D7_S173_S87


title: CD123NEG_D7_S172_S89


title: CD123NEG_D7_S170_S382


title: CD123NEG_D7_S172_S378


title: CD123NEG_D7_S171_S91


title: CD123NEG_D7_S169_S95


title: CD123NEG_D7_S168_S121


title: CD123NEG_D7_S169_S384


title: CD123NEG_D7_S167_S123


title: CD123NEG_D7_S166_S125


title: CD123NEG_D7_S165_S127


title: CD123NEG_D7_S164_S129


title: CD123NEG_D7_S163_S131


title: CD123NEG_D7_S162_S133


title: CD123NEG_D7_S160_S137


title: CD123NEG_D7_S158_S141


title: CD123NEG_D7_S159_S139


title: CD123NEG_D7_S161_S135


title: CD123NEG_D7_S156_S169


title: CD123NEG_D7_S157_S143


title: CD123NEG_D7_S152_S177


title: CD123NEG_D7_S155_S171


title: CD123NEG_D7_S150_S181


title: CD123NEG_D7_S154_S173


title: CD123NEG_D7_S153_S175


title: CD123NEG_D7_S143_S219


title: CD123NEG_D7_S142_S221


title: CD123NEG_D7_S144_S217


title: CD123NEG_D7_S137_S231


title: CD123NEG_D7_S135_S235


title: CD123NEG_D7_S133_S239


title: CD123NEG_D7_S151_S179


title: CD123NEG_D7_S149_S183


title: CD123NEG_D7_S148_S185


title: CD123NEG_D7_S147_S187


title: CD123NEG_D7_S131_S267


title: CD123NEG_D7_S130_S269


title: CD123NEG_D7_S146_S189


title: CD123NEG_D7_S129_S271


title: CD123NEG_D7_S145_S191


title: CD123NEG_D7_S141_S223


title: CD123NEG_D7_S126_S277


title: CD123NEG_D7_S139_S227


title: CD123NEG_D7_S140_S225


title: CD123NEG_D7_S138_S229


title: CD123NEG_D7_S136_S233


title: CD123NEG_D7_S134_S237


title: CD123NEG_D7_S123_S283


title: CD123NEG_D7_S132_S265


title: CD123NEG_D7_S122_S285


title: CD123NEG_D7_S120_S313


title: CD123NEG_D7_S117_S319


title: CD123NEG_D7_S115_S323


title: CD123NEG_D7_S114_S325


title: CD123NEG_D7_S113_S327


title: CD123NEG_D7_S128_S273


title: CD123NEG_D7_S111_S331


title: CD123NEG_D7_S127_S275


title: CD123NEG_D7_S108_S361


title: CD123NEG_D7_S107_S363


title: CD123NEG_D7_S105_S367


title: CD123NEG_D7_S104_S369


title: CD123NEG_D7_S125_S279


title: CD123NEG_D7_S124_S281


title: CD123NEG_D7_S102_S373


title: CD123NEG_D7_S101_S375


title: CD123NEG_D0_S98_S261


title: CD123NEG_D7_S121_S287


title: CD123NEG_D7_S119_S315


title: CD123NEG_D7_S116_S321


title: CD123NEG_D7_S118_S317


title: CD123NEG_D7_S112_S329


title: CD123NEG_D0_S96_S289


title: CD123NEG_D7_S110_S333


title: CD123NEG_D7_S109_S335


title: CD123NEG_D0_S95_S291


title: CD123NEG_D7_S106_S365


title: CD123NEG_D7_S103_S371


title: CD123NEG_D0_S94_S293


title: CD123NEG_D0_S9_S248


title: CD123NEG_D0_S93_S295


title: CD123NEG_D7_S100_S377


title: CD123NEG_D0_S92_S297


title: CD123NEG_D0_S99_S259


title: CD123NEG_D0_S8_S250


title: CD123NEG_D0_S97_S263


title: CD123NEG_D0_S88_S305


title: CD123NEG_D0_S87_S307


title: CD123NEG_D0_S86_S309


title: CD123NEG_D0_S91_S299


title: CD123NEG_D0_S90_S301


title: CD123NEG_D0_S89_S303


title: CD123NEG_D0_S85_S311


title: CD123NEG_D0_S84_S337


title: CD123NEG_D0_S83_S339


title: CD123NEG_D0_S82_S341


title: CD123NEG_D0_S81_S343


title: CD123NEG_D0_S77_S351


title: CD123NEG_D0_S80_S345


title: CD123NEG_D0_S7_S252


title: CD123NEG_D0_S78_S349


title: CD123NEG_D0_S79_S347


title: CD123NEG_D0_S71_S4


title: CD123NEG_D0_S76_S353


title: CD123NEG_D0_S6_S254


title: CD123NEG_D0_S68_S10


title: CD123NEG_D0_S75_S355


title: CD123NEG_D0_S66_S14


title: CD123NEG_D0_S74_S357


title: CD123NEG_D0_S63_S20


title: CD123NEG_D0_S73_S359


title: CD123NEG_D0_S59_S52


title: CD123NEG_D0_S56_S58


title: CD123NEG_D0_S72_S2


title: CD123NEG_D0_S70_S6


title: CD123NEG_D0_S54_S62


title: CD123NEG_D0_S69_S8


title: CD123NEG_D0_S67_S12


title: CD123NEG_D0_S65_S16


title: CD123NEG_D0_S64_S18


title: CD123NEG_D0_S53_S64


title: CD123NEG_D0_S52_S66


title: CD123NEG_D0_S51_S68


title: CD123NEG_D0_S62_S22


title: CD123NEG_D0_S60_S50


title: CD123NEG_D0_S5_S256


title: CD123NEG_D0_S61_S24


title: CD123NEG_D0_S4_S258


title: CD123NEG_D0_S58_S54


title: CD123NEG_D0_S49_S72


title: CD123NEG_D0_S57_S56


title: CD123NEG_D0_S55_S60


title: CD123NEG_D0_S47_S100


title: CD123NEG_D0_S46_S102


title: CD123NEG_D0_S45_S104


title: CD123NEG_D0_S50_S70


title: CD123NEG_D0_S42_S110


title: CD123NEG_D0_S41_S112


title: CD123NEG_D0_S48_S98


title: CD123NEG_D0_S44_S106


title: CD123NEG_D0_S40_S114


title: CD123NEG_D0_S39_S116


title: CD123NEG_D0_S43_S108


title: CD123NEG_D0_S37_S120


title: CD123NEG_D0_S36_S146


title: CD123NEG_D0_S3_S260


title: CD123NEG_D0_S38_S118


title: CD123NEG_D0_S35_S148


title: CD123NEG_D0_S32_S154


title: CD123NEG_D0_S31_S156


title: CD123NEG_D0_S34_S150


title: CD123NEG_D0_S30_S158


title: CD123NEG_D0_S33_S152


title: CD123NEG_D0_S2_S262


title: CD123NEG_D0_S23_S196


title: CD123NEG_D0_S26_S166


title: CD123NEG_D0_S25_S168


title: CD123NEG_D0_S27_S164


title: CD123NEG_D0_S1_S264


title: CD123NEG_D0_S19_S204


title: CD123NEG_D0_S29_S160


title: CD123NEG_D0_S28_S162


title: CD123NEG_D0_S17_S208


title: CD123NEG_D0_S16_S210


title: CD123NEG_D0_S164_S3


title: CD123NEG_D0_S22_S198


title: CD123NEG_D0_S24_S194


title: CD123NEG_D0_S21_S200


title: CD123NEG_D0_S20_S202


title: CD123NEG_D0_S15_S212


title: CD123NEG_D0_S18_S206


title: CD123NEG_D0_S159_S15


title: CD123NEG_D0_S163_S5


title: CD123NEG_D0_S162_S7


title: CD123NEG_D0_S150_S59


title: CD123NEG_D0_S161_S11


title: CD123NEG_D0_S158_S17


title: CD123NEG_D0_S148_S63


title: CD123NEG_D0_S146_S67


title: CD123NEG_D0_S157_S19


title: CD123NEG_D0_S156_S21


title: CD123NEG_D0_S143_S99


title: CD123NEG_D0_S160_S13


title: CD123NEG_D0_S142_S101


title: CD123NEG_D0_S13_S216


title: CD123NEG_D0_S155_S23


title: CD123NEG_D0_S154_S51


title: CD123NEG_D0_S153_S53


title: CD123NEG_D0_S138_S109


title: CD123NEG_D0_S152_S55


title: CD123NEG_D0_S137_S111


title: CD123NEG_D0_S14_S214


title: CD123NEG_D0_S151_S57


title: CD123NEG_D0_S149_S61


title: CD123NEG_D0_S141_S103


title: CD123NEG_D0_S145_S69


title: CD123NEG_D0_S144_S71


title: CD123NEG_D0_S147_S65


title: CD123NEG_D0_S131_S147


title: CD123NEG_D0_S140_S105


title: CD123NEG_D0_S139_S107


title: CD123NEG_D0_S134_S117


title: CD123NEG_D0_S125_S159


title: CD123NEG_D0_S123_S163


title: CD123NEG_D0_S136_S113


title: CD123NEG_D0_S129_S151


title: CD123NEG_D0_S135_S115


title: CD123NEG_D0_S122_S165


title: CD123NEG_D0_S133_S119


title: CD123NEG_D0_S121_S167


title: CD123NEG_D0_S128_S153


title: CD123NEG_D0_S132_S145


title: CD123NEG_D0_S126_S157


title: CD123NEG_D0_S115_S203


title: CD123NEG_D0_S113_S207


title: CD123NEG_D0_S127_S155


title: CD123NEG_D0_S118_S197


title: CD123NEG_D0_S130_S149


title: CD123NEG_D0_S12_S242


title: CD123NEG_D0_S111_S211


title: CD123NEG_D0_S117_S199


title: CD123NEG_D0_S119_S195


title: CD123NEG_D0_S124_S161


title: CD123NEG_D0_S114_S205


title: CD123NEG_D0_S120_S193


title: CD123NEG_D0_S11_S244


title: CD123NEG_D0_S112_S209


title: CD123NEG_D0_S104_S249


title: CD123NEG_D0_S116_S201


title: CD123NEG_D0_S108_S241


title: CD123NEG_D0_S110_S213


title: CD123NEG_D0_S109_S215


title: CD123NEG_D0_S10_S246


title: CD123NEG_D0_S107_S243


title: CD123NEG_D0_S105_S247


title: CD123NEG_D0_S103_S251


title: AXLSIGLEC6_S99


title: CD123NEG_D0_S100_S257


title: AXLSIGLEC6_S92


title: AXLSIGLEC6_S97


title: AXLSIGLEC6_S91


title: CD123NEG_D0_S106_S245


title: AXLSIGLEC6_S98


title: CD123NEG_D0_S102_S253


title: CD123NEG_D0_S101_S255


title: AXLSIGLEC6_S93


title: AXLSIGLEC6_S96


title: AXLSIGLEC6_S9


title: AXLSIGLEC6_S88


title: AXLSIGLEC6_S95


title: AXLSIGLEC6_S90


title: AXLSIGLEC6_S94


title: AXLSIGLEC6_S86


title: AXLSIGLEC6_S87


title: AXLSIGLEC6_S85


title: AXLSIGLEC6_S83


title: AXLSIGLEC6_S82


title: AXLSIGLEC6_S89


title: AXLSIGLEC6_S8


title: AXLSIGLEC6_S79


title: AXLSIGLEC6_S81


title: AXLSIGLEC6_S80


title: AXLSIGLEC6_S84


title: AXLSIGLEC6_S77


title: AXLSIGLEC6_S78


title: AXLSIGLEC6_S76


title: AXLSIGLEC6_S75


title: AXLSIGLEC6_S68


title: AXLSIGLEC6_S74


title: AXLSIGLEC6_S70


title: AXLSIGLEC6_S67


title: AXLSIGLEC6_S73


title: AXLSIGLEC6_S65


title: AXLSIGLEC6_S72


title: AXLSIGLEC6_S71


title: AXLSIGLEC6_S61


title: AXLSIGLEC6_S7


title: AXLSIGLEC6_S62


title: AXLSIGLEC6_S69


title: AXLSIGLEC6_S6


title: AXLSIGLEC6_S66


title: AXLSIGLEC6_S63


title: AXLSIGLEC6_S64


title: AXLSIGLEC6_S59


title: AXLSIGLEC6_S60


title: AXLSIGLEC6_S57


title: AXLSIGLEC6_S55


title: AXLSIGLEC6_S58


title: AXLSIGLEC6_S56


title: AXLSIGLEC6_S52


title: AXLSIGLEC6_S51


title: AXLSIGLEC6_S50


title: AXLSIGLEC6_S54


title: AXLSIGLEC6_S5


title: AXLSIGLEC6_S53


title: AXLSIGLEC6_S49


title: AXLSIGLEC6_S47


title: AXLSIGLEC6_S46


title: AXLSIGLEC6_S43


title: AXLSIGLEC6_S48


title: AXLSIGLEC6_S45


title: AXLSIGLEC6_S44


title: AXLSIGLEC6_S42


title: AXLSIGLEC6_S41


title: AXLSIGLEC6_S39


title: AXLSIGLEC6_S40


title: AXLSIGLEC6_S4


title: AXLSIGLEC6_S37


title: AXLSIGLEC6_S38


title: AXLSIGLEC6_S36


title: AXLSIGLEC6_S35


title: AXLSIGLEC6_S31


title: AXLSIGLEC6_S28


title: AXLSIGLEC6_S29


title: AXLSIGLEC6_S34


title: AXLSIGLEC6_S33


title: AXLSIGLEC6_S32


title: AXLSIGLEC6_S27


title: AXLSIGLEC6_S30


title: AXLSIGLEC6_S3


title: AXLSIGLEC6_S26


title: AXLSIGLEC6_S25


title: AXLSIGLEC6_S24


title: AXLSIGLEC6_S23


title: AXLSIGLEC6_S21


title: AXLSIGLEC6_S22


title: AXLSIGLEC6_S19


title: AXLSIGLEC6_S18


title: AXLSIGLEC6_S119


title: AXLSIGLEC6_S13


title: AXLSIGLEC6_S17


title: AXLSIGLEC6_S20


title: AXLSIGLEC6_S2


title: AXLSIGLEC6_S16


title: AXLSIGLEC6_S15


title: AXLSIGLEC6_S113


title: AXLSIGLEC6_S116


title: AXLSIGLEC6_S14


title: AXLSIGLEC6_S12


title: AXLSIGLEC6_S118


title: AXLSIGLEC6_S117


title: AXLSIGLEC6_S111


title: AXLSIGLEC6_S114


title: AXLSIGLEC6_S115


title: AXLSIGLEC6_S112


title: AXLSIGLEC6_S110


title: AXLSIGLEC6_S11


title: AXLSIGLEC6_S109


title: AXLSIGLEC6_S108


title: AXLSIGLEC6_S107


title: AXLSIGLEC6_S105


title: AXLSIGLEC6_S103


title: AXLSIGLEC6_S104


title: AXLSIGLEC6_S10


title: AXLSIGLEC6_S106


title: AXLSIGLEC6_S102


title: AXLSIGLEC6_S101


title: AXLSIGLEC6_S100


title: AXLSIGLEC6_S1


title: AXLSIGLEC6_CD11Cplus_S7


title: AXLSIGLEC6_CD11Cplus_S9


title: AXLSIGLEC6_CD11Cplus_S8


title: AXLSIGLEC6_CD11Cplus_S6


title: AXLSIGLEC6_CD11Cplus_S46


title: AXLSIGLEC6_CD11Cplus_S44


title: AXLSIGLEC6_CD11Cplus_S5


title: AXLSIGLEC6_CD11Cplus_S47


title: AXLSIGLEC6_CD11Cplus_S43


title: AXLSIGLEC6_CD11Cplus_S42


title: AXLSIGLEC6_CD11Cplus_S45


title: AXLSIGLEC6_CD11Cplus_S4


title: AXLSIGLEC6_CD11Cplus_S39


title: AXLSIGLEC6_CD11Cplus_S41


title: AXLSIGLEC6_CD11Cplus_S40


title: AXLSIGLEC6_CD11Cplus_S38


title: AXLSIGLEC6_CD11Cplus_S36


title: AXLSIGLEC6_CD11Cplus_S37


title: AXLSIGLEC6_CD11Cplus_S35


title: AXLSIGLEC6_CD11Cplus_S33


title: AXLSIGLEC6_CD11Cplus_S31


title: AXLSIGLEC6_CD11Cplus_S34


title: AXLSIGLEC6_CD11Cplus_S29


title: AXLSIGLEC6_CD11Cplus_S28


title: AXLSIGLEC6_CD11Cplus_S32


title: AXLSIGLEC6_CD11Cplus_S27


title: AXLSIGLEC6_CD11Cplus_S24


title: AXLSIGLEC6_CD11Cplus_S22


title: AXLSIGLEC6_CD11Cplus_S21


title: AXLSIGLEC6_CD11Cplus_S30


title: AXLSIGLEC6_CD11Cplus_S23


title: AXLSIGLEC6_CD11Cplus_S19


title: AXLSIGLEC6_CD11Cplus_S3


title: AXLSIGLEC6_CD11Cplus_S17


title: AXLSIGLEC6_CD11Cplus_S15


title: AXLSIGLEC6_CD11Cplus_S14


title: AXLSIGLEC6_CD11Cplus_S12


title: AXLSIGLEC6_CD11Cplus_S13


title: AXLSIGLEC6_CD11Cplus_S11


title: AXLSIGLEC6_CD11Cplus_S26


title: AXLSIGLEC6_CD11Cminus_S8


title: AXLSIGLEC6_CD11Cminus_S7


title: AXLSIGLEC6_CD11Cminus_S6


title: AXLSIGLEC6_CD11Cplus_S25


title: AXLSIGLEC6_CD11Cplus_S20


title: AXLSIGLEC6_CD11Cminus_S46


title: AXLSIGLEC6_CD11Cplus_S2


title: AXLSIGLEC6_CD11Cplus_S18


title: AXLSIGLEC6_CD11Cplus_S16


title: AXLSIGLEC6_CD11Cplus_S10


title: AXLSIGLEC6_CD11Cminus_S40


title: AXLSIGLEC6_CD11Cminus_S41


title: AXLSIGLEC6_CD11Cplus_S1


title: AXLSIGLEC6_CD11Cminus_S9


title: AXLSIGLEC6_CD11Cminus_S5


title: AXLSIGLEC6_CD11Cminus_S47


title: AXLSIGLEC6_CD11Cminus_S4


title: AXLSIGLEC6_CD11Cminus_S39


title: AXLSIGLEC6_CD11Cminus_S37


title: AXLSIGLEC6_CD11Cminus_S36


title: AXLSIGLEC6_CD11Cminus_S45


title: AXLSIGLEC6_CD11Cminus_S35


title: AXLSIGLEC6_CD11Cminus_S33


title: AXLSIGLEC6_CD11Cminus_S32


title: AXLSIGLEC6_CD11Cminus_S44


title: AXLSIGLEC6_CD11Cminus_S31


title: AXLSIGLEC6_CD11Cminus_S43


title: AXLSIGLEC6_CD11Cminus_S42


title: AXLSIGLEC6_CD11Cminus_S28


title: AXLSIGLEC6_CD11Cminus_S27


title: AXLSIGLEC6_CD11Cminus_S26


title: AXLSIGLEC6_CD11Cminus_S24


title: AXLSIGLEC6_CD11Cminus_S38


title: AXLSIGLEC6_CD11Cminus_S23


title: AXLSIGLEC6_CD11Cminus_S34


title: AXLSIGLEC6_CD11Cminus_S22


title: AXLSIGLEC6_CD11Cminus_S20


title: AXLSIGLEC6_CD11Cminus_S2


title: AXLSIGLEC6_CD11Cminus_S3


title: AXLSIGLEC6_CD11Cminus_S21


title: AXLSIGLEC6_CD11Cminus_S16


title: AXLSIGLEC6_CD11Cminus_S25


title: AXLSIGLEC6_CD11Cminus_S17


title: AXLSIGLEC6_CD11Cminus_S14


title: AXLSIGLEC6_CD11Cminus_S15


title: Mono_nonclassical_S99

description:
paired-end RNA-seq data
processed data file:
raw.expMatrix_DCnMono.discovery.set.submission.txt


title: Mono_nonclassical_S97


title: AXLSIGLEC6_CD11Cminus_S13


title: AXLSIGLEC6_CD11Cminus_S18


title: AXLSIGLEC6_CD11Cminus_S19


title: AXLSIGLEC6_CD11Cminus_S10


title: Mono_nonclassical_S93


title: Mono_nonclassical_S94


title: AXLSIGLEC6_CD11Cminus_S12


title: AXLSIGLEC6_CD11Cminus_S11


title: AXLSIGLEC6_CD11Cminus_S1


title: Mono_nonclassical_S98


title: Mono_nonclassical_S92


title: Mono_nonclassical_S95


title: Mono_nonclassical_S96


title: Mono_nonclassical_S90


title: Mono_nonclassical_S89


title: Mono_nonclassical_S88


title: Mono_nonclassical_S84


title: Mono_nonclassical_S83


title: Mono_nonclassical_S91


title: Mono_nonclassical_S9


title: Mono_nonclassical_S82


title: Mono_nonclassical_S87


title: Mono_nonclassical_S86


title: Mono_nonclassical_S85


title: Mono_nonclassical_S79


title: Mono_nonclassical_S78


title: Mono_nonclassical_S77


title: Mono_nonclassical_S81


title: Mono_nonclassical_S75


title: Mono_nonclassical_S74


title: Mono_nonclassical_S80


title: Mono_nonclassical_S70


title: Mono_nonclassical_S8


title: Mono_nonclassical_S7


title: Mono_nonclassical_S69


title: Mono_nonclassical_S68


title: Mono_nonclassical_S76


title: Mono_nonclassical_S73


title: Mono_nonclassical_S71


title: Mono_nonclassical_S72


title: Mono_nonclassical_S67


title: Mono_nonclassical_S66


title: Mono_nonclassical_S65


title: AXLSIGLEC6_CD11Cminus_S29


title: Mono_nonclassical_S57


title: Mono_nonclassical_S59


title: Mono_nonclassical_S56


title: Mono_nonclassical_S58


title: Mono_nonclassical_S54


title: Mono_nonclassical_S64


title: Mono_nonclassical_S63


title: Mono_nonclassical_S52


title: Mono_nonclassical_S50


title: Mono_nonclassical_S51


title: Mono_nonclassical_S62


title: Mono_nonclassical_S49


title: Mono_nonclassical_S61


title: Mono_nonclassical_S6


title: Mono_nonclassical_S60


title: Mono_nonclassical_S53


title: Mono_nonclassical_S55


title: Mono_nonclassical_S46


title: Mono_nonclassical_S5


title: Mono_nonclassical_S43


title: Mono_nonclassical_S41


title: Mono_nonclassical_S48


title: Mono_nonclassical_S47


title: Mono_nonclassical_S40


title: Mono_nonclassical_S4


title: Mono_nonclassical_S42


title: Mono_nonclassical_S39


title: Mono_nonclassical_S44


title: Mono_nonclassical_S45


title: Mono_nonclassical_S34


title: Mono_nonclassical_S29


title: Mono_nonclassical_S38


title: Mono_nonclassical_S25


title: Mono_nonclassical_S37


title: Mono_nonclassical_S33


title: Mono_nonclassical_S24


title: Mono_nonclassical_S35


title: Mono_nonclassical_S31


title: Mono_nonclassical_S32


title: Mono_nonclassical_S30


title: Mono_nonclassical_S22


title: Mono_nonclassical_S26


title: Mono_nonclassical_S27


title: Mono_nonclassical_S19


title: Mono_nonclassical_S36


title: Mono_nonclassical_S17


title: Mono_nonclassical_S15


title: Mono_nonclassical_S2


title: Mono_nonclassical_S3


title: Mono_nonclassical_S124


title: Mono_nonclassical_S16


title: Mono_nonclassical_S123


title: Mono_nonclassical_S18


title: Mono_nonclassical_S20


title: Mono_nonclassical_S28


title: Mono_nonclassical_S23


title: Mono_nonclassical_S13


title: Mono_nonclassical_S14


title: Mono_nonclassical_S21


title: Mono_nonclassical_S115


title: Mono_nonclassical_S120


title: Mono_nonclassical_S118