title: W50_WT_rep4

type: mixed

city: Carlton

first: Catherine

last: Butler

state: VIC

address: 720 Swanston St

department: The Melbourne Dental School

institute: The University of Melbourne

hyb_protocol: Slides were hybridised using either heme-excess or heme-limited samples labelled with Cy3, combined with a universal genomic reference labelled with Cy5. Prior to hybridisation, microarray slides were immersed for 1 h in blocking solution (35% formamide, 1% BSA, 0.1% SDS, 5X SSPE [1X SSPE is 150 mM NaCl, 10 mM NaH2PO4, 1 mM EDTA]) at 42ºC. After blocking, slides were briefly washed in H2O followed by 99% ethanol and then dried by centrifugation. Labelled cDNAs were resuspended in 55 µL of hybridization buffer (35% formamide, 5X SSPE, 0.1% SDS, 0.1 mg/mL Salmon Sperm DNA) and denatured at 95ºC for 5 min, and then applied to slides and covered with LifterSlips (Erie Scientific). Hybridisation was performed at 42ºC for 16 h. Following hybridisation, slides were successively washed in 0.1% SDS plus 2X SSC [1X SSC is 150 mM NaCl 15 mM sodium citrate] (5 min at 42 ºC, all further washes performed at room temperature), 0.1% SDS plus 0.1X SSC (10 min), 0.1X SSC (4 washes, 1 min each), and then quickly immersed in 0.01X SSC, then 99% ethanol and using centrifugation to dry the slides.

scan_protocol: GenePix 4000B microarray scanner (Molecular Devices) at 532 nm (Cy3) and 635 nm (Cy5) with a 10 µm resolution and laser power at 10 %. PMT setting adjusted to obtain a 1:1 ratio of Cy3:Cy5. Pictures of both channels saved as 16-bit tiff files.

data_processing: Image analysis was performed using the GenePix Pro 6.0 software (Molecular Devices), and “morph” background values were used as the background estimates in further analysis.  The LIMMA software package (Smyth, 2005) was used to normalize the within-array data by subtracting the morph background and using the loess method to fit a global loess curve. Between-array normalization was also carried out for all arrays in the series using the VSN method.

organism: Porphyromonas gingivalis W50

source_name: Wild type W50

label_protocol: cDNA was synthesized from 10 µg total RNA using the SuperScript Plus Indirect cDNA labelling system (Invitrogen) primed with 5 µg random hexamers. cDNA was labelled using the Cy3 post-labelling reactive dye pack (GE) and purified using the purification module of the Invitrogen labelling system.

growth_protocol: Porphyromonas gingivalis W50 wild type grown in continuous culture under conditions of heme-excess (BHI with 5 µg/mL hemin).

extract_protocol: Samples were stabilized with 0.2 volumes of 5% phenol in absolute ethanol, then pelleted by centrifugation and frozen in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's instructions but enhanced with mechanical lysis (Precellys 24 homogenizer - Bertin Technologies, Lysing Matrix B Glass Beads - MP Biomedicals). RNA was further purified using the Illustra RNAspin Mini RNA Isolation kit (GE) according to the manufacturer's instructions including on-column DNase treatment.

tag: strain/background

value: wild type

tag: chemostat

value: B

tag: biological replicate

source_name: Genomic DNA reference

label_protocol: 400 ng of genomic DNA was used to synthesize dUTP-incorporated DNA with the BioPrime Plus Array CGH Indirect Genomic Labelling System (Invitrogen), and then labelled using the Cy5 post-labelling reactive dye pack (GE) and purified using the purification module of the Invitrogen labelling system.

extract_protocol: Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen) in accordance with the manufacturer's instructions.


title: W50_WT_rep3

status: Public on Dec 31 2021

country: Australia

molecule: total RNA

tag: genotype/variation

value: A

molecule: genomic DNA


title: W50_WT_rep6

value: C


title: P2930_328

type: SRA

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
full-lenght RNA-seq
P2930.tsv

library_source: transcriptomic

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Mouse: Gencode release 21, assembly GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 22 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 140 pg of the amplified cDNA were fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera® libraries from 384 cells was carried out in one lane on a Illumina HiSeq2500 v4.
Full-length single-cell RNA sequencing libraries were prepared using the Smart-seq2 protocol
single cell RNA-seq (scRNA-seq)

tag: protocol

tag: cell type

value: Glioblastoma

tag: treatment

value: EGFR


title: Mouse Lung epithelial cells rep1

type: other

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Labeled RNA was hybridized to Agilent custom UCSF miRNA v3.4 multi-species 8x15K Ink-jet arrays (Agilent). Hybridizations were performed for 16 hrs according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent).

data_processing: Raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent)

molecule: other

source_name: Mouse Lung epithelial cells rep1

label_protocol: miRNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers’ protocol

growth_protocol: To prepare embryonic lung epithelium, noon of the day when a vaginal plug was detected was considered approximately E0.5. Embryos were collected in cold 1 X phosphate buffered saline (PBS). Lungs were dissected out from embryos at the E13.5 stages. Epithelium and mesenchyme were separated as reported previously86.  For adult donor cell preparation, female mice of 10-weeks of age were sacrificed and perfused with PBS. Lungs and mammary glands were harvested, minced and dissociated in buffer [5% fetal bovine serum (FBS), insulin 5 µg/ml, Penicillin-Streptomycin 100 U/ml in DMEM/F12] containing trypsin (2 mg/ml) and collagenase A (2 mg/ml) for 45 minutes and 30 minutes, respectively, at 37ºC. Primary epithelia were purified by differential centrifugation: specifically, lung and mammary epithelia were washed in dissociation buffer without collagenase and collected using a swing-bucket centrifuge at 400 X g. The process was repeated for seven and five times for lung and mammary tissues, respectively. To prepare single cells, primary epithelia from embryonic lung and adult lung and mammary gland were washed in Hank’s (Ca2+ Mg2+ free) buffer and dissociated in 0.05% Trypsin/EDTA buffer. Cells were counted using a Hausser Scientific Hemocytometer and prepared in 50% Matrigel™ (growth factor reduced, BD Biosciences) for transplantation.

extract_protocol: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: tissue

value: lung

value: epithelial cells


title: W50_WT_rep7


title: feoB_mutant_rep5

organism: Porphyromonas gingivalis

source_name: FeoB mutant

growth_protocol: Porphyromonas gingivalis FeoB mutant of W50 grown in continuous culture under conditions of heme-excess (BHI with 5 µg/mL hemin).

value: FeoB mutant

value: F


title: feoB_mutant_rep1

value: D


title: W50_WT_rep5


title: feoB_mutant_rep3

value: E


title: W50_WT_rep2


title: feoB_mutant_rep2


title: P2930_324

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_326

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_325

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_334

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_330

description:
full-lenght RNA-seq
P2930.tsv


title: SUM159, SCGB3A1 OE, biological rep3

type: RNA

city: Heidelberg

first: Tsunaki

last: Hongu

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Junior Research Group Metastatic Niches

country: Germany

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

description: Gene expression of SUM159 cells with ectopic SCGB3A1 expression

hyb_protocol: 15 μg of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Applied Biosystems™ GeneChip® Human Genome U133 Plus 2.0 Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data were normalized using quantile normalization with R using function normalize.quantiles from Bioconductor package preprocessCore.

label: biotin

organism: Homo sapiens

label_protocol: The Applied Biosystems™ Gene Chip 3’ IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100 ng total RNA. Label: Biotin.

growth_protocol: SUM159 breast cancer cells were cultured in DMEM/F12 medium (ThermoFisher Scientific) with 5% FBS, 5 μg/ml human insulin (Sigma-Aldrich), 50 U/ml penicillin (Sigma-Aldrich) and 50 μg/ml streptomycin (Sigma-Aldrich) for 1 day. Cells were trypsinized and seeded in ultra-low attachment cell culture plate at a density of 12,500 cells/ml with HuMEC-medium (Invitrogen) supplemented 0.1% BSA and B27 Supplement (Gibco).

extract_protocol: RNA extraction was performed using the QIAGEN RNeasy Mini Kit according to the manufacturer’s protocol.

treatment_protocol: Control cells and cells expressing SCGB3A1 were cultured for 5 days in ultra-low attachment cell culture plate.

value: Breast cancer cells

tag: cell line


title: SUM159, SCGB3A1 OE, biological rep1

source_name: SUM159 cells with ectopic SCGB3A1 expression


title: SUM159, empty, biological rep3

description: Gene expression of SUM159 cells with empty vec.

source_name: SUM159 cells with empty vec.


title: P2930_322

description:
full-lenght RNA-seq
P2930.tsv


title: SUM159, SCGB3A1 OE, biological rep2


title: SUM159, empty, biological rep2


title: feoB_mutant_rep4


title: feoB_mutant_rep6


title: P2930_323

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_316

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_319

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_320

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_321

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_318

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_315

description:
full-lenght RNA-seq
P2930.tsv


title: SUM159, empty, biological rep1


title: pat088_v3

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

country: Austria

institute: AIT

hyb_protocol: Hybridization was carried out overnight (16h) at 45° C in the GeneChipR Hybridization Oven 640 (Affymetrix, St. Clara, CA). Subsequent washing and staining protocols were performed with the Affymetrix Fluidics Station 450. For signal enhancement, antibody amplification was carried out using a biotinylated anti-streptavidin antibody (Vector Laboratories, U.K.), which was cross-linked by a goat IgG (Sigma, Germany) followed by a second staining with streptavidin-phycoerythrin conjugate (Molecular Probes, Invitrogen).

scan_protocol: Microarray scanning was done with the GeneChip Scanner 3000 (Affymetrix, St. Clara, CA) at 1.56 micron resolution.

data_processing: MAS 5.0 (Microarray Suite statistical algorithm, Affymetrix) probe level analysis was used employing GeneChip Operating Software (GCOS 1.4).

source_name: transbronchial biopsy

label_protocol: 3`Amplifikation One-Cycle Target Labeling and Control reagents (Affymetrix, St. Clara, CA).

extract_protocol: Qiagen Rneasy

treatment_protocol: transbronchial biopsy

value: transbronchial biopsy

tag: visit

value: healthy

value: Healthy

tag: patid


title: pat087_v3

value: II

value: O

value: Severe


title: P2930_317

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_314

description:
full-lenght RNA-seq
P2930.tsv


title: pat088_v2


title: Twin B at T1

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 265 Crittenden Blvd, Box 655c

country: USA

institute: University of Rochester

hyb_protocol: cRNA was hybridized to Affymetrix HG-U133 Plus 2.0 microarrays (Affymetrix Inc, Santa Clara, CA) and stained with streptavidin-phycoerythrin, followed by a through washing.

scan_protocol: Raw data were obtained by laser scanning imaging

data_processing: Partek Genomics Suite software, version 6.6 (Partek Inc, St. Louis, MO), was utilized for all analyses performed on microarray data.

source_name: PBMCs,control,6 hours post-injury

label_protocol: Using the GeneChip 3′ IVT Expression kit, each RNA (100 ng) sample was reverse transcribed, converted to biotinylated complementary RNA.

extract_protocol: Total RNA was isolated from PBMCs using TRIzol® Plus RNA Purification Kits (Life Technologies, Grand Island, NY), and was treated with DNase I-Amplification Grade Kits (Life Technologies).

tag: phenotype/time point

value: control twin at 6 hours post-injury

value: PBMCs


title: Twin B at T0

source_name: PBMCs,control,baseline

value: control twin at baseline


title: Twin A at T1

source_name: PBMCs,concussed,6 hours post-injury

value: concussed twin at 6 hours post-injury


title: Twin A at T2

source_name: PBMCs,concussed,7 days post-injury

value: concussed twin at 7 days post-injury


title: P2930_308

description:
full-lenght RNA-seq
P2930.tsv

value: Glioblastoma

value: EGFR


title: P2930_313

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_312

description:
full-lenght RNA-seq
P2930.tsv


title: pat088_v1


title: P2930_309

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_310

description:
full-lenght RNA-seq
P2930.tsv


title: Twin B at T2

source_name: PBMCs,control,7 days post-injury

value: control twin at 7 days post-injury


title: pat087_v2


title: pat086_v1

value: Productive


title: P2930_307

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_306

description:
full-lenght RNA-seq
P2930.tsv


title: pat085_v3


title: pat087_v1


title: pat086_v2


title: Twin A at T0

source_name: PBMCs,concussed,baseline

value: concussed twin at baseline


title: pat085_v2


title: pat084_v2

value: I


title: P2930_302

description:
full-lenght RNA-seq
P2930.tsv


title: pat084_v1

value: transbronchial biopsy


title: P2930_305

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_304

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_311

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_301

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_303

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_300

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_299

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_298

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_296

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_295

description:
full-lenght RNA-seq
P2930.tsv


title: pat082_v2


title: P2930_297

description:
full-lenght RNA-seq
P2930.tsv


title: pat081_v3


title: pat081_v1


title: pat082_v1


title: pat083_v1

value: III


title: pat083_v2


title: pat080_v3


title: P2930_294

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_292

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_293

description:
full-lenght RNA-seq
P2930.tsv


title: pat079_v2


title: pat080_v1


title: pat081_v2


title: P2930_290

description:
full-lenght RNA-seq
P2930.tsv


title: pat080_v2


title: P2930_289

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_291

description:
full-lenght RNA-seq
P2930.tsv


title: P2805_192

description:
full-lenght RNA-seq
P2805.tsv

value: PDGFR


title: P2805_191

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_189

description:
full-lenght RNA-seq
P2805.tsv


title: pat075_v2


title: pat079_v1

value: II


title: pat076_v1

value: healthy

value: Healthy


title: pat077_v3

value: Severe


title: P2805_187

description:
full-lenght RNA-seq
P2805.tsv


title: pat078_v1

value: O


title: P2805_188

description:
full-lenght RNA-seq
P2805.tsv


title: pat077_v2


title: pat077_v1


title: pat074_v2


title: pat073_v3


title: pat075_v1


title: P2805_186

description:
full-lenght RNA-seq
P2805.tsv

source_name: Empty


title: pat073_v2


title: P2805_185

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_184

description:
full-lenght RNA-seq
P2805.tsv


title: pat076_v2


title: P2805_183

description:
full-lenght RNA-seq
P2805.tsv


title: pat074_v1


title: pat073_v1


title: P2805_182

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_179

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_180

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_181

description:
full-lenght RNA-seq
P2805.tsv


title: pat072_v1


title: pat070_v1


title: pat070_v2


title: P2805_178

description:
full-lenght RNA-seq
P2805.tsv


title: pat069_v2


title: P2805_172

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_171

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_173

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_176

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_175

description:
full-lenght RNA-seq
P2805.tsv


title: pat072_v2


title: P2805_177

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_170

description:
full-lenght RNA-seq
P2805.tsv


title: pat068_v2


title: pat071_v2


title: pat069_v3


title: pat071_v1


title: pat068_v3


title: pat068_v1


title: P2805_174

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_168

description:
full-lenght RNA-seq
P2805.tsv


title: pat067_v2


title: P2805_169

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_167

description:
full-lenght RNA-seq
P2805.tsv


title: pat069_v1


title: P2805_166

description:
full-lenght RNA-seq
P2805.tsv


title: pat066_v3


title: pat066_v2


title: P2805_165

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_164

description:
full-lenght RNA-seq
P2805.tsv


title: pat066_v1


title: pat067_v3


title: P2805_160

description:
full-lenght RNA-seq
P2805.tsv


title: pat067_v1


title: P2805_161

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_163

description:
full-lenght RNA-seq
P2805.tsv


title: pat064_v2


title: pat065_v1


title: pat065_v3


title: pat065_v2


title: P2805_158

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_157

description:
full-lenght RNA-seq
P2805.tsv


title: pat064_v3


title: P2805_155

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_156

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_162

description:
full-lenght RNA-seq
P2805.tsv


title: pat063_v3


title: pat064_v1


title: P2805_152

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_190

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_153

description:
full-lenght RNA-seq
P2805.tsv


title: pat063_v1


title: P2805_159

description:
full-lenght RNA-seq
P2805.tsv


title: pat061_v3


title: P2805_150

description:
full-lenght RNA-seq
P2805.tsv


title: pat061_v2


title: pat062_v1


title: pat061_v1


title: P2805_151

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_148

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_154

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_149

description:
full-lenght RNA-seq
P2805.tsv


title: pat062_v3


title: P2805_144

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_146

description:
full-lenght RNA-seq
P2805.tsv


title: pat063_v2


title: pat060_v2


title: pat060_v1


title: pat058_v3


title: P2805_145

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_143

description:
full-lenght RNA-seq
P2805.tsv


title: pat059_v2


title: pat059_v3


title: P2805_141

description:
full-lenght RNA-seq
P2805.tsv


title: pat058_v1


title: P2805_142

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_140

description:
full-lenght RNA-seq
P2805.tsv


title: pat058_v2


title: pat056_v2


title: pat057_v2


title: pat057_v1


title: P2805_138

description:
full-lenght RNA-seq
P2805.tsv


title: pat056_v3


title: P2805_139

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_135

description:
full-lenght RNA-seq
P2805.tsv


title: pat056_v1


title: P2805_137

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_136

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_134

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_147

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_133

description:
full-lenght RNA-seq
P2805.tsv


title: pat059_v1


title: pat054_v3


title: P2805_132

description:
full-lenght RNA-seq
P2805.tsv


title: pat054_v2


title: pat052_v2


title: P2805_131

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_130

description:
full-lenght RNA-seq
P2805.tsv


title: pat054_v1


title: P2805_128

description:
full-lenght RNA-seq
P2805.tsv


title: pat051_v1


title: pat053_v2


title: P2805_129

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_127

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_126

description:
full-lenght RNA-seq
P2805.tsv


title: pat053_v1


title: pat052_v1


title: pat050_v2

value: IV


title: pat055_v1


title: pat050_v1


title: P2805_122

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_124

description:
full-lenght RNA-seq
P2805.tsv


title: pat048_v3


title: P2805_125

description:
full-lenght RNA-seq
P2805.tsv


title: pat049_v1


title: P2805_120

description:
full-lenght RNA-seq
P2805.tsv


title: pat047_v3


title: pat048_v2


title: pat047_v1


title: pat047_v2


title: P2805_121

description:
full-lenght RNA-seq
P2805.tsv


title: pat045_v3


title: P2805_119

description:
full-lenght RNA-seq
P2805.tsv


title: pat045_v2


title: P2805_118

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_116

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_123

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_115

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_114

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_117

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_113

description:
full-lenght RNA-seq
P2805.tsv


title: pat045_v1


title: P2805_112

description:
full-lenght RNA-seq
P2805.tsv


title: pat041_v2


title: pat040_v2


title: pat041_v1


title: pat044_v3


title: pat046_v3


title: P2805_111

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_109

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_110

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_108

description:
full-lenght RNA-seq
P2805.tsv


title: pat042_v1


title: pat040_v1


title: pat043_v1


title: P2805_107

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_104

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_106

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_105

description:
full-lenght RNA-seq
P2805.tsv


title: pat037_v3


title: P2805_102

description:
full-lenght RNA-seq
P2805.tsv


title: pat039_v2


title: P2805_103

description:
full-lenght RNA-seq
P2805.tsv


title: pat038_v2


title: P2805_098

description:
full-lenght RNA-seq
P2805.tsv


title: P2805_097

description:
full-lenght RNA-seq
P2805.tsv


title: pat038_v1


title: pat039_v1


title: pat037_v1


title: pat035_v3


title: pat035_v2


title: P2804_381

description:
full-lenght RNA-seq
P2804.tsv


title: pat034_v1


title: pat033_v2


title: pat037_v2


title: pat043_v2


title: P2804_384

description:
full-lenght RNA-seq
P2804.tsv


title: pat036_v1


title: pat034_v3


title: P2805_100

description:
full-lenght RNA-seq
P2805.tsv


title: P2804_383

description:
full-lenght RNA-seq
P2804.tsv


title: P2805_099

description:
full-lenght RNA-seq
P2805.tsv


title: P2804_382

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_377

description:
full-lenght RNA-seq
P2804.tsv


title: P2805_101

description:
full-lenght RNA-seq
P2805.tsv


title: P2804_379

description:
full-lenght RNA-seq
P2804.tsv


title: pat034_v2


title: P2804_375

description:
full-lenght RNA-seq
P2804.tsv


title: pat035_v1


title: pat032_v1


title: P2804_378

description:
full-lenght RNA-seq
P2804.tsv


title: pat030_v3


title: pat031_v1


title: pat031_v2


title: pat033_v1


title: P2804_373

description:
full-lenght RNA-seq
P2804.tsv


title: pat028_v3


title: P2804_374

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_370

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_376

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_380

description:
full-lenght RNA-seq
P2804.tsv


title: pat030_v2


title: pat028_v2


title: P2804_372

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_368

description:
full-lenght RNA-seq
P2804.tsv


title: pat029_v1


title: P2804_371

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_365

description:
full-lenght RNA-seq
P2804.tsv


title: pat027_v1


title: pat029_v2


title: P2804_363

description:
full-lenght RNA-seq
P2804.tsv


title: pat027_v3


title: P2804_369

description:
full-lenght RNA-seq
P2804.tsv


title: pat026_v1


title: P2804_366

description:
full-lenght RNA-seq
P2804.tsv


title: pat025_v3


title: P2804_367

description:
full-lenght RNA-seq
P2804.tsv


title: pat028_v1


title: P2804_364

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_362

description:
full-lenght RNA-seq
P2804.tsv


title: pat026_v2


title: pat026_v3


title: P2804_359

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_361

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_360

description:
full-lenght RNA-seq
P2804.tsv


title: pat024_v2


title: pat025_v1


title: pat023_v2


title: pat027_v2


title: pat025_v2


title: P2804_353

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_356

description:
full-lenght RNA-seq
P2804.tsv


title: pat023_v1


title: pat022_v1


title: pat022_v2


title: P2804_352

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_355

description:
full-lenght RNA-seq
P2804.tsv


title: pat024_v1


title: P2804_357

description:
full-lenght RNA-seq
P2804.tsv


title: pat021_v3


title: pat022_v3


title: pat020_v3


title: P2804_354

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_358

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_350

description:
full-lenght RNA-seq
P2804.tsv


title: pat021_v1


title: pat021_v2


title: P2804_348

description:
full-lenght RNA-seq
P2804.tsv


title: pat023_v3


title: P2804_351

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_349

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_346

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_345

description:
full-lenght RNA-seq
P2804.tsv


title: pat018_v2


title: pat020_v1


title: pat018_v3


title: pat019_v1


title: pat020_v2


title: P2804_341

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_347

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_339

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_338

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_342

description:
full-lenght RNA-seq
P2804.tsv


title: pat017_v1


title: P2804_336

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_344

description:
full-lenght RNA-seq
P2804.tsv


title: pat017_v2


title: pat018_v1


title: P2804_337

description:
full-lenght RNA-seq
P2804.tsv


title: pat016_v1


title: pat016_v2


title: P2804_333

description:
full-lenght RNA-seq
P2804.tsv


title: pat014_v2


title: pat017_v3


title: P2804_331

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_343

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_335

description:
full-lenght RNA-seq
P2804.tsv


title: pat015_v1


title: P2804_329

description:
full-lenght RNA-seq
P2804.tsv


title: pat013_v1


title: pat011_v3


title: pat012_v1


title: P2804_334

description:
full-lenght RNA-seq
P2804.tsv


title: pat016_v3


title: P2804_330

description:
full-lenght RNA-seq
P2804.tsv


title: pat011_v2


title: P2804_332

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_326

description:
full-lenght RNA-seq
P2804.tsv


title: pat014_v1


title: P2804_328

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_324

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_327

description:
full-lenght RNA-seq
P2804.tsv


title: pat010_v1


title: P2804_323

description:
full-lenght RNA-seq
P2804.tsv


title: pat010_v3


title: P2804_325

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_340

description:
full-lenght RNA-seq
P2804.tsv


title: pat011_v1


title: pat013_v2


title: pat009_v2


title: P2804_322

description:
full-lenght RNA-seq
P2804.tsv


title: pat009_v3


title: pat009_v1


title: P2804_319

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_318

description:
full-lenght RNA-seq
P2804.tsv


title: pat032_v2


title: P2804_317

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_316

description:
full-lenght RNA-seq
P2804.tsv


title: pat008_v2


title: P2804_313

description:
full-lenght RNA-seq
P2804.tsv


title: pat006_v1


title: P2804_320

description:
full-lenght RNA-seq
P2804.tsv


title: pat007_v3


title: P2804_312

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_321

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_315

description:
full-lenght RNA-seq
P2804.tsv


title: pat007_v1


title: P2804_314

description:
full-lenght RNA-seq
P2804.tsv


title: pat006_v3


title: pat008_v1


title: P2804_308

description:
full-lenght RNA-seq
P2804.tsv


title: pat007_v2


title: pat005_v2


title: P2804_307

description:
full-lenght RNA-seq
P2804.tsv


title: pat005_v1


title: pat015_v2


title: pat004_v3


title: pat002_v3


title: P2804_311

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_309

description:
full-lenght RNA-seq
P2804.tsv


title: pat004_v1


title: pat003_v1


title: P2804_306

description:
full-lenght RNA-seq
P2804.tsv


title: pat002_v1


title: pat003_v2


title: pat002_v2


title: P2804_301

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_298

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_305

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_299

description:
full-lenght RNA-seq
P2804.tsv


title: pat001_v1


title: P2804_304

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_303

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_294

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_302

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_292

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_296

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_297

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_295

description:
full-lenght RNA-seq
P2804.tsv


title: IL17A 4

city: New York

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

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

source_name: IL17A 200ng/ml IL17A

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subject

tag: group

tag: stimulation

value: IL17A 200ng/ml

value: keratinocyte


title: P2804_290

description:
full-lenght RNA-seq
P2804.tsv

value: Glioblastoma


title: pat004_v2


title: P2804_289

description:
full-lenght RNA-seq
P2804.tsv


title: Control 3

source_name: medium Control

value: Control

value: medium


title: P2803_288

description:
full-lenght RNA-seq
P2803.tsv


title: IL17A 6


title: IL36G 8

source_name: IL36G 100ng/ml IL36G

value: IL36G 100ng/ml


title: IL36G 9


title: IL17A 5


title: Control 2


title: IL36G 7


title: IL36GplusIL17A 10

source_name: IL36G 100ng/ml + IL17A 200ng/ml IL36GplusIL17A

value: IL36G 100ng/ml + IL17A 200ng/ml


title: IL36GplusIL17A 11


title: Control 1

source_name: medium  Control


title: IL36GplusIL17A 12


title: P2803_287

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_285

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_286

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_284

description:
full-lenght RNA-seq
P2803.tsv


title: P2804_291

description:
full-lenght RNA-seq
P2804.tsv


title: P2804_293

description:
full-lenght RNA-seq
P2804.tsv


title: P2803_280

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_283

description:
full-lenght RNA-seq
P2803.tsv


title: NHLF3 co-culture

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

hyb_protocol: Following fragmentation and labeling, ss-cDNA were hybridized for 16 hr at 45°C oto Clariom S Human Arrays. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix, P/N 00-0079).

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

data_processing: The raw CEL files were normalized using RMA background correction with quantile normalization, log2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes were considered significant if p-value with FDR ≤ 0.05 and fold-change of >2 or < -2.

source_name: Normal lung fibroblast donor 3 co-culture

label_protocol: Affymetrix GeneChipTM WT PLUS Reagent Kit

growth_protocol: Cells were grown at 37˚C and 5% CO2 in 24-well Boyden chamber (Transwell) plates  (0.4μm pore) with fibroblasts plated in the well and 621-101 cells in the insert as required. Medium was phenol red free DMEM-F12 with 10nM β-oestradiol.

extract_protocol: Cells were washed with phosphate buffered saline then total RNA extracted using GenElute™ Mammalian Total RNA Miniprep Kit (Sigma, Dorset, UK), and contaminating genomic DNA was removed using On-Column DNase I digest set (Sigma, Dorset, UK), according to the manufacturer's protocols.

treatment_protocol: Cells were cultured for 96 hours in monoculture (no 621 cells) or co-culture (+ 621 cells)

tag: individual

value: donor 3

tag: disease state

value: Normal

value: NHLFs

tag: growth conditions

value: co-culture


title: NHLF2 control/monoculture

source_name: Normal lung fibroblast donor 2 control/monoculture

value: donor 2

value: control/monoculture


title: LAF3 control/monoculture

source_name: LAF donor 3 control/monoculture

value: LAM

value: LAFs


title: NHLF1 co-culture

source_name: Normal lung fibroblast donor 1 co-culture

value: donor 1


title: LAF2 co-culture

source_name: LAF donor 2 co-culture


title: LAF1 control/monoculture

source_name: LAF donor 1 control/monoculture


title: P2803_281

description:
full-lenght RNA-seq
P2803.tsv


title: NHLF2 co-culture

source_name: Normal lung fibroblast donor 2 co-culture


title: P2803_277

description:
full-lenght RNA-seq
P2803.tsv


title: LAF2 control/monoculture

source_name: LAF donor 2 control/monoculture


title: NHLF3 control/monoculture

source_name: Normal lung fibroblast donor 3 control/monoculture


title: LAF1 co-culture

source_name: LAF donor 1 co-culture


title: NHLF1 control/monoculture

source_name: Normal lung fibroblast donor 1 control/monoculture


title: LAF3 co-culture

source_name: LAF donor 3 co-culture


title: P2803_279

description:
full-lenght RNA-seq
P2803.tsv


title: SUM-LM1, treated with Activin B, biological rep2

description: Gene expression of SUM-LM1 cells treated with recombinant Activin B

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Applied Biosystems™ GeneChip® Human Genome U133 Plus 2.0 Arrays.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore.

label_protocol: The Applied Biosystems™ Gene Chip 3’ IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 50 ng total RNA. Label: Biotin.

growth_protocol: SUM-LM1 breast cancer cells were cultured in DMEM/F12 medium (ThermoFisher Scientific) with 5% FBS, 5 ug/ml human insulin (Sigma-Aldrich), 50 U/ml penicillin (Sigma-Aldrich) and 50 ug/ml streptomycin (Sigma-Aldrich) for 1 day. Cells were tripsinized and seeded in ultra-low attachment cell culture plate at a density of 12,500 cells/ml with HuMEC-medium (Invitrogen) supplemented 0.1% BSA with or without 50 ng/ml of recombinant human Activin B (R&D systems).

treatment_protocol: Cells were stimulated with 50 ng/ml recombinant human Activin B or vehicle (0.1% BSA/PBS) for 6 hrs.

value: Breast cancer cells

value: Activin B


title: P2803_282

description:
full-lenght RNA-seq
P2803.tsv


title: SUM-LM1, treated with Activin B, biological rep3

source_name: SUM-LM1 cells treated with recombinant Activin B


title: P2803_276

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_275

description:
full-lenght RNA-seq
P2803.tsv


title: pat012_v2

source_name: transbronchial biopsy

value: transbronchial biopsy

value: O

value: I

value: Productive


title: P2803_274

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: P2803_278

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_273

description:
full-lenght RNA-seq
P2803.tsv


title: SUM-LM1, treated with control vehicle, biological rep1

description: Gene expression of SUM-LM1 cells treated with vehicle

source_name: SUM-LM1 cells treated with vehicle

value: Vehicle


title: P2803_272

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_271

description:
full-lenght RNA-seq
P2803.tsv


title: SUM-LM1, treated with Activin B, biological rep1


title: SUM-LM1, treated with control vehicle, biological rep3


title: P2803_269

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_268

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_266

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_267

description:
full-lenght RNA-seq
P2803.tsv


title: pop4

city: Suita

first: Fumihiro

last: Fujiki

address: Yamada-oka, 1-7

country: Japan

institute: Osaka University Graduate School of Medicine

description:
EA0565_03
Gene expression data from Terminal E population of CD4+ T cell clone.

scan_protocol: Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed GeneChip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

data_processing: The data were analyzed with MAS5 statistical Algorithm using Expression Console. The trimmed mean target intensity of each array was arbitrarily set to 500 (TGT500).

source_name: CD62L-CD127- cells from CD4+ T cell clone

growth_protocol: A WT1-specific CD4+ T cell clone was expanded by the stimulation with WT1 peptide-pulsed dendritic cells and IL-2 in 10% AB serum/X-VIVO 15 medium.

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

tag: differentiation stage

value: terminal effector


title: P2803_265

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_264

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_263

description:
full-lenght RNA-seq
P2803.tsv


title: pop2

description:
EA0565_02
Gene expression data from EM population of CD4+ T cell clone.

hyb_protocol: Detailed GeneChip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

source_name: CD62L-CD127+ cells from CD4+ T cell clone

value: effector memory


title: P2803_270

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_262

description:
full-lenght RNA-seq
P2803.tsv


title: CN Tissue

city: Seoul

first: Sun Ha

last: Paek

address: 101 Daehak-ro,  Jongno-gu

department: Neurosurgery

country: South Korea

institute: Seoul National University

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human U133Plus 2.0 Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The MAS 5.0 algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: CN patient

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Methods for establishment of primary cultures for this study were approved by the Institutional Review Board (IRB) at Seoul National University Hospital (IRB No; C-0710-040-223).  Tissues were mechanically dissected and enzymatically dissociated to single-cell suspensions using papain (Sigma, St. Louis, MO) and DNase I (Sigma) as described previously (Shin et al., 2010). The cells were then suspended in DMEM/F12 (Invitrogen, Carlsbad, CA) supplemented with 5 ㎍/ml insulin (Sigma), 50 ㎍/ml transferrin (Sigma), 30 nM selenium chloride (Sigma), and 5 ㎍/ml fibronectin (Sigma) (ITSFn medium),

extract_protocol: RNA was isolated from cell pellets with the RNeasy Mini Kit (Qiagen).

tag: type

value: Tumor tissue


title: P2804_310

description:
full-lenght RNA-seq
P2804.tsv


title: P2803_260

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_261

description:
full-lenght RNA-seq
P2803.tsv


title: CN-tumor shperes

value: Primary tumor cells


title: pop1

description:
EA0565_01
Gene expression data from CM population of CD4+ T cell clone.

source_name: CD62L+CD127+ cells from CD4+ T cell clone

label_protocol: Detailed GeneChip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

value: central memory


title: CN-differentiated cells


title: P2803_259

description:
full-lenght RNA-seq
P2803.tsv


title: Fetal-SVZ-derived NSCs

source_name: Fatal disease-caused aborted fetal brain


title: P2803_256

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_258

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_254

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_253

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_257

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 498pB from patient 3429

city: Innsbruck

first: Stefan

last: Schmidt

address: Anichstr. 35

institute: Medical University Innsbruck

hyb_protocol: Purified cRNA was fragmented and 20 µg were used for GeneChip hybridization following the manafacturer’s protocols (Affymetrix GeneChip Expression Analysis Technical Manual Revison #4; Eukaryotic Target Preparation, Revison #3). After staining and washing of the hybridized arrays in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.

scan_protocol: Fluorescence intensity signals were read by an Affymetrix 3000 scanner

data_processing: Image analysis was performed with the GCOS software (version 1.2) and for subsequent bioinformatics analysis the statistical programming language “R” (V2.3) and additional software package from the BioConductor library (Release 2.6) were used. Briefly, for identifying genes predicting imatinib response in this group of pre-treated CML patients   we followed a main workflow consisting of filtering genes by variance of expression, consecutive identification of differentially expressed genes and eventually applying linear discriminatory analysis for response prediction. This approach was run in a nested-cross validation manner, in which the full data set was at random divided into test and training set and this division was repeated 40 times. The resulting training sets were again split into 40 randomly chosen training and test-subsets. Within each of these training subsets feature selection and all pre-processing steps (filtering, differential expression) were performed. Features were selected for testing in the prediction algorithm based on their differential expression calculated by t-test and adjusted for multiple testing using Benjamini-Hochberg correction, if they showed a at least 1.5-fold difference in expression levels and had a adjusted significance <0.01%.

source_name: peripheral whole blood sample prior to treatment

label_protocol: Using One Cycle cDNA Synthesis- and One Cycle Target Labelling-Kit from Affymetrix biotinylated hybridization targets were generated from 1.5 µg total RNA.  Purified oligo-dT-T7-primed double-stranded cDNA was amplified by T7 polymerase in single round cRNA amplification step. Incorporation of a modified nucleotide during the latter step allowed subsequent biotinylation. Purified cRNA was fragmented and 20 µg were used for GeneChip hybridization following the manufacturer’s protocols.

growth_protocol: not applicable,no cell culture involved

extract_protocol: Peripheral whole blood samples, preserved in PAXgene tubes containing an RNA stabilizing agent,  stored at or below -20°C , processing was performed using the Affymetrix Blood RNA concentration kit according to the manufacturers' instructions. In brief, blood cells were lyzed sedimented and pelleted, Following homogenization by centrifugation through shredder columns the supernatant was transferred, centrifuged and RNA bound to column membranesDNA was digested by DNAse I treatment prior to concentration using the Affymetrix Blood RNA concentration kit.   Total RNA was consecutively depleted of haemoglobin mRNA applying the Globin Reduction kit following the manufacturer’s protocol (Preanalytix, Switzerland).

treatment_protocol: primary peripheral whole blood samples prior treatment (n=135), subset  after 6 weeks of treatment (n=65) either after 400mg imatinib once daily or 800mg imatinib once daily

tag: molecular response

value: not available

tag: gender

value: female

tag: pretreatment hydroxyurea

value: yes

tag: pretreatment interferon

tag: pretreatment busulfan

value: no

tag: pretreatment others

tag: dose

value: Imatinib 400 mg/day

tag: time point

tag: time

value: baseline

value: patient 3429

value: peripheral blood

value: prior to treatment

value: chronic myeloid leukemia


title: P2803_255

description:
full-lenght RNA-seq
P2803.tsv

tag: protocol

tag: cell type

value: Glioblastoma

tag: treatment


title: Chip No: 201pB from patient 3346

source_name: peripheral whole blood sample after 6 weeks of treatment

value: MMR

value: 6 wk

tag: subject

value: patient 3346

tag: tissue

value: imatinib


title: Chip No: 399pB from patient 3417

value: male

value: patient 3417

tag: disease state


title: Chip No: 569pB from patient 3466

value: Imatinib 800 mg/day

value: patient 3466


title: Chip No: 508pB from patient 3457

value: female

value: yes

value: patient 3457


title: Chip No: 549pB from patient 3434

value: no

value: baseline

value: patient 3434


title: P2803_251

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 282pB from patient 3365

value: Imatinib 400 mg/day

value: patient 3365

value: peripheral blood


title: Chip No: 231pB from patient 3333

value: patient 3333

value: chronic myeloid leukemia


title: P2803_248

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: P2803_250

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_252

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 237pB from patient 3354

value: MMR

value: 6 wk

value: patient 3354

value: imatinib


title: P2803_247

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_249

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 347pB from patient 3371

value: male

value: patient 3371

value: prior to treatment


title: Chip No: 262pB from patient 3339

value: female

value: yes

value: Imatinib 800 mg/day

value: patient 3339


title: Chip No: 284pB from patient 3358

value: no

value: Imatinib 400 mg/day

value: patient 3358


title: Chip No: 360pB from patient 3406

value: patient 3406

value: peripheral blood


title: Chip No: 382pB from patient 3391

value: baseline

value: patient 3391

value: chronic myeloid leukemia


title: Chip No: 307pB from patient 3342

value: MMR

value: 6 wk

value: patient 3342


title: Chip No: 279pB from patient 3364

value: patient 3364


title: P2803_245

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: Chip No: 349pB from patient 3380

value: female

value: patient 3380

value: prior to treatment


title: P2803_246

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_243

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_241

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_244

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_242

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 239pB from patient 3357

value: yes

value: Imatinib 800 mg/day

value: patient 3357

value: imatinib


title: P2803_240

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_238

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 541pB from patient 3484

value: no

value: patient 3484


title: P2803_239

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 500pB from patient 3427

value: male

value: baseline

value: patient 3427

value: peripheral blood


title: Chip No: 536pB from patient 3451

value: MMR

value: Imatinib 400 mg/day

value: patient 3451

value: chronic myeloid leukemia


title: Chip No: 197pB from patient 3349

value: not available

value: 6 wk

value: patient 3349


title: Chip No: 236pB from patient 3354

value: female

value: yes

value: patient 3354

value: prior to treatment


title: P2803_235

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: Chip No: 260pB from patient 3337

value: no

value: Imatinib 800 mg/day

value: patient 3337

value: imatinib


title: P2803_237

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 501pB from patient 3453

value: male

value: baseline

value: patient 3453

value: peripheral blood


title: Chip No: 556pB from patient 3480

value: MMR

value: patient 3480

value: chronic myeloid leukemia


title: Chip No: 316pB from patient 3367

value: patient 3367


title: P2803_234

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_233

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 540pB from patient 3454

value: female

value: Imatinib 400 mg/day

value: patient 3454


title: P2803_231

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_232

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 372pB from patient 3347

value: yes

value: patient 3347

value: prior to treatment


title: P2803_229

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: P2803_230

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_236

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_228

description:
full-lenght RNA-seq
P2803.tsv


title: SUM-LM1, treated with control vehicle, biological rep2

value: Breast cancer cells

tag: cell line

value: Vehicle


title: P2803_226

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_225

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_224

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 560pB from patient 3478

value: male

value: no

value: patient 3478


title: P2803_222

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_227

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_220

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 505pB from patient 3477

value: baseline

value: patient 3477

value: peripheral blood


title: P2803_221

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 370pB from patient 3407

value: MMR

value: Imatinib 800 mg/day

value: patient 3407

value: chronic myeloid leukemia


title: Chip No: 322pB from patient 3388

value: patient 3388


title: Chip No: 429pB from patient 3428

value: female

value: yes

value: Imatinib 400 mg/day

value: patient 3428


title: P2803_219

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: Chip No: 319pB from patient 3390

value: 6 wk

value: patient 3390

value: imatinib


title: P2803_217

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_218

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 562pB from patient 3340

value: male

value: no

value: patient 3340

value: prior to treatment


title: P2803_223

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 373pB from patient 3341

value: baseline

value: patient 3341

value: peripheral blood


title: Chip No: 216pB from patient 3351

value: not available

value: patient 3351

value: chronic myeloid leukemia


title: Chip No: 218pB from patient 3329

value: female

value: yes

value: patient 3329


title: Chip No: 266pB from patient 3372

value: MMR

value: Imatinib 400 mg/day

value: patient 3372


title: Chip No: 243pB from patient 3335

value: Imatinib 800 mg/day

value: 6 wk

value: patient 3335

value: imatinib


title: Chip No: 286pB from patient 3359

value: no

value: patient 3359


title: Chip No: 428pB from patient 3445

value: baseline

value: patient 3445

value: prior to treatment


title: Chip No: 320pB from patient 3389

value: male

value: patient 3389

value: peripheral blood


title: Chip No: 329pB from patient 3360

value: female

value: yes

value: patient 3360

value: chronic myeloid leukemia


title: Chip No: 318pB from patient 3390

value: MMR

value: Imatinib 400 mg/day

value: patient 3390


title: Chip No: 275pB from patient 3370

value: patient 3370


title: P2803_216

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: P2803_215

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_214

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_211

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 245pB from patient 3344

value: no

value: Imatinib 800 mg/day

value: 6 wk

value: patient 3344

value: imatinib


title: P2803_213

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_212

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_210

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 312pB from patient 3373

value: male

value: baseline

value: patient 3373

value: prior to treatment


title: Chip No: 542pB from patient 3462

value: female

value: yes

value: patient 3462

value: peripheral blood


title: P2803_208

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_205

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_206

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 354pB from patient 3331

value: MMR

value: patient 3331

value: chronic myeloid leukemia


title: Chip No: 567pB from patient 3493

value: Imatinib 400 mg/day

value: patient 3493


title: Chip No: 254pB from patient 3361

value: no

value: patient 3361


title: Chip No: 350pB from patient 3380

value: Imatinib 800 mg/day

value: 6 wk

value: patient 3380


title: Chip No: 277pB from patient 3369

value: baseline

value: patient 3369


title: Chip No: 310pB from patient 3376

value: male

value: patient 3376

value: prior to treatment


title: Chip No: 552pB from patient 3461

value: female

value: yes

value: patient 3461


title: P2803_207

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: P2803_200

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_197

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_203

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_202

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_204

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_199

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 232pB from patient 3353

value: MMR

value: patient 3353

value: peripheral blood

value: chronic myeloid leukemia


title: P2803_198

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 241pB from patient 3356

value: no

value: patient 3356

value: imatinib


title: Chip No: 328pB from patient 3360

value: Imatinib 400 mg/day

value: patient 3360


title: Chip No: 194pB from patient 3348

value: Imatinib 800 mg/day

value: baseline

value: patient 3348


title: Chip No: 543pB from patient 3474

value: patient 3474

value: prior to treatment


title: Chip No: 317pB from patient 3367

value: male

value: yes

value: 6 wk

value: patient 3367


title: P2803_201

description:
full-lenght RNA-seq
P2803.tsv

value: Glioblastoma


title: Chip No: 287pB from patient 3326

value: MMR

value: patient 3326

value: peripheral blood


title: Chip No: 566pB from patient 3494

value: no

value: patient 3494

value: chronic myeloid leukemia


title: Chip No: 497pB from patient 3408

value: Imatinib 400 mg/day

value: patient 3408


title: Chip No: 450pB from patient 3396

value: female

value: Imatinib 800 mg/day

value: patient 3396

value: imatinib


title: P2803_193

description:
full-lenght RNA-seq
P2803.tsv


title: P2802_096

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_095

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_094

description:
full-lenght RNA-seq
P2802.tsv


title: P2803_194

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_195

description:
full-lenght RNA-seq
P2803.tsv


title: P2803_196

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 376pB from patient 3396

value: baseline

value: prior to treatment


title: P2802_093

description:
full-lenght RNA-seq
P2802.tsv


title: P2803_209

description:
full-lenght RNA-seq
P2803.tsv


title: Chip No: 554pB from patient 3469

value: male

value: yes

value: patient 3469


title: Chip No: 384pB from patient 3395

value: patient 3395


title: Chip No: 571pB from patient 3483

value: patient 3483


title: Chip No: 563pB from patient 3440

value: patient 3440

value: peripheral blood


title: Chip No: 261pB from patient 3361

value: no

value: 6 wk

value: patient 3361


title: Chip No: 281pB from patient 3365

value: Imatinib 400 mg/day

value: patient 3365

value: chronic myeloid leukemia


title: Chip No: 327pB from patient 3328

value: MMR

value: female

value: patient 3328


title: Chip No: 368pB from patient 3355

value: patient 3355

value: imatinib


title: P2802_092

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: P2802_091

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 396pB from patient 3413

value: yes

value: Imatinib 800 mg/day

value: baseline

value: patient 3413

value: prior to treatment


title: P2802_090

description:
full-lenght RNA-seq
P2802.tsv

source_name: Empty


title: P2802_085

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_088

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_089

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_086

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_087

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_083

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_084

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_082

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_080

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_081

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 555pB from patient 3472

value: male

value: no

value: patient 3472

value: peripheral blood


title: P2802_079

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 449pB from patient 3387

value: Imatinib 400 mg/day

value: 6 wk

value: patient 3387


title: P2802_077

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 313pB from patient 3373

value: MMR

value: patient 3373

value: chronic myeloid leukemia


title: Chip No: 276pB from patient 3370

value: female

value: patient 3370

value: imatinib


title: Chip No: 257pB from patient 3336

value: yes

value: patient 3336


title: Chip No: 364pB from patient 3382

value: patient 3382


title: Chip No: 325pB from patient 3327

value: Imatinib 800 mg/day

value: patient 3327


title: Chip No: 259pB from patient 3337

value: male

value: no

value: baseline

value: patient 3337

value: prior to treatment


title: Chip No: 217pB from patient 3351

value: Imatinib 400 mg/day

value: 6 wk

value: patient 3351

value: peripheral blood


title: Chip No: 380pB from patient 3397

value: MMR

value: female

value: patient 3397

value: chronic myeloid leukemia


title: Chip No: 355pB from patient 3381

value: yes

value: patient 3381


title: Chip No: 196pB from patient 3349

value: patient 3349


title: P2802_078

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 510pB from patient 3430

value: patient 3430


title: P2802_075

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_073

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_076

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_072

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_074

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_069

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_070

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_071

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_068

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 306pB from patient 3342

value: no

value: Imatinib 800 mg/day

value: patient 3342


title: P2802_064

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 219pB from patient 3329

value: patient 3329

value: imatinib


title: P2802_066

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 545pB from patient 3386

value: Imatinib 400 mg/day

value: 6 wk

value: patient 3386


title: Chip No: 547pB from patient 3456

value: baseline

value: patient 3456

value: peripheral blood

value: prior to treatment


title: Chip No: 400pB from patient 3421

value: male

value: yes

value: patient 3421

value: chronic myeloid leukemia


title: Chip No: 454pB from patient 3400

value: MMR

value: female

value: patient 3400


title: Chip No: 234pB from patient 3330

value: no

value: Imatinib 800 mg/day

value: patient 3330


title: P2802_063

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: P2802_065

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_062

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 351pB from patient 3383

value: patient 3383


title: Chip No: 256pB from patient 3345

value: Imatinib 400 mg/day

value: 6 wk

value: patient 3345

value: imatinib


title: Chip No: 568pB from patient 3464

value: baseline

value: patient 3464

value: peripheral blood

value: prior to treatment


title: Chip No: 371pB from patient 3334

value: yes

value: patient 3334

value: chronic myeloid leukemia


title: Chip No: 546pB from patient 3471

value: MMR

value: male

value: patient 3471


title: P2802_061

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_067

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 353pB from patient 3331

value: no

value: Imatinib 800 mg/day

value: patient 3331


title: Chip No: 558pB from patient 3489

value: Imatinib 400 mg/day

value: patient 3489


title: P2802_060

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 379pB from patient 3392

value: female

value: patient 3392


title: Chip No: 214pB from patient 3343

value: 6 wk

value: patient 3343

value: imatinib


title: P2802_059

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 539pB from patient 3459

value: yes

value: baseline

value: patient 3459

value: peripheral blood

value: prior to treatment


title: Chip No: 564pB from patient 3495

value: not available

value: patient 3495

value: chronic myeloid leukemia


title: Chip No: 330pB from patient 3375

value: MMR

value: no

value: patient 3375


title: P2802_058

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 352pB from patient 3383

value: female

value: Imatinib 800 mg/day

value: patient 3383


title: Chip No: 503pB from patient 3435

value: male

value: patient 3435


title: P2802_057

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_054

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_056

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_053

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 263pB from patient 3339

value: yes

value: 6 wk

value: patient 3339

value: imatinib


title: P2802_051

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_052

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_055

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_047

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_050

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_049

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_045

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_046

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_048

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_043

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_044

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_042

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_040

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 366pB from patient 3401

value: Imatinib 400 mg/day

value: patient 3401

value: peripheral blood


title: P2802_041

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 424pB from patient 3410

value: baseline

value: patient 3410

value: prior to treatment

value: chronic myeloid leukemia


title: Chip No: 565pB from patient 3486

value: no

value: patient 3486


title: Chip No: 423pB from patient 3423

value: MMR

value: female

value: Imatinib 800 mg/day

value: patient 3423


title: P2802_039

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 198pB from patient 3350

value: yes

value: patient 3350


title: P2802_038

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 496pB from patient 3402

value: patient 3402


title: Chip No: 308pB from patient 3375

value: Imatinib 400 mg/day

value: patient 3375


title: Chip No: 548pB from patient 3473

value: male

value: patient 3473

value: peripheral blood


title: Chip No: 278pB from patient 3369

value: 6 wk

value: patient 3369

value: imatinib


title: Chip No: 242pB from patient 3335

value: not available

value: no

value: baseline

value: patient 3335

value: prior to treatment

value: chronic myeloid leukemia


title: P2802_037

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 448pB from patient 3387

value: yes

value: patient 3387


title: Chip No: 383pB from patient 3399

value: Imatinib 800 mg/day

value: patient 3399


title: Chip No: 326pB from patient 3328

value: female

value: Imatinib 400 mg/day

value: patient 3328


title: Chip No: 230pB from patient 3333

value: patient 3333

value: peripheral blood


title: Chip No: 233pB from patient 3353

value: male

value: 6 wk

value: patient 3353

value: imatinib


title: Chip No: 422pB from patient 3422

value: no

value: baseline

value: patient 3422


title: Chip No: 395pB from patient 3400

value: MMR

value: patient 3400

value: prior to treatment

value: chronic myeloid leukemia


title: P2802_035

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: P2802_036

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 559pB from patient 3482

value: female

value: yes

value: patient 3482


title: Chip No: 267pB from patient 3372

value: not available

value: Imatinib 400 mg/day

value: patient 3372


title: P2802_034

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 315pB from patient 3366

value: male

value: 6 wk

value: patient 3366

value: peripheral blood


title: Chip No: 348pB from patient 3371

value: no

value: patient 3371

value: imatinib


title: P2802_032

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_031

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 255pB from patient 3345

value: MMR

value: baseline

value: patient 3345


title: P2802_030

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 504pB from patient 3475

value: female

value: patient 3475

value: prior to treatment

value: chronic myeloid leukemia


title: P2802_027

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_029

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_033

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_028

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_026

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_025

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_024

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_023

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_021

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 240pB from patient 3356

value: yes

value: Imatinib 800 mg/day

value: patient 3356


title: P2802_020

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 280pB from patient 3364

value: 6 wk

value: patient 3364


title: P2802_018

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_017

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_016

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_022

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_014

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 273pB from patient 3368

value: male

value: patient 3368

value: peripheral blood


title: P2802_019

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 537pB from patient 3447

value: no

value: Imatinib 400 mg/day

value: patient 3447


title: Chip No: 427pB from patient 3446

value: MMR

value: baseline

value: patient 3446


title: Chip No: 502pB from patient 3463

value: patient 3463


title: Chip No: 264pB from patient 3325

value: patient 3325

value: prior to treatment


title: Chip No: 426pB from patient 3385

value: yes

value: patient 3385

value: chronic myeloid leukemia


title: Chip No: 321pB from patient 3389

value: Imatinib 800 mg/day

value: 6 wk

value: patient 3389

value: imatinib


title: Chip No: 365pB from patient 3401

value: female

value: patient 3401

value: peripheral blood


title: Chip No: 314pB from patient 3366

value: male

value: no

value: Imatinib 400 mg/day

value: patient 3366


title: P2802_013

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 509pB from patient 3467

value: baseline

value: patient 3467


title: Chip No: 200pB from patient 3346

value: MMR

value: yes

value: patient 3346

value: prior to treatment


title: Chip No: 397pB from patient 3414

value: Imatinib 800 mg/day

value: patient 3414

value: chronic myeloid leukemia


title: Chip No: 369pB from patient 3398

value: female

value: patient 3398


title: Chip No: 453pB from patient 3407

value: 6 wk

value: patient 3407

value: peripheral blood

value: imatinib


title: Chip No: 283pB from patient 3358

value: no

value: Imatinib 400 mg/day

value: patient 3358


title: P2802_015

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: Chip No: 356pB from patient 3381

value: male

value: patient 3381


title: P2802_012

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 323pB from patient 3388

value: yes

value: patient 3388


title: P2802_009

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_010

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_007

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 378pB from patient 3394

value: baseline

value: patient 3394

value: prior to treatment


title: P2802_006

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_011

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 375pB from patient 3338

value: female

value: Imatinib 800 mg/day

value: patient 3338

value: chronic myeloid leukemia


title: P2802_008

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_005

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 228pB from patient 3332

value: patient 3332

value: peripheral blood


title: P2802_003

description:
full-lenght RNA-seq
P2802.tsv


title: Chip No: 235pB from patient 3330

value: no

value: 6 wk

value: patient 3330

value: imatinib


title: Chip No: 550pB from patient 3488

value: male

value: patient 3488


title: Chip No: 506pB from patient 3452

value: MMR

value: yes

value: Imatinib 400 mg/day

value: patient 3452


title: Chip No: 544pB from patient 3391

value: patient 3391


title: P2802_001

description:
full-lenght RNA-seq
P2802.tsv

value: Glioblastoma


title: P2776_384

description:
full-lenght RNA-seq
P2776.tsv

value: PDGFR


title: P2776_382

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_380

description:
full-lenght RNA-seq
P2776.tsv


title: P2802_004

description:
full-lenght RNA-seq
P2802.tsv


title: P2802_002

description:
full-lenght RNA-seq
P2802.tsv


title: P2776_379

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_381

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 361pB from patient 3404

value: female

value: baseline

value: patient 3404

value: prior to treatment


title: Chip No: 455pB from patient 3393

value: no

value: Imatinib 800 mg/day

value: patient 3393

value: peripheral blood

value: chronic myeloid leukemia


title: Chip No: 238pB from patient 3357

value: patient 3357


title: P2776_383

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_378

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_377

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_375

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 215pB from patient 3344

value: MMR

value: male

value: patient 3344


title: Chip No: 357pB from patient 3384

value: not available

value: yes

value: patient 3384


title: Chip No: 363pB from patient 3382

value: Imatinib 400 mg/day

value: patient 3382


title: Chip No: 229pB from patient 3332

value: 6 wk

value: patient 3332

value: imatinib


title: Chip No: 507pB from patient 3479

value: no

value: baseline

value: patient 3479

value: prior to treatment


title: Chip No: 213pB from patient 3343

value: Imatinib 800 mg/day

value: patient 3343

value: peripheral blood

value: chronic myeloid leukemia


title: Chip No: 557pB from patient 3465

value: female

value: patient 3465


title: Chip No: 285pB from patient 3359

value: MMR

value: yes

value: patient 3359


title: Chip No: 274pB from patient 3368

value: male

value: patient 3368


title: Chip No: 452pB from patient 3405

value: 6 wk

value: patient 3405


title: P2776_374

description:
full-lenght RNA-seq
P2776.tsv

value: Glioblastoma

value: PDGFR


title: Chip No: 499pB from patient 3409

value: no

value: Imatinib 400 mg/day

value: baseline

value: patient 3409


title: Chip No: 553pB from patient 3468

value: Imatinib 800 mg/day

value: patient 3468

value: peripheral blood

value: prior to treatment


title: Chip No: 367pB from patient 3355

value: female

value: patient 3355

value: chronic myeloid leukemia


title: P2776_372

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 265pB from patient 3325

value: male

value: yes

value: patient 3325

value: imatinib


title: P2776_369

description:
full-lenght RNA-seq
P2776.tsv

value: Glioblastoma


title: P2776_368

description:
full-lenght RNA-seq
P2776.tsv

value: PDGFR


title: P2776_370

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_376

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_371

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_373

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_367

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_366

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_365

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_363

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_364

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_361

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_362

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 362pB from patient 3404

value: no

value: 6 wk

value: patient 3404


title: Chip No: 288pB from patient 3326

value: MMR

value: Imatinib 400 mg/day

value: patient 3326


title: Chip No: 195pB from patient 3348

value: Imatinib 800 mg/day

value: patient 3348

value: peripheral blood


title: Chip No: 425pB from patient 3352

value: female

value: baseline

value: patient 3352

value: prior to treatment


title: Chip No: 377pB from patient 3393

value: yes

value: patient 3393

value: chronic myeloid leukemia


title: P2776_360

description:
full-lenght RNA-seq
P2776.tsv

value: Glioblastoma

value: PDGFR


title: Chip No: 398pB from patient 3416

value: no

value: patient 3416


title: Chip No: 570pB from patient 3481

value: male

value: patient 3481


title: Chip No: 359pB from patient 3406

value: Imatinib 400 mg/day

value: patient 3406


title: P2776_358

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_359

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_356

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_357

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 451pB from patient 3398

value: Imatinib 800 mg/day

value: 6 wk

value: patient 3398

value: imatinib


title: P2776_355

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_354

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 258pB from patient 3336

value: patient 3336

value: peripheral blood


title: Chip No: 561pB from patient 3485

value: female

value: yes

value: baseline

value: patient 3485

value: prior to treatment


title: Chip No: 324pB from patient 3327

value: not available

value: no

value: patient 3327

value: chronic myeloid leukemia


title: Chip No: 551pB from patient 3455

value: Imatinib 400 mg/day

value: patient 3455


title: Chip No: 374pB from patient 3405

value: Imatinib 800 mg/day

value: patient 3405


title: Chip No: 511pB from patient 3412

value: MMR

value: patient 3412


title: Chip No: 311pB from patient 3376

value: male

value: 6 wk

value: patient 3376

value: imatinib


title: P2776_352

description:
full-lenght RNA-seq
P2776.tsv

value: Glioblastoma

value: PDGFR


title: P2776_351

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_353

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 538pB from patient 3460

value: yes

value: baseline

value: patient 3460

value: peripheral blood

value: prior to treatment


title: Chip No: 358pB from patient 3384

value: patient 3384

value: chronic myeloid leukemia


title: P2776_350

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_347

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 381pB from patient 3386

value: female

value: no

value: Imatinib 400 mg/day

value: patient 3386


title: P2776_346

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_345

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_342

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_343

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_341

description:
full-lenght RNA-seq
P2776.tsv


title: OVPAIR-4.1

type: genomic

city: Amsterdam

first: Philip

middle: C

last: Schouten

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Sample 51

hyb_protocol: According to manufacterer's protocol (Nimblegen Roche)

scan_protocol: 2 um double pass

data_processing: Nimblescan, grid tiff files, generate pair reports followed by using the NimbleScan DNAcopy procedure at default settings

label_protocol: With the ENZO 42760 labeling kit for array CGH: 20 uL primers (vial 1) with 500 ng of genomic tumor DNA or Promega Female reference DNA (GG1521) in 19 ul of nuclease free water for 10 minutes at 99 C in pcr machine, followed by 10 minutes of cooling to 4 degrees. Snap freeze and spin. While on ice add 11 ul Cy3 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to tumor DNA, and 11 ul Cy5 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to reference DNA and incubate in PCR machine for 4 hours at 37 C. Then add 5ul stop buffer (vial 5). To remove excess nucleotides with Qiagen MinElute PCR purification kit add 275 uL binding buffer (PB) to sample and reference. Put on minElute column and spin 60 sec on 16000 rcf. Add 700 ul Wash Buffer (PE) and centrifuge 60 secs at 16000 rcf. Dry columns by spinning another 60 secs at 16000 rcf. Elute the DNA in 2 steps by adding 2x 10.5 ul of elution buffer (EB). Pool equal amounts of tumor and reference DNA and speedvac into a pellet.

extract_protocol: 10 x 10 u slices containing at least 60% tumour cells were cleared of paraffin (2 x 5 min xylene, 2 x 30 s 100% ethanol, 30s 90% ethanol, 30 s 70% ethanol, and rinsed with H2O), treated with 1 M NaSCN at 37 C overnight, and sections of interest (>70% tumour cells) were scraped in 200 ul buffer ATL (Qiagen, cat. no. 51304). 27 ul of proteinase K (15 ug/ull, Roche, cat. no.3115879001) was immediately added, as well as at the end of the day, and at the beginning and end of the next day; samples were constantly shaken at 37 C during the time of digestion. The following day, 40 ul RNase A (20 ug/ul, Sigma, cat. no. R5500) was added to the sample, vortexed, and incubated for 2 min at room temperature. 400 ul of buffer AL (Qiagen, cat.no.51304) was added and incubated for 10 min at 70 C. 420 ul of 100% ethanol was added and vortexed. The sample mixture was spun on a spincolumn (Qiagen, cat. no. 51304) for 1 min at 8,000 rpm. The column was sequentially washed with 500 ul of the following reagents and spun for 1 min at 8,000 rpm: AW1, AW2, and twice with 80% ethanol. The column was spun dry for 3 min at 14,000 rpm. The sample was eluted with 50 ul of AE buffer by spinning for 1 min at 8,000 rpm. (Joosse, SA et al, Breast Cancer Res Treat, 2009)

tag: training group

value: CONTROL

value: ovarian cancer tumor

source_name: Promega Human Reference DNA Female


title: OVPAIR-4.2

description: Sample 52


title: OVPAIR-3.3

description: Sample 50


title: OVPAIR-3.1

description: Sample 48


title: OVPAIR-3.2

description: Sample 49


title: OVPAIR-2.3

description: Sample 47


title: P2776_348

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_349

description:
full-lenght RNA-seq
P2776.tsv


title: OVPAIR-1.1

description: Sample 43


title: OVPAIR-2.2

description: Sample 46


title: P2776_344

description:
full-lenght RNA-seq
P2776.tsv


title: 39013

description: Sample 39


title: P2776_340

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_339

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_338

description:
full-lenght RNA-seq
P2776.tsv


title: OVPAIR-2.1

description: Sample 45


title: OVPAIR-1.3

description: Sample 44


title: P2776_334

description:
full-lenght RNA-seq
P2776.tsv


title: 39026

description: Sample 41


title: 39035

description: Sample 40


title: 39055

description: Sample 34


title: 39022

description: Sample 42


title: P2776_337

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_335

description:
full-lenght RNA-seq
P2776.tsv


title: 39019

description: Sample 37


title: 63983

description: Sample 35


title: P2776_336

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_333

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_332

description:
full-lenght RNA-seq
P2776.tsv


title: 39024

description: Sample 36


title: P2776_330

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_328

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_331

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_329

description:
full-lenght RNA-seq
P2776.tsv


title: 39027

description: Sample 30


title: 39037

description: Sample 38


title: P2776_327

description:
full-lenght RNA-seq
P2776.tsv


title: 63997

description: Sample 29


title: 39039

description: Sample 33


title: 39020

description: Sample 32


title: 39002

description: Sample 31


title: P2776_326

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_324

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_322

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_323

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_320

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_321

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_319

description:
full-lenght RNA-seq
P2776.tsv


title: 63977

description: Sample 27


title: 639119

description: Sample 28


title: P2776_325

description:
full-lenght RNA-seq
P2776.tsv


title: BO.031

description: Sample 25


title: 39005

description: Sample 26


title: P2776_318

description:
full-lenght RNA-seq
P2776.tsv


title: BO.043

description: Sample 24


title: P2776_317

description:
full-lenght RNA-seq
P2776.tsv


title: BO.038

description: Sample 23


title: P2776_316

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_314

description:
full-lenght RNA-seq
P2776.tsv


title: Chip No: 199pB from patient 3350

tag: molecular response

value: MMR

value: 6 wk

value: patient 3350


title: BO.020

description: Sample 20

tag: gender


title: P2776_313

description:
full-lenght RNA-seq
P2776.tsv

value: Glioblastoma

value: PDGFR


title: BO.021

description: Sample 18


title: BO.014

description: Sample 17


title: BO.015

description: Sample 15


title: P2776_315

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_312

description:
full-lenght RNA-seq
P2776.tsv


title: BO.039

description: Sample 16


title: BO.041

description: Sample 21


title: P2776_311

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_310

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_309

description:
full-lenght RNA-seq
P2776.tsv


title: BO.036

description: Sample 19


title: BO.030

description: Sample 11


title: BO.008

description: Sample 22


title: P2776_307

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_308

description:
full-lenght RNA-seq
P2776.tsv


title: BO.007

description: Sample 10


title: BO.026

description: Sample 13


title: P2776_306

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_305

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_303

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_304

description:
full-lenght RNA-seq
P2776.tsv


title: BO.034

description: Sample 14


title: BO.037

description: Sample 12


title: P2776_297

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_301

description:
full-lenght RNA-seq
P2776.tsv


title: RSV1

city: Kongens Lyngby

first: Xiao

last: Wang

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

data_processing:
raw reads containing ploy N (Percentage of uncertain N ≥ 10%) A/T/G/C, with 5’ adapter contaminants, without 3’ adapters or insert tags and low-quality reads (Percentage of Qphred less than 20 ≥ 50%)
The miRNA tags were mapped to the reference genome of Bos taurus (UMD_3.1.1/bosTau8) by Bowtie software (version 0.12.9)
The mapped miRNA tags were used to seek the known miRNAs using miRBase20.0 as the reference, so the potential miRNA and the secondary structures were obtained by mirdeep2 software
Genome_build: UMD_3.1.1/bosTau8
Supplementary_files_format_and_content: Tab-delimited text files include DE genes

organism: Bos taurus

source_name: Case group

growth_protocol: Following the RSV formulating method in the previous study (Li et al., 2015), 105 μM mother solution was formulated by using 22.8 mg RSV (Molar mass = 228) (Sangon Biotech, Shanghai, China) dissolved into 1 mL Dimethyl sulfoxide (DMSO; Sangon Biotech , Shanghai, China). Afterwards, 1 uL mother solution and 1 uL pure DMSO diluted into 5 mL DM.

extract_protocol: Libraries were prepared according to Illumina's instructions

treatment_protocol: One group of cells was treated with constant doses of 20 μM RSV in DM (i.e., 1uL mother solution added in 5 mL DM), which is the case group. Another group of cells was treated with 1 uL DMSO as the control group.

value: Primary myoblasts

value: fetal beef longissimus dorsi muscle

value: 20 μM resveratrol


title: DMSO3

source_name: Control group

value: DMSO


title: DMSO2


title: BO.024

description: Sample 9


title: BO.028

description: Sample 7


title: P2776_295

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_296

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_294

description:
full-lenght RNA-seq
P2776.tsv


title: BO.042

description: Sample 8


title: BO.035

description: Sample 6


title: H3K27me3_rep2

city: Kyoto

first: Shuntaro

last: Ikeda

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

institute: Kyoto University

library_source: genomic

data_processing:
Sequencing reads were aligned to the bovine genome (Bos_taurus_UMD_3.1.1/bosTau8, Jun. 2014) using Bowtie (version 1.1.1). The peaks were called in the ChIP samples relative to the baseline using Model-based Analysis of ChIP-Seq (MACS, version 1.4.2) with following options; --nomodel --nolambda --shiftsize=300.
Genome_build: bosTau8
Supplementary_files_format_and_content: wig.gz files of called peaks

source_name: bovine blastocysts

growth_protocol: Bovine blastocysts were in vitro produced by in vitro fertilization (IVF) and further cultured in mSOF up to day 8 (IVF = day 0).

extract_protocol:
Blastocyst-stage embryos at 192 h post IVF were collected as approximately 15 embryos per biological replicate for ChIP. ChIP for small cell numbers was performed with a Low Cell ChIP-Seq Kit (Active Motif) according to the manufacturer’s manual (version A3) with some modifications. The blastocysts were freed from the zona pellucida by using pronase before crosslinking with formaldehyde. After crosslink-quenching, the sample was sonicated to shear chromatin using a Bioruptor UCD-250 (Cosmo Bio) for 30 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 2 min at 18,000 x g and the supernatant (200 μL) was transferred to a new tube. The 200-µL sample of sheared chromatin was divided into a 10-µL aliquot as “input” and the rest (190 µl). The latter aliquot was processed for ChIP using 3.2 µg anti-H3K27me3 antibody (C15410069, Diagenode) as indicated in the user manual. The input and ChIPed DNA was decrosslinked, purified, and resuspended in 40 µL low-EDTA TE buffer.
Sequencing libraries of the ChIPed DNA were constructed by using Next Gen DNA Library Kit and Next Gen Indexing Kit (Active Motif) following the manufacturer’s instruction.

treatment_protocol: The culture was chemically semi-defined (bovine serum albumin was added) and performed under low oxygen tension (5%).

tag: sourse

value: in vitro produced

tag: day after ivf

value: day 8

tag: chip antibody

value: Diagenode C15410069


title: BO.006

description: Sample 1

value: female


title: H3K27me3_rep1


title: BO.009

description: Sample 5


title: BO.023

description: Sample 3


title: RSV3


title: BO.040

description: Sample 4


title: P2776_302

description:
full-lenght RNA-seq
P2776.tsv


title: IG116-Δcrp_2

city: Uppsala

first: Ankita

last: Pal

address: Husargatan 3

department: Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

description:
IG116-crp_S2
processed data file: counts_new.txt

data_processing:
Illumina Hi-seq 2500 used for sequencing
CUTADAPT used for removing adapter sequence and low-quality reads (q >= 20)
BWA used for reads mapping and alignment to reference genome (GenBank accession no. NC 000391.3)
Samtools used for compressing alignment files and sorting
FeatureCounts used for assigning counts at gene level
EdgeR used for differential gene expression analysis
Genome_build: Reference genome used: E.coli K-12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: tab delimited .txt file containing raw reads count (counts_new.txt)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacteria grown in M9+ glucose + 40 mM MOPS

growth_protocol: Escherichia coli cells grown in a bioreactor under glucose-limited chemostat condition and batch condition with M9+glucose+ 40mM MOPS at 37 degree Celcius and 700 rpm and total RNA extracted after 3-5 residence times in steady state and at exponential phase, respectively.

extract_protocol:
Total RNA extraction was done using the TRIzol-chloroform method. DNase treatment was done to remove any DNA contamination after which enrichment for mRNA was done using the MicrobExpress Kit.
Single-end, strand specific libraries for RNA sequencing were prepared using NEBNext Ultra II Directional RNA library kit.The sequencing was carried out on HiSeq 2500 Rapid Run Mode using 1x50 bp single-end reads.

tag: genotype/variation

tag: culture/growth condition

value: batch exponential phase

tag: molecule type

value: Ribo-depleted mRNA


title: IG116-Δcrp_1

description:
IG116-crp_S1
processed data file: counts_new.txt


title: EvoCrp3_2_chemostat

description:
EvoCrp3_chemostat_S2
processed data file: counts_new.txt

source_name: Bacteria grown in glucose -limited chemostat containing M9+ glucose + 40 mM MOPS

value: adaptively evolved mutant of {delta}crp

value: chemostat culture


title: BO.025

description: Sample 2

value: ovarian cancer tumor


title: DMSO1


title: P2776_292

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_293

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_291

description:
full-lenght RNA-seq
P2776.tsv


title: P2776_290

description:
full-lenght RNA-seq
P2776.tsv


title: EvoCrp1_2_chemostat

description:
EvoCrp1_chemostat_S2
processed data file: counts_new.txt


title: P2775_287

description:
full-lenght RNA-seq
P2775.tsv

source_name: S94F1_P3 Inv

value: EGFR


title: P2776_289

description:
full-lenght RNA-seq
P2776.tsv


title: EvoCrp3_1_chemostat

description:
EvoCrp3_chemostat_S1
processed data file: counts_new.txt


title: EvoCrp1_1_chemostat

description:
EvoCrp1_chemostat_S1
processed data file: counts_new.txt


title: P2775_288

description:
full-lenght RNA-seq
P2775.tsv


title: Δcrp_2_chemostat

description:
CRP_chemostat_S2
processed data file: counts_new.txt

value: {delta}crp


title: Δcrp_1_chemostat

description:
CRP_chemostat_S1
processed data file: counts_new.txt


title: P2775_285

description:
full-lenght RNA-seq
P2775.tsv

value: Glioblastoma


title: Wild type K12MG1655_1_chemostat

description:
WT_chemostat_S1
processed data file: counts_new.txt

value: Wild type K12MG1655


title: P2775_283

description:
full-lenght RNA-seq
P2775.tsv

source_name: empty


title: P2775_286

description:
full-lenght RNA-seq
P2775.tsv


title: Wild type K12MG1655_2_chemostat

description:
WT_chemostat_S2
processed data file: counts_new.txt


title: P2775_280

description:
full-lenght RNA-seq
P2775.tsv

source_name: S94F1_P3 Core


title: EvoCrp5_1

description:
Evocrp5_S1
processed data file: Raw_counts.txt

data_processing:
Illumina Hi-seq 2500 used for sequencing.
CUTADAPT used for removing adapter sequence and low-quality reads (q >= 20).
BWA used for read mapping and alignment to reference genome (GenBank accession no. NC_000913.3).
Samtools used for compressing alignment files and sorting.
FeatureCounts used for assigning counts at gene level.
EdgeR used for differential gene expression analysis.
Genome_build: Reference genome used: E.coli K12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited .txt file containing raw reads count.

growth_protocol: Escherichia coli cells grown in a bioreactor under aerobic conditions with M9+glucose+ 40mM MOPS at 37 degree Celsius and 700 rpm till exponential phase.

extract_protocol:
Total RNA extracted at exponential phase.
Total RNA extraction was done using the TRIzol-chloroform method. DNase treatment was done to remove any DNA contamination after which enrichment for mRNA was done using the MicrobExpress Kit.
Single-end, strand specific libraries for RNA sequencing were prepared using NEBNext Ultra II Directional RNA library kit. The sequencing was carried out on HiSeq 2500 Rapid Run Mode using 1x50 bp single-end reads.

tag: genotype

value: Adaptively evolved mutant of <delta>crp

tag: media

value: Glucose minimal media

tag: growth phase

value: Exponential


title: P2775_282

description:
full-lenght RNA-seq
P2775.tsv

tag: protocol

tag: cell type

tag: treatment


title: P2775_284

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_281

description:
full-lenght RNA-seq
P2775.tsv


title: EvoCrp3_2

description:
Evocrp3_S2
processed data file: Raw_counts.txt


title: EvoCrp4_1

description:
Evocrp4_S1
processed data file: Raw_counts.txt


title: EvoCrp5_2

description:
Evocrp5_S2
processed data file: Raw_counts.txt


title: P2775_279

description:
full-lenght RNA-seq
P2775.tsv


title: EvoCrp4_2

description:
Evocrp4_S2
processed data file: Raw_counts.txt


title: P2775_278

description:
full-lenght RNA-seq
P2775.tsv


title: EvoCrp3_1

description:
Evocrp3_S1
processed data file: Raw_counts.txt


title: EvoCrp2_2

description:
Evocrp2_S2
processed data file: Raw_counts.txt


title: EvoCrp2_1

description:
Evocrp2_S1
processed data file: Raw_counts.txt


title: EvoCrp1_2

description:
Evocrp1_S2
processed data file: Raw_counts.txt


title: P2775_275

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_274

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_277

description:
full-lenght RNA-seq
P2775.tsv


title: EvoCrp1_1

description:
Evocrp1_S1
processed data file: Raw_counts.txt


title: P2775_276

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_273

description:
full-lenght RNA-seq
P2775.tsv


title: Δcrp_2

description:
CRP_S2
processed data file: Raw_counts.txt

value: <delta>crp


title: P2775_272

description:
full-lenght RNA-seq
P2775.tsv


title: Δcrp_1

description:
CRP_S1
processed data file: Raw_counts.txt


title: P2775_271

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_270

description:
full-lenght RNA-seq
P2775.tsv


title: P2775_269

description:
full-lenght RNA-seq
P2775.tsv