title: BloodGT259

description: DishQualityControl 0.996


title: BloodGT277

status: Public on Feb 19 2018

type: genomic

city: Wageningen

first: Veronika

last: Laine

address: Droevendaalsesteeg 10

department: Animal Ecology

country: Netherlands

institute: NIOO-KNAW

description: DishQualityControl 0.998

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing:
A total of 3.116 great tits were genotyped using a custom made Affymetrix® great tit 650K SNP chip at Edinburgh Genomics (Edinburgh, United Kingdom). SNP calling was done following the Affymetrix® best practices workflow by using the Axiom® Analysis Suite 1.1.
The processed data file "SamValuesAll.txt" includes the Genotype Call (SNP call): AA (0), AB (1), BB (2), and NoCall (3); Columns with header 'A' or 'B' represent the raw signal intensity from the probes targeting each allele (i.e. A and B).

label: Biotin

molecule: genomic DNA

organism: Parus major

source_name: wild

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Whole blood samples were stored in either 1 ml Cell Lysis Solution (Gentra Puregene Kit, Qiagen, USA) or Queens buffer. DNA was extracted by using the FavorPrep 96-Well Genomic DNA Extraction Kit (Favorgen Biotech corp.). DNA quality and DNA concentration were measured on a Nanodrop 2000 (Thermo Scientific).

tag: tissue

value: blood

tag: Sex

value: female


title: BloodGT256

description: DishQualityControl 0.997


title: BloodGT274

description: DishQualityControl 0.98


title: BloodGT254

description: DishQualityControl 0.996


title: BloodGT251

description: DishQualityControl 0.995


title: BloodGT250

description: DishQualityControl 0.994


title: BloodGT248

description: DishQualityControl 0.995


title: BloodGT270

description: DishQualityControl 0.997


title: BloodGT253

description: DishQualityControl 0.993


title: BloodGT252

description: DishQualityControl 0.994


title: BloodGT249

description: DishQualityControl 0.994


title: BloodGT247

description: DishQualityControl 0.985


title: BloodGT246

description: DishQualityControl 0.996


title: BloodGT263

description: DishQualityControl 0.995


title: BloodGT244

description: DishQualityControl 0.998


title: BloodGT241

description: DishQualityControl 0.998


title: BloodGT239

description: DishQualityControl 0.994


title: BloodGT240

description: DishQualityControl 0.992


title: BloodGT238

description: DishQualityControl 0.995


title: BloodGT235

description: DishQualityControl 0.995


title: BloodGT233

description: DishQualityControl 0.997


title: BloodGT232

description: DishQualityControl 0.998


title: BloodGT230

description: DishQualityControl 0.994


title: BloodGT229

description: DishQualityControl 0.994


title: BloodGT231

description: DishQualityControl 0.993


title: BloodGT228

description: DishQualityControl 0.996


title: BloodGT227

description: DishQualityControl 0.993


title: BloodGT245

description: DishQualityControl 0.995


title: BloodGT225

description: DishQualityControl 0.993


title: BloodGT222

description: DishQualityControl 0.993


title: BloodGT226

description: DishQualityControl 0.993


title: BloodGT224

description: DishQualityControl 0.996


title: BloodGT220

description: DishQualityControl 0.998


title: BloodGT223

description: DishQualityControl 0.996


title: BloodGT242

description: DishQualityControl 0.997


title: BloodGT219

description: DishQualityControl 0.995


title: BloodGT243

description: DishQualityControl 0.995


title: BloodGT218

description: DishQualityControl 0.992


title: BloodGT217

description: DishQualityControl 0.995


title: BloodGT216

description: DishQualityControl 0.998


title: BloodGT215

description: DishQualityControl 0.996


title: BloodGT214

description: DishQualityControl 0.997


title: BloodGT213

description: DishQualityControl 0.995


title: BloodGT237

description: DishQualityControl 0.993


title: BloodGT236

description: DishQualityControl 0.994


title: BloodGT234

description: DishQualityControl 0.995


title: BloodGT212

description: DishQualityControl 0.995


title: BloodGT211

description: DishQualityControl 0.992


title: BloodGT210

description: DishQualityControl 0.996


title: BloodGT208

description: DishQualityControl 0.998


title: BloodGT207

description: DishQualityControl 0.997


title: BloodGT205

description: DishQualityControl 0.995


title: BloodGT202

description: DishQualityControl 0.992


title: BloodGT206

description: DishQualityControl 0.996


title: BloodGT221

description: DishQualityControl 0.998


title: BloodGT203

description: DishQualityControl 0.997


title: BloodGT204

description: DishQualityControl 0.995


title: BloodGT199

description: DishQualityControl 0.988


title: BloodGT197

description: DishQualityControl 0.998


title: BloodGT200

description: DishQualityControl 0.998


title: BloodGT195

description: DishQualityControl 0.995


title: BloodGT198

description: DishQualityControl 0.995


title: BloodGT189

description: DishQualityControl 0.996


title: BloodGT194

description: DishQualityControl 0.983


title: BloodGT201

description: DishQualityControl 0.995


title: BloodGT193

description: DishQualityControl 0.997


title: BloodGT182

description: DishQualityControl 0.993


title: BloodGT191

description: DishQualityControl 0.993


title: BloodGT181

description: DishQualityControl 0.993


title: BloodGT190

description: DishQualityControl 0.997


title: BloodGT192

description: DishQualityControl 0.997


title: BloodGT188

description: DishQualityControl 0.997


title: BloodGT184

description: DishQualityControl 0.997


title: BloodGT185

description: DishQualityControl 0.996


title: BloodGT209

description: DishQualityControl 0.995


title: BloodGT183

description: DishQualityControl 0.994


title: BloodGT186

description: DishQualityControl 0.993


title: BloodGT187

description: DishQualityControl 0.994


title: BloodGT176

description: DishQualityControl 0.993


title: BloodGT175

description: DishQualityControl 0.993


title: BloodGT196

description: DishQualityControl 0.993


title: BloodGT179

description: DishQualityControl 0.992


title: BloodGT177

description: DishQualityControl 0.99


title: BloodGT178

description: DishQualityControl 0.997


title: BloodGT164

description: DishQualityControl 0.993


title: BloodGT173

description: DishQualityControl 0.994


title: BloodGT174

description: DishQualityControl 0.995


title: BloodGT169

description: DishQualityControl 0.994


title: BloodGT170

description: DishQualityControl 0.996


title: BloodGT167

description: DishQualityControl 0.996


title: BloodGT180

description: DishQualityControl 0.99


title: BloodGT165

description: DishQualityControl 0.99


title: BloodGT166

description: DishQualityControl 0.993


title: BloodGT163

description: DishQualityControl 0.99


title: BloodGT162

description: DishQualityControl 0.995


title: BloodGT161

description: DishQualityControl 0.997


title: BloodGT160

description: DishQualityControl 0.991


title: BloodGT158

description: DishQualityControl 0.993


title: BloodGT157

description: DishQualityControl 0.99


title: BloodGT156

description: DishQualityControl 0.991


title: BloodGT155

description: DishQualityControl 0.996


title: BloodGT171

description: DishQualityControl 0.996


title: BloodGT153

description: DishQualityControl 0.993


title: BloodGT168

description: DishQualityControl 0.993


title: BloodGT154

description: DishQualityControl 0.988


title: BloodGT172

description: DishQualityControl 0.996


title: BloodGT152

description: DishQualityControl 0.995


title: BloodGT151

description: DishQualityControl 0.997


title: BloodGT150

description: DishQualityControl 0.996


title: BloodGT149

description: DishQualityControl 0.995


title: BloodGT146

description: DishQualityControl 0.997


title: BloodGT148

description: DishQualityControl 0.988


title: BloodGT143

description: DishQualityControl 0.995


title: BloodGT141

description: DishQualityControl 0.996


title: BloodGT147

description: DishQualityControl 0.995


title: BloodGT145

description: DishQualityControl 0.991


title: BloodGT142

description: DishQualityControl 0.992


title: BloodGT144

description: DishQualityControl 0.994


title: BloodGT159

description: DishQualityControl 0.997


title: BloodGT135

description: DishQualityControl 0.998


title: BloodGT138

description: DishQualityControl 0.993


title: BloodGT137

description: DishQualityControl 0.985


title: BloodGT133

description: DishQualityControl 0.988


title: BloodGT129

description: DishQualityControl 0.991


title: BloodGT139

description: DishQualityControl 0.993


title: BloodGT140

description: DishQualityControl 0.995


title: BloodGT131

description: DishQualityControl 0.967


title: BloodGT127

description: DishQualityControl 0.996


title: BloodGT128

description: DishQualityControl 0.993


title: BloodGT126

description: DishQualityControl 0.981


title: BloodGT134

description: DishQualityControl 0.995


title: BloodGT132

description: DishQualityControl 0.995


title: BloodGT130

description: DishQualityControl 0.99


title: BloodGT124

description: DishQualityControl 0.993


title: BloodGT123

description: DishQualityControl 0.994


title: BloodGT125

description: DishQualityControl 0.993


title: BloodGT121

description: DishQualityControl 0.993


title: BloodGT120

description: DishQualityControl 0.997


title: BloodGT122

description: DishQualityControl 0.993


title: BloodGT136

description: DishQualityControl 0.998


title: BloodGT117

description: DishQualityControl 0.987


title: BloodGT116

description: DishQualityControl 0.995


title: BloodGT115

description: DishQualityControl 0.997


title: BloodGT114

description: DishQualityControl 0.995


title: BloodGT118

description: DishQualityControl 0.998


title: BloodGT119

description: DishQualityControl 0.998


title: BloodGT111

description: DishQualityControl 0.996


title: BloodGT113

description: DishQualityControl 0.991


title: BloodGT110

description: DishQualityControl 0.994


title: BloodGT109

description: DishQualityControl 0.99


title: BloodGT112

description: DishQualityControl 0.994


title: BloodGT108

description: DishQualityControl 0.995


title: BloodGT107

description: DishQualityControl 0.995


title: BloodGT106

description: DishQualityControl 0.992


title: BloodGT105

description: DishQualityControl 0.994


title: BloodGT104

description: DishQualityControl 0.998


title: BloodGT103

description: DishQualityControl 0.994


title: NZOHFD12

type: RNA

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014868 Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

molecule: total RNA

organism: Mus musculus

label_protocol: Cy3-labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated according to the manufacturer's instructions using TRI reagent (Sigma-Aldrich). RNA integrity was measured on LabChips in an Agilent bioanalyzer, and RNA concentration was determined spectrophotometrically using a Nanodrop spectrophotometer (Thermo Scientific).

treatment_protocol: Mice were kept on a carbohydrate-free high-fat diet until the age of 18 wks. Afterwards, diet was switched to a carbohydrate-containing diet to induce glucolipotoxic stress. After 48 h pancreatic islets were isolated for transcriptome analysis.

tag: strain

value: NZO/HiBomDife

tag: susceptibility to diet-induced diabetes

value: diabetes-prone

tag: gender

value: male

tag: time point

value: 2d after switch from carbohydrate-free to carbohydrate-containing diet

value: pancreatic islets


title: obobHFD5

value: diabetes-resistant


title: obobHFD6


title: NZOHFD11


title: yda11 PcBMM_3dpi_rep2

city: Madrid

first: Sara

last: Sopeña Torres

address: Campus Montegancedo - Autovia M40 km.38

country: Spain

institute: Centro de Biotecnologia y Genomica de Plantas (UPM-INIA)

description:
Gene expression at 3 days post-inoculation in PcBMM-infected yda11 plants, replicate 2
yda11_P3_2
yda11, PcBMM infection, 3dpi, replicate 2

hyb_protocol: The complementary RNA was used to hybridize ATH1 Arabidopsis GeneChip (Affymetrix) following the manufacturer’s protocol.

scan_protocol: The array images were analyzed with a GenePix 4000B scanner (Molecular Devices) at 10mm resolution.

data_processing: The images were quantified with GenePix Pro 5.1.

label: biotin

organism: Arabidopsis thaliana

source_name: yda11, PcBMM infection, 3dpi

label_protocol: cDNA was synthesized from 4 mg of total RNA using One-cycle target labeling and control reagents to produce biotin labeled cRNA.

growth_protocol: Arabidopsis thaliana plants were grown in phytochambers on a sterilized mixture of soil and vermiculite (3:1) with a 10 h day/14 h night photoperiod, a temperature of 22ºC day/20ºC night and 50% relative humidity. Light intensity was fixed to 120–150 umol m-2 s-1 (Hernández-Blanco et al., 2007)

extract_protocol: Frozen samples were ground using mortar and pestle and total RNA was extracted with a phenol/chloroform method, as described in Berrocal-Lobo et al., 2002. Total RNA was further purified using the RNeasy Kit (Qiagen) and quantified with a NanoDrop ND-100 spectrophotometer (Thermo Scientific). RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies.

treatment_protocol: 3-week-old Arabidopsis plants were spray-inoculated with a spore suspension (4 x 10^6 spores/ml) of PcBMM (0.6 ml per pot containing 9 plants) or with water (mock treatment). After inoculation, plants were transferred to a growth chamber with a 10 h day/14 h night photoperiod, a temperature of 24ºC day/22ºC night, and light intensity was maintained at 120–150 umol m-2 s-1. Inoculated plants were kept under high humidity in covered trays. Samples were collected 1 and 3 days after inoculation and frozen in liquid nitrogen.

tag: background

tag: genotype

tag: age

tag: treatment

value: PcBMM

tag: time

value: rosettes


title: BloodGT102

description: DishQualityControl 0.998


title: TNBC primary tumor [DFHCC06-202_Sample_20]

city: Lyngby

first: Nicolai

middle: Juul

last: Birkbak

address: Kemitorvet, Build. 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

description: Gene expression data from pretreatment biopsy from triple negative breast cancer patient

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Human U133 plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Expression values were calculated with the RMA algorithm.

organism: Homo sapiens

source_name: Human breast tumor core biopsy

label_protocol: Gene expression profiling was then performed on Affymetrix U133 Plus 2.0 microarrays at the Dana-Farber/Harvard Cancer Center array core facility

extract_protocol: Two 5μm frozen sections were stained with hematoxylin and eosin, manually scraped to remove normal stroma and enrich for tumor cells, and RNA was extracted using the Absolutely RNA Nanoprep kit (Stratagene)

treatment_protocol: Core biopsy was obtained prior to adjuvant chemotherapy with cisplatin and bevacizumab

value: primary breast tumor

tag: millerpayne

tag: rcbscore

tag: response

tag: pcr

tag: brcastatus

value: neg/neg/neg


title: TNBC primary tumor [DFHCC06-202_Sample_6]

value: WT


title: TNBC primary tumor [DFHCC06-202_Sample_4]


title: TNBC primary tumor [DFHCC06-202_Sample_17]


title: TNBC primary tumor [DFHCC06-202_Sample_48]


title: TNBC primary tumor [DFHCC06-202_Sample_41]


title: yda11 PcBMM_3dpi_rep3

description:
Gene expression at 3 days post-inoculation in PcBMM-infected yda11 plants, replicate 3
yda11_P3_3
yda11, PcBMM infection, 3dpi, replicate 3


title: TNBC primary tumor [DFHCC06-202_Sample_37]


title: TNBC primary tumor [DFHCC06-202_Sample_32]


title: yda11 mock_3dpi_rep3

description:
Gene expression at 3 days post-inoculation in mock-treated yda11 plants, replicate 3
yda11_M3_3
yda11, mock treatment, 3dpi, replicate 3

source_name: yda11, mock treatment, 3dpi

value: water (mock)


title: TNBC primary tumor [DFHCC06-202_Sample_9]


title: TNBC primary tumor [DFHCC06-202_Sample_15]


title: yda11 PcBMM_3dpi_rep1

description:
Gene expression at 3 days post-inoculation in PcBMM-infected yda11 plants, replicate 1
yda11_P3_1
yda11, PcBMM infection, 3dpi, replicate 1


title: TNBC primary tumor [DFHCC06-202_Sample_3]


title: TNBC primary tumor [DFHCC06-202_Sample_13]


title: TNBC primary tumor [DFHCC06-202_Sample_11]


title: obobHFD4


title: TNBC primary tumor [DFHCC06-202_Sample_30]


title: BloodGT100

description: DishQualityControl 0.995


title: TNBC primary tumor [DFHCC06-202_Sample_2]


title: BloodGT99

description: DishQualityControl 0.993


title: NZOHFD10


title: TNBC primary tumor [DFHCC06-202_Sample_27]


title: TNBC primary tumor [DFHCC06-202_Sample_12]


title: BloodGT98

description: DishQualityControl 0.992


title: yda11 mock_3dpi_rep1

description:
Gene expression at 3 days post-inoculation in mock-treated yda11 plants, replicate 1
yda11_M3_1
yda11, mock treatment, 3dpi, replicate 1


title: TNBC primary tumor [DFHCC06-202_Sample_49]


title: BloodGT101

description: DishQualityControl 0.993


title: yda11 mock_3dpi_rep2

description:
Gene expression at 3 days post-inoculation in mock-treated yda11 plants, replicate 2
yda11_M3_2
yda11, mock treatment, 3dpi, replicate 2


title: TNBC primary tumor [DFHCC06-202_Sample_10]


title: yda11 PcBMM_1dpi_rep3

description:
Gene expression at 1 day post-inoculation in PcBMM-infected yda11A plants, replicate 3
yda11_P1_3
yda11, PcBMM infection, 1dpi, replicate 3

source_name: yda11, PcBMM infection, 1dpi


title: BloodGT97

description: DishQualityControl 0.998


title: BloodGT96

description: DishQualityControl 0.997


title: yda11 PcBMM_1dpi_rep2

description:
Gene expression at 1 day post-inoculation in PcBMM-infected yda11 plants, replicate 2
yda11_P1_2
yda11, PcBMM infection, 1dpi, replicate 2


title: yda11 PcBMM_1dpi_rep1

description:
Gene expression at 1 day post-inoculation in PcBMM-infected yda11 plants, replicate 1
yda11_P1_1
yda11, PcBMM infection, 1dpi, replicate 1


title: prima800329 Follicular Lymphoma

city: Pierre Bénite

first: Bruno

last: Tesson

address: Centre Hospitalier Lyon-Sud  Secteur Sainte Eugénie - Pavillon 6D

department: Bioinformatics

country: France

institute: Institut Carnot CALYM

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on the GeneChip® Human Genome U133 Plus 2.0 array (Affymetrix) using the Affymetrix Hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner (Affymetrix) and software AGCC.

data_processing: GC-RMA with option fast=FALSE

source_name: Follicular Lymphoma

label_protocol: Reverse transcription and In Vitro Transcription were performed on 100ng of total RNA using the GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Not applicable

extract_protocol: Extraction of total RNA was performed using the miRNeasy mini kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.

treatment_protocol: Fresh frozen tissues stored at -80°C.

value: Male

value: Follicular Lymphoma

tag: hybridizationdate

tag: rnaextractiondate


title: prima800112 Follicular Lymphoma

value: Female

tag: tissue


title: prima800331 Follicular Lymphoma


title: prima700679 Follicular Lymphoma


title: yda11 mock_1dpi_rep3

description:
Gene expression at 1 day post-inoculation in mock-treated yda11 plants, replicate 3
yda11_M1_3
yda11, mock treatment, 1dpi, replicate 3

source_name: yda11, mock treatment, 1dpi


title: BloodGT95

description: DishQualityControl 0.993

value: blood

tag: Sex


title: prima800338 Follicular Lymphoma


title: prima700678 Follicular Lymphoma


title: TNBC primary tumor [DFHCC06-202_Sample_14]


title: BloodGT94

description: DishQualityControl 0.996

value: female


title: BloodGT92

description: DishQualityControl 0.993


title: TNBC primary tumor [DFHCC06-202_Sample_19]


title: BloodGT93

description: DishQualityControl 0.993


title: yda11 mock_1dpi_rep2

description:
Gene expression at 1 day post-inoculation in mock-treated yda11 plants, replicate 2
yda11_M1_2
yda11, mock treatment, 1dpi, replicate 2


title: yda11 mock_1dpi_rep1

description:
Gene expression at 1 day post-inoculation in mock-treated yda11 plants, replicate 1
yda11_M1_1
yda11, mock treatment, 1dpi, replicate 1


title: prima700663 Follicular Lymphoma


title: prima700656 Follicular Lymphoma


title: prima700676 Follicular Lymphoma


title: prima700650 Follicular Lymphoma


title: prima700652 Follicular Lymphoma


title: prima700657 Follicular Lymphoma


title: prima700649 Follicular Lymphoma


title: yda11 t0_rep3

description:
Gene expression in non-treated yda11 plants, replicate 3
yda11_T0_3
yda11, time zero, replicate 3

source_name: yda11, time zero

value: no treatment

value: time zero


title: prima700629 Follicular Lymphoma


title: yda11 t0_rep2

description:
Gene expression in non-treated yda11 plants, replicate 2
yda11_T0_2
yda11, time zero, replicate 2


title: prima700622 Follicular Lymphoma


title: prima700621 Follicular Lymphoma


title: BloodGT91

description: DishQualityControl 0.991


title: prima700620 Follicular Lymphoma


title: BloodGT90

description: DishQualityControl 0.996


title: BloodGT89

description: DishQualityControl 0.993


title: BloodGT88

description: DishQualityControl 0.998


title: BloodGT87

description: DishQualityControl 0.996


title: BloodGT86

description: DishQualityControl 0.992


title: prima700617 Follicular Lymphoma


title: BloodGT85

description: DishQualityControl 0.996


title: Col-0 PcBMM_3dpi_rep3

description:
Gene expression at 3 days post-inoculation in PcBMM-infected wild-type plants, replicate 3
Col_P3_3
Col-0, PcBMM infection, 3dpi, replicate 3

source_name: Col-0, PcBMM infection, 3dpi

value: wild-type


title: prima700619 Follicular Lymphoma


title: BloodGT84

description: DishQualityControl 0.992


title: Col-0 PcBMM_3dpi_rep2

description:
Gene expression at 3 days post-inoculation in PcBMM-infected wild-type plants, replicate 2
Col_P3_2
Col-0, PcBMM infection, 3dpi, replicate 2


title: prima700613 Follicular Lymphoma


title: Col-0 mock_3dpi_rep3

description:
Gene expression at 3 days post-inoculation in mock-treated wild-type plants, replicate 3
Col_M3_3
Col-0, mock treatment, 3dpi, replicate 3

source_name: Col-0, mock treatment, 3dpi


title: yda11 t0_rep1

description:
Gene expression in non-treated yda11 plants, replicate 1
yda11_T0_1
yda11, time zero, replicate 1


title: Col-0 PcBMM_3dpi_rep1

description:
Gene expression at 3 days post-inoculation in PcBMM-infected wild-type plants, replicate 1
Col_P3_1
Col-0, PcBMM infection, 3dpi, replicate 1


title: Col-0 mock_3dpi_rep2

description:
Gene expression at 3 days post-inoculation in mock-treated wild-type plants, replicate 2
Col_M3_2
Col-0, mock treatment, 3dpi, replicate 2


title: prima700565 Follicular Lymphoma


title: BloodGT83

description: DishQualityControl 0.996


title: prima700572 Follicular Lymphoma


title: prima700611 Follicular Lymphoma


title: Col-0 PcBMM_1dpi_rep3

description:
Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants, replicate 3
Col_P1_3
Col-0, PcBMM infection, 1dpi, replicate 3

source_name: Col-0, PcBMM infection, 1dpi


title: prima700548 Follicular Lymphoma


title: prima700603 Follicular Lymphoma


title: prima700571 Follicular Lymphoma


title: prima700558 Follicular Lymphoma


title: Col-0 mock_3dpi_rep1

description:
Gene expression at 3 days post-inoculation in mock-treated wild-type plants, replicate 1
Col_M3_1
Col-0, mock treatment, 3dpi, replicate 1


title: prima700555 Follicular Lymphoma


title: prima700570 Follicular Lymphoma


title: BloodGT82

description: DishQualityControl 0.996


title: prima700569 Follicular Lymphoma


title: prima700550 Follicular Lymphoma


title: prima700584 Follicular Lymphoma


title: BloodGT80

description: DishQualityControl 0.983

value: male


title: prima700549 Follicular Lymphoma


title: Col-0 PcBMM_1dpi_rep1

description:
Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants, replicate 1
Col_P1_1
Col-0, PcBMM infection, 1dpi, replicate 1


title: Col-0 PcBMM_1dpi_rep2

description:
Gene expression at 1 day post-inoculation in PcBMM-infected wild-type plants, replicate 2
Col_P1_2
Col-0, PcBMM infection, 1dpi, replicate 2


title: Col-0 mock_1dpi_rep2

description:
Gene expression at 1 day post-inoculation in mock-treated wild-type plants, replicate 2
Col_M1_2
Col-0, mock treatment, 1dpi, replicate 2

source_name: Col-0, mock treatment, 1dpi


title: Col-0 mock_1dpi_rep3

description:
Gene expression at 1 day post-inoculation in mock-treated wild-type plants, replicate 3
Col_M1_3
Col-0, mock treatment, 1dpi, replicate 3


title: prima700544 Follicular Lymphoma


title: prima700547 Follicular Lymphoma


title: prima700442 Follicular Lymphoma


title: prima700454 Follicular Lymphoma


title: prima700543 Follicular Lymphoma


title: BloodGT79

description: DishQualityControl 0.996


title: prima700432 Follicular Lymphoma


title: BloodGT78

description: DishQualityControl 0.994


title: BloodGT81

description: DishQualityControl 0.994


title: BloodGT77

description: DishQualityControl 0.993


title: BloodGT76

description: DishQualityControl 0.996


title: prima700439 Follicular Lymphoma


title: BloodGT75

description: DishQualityControl 0.995


title: BloodGT74

description: DishQualityControl 0.996


title: prima700377 Follicular Lymphoma


title: BloodGT73

description: DishQualityControl 0.993


title: prima700440 Follicular Lymphoma


title: prima700366 Follicular Lymphoma


title: prima700362 Follicular Lymphoma


title: Col-0 t0_rep2

description:
Gene expression in non-treated wild-type plants, replicate 2
Col_T0_2
Col-0, time zero, replicate 2

source_name: Col-0, time zero


title: prima700376 Follicular Lymphoma


title: Col-0 t0_rep1

description:
Gene expression in non-treated wild-type plants, replicate 1
Col_T0_1
Col-0, time zero, replicate 1


title: Col-0 mock_1dpi_rep1

description:
Gene expression at 1 day post-inoculation in mock-treated wild-type plants, replicate 1
Col_M1_1
Col-0, mock treatment, 1dpi, replicate 1


title: BloodGT72

description: DishQualityControl 0.996


title: prima700363 Follicular Lymphoma


title: Col-0 t0_rep3

description:
Gene expression in non-treated wild-type plants, replicate 3
Col_T0_3
Col-0, time zero, replicate 3


title: prima700384 Follicular Lymphoma


title: prima600030 Follicular Lymphoma


title: prima700345 Follicular Lymphoma


title: prima700338 Follicular Lymphoma


title: Cn_RNA1

type: SRA

city: San Francisco

first: Jordan

middle: Emily

last: Burke

state: CA

address: N374 Genentech Hall, 600 16th Street

department: Biochemistry and Biophysics

country: USA

institute: University of California, San Francisco

description:
RNA from whole cell extract. polyA selected
polyA RNA-seq

library_source: transcriptomic

data_processing:
For 3' end profiling, spliceosome-bound RNA-seq and polyA RNA-seq:
Illumina adaptor removed from read 3' ends using an in-house script
Reads collapsed with fastx_collapser
6 nt barcode removed from 5' end of read using an in-house script
Reads were aligned to the  genome with bowtie v 1.1.2
For junction and branch profiling:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads aligned to genome using tophat v2.1.1
Branches detected using an in-house script
Genome_build: CNA3
Genome_build: R64-2-1_20150113
Genome_build: ASM294v2.30
Supplementary_files_format_and_content: bedgraph, csv, bed

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: An overnight saturated culture grown in YPAD was diluted to 0.001-0.003 OD in 2 L YPAD and grown at 30C with shaking. At 1 OD, 1% additional glucose was added. Cultures were harvested at 2 OD.

extract_protocol:
Cells were lysed by cryo-milling 3X 2 min at 10 cps (2 min rest between) in a SPEX sample prep 6870. RNA from lysate or affinity purified spliceosomes was extracted by treatment with Proteinase K followed by phenol/chloroform extraction.
Spliceosome profiling

tag: strain

value: wild type


title: Cn_RNA2


title: Cn RNase plus 1

description:
RNA from affinity purified spliceosomes
Spliceosome-bound RNA-seq

source_name: yeast, Prp19-2XFLAG


title: prima700369 Follicular Lymphoma

tag: gender


title: Cn RNase plus 2


title: Cn RNase minus 2


title: prima700020 Follicular Lymphoma


title: BloodGT71

description: DishQualityControl 0.995


title: Cn RNase minus 1


title: prima601369 Follicular Lymphoma


title: prima601368 Follicular Lymphoma


title: prima601367 Follicular Lymphoma


title: prima700018 Follicular Lymphoma


title: BloodGT70

description: DishQualityControl 0.99


title: BloodGT69

description: DishQualityControl 0.995


title: prima601129 Follicular Lymphoma


title: BloodGT67

description: DishQualityControl 0.995


title: BloodGT68

description: DishQualityControl 0.993


title: CM764G-B

data_processing:
library strategy: splicesome profiling
For 3' end profiling, spliceosome-bound RNA-seq and polyA RNA-seq:
Illumina adaptor removed from read 3' ends using an in-house script
Reads collapsed with fastx_collapser
6 nt barcode removed from 5' end of read using an in-house script
Reads were aligned to the  genome with bowtie v 1.1.2
For junction and branch profiling:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads aligned to genome using tophat v2.1.1
Branches detected using an in-house script
Genome_build: CNA3
Genome_build: R64-2-1_20150113
Genome_build: ASM294v2.30
Supplementary_files_format_and_content: bedgraph, csv, bed

source_name: C. neoformans_Prp19-2XFLAG

extract_protocol: Cells were lysed by cryo-milling 3X 2 min at 10 cps (2 min rest between) in a SPEX sample prep 6870. RNA from lysate or affinity purified spliceosomes was extracted by treatment with Proteinase K followed by phenol/chloroform extraction.

tag: strain info.

tag: molecule subtype

value: RNA from affinity purified spliceosomes

tag: experiment type

value: Spliceosome-bound RNA-seq, galactose substituted for glucose in YPAD medium


title: BloodGT66

description: DishQualityControl 0.993


title: CM764G-W

value: RNA from whole cell extract. polyA selected

value: polyA RNA-seq, galactose substituted for glucose in YPAD medium


title: CM763G-B


title: BloodGT65

description: DishQualityControl 0.995


title: CJB67G-W


title: prima601115 Follicular Lymphoma


title: BloodGT64

description: DishQualityControl 0.985


title: CJB67G-B


title: prima601096 Follicular Lymphoma


title: CM763G-W


title: prima601362 Follicular Lymphoma


title: prima601110 Follicular Lymphoma


title: prima601046 Follicular Lymphoma


title: prima601085 Follicular Lymphoma


title: prima601084 Follicular Lymphoma


title: prima601091 Follicular Lymphoma


title: prima601114 Follicular Lymphoma


title: CJB67G-A

value: 3' end profiling, galactose substituted for glucose in YPAD medium


title: prima600896 Follicular Lymphoma


title: BloodGT63

description: DishQualityControl 0.992


title: prima601042 Follicular Lymphoma


title: BloodGT62

description: DishQualityControl 0.995


title: CJB66G-B


title: prima601089 Follicular Lymphoma


title: prima600849 Follicular Lymphoma


title: prima600865 Follicular Lymphoma


title: prima601058 Follicular Lymphoma


title: BloodGT61

description: DishQualityControl 0.992


title: CJB66G-A


title: BloodGT60

description: DishQualityControl 0.993


title: CJB66G-W


title: prima600876 Follicular Lymphoma


title: BloodGT58

description: DishQualityControl 0.994


title: CJB67D-W

value: polyA RNA-seq


title: BloodGT59

description: DishQualityControl 0.994


title: CJB67D-A

value: 3' end profiling


title: prima600837 Follicular Lymphoma

value: Male


title: prima600842 Follicular Lymphoma

value: Follicular Lymphoma


title: prima600787 Follicular Lymphoma

value: Female


title: prima600847 Follicular Lymphoma


title: prima600834 Follicular Lymphoma


title: prima600746 Follicular Lymphoma


title: CJB67D-B

value: Spliceosome-bound RNA-seq


title: BloodGT57

description: DishQualityControl 0.988

value: blood

value: female


title: BloodGT56

description: DishQualityControl 0.994


title: CJB66D-A


title: prima600737 Follicular Lymphoma


title: CJB66D-B


title: CJB66D-W


title: prima600769 Follicular Lymphoma


title: BloodGT55

description: DishQualityControl 0.995


title: BloodGT54

description: DishQualityControl 0.994


title: prima600726 Follicular Lymphoma


title: prima600721 Follicular Lymphoma


title: prima600736 Follicular Lymphoma


title: prima600765 Follicular Lymphoma


title: prima600748 Follicular Lymphoma


title: prima600718 Follicular Lymphoma


title: BloodGT53

description: DishQualityControl 0.988


title: prima600713 Follicular Lymphoma


title: CM763 branch

description: processed data file: Cneoformans_branches.csv

value: Branch profiling


title: prima600720 Follicular Lymphoma


title: prima600690 Follicular Lymphoma


title: BloodGT51

description: DishQualityControl 0.996


title: CM764 branch


title: CM763 junction

value: Junction profiling


title: prima600672 Follicular Lymphoma


title: prima600482 Follicular Lymphoma


title: prima600501 Follicular Lymphoma


title: CM764-B


title: CM764-A

description: processed data file: Cn_CP_peaks_new.bedgraph


title: BloodGT50

description: DishQualityControl 0.993


title: CM764-W


title: prima600686 Follicular Lymphoma


title: BloodGT52

description: DishQualityControl 0.993


title: prima600496 Follicular Lymphoma


title: BloodGT49

description: DishQualityControl 0.993


title: prima600510 Follicular Lymphoma


title: prima600476 Follicular Lymphoma


title: prima600696 Follicular Lymphoma


title: BloodGT45

description: DishQualityControl 0.995


title: BloodGT48

description: DishQualityControl 0.992


title: CM764 junction


title: prima600472 Follicular Lymphoma


title: BloodGT47

description: DishQualityControl 0.995


title: prima600484 Follicular Lymphoma


title: CM763-W


title: CM763-A


title: prima600402B Follicular Lymphoma


title: BloodGT44

description: DishQualityControl 0.997


title: prima600405 Follicular Lymphoma


title: prima600448 Follicular Lymphoma


title: BloodGT46

description: DishQualityControl 0.991


title: prima600444 Follicular Lymphoma


title: prima600492 Follicular Lymphoma


title: CM763-B


title: CM018-B

source_name: C. neoformans_untagged


title: BloodGT42

description: DishQualityControl 0.992

source_name: wild


title: prima600418 Follicular Lymphoma


title: CM018-A


title: prima600402A Follicular Lymphoma extra biopsy


title: prima600450 Follicular Lymphoma


title: BloodGT40

description: DishQualityControl 0.996


title: BloodGT39

description: DishQualityControl 0.991


title: BloodGT41

description: DishQualityControl 0.996


title: BloodGT43

description: DishQualityControl 0.995


title: BloodGT38

description: DishQualityControl 0.99


title: BloodGT37

description: DishQualityControl 0.996


title: prima600396 Follicular Lymphoma


title: BloodGT35

description: DishQualityControl 0.996


title: BloodGT36

description: DishQualityControl 0.994


title: BloodGT34

description: DishQualityControl 0.997


title: prima600398 Follicular Lymphoma


title: Foxp1wt/flox B cells_unstimulated_rep2

city: Munich

first: Silvia

last: Thoene

address: Ismaninger Str. 22

institute: Klinikum rechts der Isar der TUM

hyb_protocol: Labeled cDNA was hybridized to Affymetrix 430 2.0 microarrays and stained according to standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocol.

data_processing: Data have been analyzed using R statistical packages from bioconductor (http://www.bioconductor.org/). Pre-processing (background correction, normalization, summarization of probe-sets) has been performed using the package gcrma.

source_name: Foxp1wt/flox B cells_unstimulated

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocols.

growth_protocol: B220+ B cells have been isolated from murine spleen by FACS.

extract_protocol: Total RNA has been extracted using using the RNAeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells have been incubated in for four hours, with or without addition of IgM.

tag: strain background

value: mixed; 129/Sv-C57BL/6

tag: genotype/variation

value: spleen

tag: cell type

value: B220+ B cells

tag: stimulated with

value: none (unstimulated)


title: BloodGT33

description: DishQualityControl 0.995


title: Foxp1wt/flox B cells_unstimulated_rep3


title: prima600354 Follicular Lymphoma


title: BloodGT31

description: DishQualityControl 0.994


title: Foxp1wt/flox B cells_IgM-stimulated_rep3

source_name: Foxp1wt/flox B cells_IgM-stimulated

value: IgM for 4 hours


title: prima600383 Follicular Lymphoma


title: Foxp1wt/flox B cells_IgM-stimulated_rep2


title: Foxp1wt/flox B cells_unstimulated_rep1


title: Foxp1wt/flox B cells_IgM-stimulated_rep1


title: prima600341 Follicular Lymphoma


title: prima600302 Follicular Lymphoma


title: BloodGT30

description: DishQualityControl 0.998


title: prima600303 Follicular Lymphoma


title: Foxp1flox/del B cells_unstimulated_rep1

source_name: Foxp1flox/del B cells_unstimulated


title: Foxp1flox/del B cells_unstimulated_rep3


title: prima600301 Follicular Lymphoma


title: Foxp1flox/del B cells_unstimulated_rep2


title: prima600251 Follicular Lymphoma


title: BloodGT32

description: DishQualityControl 0.985


title: BloodGT29

description: DishQualityControl 0.989


title: prima600244 Follicular Lymphoma


title: Foxp1flox/del B cells_IgM-stimulated_rep2

source_name: Foxp1flox/del B cells_IgM-stimulated


title: prima600243 Follicular Lymphoma

source_name: Follicular Lymphoma


title: BloodGT27

description: DishQualityControl 0.995


title: prima600414 Follicular Lymphoma


title: prima600370 Follicular Lymphoma


title: BloodGT25

description: DishQualityControl 0.998


title: prima600375 Follicular Lymphoma


title: BloodGT22

description: DishQualityControl 0.997


title: BloodGT23

description: DishQualityControl 0.993


title: BloodGT26

description: DishQualityControl 0.996


title: BloodGT28

description: DishQualityControl 0.992


title: BloodGT21

description: DishQualityControl 0.992


title: Foxp1flox/del B cells_IgM-stimulated_rep3


title: BloodGT24

description: DishQualityControl 0.994


title: Foxp1flox/del B cells_IgM-stimulated_rep1


title: BloodGT20

description: DishQualityControl 0.994


title: prima600223 Follicular Lymphoma


title: BloodGT19

description: DishQualityControl 0.992


title: prima600222 Follicular Lymphoma


title: BloodGT18

description: DishQualityControl 0.996


title: BloodGT17

description: DishQualityControl 0.992


title: prima600242 Follicular Lymphoma


title: prima600182 Follicular Lymphoma


title: prima600210 Follicular Lymphoma


title: prima600189 Follicular Lymphoma


title: prima600127 Follicular Lymphoma


title: BMDM_IL-4_18hr

city: Daejeon

first: Saet-Byel

last: Jung

address: 266, Munhwa-ro, Jung-gu

department: School of medicine

country: South Korea

institute: Chungnam national university

description: Gene expression after 18hr in mouse macrophages treated with IL-4

hyb_protocol: Labeled cRNA was applied microarray (Agilent technologies, 8x60K) using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: The microarray chip was scanned using Agilent’s DNA microarray scanner and the raw signal density was acquired from feature Extraction software.

data_processing: The differential gene expression was classified by Benjamini-Hochberg's false discovery ratio method. GeneSpring GX12 software. Gene ontology and KEGG pathway for the  differential expressed genes was analyzed using GeneSpring GX 12 (Agilent Technologies, San Carlos, CA) and DAVID Bioinformatics tools (National Institute of Allergy and Infectious Diseases, NIH).

source_name: BMDM, treated with IL-4, 18 hours

label_protocol: Cyanine 3-labeled cRNA (complementary RNA) was generated from Agilent’s Low RNA Input Linear Amplification kit with 500ng total RNA. Labeled cRNA was also measured using Nanodrop spectrophotometer.

extract_protocol: Total RNA from cell was isolated using Trizol Reagent (Molecular Research Center, Cincinnati, OH, USA), according to the manufacturer’s instructions. Total RNA was quantified by absorbance at 260 nm and the integrity of total RNA was checked by Bioanalyzer2100 (Agilent, CA, USA).

value: male

value: macrophages


title: prima600120 Follicular Lymphoma


title: prima600126 Follicular Lymphoma


title: BMDM_UN_18hr

source_name: BMDM, untreated


title: BloodGT16

description: DishQualityControl 0.992


title: prima600118 Follicular Lymphoma


title: prima600335 Follicular Lymphoma


title: prima600107 Follicular Lymphoma


title: BloodGT13

description: DishQualityControl 0.997


title: BloodGT14

description: DishQualityControl 0.996


title: prima600131 Follicular Lymphoma


title: prima600104 Follicular Lymphoma


title: BloodGT12

description: DishQualityControl 0.992


title: BloodGT11

description: DishQualityControl 0.993


title: prima600098 Follicular Lymphoma


title: BloodGT10

description: DishQualityControl 0.996


title: BloodGT15

description: DishQualityControl 0.99


title: BloodGT7

description: DishQualityControl 0.993


title: prima600031 Follicular Lymphoma


title: prima600097 Follicular Lymphoma


title: prima700343 Follicular Lymphoma


title: BloodGT9

description: DishQualityControl 0.996


title: BloodGT8

description: DishQualityControl 0.994


title: prima600026 Follicular Lymphoma


title: prima600029 Follicular Lymphoma


title: prima600047 Follicular Lymphoma


title: BloodGT5

description: DishQualityControl 0.994


title: BloodGT6

description: DishQualityControl 0.995


title: prima600025 Follicular Lymphoma


title: BloodGT4

description: DishQualityControl 0.993


title: Sp1 branch

description: processed data file: Spombe_branches.csv

organism: Schizosaccharomyces pombe

source_name: S. pombe_Prp19-4XTAP

value: RNA from affinity purified spliceosomes


title: Sp2 branch


title: Sp2 junction


title: BloodGT2

description: DishQualityControl 0.991


title: BloodGT1

description: DishQualityControl 0.995


title: prima600021 Follicular Lymphoma


title: SpWT-B

source_name: S. pombe_untagged


title: Sp1 junction


title: SpWT-W

value: RNA from whole cell extract. polyA selected


title: prima600022 Follicular Lymphoma


title: prima600023 Follicular Lymphoma

value: Male


title: prima600015 Follicular Lymphoma

value: Follicular Lymphoma


title: SpWT-A

description: processed data file: Sp_CP_peaks_new.bedgraph


title: Sp2-W


title: Sp2-B


title: BloodGT3

description: DishQualityControl 0.994


title: Sp2-A


title: Sp1-B


title: Sp1-W


title: ScWT-W

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae_BY4741

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: Sc19TAP1-W

source_name: S. cerevisiae_YLL036C 5GS3-C2

value: YLL036C 5GS3-C2

value: Prp19-TAP (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)


title: ScWT-B


title: Sc19TAP2-B


title: Sc19TAP2-W


title: Sc19TAP1-B


title: ScWT-A

description: processed data file: Sc_CP_peaks_new.bedgraph


title: prima600012 Follicular Lymphoma

value: Female


title: Sc19TAP1-A


title: Sc19TAP2-A


title: Sp1-A


title: WGBS_ZF2CACTA1-TET1cd_T2plus

status: Public on Feb 18 2018

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

description: WGBS_ZF2CACTA1-TET1cd_T2 +

library_source: genomic

data_processing:
Raw sequencing reads were aligned to the TAIR10 genome using BSMAP (49) by allowing up to 2 mismatches and only retaining reads mapped to one location. Methylation ratio are calculated by #C/(#C+#T) for all CG, CHG and CHH sites. Reads with 3 consecutive methylated CHH sites were discarded since they are likely to be unconverted reads as described before (50).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text and bigwig

growth_protocol: All the plants used in this study were in the Columbia-0 ecotype (Col-0) and were grown under long day conditions (16 hours light, 8 hours dark).  Leaf tissues were collected and used for the WGBS and RNAseq procedure

extract_protocol:
DNA was extracted using a CTAB-based method
100ng of DNA were used to make libraries using the Nugen Ultralow Methyl-seq kit (Ovation).

value: Leaf

tag: genotype

tag: ecotype

value: Columbia


title: WGBS_ZF1CACTA1-TET1cd_T2minus

description: WGBS_ZF1CACTA1-TET1cd_T2 -


title: WGBS_col_for_ZFCACTA1-TET1cd_T2


title: WGBS_ZF2CACTA1-TET1cd_T2


title: WGBS_ZF1CACTA1-TET1cd_T1


title: WT 2

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

institute: Korea Institute of Ocean Science and Technology

description: This sample is Thermococcus onnurineus NA1 wild type. It is the second of two mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: The concentrated Cy5-labelled cDNAs were resuspended in 30 ml of hybridization solution. Labelled cDNAs were placed on the microarray and covered by a MAUI Mixer hybridization chamber (BioMicro Systems). The slides were hybridized for 12 h at 42℃ by MAUI 12-bay system (BioMicro Systems). The hybridized slides were washed in 2X saline-sodium citrate (SSC)/0.1% sodium dodecyl sulphate (SDS) for 2 min, 1X SSC for 3 min, and then 0.2X SSC for 2 min at room temperature. The slides were centrifuged at 1,000g for 20s to dry them.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Molecular Devices).

data_processing:
The data were extracted using NimbleScan 2.4 software (Roche NimbleGen). Array normalization was performed using the median polish and quantile normalization method (Amaratunga, D. & Cabrera, J. J. Am. Stat. Assoc. 96, 1161–1170 (2001)).
Normalized expression values for the individual probes were used to obtain the expression values for a given ORF using the robust multi-array average (RMA) procedure as described (Irizarry, R. A. et al. Biostatistics 4, 249–264 (2003)). Finally, n-fold change ratios (R) were calculated using the RMA-processed expression values (RMA calls) obtained for a particular gene in the sample. Data analysis was performed using GeneSpring GX 7.3.1 (Agilent Technologies). Sample data table contains RMA-normalized, averaged gene-level signal intensity (i.e. values in the 'EXPRS' column in processed data *RMA.calls file)

organism: Thermococcus onnurineus NA1

source_name: Thermococcus onnurineus NA1 wild type

label_protocol: Total RNA samples (5 ug) were labelled with Cy5 dye-conjugated dCTP (Amersham) by reverse transcription using SuperScript II reverse transcriptase (Invitrogen). The labelled cDNA mixtures were then concentrated by ethanol precipitation.

growth_protocol: To examine the growth of strains on formate, modified medium 1 (Sokolova, T. G. et al. Extremophiles 8, 317-323 (2004)).  including 35 g/L NaCl and 1 g/L yeast extract was used in the presence of 10 g/L sodium formate. Trace elements and vitamins were added and the pH was adjusted to 6.0–7.0. All incubations were carried out at 80 ℃ under anaerobic conditions

extract_protocol: After cell harvest, RNA samples were prepared using TRIzol reagent. Genomic DNA was eliminated by DNaseI.

value: Wild-type

tag: media


title: overexpression of frh gene cluster 1

description: This sample is overexpression of frh gene cluster mutant. It is the first of two mutant biological replicates used in this experiment, each from separate cultures. Its control samples were WT1 and WT2

source_name: The overexpression of frh gene cluster in T. onnurineus NA1

value: overexpression of frh gene cluster


title: overexpression of frh gene cluster 2

description: This sample is overexpression of frh gene cluster mutant. It is the second of two mutant biological replicates used in this experiment, each from separate cultures. Its control samples were WT1 and WT2


title: frhA deletion 2

description: This sample is a frhA gene deletion mutant. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. Its control samples were WT1 and WT2

source_name: The frhA gene was deleted in T. onnurineus NA1

value: frhA gene deletion


title: frhA deletion 1

description: This sample is a frhA gene deletion mutant. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. Its control samples were WT1 and WT2


title: WT

description: This sample is Thermococcus onnurineus NA1 wild-type strain. It was used as control sample to compare TON_0282 gene deletion mutant.


title: WGBS_col_for_CACTA1g2-SunTag_T1


title: WGBS_CACTA1g2-SunTag22aa-2_T1


title: WGBS_CACTA1g2-SunTag22aa-1_T1


title: TON_0282 deletion

description: This sample is a TON_0282 gene deletion mutant.

source_name: The TON_0282 gene was deleted in T. onnurineus NA1

value: TON_0282 gene deletion


title: WT 1

description: This sample is Thermococcus onnurineus NA1 wild type. It is the first of two mutant biological replicates used in this experiment, each from separate cultures.


title: WGBS_ZF1CACTA1-TET1cd_T2plus

description: WGBS_ZF1CACTA1-TET1cd_T2 +


title: WGBS_ZF2CACTA1-TET1cd_T2minus

description: WGBS_ZF2CACTA1-TET1cd_T2 -


title: WGBS_fwa_for_FWAg4-SunTag_T2


title: WGBS_col_for_FWAg4-SunTag_T2


title: WGBS_FWAg4-SunTag22aa-1plus_T2

description: WGBS_FWAg4-SunTag22aa-1 +_T2


title: Alcoholic_cirrhosis_64

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Affymetrix assay system manual

data_processing: Raw scan data (.cel files) were normalized by Robust Multiarray Average (RMA) algorithm implemented in GenePattern ExpressionFileCreator module (www.broadinstitute.org/genepattern).

source_name: Alcoholic_cirrhosis, liver tissue

extract_protocol: RNA was isolated using AllPrepDNA/RNA mini kit (Qiagen) according to manufacturer’s protocol.

tag: disease status

value: Alcoholic cirrhosis

value: liver


title: Alcoholic_cirrhosis_66

scan_protocol: Refer to the Affymetrix assay system manual


title: Alcoholic_cirrhosis_62

label_protocol: Refer to the Affymetrix assay system manual


title: Alcoholic_cirrhosis_63


title: Alcoholic_cirrhosis_67


title: Alcoholic_cirrhosis_65


title: Alcoholic_cirrhosis_60


title: Alcoholic_cirrhosis_59


title: WGBS_FWAg4-SunTag22aa-2plus_T2

description: WGBS_FWAg4-SunTag22aa-2 +_T2


title: WGBS_FWAg4-SunTag14aa-1plus_T2

description: WGBS_FWAg4-SunTag14aa-1 +_T2


title: WGBS_FWAg4-SunTag22aa-2minus_T2

description: WGBS_FWAg4-SunTag22aa-2 -_T2


title: WGBS_col_for_NG-SunTag_T1


title: WGBS_FWAg4-SunTag22aa-1minus_T2

description: WGBS_FWAg4-SunTag22aa-1 -_T2


title: WGBS_NG-SunTag14aa-2_T1


title: WGBS_FWAg4-SunTag14aa-1minus_T2

description: WGBS_FWAg4-SunTag14aa-1 -_T2


title: WGBS_NG-SunTag22aa-1_T1


title: Alcoholic_cirrhosis_58


title: WGBS_col_for_SunTag_T1_rep1


title: WGBS_NG-SunTag14aa-1_T1


title: Alcoholic_cirrhosis_53


title: Alcoholic_cirrhosis_54


title: WGBS_NG-SunTag22aa-2_T1


title: Alcoholic_cirrhosis_51


title: Alcoholic_cirrhosis_55


title: Alcoholic_cirrhosis_52


title: Alcoholic_cirrhosis_61


title: WGBS_col_for_SunTag_T1_rep2


title: Alcoholic_cirrhosis_49


title: Alcoholic_cirrhosis_57


title: Alcoholic_cirrhosis_56


title: Alcoholic_cirrhosis_46


title: WGBS_FWAg4-SunTag22aa-2_T1


title: WGBS_FWAg4-SunTag22aa-1_T1


title: WGBS_col_for_ZF108-TET1cd_T3


title: WGBS_FWAg4-SunTag14aa-2_T1


title: WGBS_FWAg4-SunTag14aa-1_T1


title: WGBS_ZF108-TET1cd-2minus_T3

description: WGBS_ZF108-TET1cd-2 - _T3


title: Alcoholic_cirrhosis_47


title: WGBS_ZF108-TET1cd-2plus_T3

description: WGBS_ZF108-TET1cd-2 +_T3


title: Alcoholic_cirrhosis_42


title: Alcoholic_cirrhosis_43


title: Alcoholic_cirrhosis_44


title: Alcoholic_cirrhosis_50


title: Alcoholic_cirrhosis_48


title: Alcoholic_cirrhosis_45


title: WGBS_ZF108-TET1cd-1plus_T3

description: WGBS_ZF108-TET1cd-1 +_T3


title: WGBS_col_for_ZF108-TET1cd_T1_rep2


title: Alcoholic_cirrhosis_40


title: WGBS_ZF108-TET1cd-1minus_T3

description: WGBS_ZF108-TET1cd-1 - _T3


title: WGBS_col_for_ZF108-TET1cd_T1_rep1


title: Alcoholic_cirrhosis_41


title: RNAseq_ZF2CACTA1-TET1cd_T1

data_processing:
Reads were first aligned to TAIR10 gene annotation using Tophat (47) by allowing up to two mismatches and only keeping reads that mapped to one location. When reads did not map to the annotated genes, the reads were mapped to the TAIR10 genome. Number of reads mapping to genes were calculated by HTseq (48) with default parameters. Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads) using customized R scripts.
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text and bigwig

extract_protocol:
RNA was extracted using Direct-zol RNA Miniprep kit (Zymo).
For RNAseq involving ZF108-TET1cd and ZF108-YPet plants, 75ng of total RNA was used to prepare libraries using the Neoprep stranded mRNA-seq kit (Illumina). For RNAseq involving, ZF1CACTA1-TET1cd, ZF2CACTA1-TET1cd, SunTag14aa-TET1cd and SunTag22aa-TET1cd plants, 1μg of total RNA was used to prepare libraries using the TruSeq Stranded mRNA-seq kit (Illumina).


title: WGBS_ZF108-TET1cd-2_T1


title: WGBS_ZF108-TET1cd-3_T1


title: WGBS_ZF108-TET1cd-1_T1


title: RNAseq_ZF1CACTA1-TET1cd_T1


title: WGBS_ZF108-TET1cd-4_T1


title: Alcoholic_cirrhosis_39


title: Mild_acute_alcoholic_hepatitis_13

value: Mild acute alcoholic hepatitis


title: RNAseq_fwa_for_FWAg4-SunTag_T1

molecule: polyA RNA


title: Alcoholic_cirrhosis_36


title: Mild_acute_alcoholic_hepatitis_11


title: RNAseq_col_for_FWAg4-SunTag_T1_rep5


title: Mild_acute_alcoholic_hepatitis_12


title: RNAseq_col_for_FWAg4-SunTag_T1_rep4


title: Alcoholic_cirrhosis_37


title: Mild_acute_alcoholic_hepatitis_08


title: Mild_acute_alcoholic_hepatitis_09


title: RNAseq_col_for_FWAg4-SunTag_T1_rep3


title: Alcoholic_cirrhosis_38


title: RNAseq_col_for_FWAg4-SunTag_T1_rep1


title: Mild_acute_alcoholic_hepatitis_10


title: RNAseq_FWAg4-SunTag22aa-2_T1


title: RNAseq_col_for_FWAg4-SunTag_T1_rep2


title: RNAseq_FWAg4-SunTag14aa-2_T1


title: RNAseq_FWAg4-SunTag14aa-1_T1


title: Mild_acute_alcoholic_hepatitis_04


title: Mild_acute_alcoholic_hepatitis_07


title: alcoholic_steatosis_6

source_name: alcoholic_steatosis, liver tissue

value: Alcoholic steatosis


title: alcoholic_steatosis_4


title: Mild_acute_alcoholic_hepatitis_03


title: alcoholic_steatosis_3


title: alcoholic_steatosis_5


title: Mild_acute_alcoholic_hepatitis_06


title: alcoholic_steatosis_2


title: RNAseq_ZF108-TET1cd-2-1_T3


title: alcoholic_steatosis_1


title: RNAseq_ZF108-TET1cd-2-2_T3


title: RNAseq_ZF108-TET1cd-2-3_T3


title: RNAseq_ZF108-TET1cd-1-2_T3


title: RNAseq_ZF108-TET1cd-2-4_T3


title: RNAseq_ZF108-TET1cd-1-4_T3


title: RNAseq_FWAg4-SunTag22aa-1_T1


title: RNAseq_ZF108-TET1cd-1-1_T3


title: RNAseq_ZFYPET-2-4_T3

value: ZF-Ypet


title: RNAseq_ZFYPET-2-3_T3


title: RNAseq_ZFYPET-2-2_T3


title: RNAseq_ZFYPET-1-4_T3


title: RNAseq_ZFYPET-2-1_T3


title: Alcoholic_cirrhosis_31


title: Alcoholic_cirrhosis_33


title: Alcoholic_cirrhosis_27


title: Alcoholic_cirrhosis_30


title: Alcoholic_cirrhosis_29


title: RNAseq_col0_for_ZF108-TET1cd_T3_rep4


title: Alcoholic_cirrhosis_24


title: Alcoholic_cirrhosis_26


title: Alcoholic_cirrhosis_34


title: RNAseq_col0_for_ZF108-TET1cd_T3_rep2


title: RNAseq_ZFYPET-1-3_T3


title: Alcoholic_cirrhosis_28


title: RNAseq_ZFYPET-1-1_T3


title: RNAseq_ZF108-TET1cd-1-3_T3


title: RNAseq_col0_for_ZF108-TET1cd_T3_rep3


title: Alcoholic_cirrhosis_19


title: Alcoholic_cirrhosis_22


title: RNAseq_ZFYPET-1-2_T3


title: RNAseq_col0_for_ZF108-TET1cd_T3_rep1


title: RNAseq_ZF108-TET1cd-4_T1

value: Inflorescence


title: Alcoholic_cirrhosis_21


title: Alcoholic_cirrhosis_20


title: Alcoholic_cirrhosis_25


title: RNAseq_ZF108-TET1cd-1_T1


title: Alcoholic_cirrhosis_23


title: RNAseq_ZF108-TET1cd-2_T1


title: Mild_acute_alcoholic_hepatitis_05


title: Alcoholic_cirrhosis_17


title: Alcoholic_cirrhosis_16


title: RNAseq_col_for_ZF108-TET1cd_T1


title: Alcoholic_cirrhosis_18


title: RNAseq_ZF108-TET1cd-3_T1


title: Alcoholic_cirrhosis_15


title: RNAseq_fwa_for_ZF108-TET1cd_T1


title: Alcoholic_cirrhosis_12


title: Alcoholic_cirrhosis_14


title: Alcoholic_cirrhosis_11


title: Alcoholic_cirrhosis_13


title: Alcoholic_cirrhosis_10


title: Alcoholic_cirrhosis_07


title: Alcoholic_cirrhosis_09


title: MSAH21

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

tag: cohort

value: MSMC cohort

tag: outcome at 6 months

value: Dead or liver transplantation


title: MSAH19

scan_protocol: Refer to the NanoString nCounter Assay System Manual

tag: tissue


title: MSAH20

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Alive


title: MSAH16


title: Mild_acute_alcoholic_hepatitis_01


title: Mild_acute_alcoholic_hepatitis_02


title: Alcoholic_cirrhosis_35


title: A2848_51

source_name: liver tissue

value: Validation cohort (BRAH)


title: Alcoholic_cirrhosis_01


title: A2848_50


title: MSAH14


title: A2848_52


title: Alcoholic_cirrhosis_04


title: MSAH18


title: A2848_48


title: MSAH15


title: MSAH12


title: MSAH11


title: Alcoholic_cirrhosis_03


title: Alcoholic_cirrhosis_05


title: A2848_46


title: Alcoholic_cirrhosis_02


title: A2848_47


title: A2848_45


title: MSAH09


title: MSAH13


title: A2848_61


title: A2848_49


title: MSAH08


title: A2848_44


title: Alcoholic_cirrhosis_32


title: MSAH07


title: A2848_43


title: MSAH10


title: MSAH05


title: MSAH04


title: MSAH06


title: MSAH03


title: A2848_42


title: A2848_38


title: BRAH099

value: BRAH cohort


title: MSAH01


title: BRAH096


title: BRAH097


title: MSAH02


title: BRAH098


title: BRAH094


title: BRAH095


title: A2848_37


title: A2848_41


title: A2848_14


title: A2848_13


title: BRAH093


title: BRAH092


title: A2848_19


title: A2848_17


title: BRAH090


title: A2848_20


title: A2848_39


title: Alcoholic_cirrhosis_06


title: A2848_11


title: A2848_36


title: A2848_15


title: A2848_16


title: A2848_40


title: A2848_18


title: A2848_07


title: A2848_09


title: BRAH086


title: BRAH088


title: BRAH087


title: BRAH085


title: A2848_10


title: BRAH084


title: BRAH082


title: BRAH091


title: BRAH081


title: BRAH080


title: A2848_02


title: BRAH083


title: A2848_06


title: A2848_03


title: BRAH079


title: BRAH077


title: BRAH089


title: A2848_08


title: BRAH076


title: A2465_069

value: Derivation cohort (BRAH)


title: A2848_05


title: A2848_12


title: BRAH071


title: A2465_063


title: A2465_070


title: Alcoholic_cirrhosis_08


title: A2848_01


title: A2465_066


title: BRAH067


title: A2465_071


title: A2848_04


title: A2465_067


title: A2465_068


title: BRAH078


title: BRAH075


title: BRAH072


title: BRAH064


title: BRAH074


title: BRAH062


title: BRAH061


title: BRAH060


title: A2465_060


title: BRAH073


title: BRAH066


title: BRAH068


title: BRAH069


title: A2465_052


title: A2465_051


title: A2465_058


title: A2465_061


title: BRAH065


title: BRAH057


title: BRAH063


title: A2465_049


title: BRAH070


title: A2465_053


title: A2465_047


title: A2465_064


title: BRAH056


title: A2465_059


title: A2465_057


title: A2465_054


title: BRAH052


title: BRAH053


title: A2465_050


title: A2465_045


title: BRAH059


title: BRAH050


title: A2465_044


title: BRAH048


title: A2465_055


title: BRAH046


title: BRAH047


title: A2465_056


title: BRAH058


title: A2465_048


title: BRAH051


title: A2465_042


title: BRAH054


title: A2465_034


title: A2465_040


title: A2465_039


title: BRAH044


title: A2465_038


title: A2465_046


title: BRAH043


title: A2465_041


title: BRAH039


title: BRAH042


title: A2465_043


title: BRAH040


title: BRAH037


title: BRAH036


title: BRAH035


title: BRAH038


title: BRAH033


title: A2465_025


title: A2465_037


title: A2465_036


title: A2465_024


title: A2465_033


title: A2465_032


title: BRAH032


title: A2465_027


title: A2465_023


title: A2465_029


title: A2465_020


title: A2465_026


title: A2465_018


title: BRAH030


title: A2465_021


title: A2465_031


title: A2465_030


title: A2465_062


title: BRAH029


title: A2465_017


title: A2465_015


title: A2465_022


title: BRAH028


title: A2465_014


title: A2465_013


title: A2465_019


title: A2465_011


title: A2465_016


title: BRAH024


title: A2465_009


title: BRAH023


title: A2465_008


title: BRAH026


title: BRAH025


title: A2465_012


title: A2465_007


title: BRAH022


title: BRAH020


title: BRAH021


title: A2465_005


title: A2465_003


title: BRAH019


title: A2465_004


title: BRAH018


title: A2465_002


title: A2465_001


title: A2299_094


title: A2465_010


title: A2465_006


title: WT_CD4+_cDC_exp2

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90040, Version 6.5, May 2010).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-60502) at 100% in Green channel, with a scan resolution of 3 um.

data_processing: Data are extracted with Agilent Feature Extraction Software and normalized.

label_protocol: Total RNA was labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen) or NucleoSpin RNA (MACHEREY-NAGEL) according to the manufacturers' instructions.

treatment_protocol: Progenitor and mature hematopoietic cells were isolated by cell sorting.

value: CD4+ cDC

value: wildtype

tag: cell isolation type

value: Primary isolated cells

value: Spleen

tag: sorting methods

value: MACS sorting

tag: surface markers


title: BRAH017


title: BRAH015


title: BRAH014


title: New born control 2

city: Al Ain

first: Ranjit

last: Vijayan

state: Abu Dhabi

address: PO Box 15551

department: Biology

country: United Arab Emirates

institute: United Arab Emirates University

description:
NB_Control_2
This sample is from normal birth weight (25th-75th percentile) new born (1 day old) pups. Second of 3 biologial replicates.

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

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

data_processing: The raw data was subjected to RMA (Robust Multi-Array) Analysis and background correction as implemented in the rma package in R.

organism: Rattus norvegicus

source_name: Newborn control

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

growth_protocol: 24 female (~200-210 g) and 12 male (340 to 350 g) ~10-12 week old Wistar rats were mated in 12 groups, each comprising 2 females and a male

extract_protocol: RNA was extracted from skeletal muscle tissues using TRIzol reagent (Applied Biosystems, Thermo Fisher Scientific, USA) according to manufacturer’s protocol. RNA quality and concentration was determined by using an Agilent 2100 bioanalyzer.

treatment_protocol: On delivery, the pups were weighed and grouped as either of lower (LBW) (5-25th percentile) or average (ABW) (50th-75th percentile) birth weight. Each litter size was adjusted to eight pups per lactating female

tag: strain

value: Wistar

tag: gender

value: male

tag: age of rats (days)

tag: birth weight (percentile)

value: Skeletal muscle


title: A2299_095


title: New born control 3

description:
NB_Control_3
This sample is from normal birth weight (25th-75th percentile) new born (1 day old) pups. Third of 3 biologial replicates.


title: BRAH012

value: liver


title: WT_Neu_exp2

value: Neutrophils

value: Bone marrow

value: FACS sorting

value: CD11b(+) Ly6G(hi)


title: Normal birth weight adult rats 2

description:
NBW_AR_2
This sample is from normal birth weight (25th-75th percentile) 145-day old adult rats. Second of 3 biologial replicates.

source_name: Normal birth weight adult rats


title: WT_CD4+_cDC_exp1


title: Low birth weight new born 2

description:
LBW_NB_2
This sample is from low birth weight (5th-25th percentile) new born (1 day old) pups. Second of 3 biologial replicates.

source_name: Low birth weight newborn


title: BRAH011

value: Dead or liver transplantation


title: New born control 1

description:
NB_Control_1
This sample is from normal birth weight (25th-75th percentile) new born (1 day old) pups. First of 3 biologial replicates.


title: Low birth weight new born 1

description:
LBW_NB_1
This sample is from low birth weight (5th-25th percentile) new born (1 day old) pups. First of 3 biologial replicates.


title: WT_Neu_exp1


title: A2299_091


title: Normal birth weight adult rats 1

description:
NBW_AR_1
This sample is from normal birth weight (25th-75th percentile) 145-day old adult rats. First of 3 biologial replicates.


title: BRAH010

value: Alive


title: BRAH013

value: BRAH cohort


title: WT_CD8+_cDC_exp1

value: CD8+ cDC

value: MACS sorting followed by FACS sorting


title: Normal birth weight adult rats 3

description:
NBW_AR_3
This sample is from normal birth weight (25th-75th percentile) 145-day old adult rats. Third of 3 biologial replicates.


title: Lwt1_1

city: Wuhan

first: Weihui

last: Li

address: 1 str Sizisan

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium_smegmatis_MC2_155_uid57701 whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped (FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Mycobacterium%20smegmatis%20MC2%20155
Supplementary_files_format_and_content: gene_expression-1.xls file includes FPKM values for each Sample

organism: Mycolicibacterium smegmatis

source_name: wild-type strain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNeasy Mini Kit (Cat#74106, Qiagen) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: Lwt2_1


title: Lwt3_1


title: WT_CD8+_cDC_exp2

tag: cell type

value: wildtype


title: L583_1

source_name: hpoR mutant

value: Msm hpoR::hyg/pMV261


title: Low birth weight adult rats on normal diet 3

description:
LBW_AR_ND_3
This sample is from low birth weight (5th-25th percentile) 145-day old adult rats. Third of 3 biologial replicates.


title: Low birth weight adult rats on normal diet 2

description:
LBW_AR_ND_2
This sample is from low birth weight (5th-25th percentile) 145-day old adult rats. Second of 3 biologial replicates.


title: Low birth weight adult rats on normal diet 1

description:
LBW_AR_ND_1
This sample is from low birth weight (5th-25th percentile) 145-day old adult rats. First of 3 biologial replicates.


title: WT_Ly6C+_Mo_exp2

value: Ly6C+ Monocyte progenitor

value: Primary isolated cells


title: WT_Ly6C+_Mo_exp1


title: L581_1


title: WT_pre-cDC_exp2

value: precursors of classical dendritic cells


title: BRAH009


title: BRAH008


title: BRAH004


title: BRAH003


title: BRAH007


title: BRAH002


title: IRF8KO_GMP_exp1

value: granulocyte-monocyte progenitors


title: L582_1


title: Low birth weight new born 3

description:
LBW_NB_3
This sample is from low birth weight (5th-25th percentile) new born (1 day old) pups. Third of 3 biologial replicates.

value: Wistar

value: male

value: Skeletal muscle


title: WT_pre-cDC_exp1

value: Bone marrow


title: BRAH005

value: liver


title: WT_CDP_exp1

value: common dendritic cell progenitors


title: IRF8KO_GMP_exp2


title: WT_GMP_exp1


title: WT_CDP_exp2


title: BRAH006

value: Dead or liver transplantation


title: SK-N-BE(2) GSK-J4 rep1

status: Public on Feb 17 2018

city: Richmond

first: Timothy

middle: L

last: Lochmann

state: VA

address: 521 N 11th St

department: OCMB

institute: Virginia Commonwealth University

data_processing:
RNA-seq quality was confirmed by FastQC
RNA-seq data was mapped to ENSEMBL hg38 release 85 assembly using the STAR aligner under default settings
Aligned read files were counted using SummerizedExperiment in R.
Genes with no reads across all samples within each cell line were removed from analysis prior to differential analysis.
Summarized data sets were compared for differential expression by DESeq2 under default settings.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated text files (.csv) contain gene expression data for each cell line. Data includes ENSEMBL gene identifier, mean expression, Log2 fold change, Standard error, p-value, fdr adjusted p-value, and gene symbol.

source_name: Neuroblastoma

extract_protocol:
Total RNA was harvested by TriZol reagent and ribosomal RNA was removed by polyA capture prior to library generation.
Libraries were created with the KAPA Stranded mRNA-seq Kit.

treatment_protocol: All treatments were with 1µM GSK-J4 for 72 hours.

tag: cell line

value: neuroblastoma cell line

tag: gsk-j4 sensitivity

value: resistant

tag: mycn

value: amplified


title: WT_GMP_exp2

tag: genotype

value: MACS sorting followed by FACS sorting


title: SK-N-FI No Rx rep2

value: SK-N-FI

value: sensitive

value: wildtype


title: SK-N-BE(2) No Rx rep1


title: SK-N-BE(2) GSK-J4 rep3


title: IMR5 72h GSK-J4 rep2


title: SK-N-BE(2) GSK-J4 rep2


title: SK-N-FI 72h GSK-J4 rep3


title: SK-N-FI 72h GSK-J4 rep1


title: SK-N-BE(2) No Rx rep3


title: IMR5 72h GSK-J4 rep3


title: SK-N-FI No Rx rep3


title: IMR5 No Rx rep3


title: SK-N-BE(2) No Rx rep2


title: IMR5 72h GSK-J4 rep1


title: SK-N-FI 72h GSK-J4 rep2


title: IMR5 No Rx rep1


title: IMR5 No Rx rep2


title: SK-N-FI No Rx rep1


title: LAN5 72h GSK-J4 rep1


title: LAN5 No Rx rep1


title: LAN5 No Rx rep2


title: LAN5 No Rx rep3


title: #4_NAH7-harboring_8h_2

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

hyb_protocol: The labelled samples were hybridized individually with each chip using a GeneChip Hybridization Oven 640 (Affymetrix) at 60 rpm and 50°C for 16 h. The chips were then washed and stained using a Hybridization, Wash and Stain Kit (Affymetrix) according to a modified version of the FleX450-0005 protocol of the GeneChip Fluidics station 450 (Affymetrix)

scan_protocol: Signals were detected using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
KT2440b520511FR-3.bpmap: BPMAP for the forward strand of KT2440 chromosome
KT2440b520511FF-3.bpmap: BPMAP for the reverse strand of KT2440 chromosome

organism: Pseudomonas putida

source_name: cDNA prepared from KT2440 (substrain #4) harboring NAH7 plasmid sampled in stationary phase

label_protocol: Labelling of the cDNA was achieved using a GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Each strain was grown in 5 ml of LB at 300 strokes/min for 14-14.5 h (pre-culture) and then washed and transferred into 100-ml of NMM-4 buffer (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 0.1% succinate adjusting its turbidity (600 nm) at 0.05. The resultant culture was incubated on a rotary shaker at 120 rpm and cell growth was monitored in by measuring its turbidity (600 nm) until its log phase (4 h after inoculation) and early stationary phase (8 h after inoculation).

extract_protocol: Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel). cDNA was synthesized using SuperScript II (Invitrogen, Carlsbad, CA) in the presence of actinomycin D (Sigma, St.Louis, MO) to prevent generation of spurious second-strand cDNA.

treatment_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA) to stabilize RNA of them.


title: #4_pCAR1-harboring_8h_2

source_name: cDNA prepared from KT2440 (substrain #4) harboring pCAR1 plasmid sampled in stationary phase


title: #4_NAH7-harboring_8h_1


title: #4_pCAR1-harboring_8h_1


title: #4_RP4-harboring_8h_2

source_name: cDNA prepared from KT2440 (substrain #4) harboring RP4 plasmid sampled in stationary phase


title: #4_RP4-harboring_8h_1


title: #4_plasmid-free_8h_2

source_name: cDNA prepared from plasmid-free KT2440 (substrain #4) sampled in stationary phase


title: #4_plasmid-free_8h_1


title: LAN5 72h GSK-J4 rep3


title: LAN5 72h GSK-J4 rep2


title: #4_NAH7-harboring_4h_2

source_name: cDNA prepared from KT2440 (substrain #4) harboring NAH7 plasmid sampled in log phase


title: #4_pCAR1-harboring_4h_2

source_name: cDNA prepared from KT2440 (substrain #4) harboring pCAR1 plasmid sampled in log phase


title: #2_NAH7-harboring_8h_2

source_name: cDNA prepared from KT2440 (substrain #2) harboring NAH7 plasmid sampled in stationary phase


title: #4_plasmid-free_4h_2

source_name: cDNA prepared from plasmid-free KT2440 (substrain #4) sampled in log phase


title: #4_plasmid-free_4h_1


title: #4_RP4-harboring_4h_2

source_name: cDNA prepared from KT2440 (substrain #4) harboring RP4 plasmid sampled in log phase


title: #4_RP4-harboring_4h_1


title: #2_NAH7-harboring_8h_1


title: #2_RP4-harboring_8h_2

source_name: cDNA prepared from KT2440 (substrain #2) harboring RP4 plasmid sampled in stationary phase


title: #2_pCAR1-harboring_8h_1

source_name: cDNA prepared from KT2440 (substrain #2) harboring pCAR1 plasmid sampled in stationary phase


title: #2_plasmid-free_8h_1

source_name: cDNA prepared from plasmid-free KT2440 (substrain #2) sampled in stationary phase


title: #4_NAH7-harboring_4h_1


title: #4_pCAR1-harboring_4h_1


title: #2_NAH7-harboring_4h_2

source_name: cDNA prepared from KT2440 (substrain #2) harboring NAH7 plasmid sampled in log phase


title: #2_NAH7-harboring_4h_1


title: #2_pCAR1-harboring_4h_2

source_name: cDNA prepared from KT2440 (substrain #2) harboring pCAR1 plasmid sampled in log phase


title: #2_pCAR1-harboring_4h_1


title: #2_plasmid-free_4h_2

source_name: cDNA prepared from plasmid-free KT2440 (substrain #2) sampled in log phase


title: #2_RP4-harboring_8h_1


title: #2_pCAR1-harboring_8h_2


title: #2_RP4-harboring_4h_2

source_name: cDNA prepared from KT2440 (substrain #2) harboring RP4 plasmid sampled in log phase


title: #2_plasmid-free_4h_1


title: #2_plasmid-free_8h_2


title: HS1-11 N3 DNA rep3

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

institute: University of Luebeck

description:
telencephalon
There are three raw files per sample. Two files (15 bp) represent read 1 and read 2  of paired-end sequencing. One file (10 bp) contains the technical reads with the  unique molecular identifiers (UMIs) for each RNA or DNA molecule, allowing to computationally reduce the effects of PCR amplification biases.

data_processing:
Library strategy: lentivirus-based massively parallel reporter assay (lentiMPRA)
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis softwarre. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
Barcodes (consensus called paired-end reads) and UMI sequences containing unresolved bases (N) or not matching the designed length of 15bp were excluded. Each barcode x UMI pair was counted only once and only barcodes matching perfectly to those included the oligo design considered. To determine RNA/DNA ratios per insert, we summed up the counts of all barcodes belonging to the same insert and determined the ratio of the average of normalized counts.
Genome_build: GRCh37
Supplementary_files_format_and_content: All processed data files are in gzip-compressed tab-separated text file format. DNA.tsv.gz and RNA.tsv.gz files contain assigned RNA and DNA barcode counts. HAR_design.tsv.gz and HAR-permutation_design.tsv.gz and contain all designed oligo sequences for HAR and HAR-permutation experiments, respectively.

source_name: Human glial progenitor cells

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen). Messenger RNA (mRNA) was purified from the total RNA using Oligotex mRNA mini kit (Qiagen) and treated with Turbo DNase to remove contaminating DNA.
mRNA was reverse transcribed with SuperScript II (Invitrogen) using a primer downstream from the barcode. Resulting cDNA was split into multiple reactions to reduce PCR jack-potting effects and cDNA amplification performed with Kapa Robust polymerase for three cycles, incorporating unique molecular identifiers (UMIs) of 10 bp length. PCR products were cleaned with AMPure XP beads (Beckman Coulter) to remove primers and concentrate samples. These products underwent a second round of amplification in 8 reactions per replicate for 15 cycles, with a reverse primer containing only P7. All reactions were pooled and run on agarose gels for size selection and submitted for sequencing. For DNA, each replicate was amplified for 3 cycles with UMI-incorporating primers, just as the RNA. First round products were cleaned up with AMPure XP beads, and amplified in split reactions, each for 20 cycles. Again, reactions were pooled and gel-purified and sequenced.

treatment_protocol: For the lentiMPRA, 6 million human iPSC-derived neural progenitor cells were plated on a 15 cm dish and cultured for 24 hours. The cells were infected with integrating lentivirus libraries and incubated for 4 days, when they have an estimated 50-100 viral particles/cell. Three independent replicate cultures were infected.

tag: iPSc line name

value: iPSC-derived neural progenitors

tag: developmental stage


title: HS1-11 N3 DNA rep2


title: HS1-11 N3 DNA rep1


title: Pt5C N3 DNA rep2

data_processing:
Library strategy: lentivirus-based massively parallel reporter assay (lentiMPRA)
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis softwarre. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
Barcodes (consensus called paired-end reads) and UMI sequences containing unresolved bases (N) or not matching the designed length of 15bp were excluded. Each barcode x UMI pair was counted only once and only barcodes matching perfectly to those included the oligo design considered. To determine RNA/DNA ratios per insert, we summed up the counts of all barcodes belonging to the same insert and determined the ratio of the average of normalized counts.
Genome_build: GRCh37
Supplementary_files_format_and_content: All processed data files are in gzip-compressed tab-separated text file format. DNA.tsv.gz and RNA.tsv.gz files contain assigned RNA and DNA barcode counts.

organism: Pan troglodytes

source_name: Chimpanzee glial progenitor cells

treatment_protocol: For the lentiMPRA, 6 million chimpanzee iPSC-derived neural progenitor cells were plated on a 15 cm dish and cultured for 24 hours. The cells were infected with integrating lentivirus libraries and incubated for 4 days, when they have an estimated 50-100 viral particles/cell. Three independent replicate cultures were infected.


title: Pt5C N3 DNA rep1


title: WTc N3 HAR permutation DNA rep3

value: WTc


title: Pt2A N3 HAR permutation DNA rep3


title: WTc N3 HAR permutation DNA rep2


title: Pt5C N3 DNA rep3


title: #2_RP4-harboring_4h_1


title: WTc N3 DNA rep3


title: Pt2A N3 HAR permutation DNA rep2


title: Pt5C N2 DNA rep2

source_name: Chimpanzee neural progenitor cells


title: WTc N3 HAR permutation DNA rep1


title: Pt2A N3 DNA rep2


title: HS1-11 N2 DNA rep2

source_name: Human neural progenitor cells


title: Pt2A N3 DNA rep3


title: WTc N3 DNA rep1


title: Pt2A N2 HAR permutation DNA rep3


title: Pt2A N3 DNA rep1


title: Pt2A N3 HAR permutation DNA rep1


title: Pt5C N2 DNA rep3


title: Pt2A N2 HAR permutation DNA rep2


title: HS1-11 N2 DNA rep3


title: HS1-11 N2 DNA rep1


title: Pt2A N2 DNA rep2


title: WTc N2 HAR permutation DNA rep2


title: Pt5C N3 RNA rep1


title: WTc N2 HAR permutation DNA rep1


title: Pt5C N3 RNA rep3


title: WTc N2 HAR permutation DNA rep3


title: WTc N3 DNA rep2


title: HS1-11 N3 RNA rep2


title: Pt2A N2 DNA rep1


title: HS1-11 N3 RNA rep3


title: WTc N2 DNA rep2


title: Pt2A N2 DNA rep3


title: Pt2A N3 HAR permutation RNA rep2


title: HS1-11 N3 RNA rep1


title: Pt2A N3 HAR permutation RNA rep3


title: Pt2A N3 HAR permutation RNA rep1


title: WTc N2 DNA rep3


title: Pt2A N2 HAR permutation DNA rep1


title: Pt5C N3 RNA rep2


title: Pt5C N2 DNA rep1


title: Pt2A N3 RNA rep2


title: WTc N3 HAR permutation RNA rep1


title: Pt2A N3 RNA rep1


title: HS1-11 N2 RNA rep3


title: HS1-11 N2 RNA rep2


title: WTc N3 HAR permutation RNA rep3


title: Pt2A N3 RNA rep3


title: WTc N3 RNA rep3


title: WTc N2 HAR permutation RNA rep1


title: WTc N2 DNA rep1


title: Pt5C N2 RNA rep3


title: Pt5C N2 RNA rep2


title: WTc N3 HAR permutation RNA rep2


title: Rev-erba KO3

city: Duarte

first: Ke

last: Ma

address: 1500 E Duarte Road

department: Diabetes Complications & Metabolism

institute: City of Hope

description: KO myoblast sample 3

hyb_protocol: Biotinylated cRNA samples were hybridized to arrays at 58°C for 18 hours according to manufacturer's protocol.

scan_protocol: Arrays were scanned using Illumina BeadArray Reader using standard scanning protocol

data_processing: Unmodified microarray data obtained from GenomeStudio were background-subtracted and quantile-normalized using the lumi package and analyzed with the limma package within R.

source_name: Primary myoblast

label_protocol: cRNA synthesis and biotin labeling were performed using Illumina TotalPrep-96 RNA Amplification Kit (Ambion/ThermoScientific) according to manufacturer's protocol. Labeling in vitro transcription reaction was performed at 37°C for 14 hours.

growth_protocol: Myoblasts were grown in growth media containing F-10 medium supplemented with 20% FBS and 5 ng/ml bFGF in collagen-coated plates

extract_protocol: Total RNA from three independent primary myoblast samples were extracted using Qiagen RNAeasy Mini kit.  cRNA using Illumina TotalPrep RNA amplification kit (Thermo Scientific).

treatment_protocol: Normal primary myoblast growth condition

value: Male

tag: age

value: 6 weeks old


title: WTc N2 HAR permutation RNA rep3


title: HS1-11 N2 RNA rep1


title: WTc N2 HAR permutation RNA rep2


title: Pt2A N2 HAR permutation RNA rep3


title: Pt5C N2 RNA rep1


title: Rev-erba KO2

description: KO myoblast sample 2


title: WTc N2 RNA rep2


title: WTc N3 RNA rep2


title: Pt2A N2 HAR permutation RNA rep1


title: WTc N2 RNA rep3


title: WTc N2 RNA rep1


title: WTc N3 RNA rep1


title: Pt2A N2 RNA rep3


title: Rev-erba WT1

description: WT myoblast sample 1


title: Pt2A N2 HAR permutation RNA rep2


title: Rev-erba KO1

description: KO myoblast sample 1


title: Rev-erba WT2

description: WT myoblast sample 2


title: Rev-erba WT3

description: WT myoblast sample 3


title: Pt2A N2 RNA rep2


title: Pt2A N2 RNA rep1


title: Control_replicate_2

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v1.2)
Data normalization, dimension reduction, and differential expression analysis were performed using the Seurat R package (v2.2.0)
Single cell signatures scoring was performed using the FastProject software (v1.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; genes.tsv is list of genes detected in samples

source_name: Immune Infiltrate

growth_protocol: Adar1 null tumors or control tumors (2 million cells each) were implanted with matrigel into C57BL/6 mice. On day 14 after implantation, tumors were extracted and processed as noted below

extract_protocol:
Tumors were dissected from the surrounding fascia, mechanically minced and treated with collagenase P and DNAse I for 10 minutes at 37C. Tumor-infiltrating leukocytes were enriched using Optiprep (Sigma) density gradient followed by CD45+ MACS positive selection (Miltenyi). Cells were counted and loaded onto the 10x device (10x Genomics).
Library construction was performed as per standard 10x protocol (Manual CG00052 Rev B) for 10X single-cell 3' RNA-seq v2

value: CD45+ cells extracted from B16-F10 control melanoma tumors

tag: background strain

value: control

tag: tissue

value: melanoma tumors

tag: isolation of cd45+ cells from tumors


title: Adar__replicate_2

value: CD45+ cells extracted from B16-F10 Adar1 null melanoma tumors

value: Adar1 null

value: CD45+ MACS positive selection (Miltenyi)


title: Control_replicate_1


title: Adar_replicate_1


title: siTP53 10Gy4h rep3

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description:
siTP53-transfected-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG-7926_10Gy_3_si_p53_lib80491_4027_7_1

data_processing:
alignment to hg19, hisat 2.0.5
feature counting, featureCounts
normalization, DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: txt file, normalized expression values

source_name: U2OS cells

growth_protocol: The wild-type U2-OS cells were purchased from ATCC (HTB-96) and used as a primary model. Cells were grown in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (HyClone) and gentamicin (40 mg/mL; Krka) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from 1x106 cells using RNeasy Mini Kit (Qiagen) and treated on-column with DNase using the RNase-Free DNase Set (Qiagen).
RNA libraries were prepared for sequencing using 1ug RNA according to the standard Illumina protocols

treatment_protocol: For expression analysis wild type and transfected cells were used. Cells were transiently transfected with 10 nM siRNA (Eurofins) using INTERFERin® Kit (Polyplus Transfection) for 48 hours using sequences specific for TP53 gene, RELA gene, or control siRNA. Any treatment started 48 h after inoculation of cells (wild type cells) or after 48h of siRNA transfection (transfected cells); all steps, with the exception of irradiation, were carried out at 37 °C and 5% CO2. For gene expression analysis cells were irradiated with 4 or 10 Gy IR dose at a 1Gy/min dose rate using 6 MeV photons (generated by linear accelerator Clinac 600, Varian), the medium was replaced with a fresh one, and then cells were harvested 4 hours after irradiation.

tag: tumor

value: osteosarcoma

tag: Sex

value: female

value: 15 years

tag: tissue/cells

value: bone


title: siTP53 10Gy4h rep1

description:
siTP53-transfected-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG-7926_10Gy_1_si_p53_lib80453_3900_1_1


title: siTP53 4Gy4h rep3

description:
siTP53-transfected-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG-7926_4Gy_3_si_p53_lib80487_4027_4056_1_1


title: adult Can_5

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

description: adult Can

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Hippocampus

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

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: strain

value: Hippocampus


title: adult Veh_3

description: adult Veh


title: adult Can_4

description: adult Can


title: adult Veh_5

description: adult Veh


title: siTP53 4Gy4h rep2

description:
siTP53-transfected-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG-7926_4Gy_2_si_p53_lib80468_4027_4_1


title: siTP53 10Gy4h rep2

description:
siTP53-transfected-transfected cells irradiated with 10Gy (1Gy/min) & 4h recovery
NG-7926_10Gy_2_si_p53_lib80472_4027_5_1


title: adult Can_3

description: adult Can


title: adult Veh_4

description: adult Veh


title: p28 Can_4

description: p28 Can


title: p28 Veh_4

description: p28 Veh


title: adult Veh_2

description: adult Veh


title: p28 Can_3

description: p28 Can


title: human colorectal tumor tissue, patient sample 49

city: Guangzhou

first: Huanliang

address: 26 Yuancun Er Heng Road

institute: Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-sen University

description: LncRNA and gene expression in colon cancer tissue

hyb_protocol: 600ng of Cy3-labelled linearly amplified aRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1  (Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2  (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x180k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: tumor tissue

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

extract_protocol: RNA was prepared using the RNeasy mini kit (Qiagen, GmBH, Germany) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fresh samples obtained from surgery were protected in RNAlater and kept in liquid nitrogen.

value: tumor tissue

tag: patient diagnosis

value: colon cancer

tag: gender


title: p28 Veh_3

description: p28 Veh


title: human colorectal normal tissue, patient sample 45

description: LncRNA and gene expression in colon paraneoplastic tissue

source_name: adjacent non-tumor tissue

value: adjacent non-tumor tissue

value: male


title: human colorectal normal tissue, patient sample 44

description: LncRNA and gene expression in rectal paraneoplastic tissue

value: rectal cancer


title: human colorectal normal tissue, patient sample 49


title: adult Veh_1

description: adult Veh


title: human colorectal tumor tissue, patient sample 45


title: human colorectal tumor tissue, patient sample 44

description: LncRNA and gene expression in rectal cancer tissue


title: siTP53 4Gy4h rep1

description:
siTP53-transfected-transfected cells irradiated with 4Gy (1Gy/min) & 4h recovery
NG-7926_4Gy_1_si_p53_lib80449_3900_8_1


title: human colorectal normal tissue, patient sample 25


title: p28 Veh_2

description: p28 Veh


title: adult Can_2

description: adult Can


title: p28 Can_2

description: p28 Can


title: p28 Veh_1

description: p28 Veh


title: siTP53 ctr rep1

description:
untreated control siTP53-transfected-transfected cells
NG-7926_ctr_1_si_p53_lib80438_3949_3949_2_1


title: human colorectal tumor tissue, patient sample 25


title: human colorectal normal tissue, patient sample 24


title: GC3

status: Public on Feb 16 2018

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Data from mice were aligned to the mm9 reference transcriptome using Tophat, and analyzed using voom and limma packages to generate differential expression signatures
Genome_build: mm9
Supplementary_files_format_and_content: Counts in tab delimited text files generated using HTSeq-count against Ensembl v67 annotation

source_name: Brain

extract_protocol:
Total RNA was isolated from frozen dissected NAc tissue using QIAzol lysis reagent and purified using the RNAeasy mini kit (Qiagen). RNA integrity was assayed using an Aligent 2100 Bioanalyzer (Aligent, Santa Clara CA).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA).

tag: region

value: NAc

tag: condition

value: Control

value: GFP

value: Male


title: GC1


title: GC5


title: GC7


title: GC4


title: GC9


title: GC8


title: GC6


title: GC10


title: GC2