title: Monocyte-Specific DNA Methylation Sample 340

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 338

status: Public on Jun 22 2024

type: genomic

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

country: USA

institute: University of Hawaii at Manoa

description: normal monocyte enriched sample

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1.0 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina HiScanSQ System following standard protocols

data_processing:
minfi for quality control, along with ENmix package for normalization in R environment 4.1
average beta value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: monocyte

label_protocol: Standard Illumina Protocol

extract_protocol: Monocytes were enriched from peripheral blood mononuclear cells using the EasySep Magnetic cell separator for the EasySep Human Monocyte Enrichment Kit without CD16 Depletion following the manufacturers protocols. Enriched monocytes were isolated for genomic DNA using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit following standard protocols.

tag: cell type

value: monocyte

tag: Sex

value: Female

tag: race

value: Native Hawaiian


title: Monocyte-Specific DNA Methylation Sample 364

description: normal monocyte enriched sample

value: Male


title: Monocyte-Specific DNA Methylation Sample 337

description: normal monocyte enriched sample

value: White


title: Monocyte-Specific DNA Methylation Sample 359

description: normal monocyte enriched sample

value: Japanese American


title: Monocyte-Specific DNA Methylation Sample 333

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 331

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 350

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 332

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 330

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 335

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 334

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 329

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 324

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 328

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 325

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 327

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 321

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 322

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 323

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 320

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 319

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 317

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 318

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 315

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 314

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 312

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 311

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 339

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 310

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 336

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 309

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 308

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 326

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 307

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 304

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 301

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 305

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 302

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 306

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 303

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 299

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 296

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 295

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 298

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 316

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 297

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 300

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 292

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 313

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 290

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 291

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 288

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 289

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 293

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 285

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 287

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 286

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 283

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 284

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 281

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 282

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 278

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 280

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 279

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 277

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 275

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 274

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 276

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 294

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 267

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 268

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 269

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 264

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 266

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 261

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 260

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 259

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 258

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 256

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 254

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 255

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 253

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 251

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 249

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 250

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 248

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 252

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 273

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 272

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 246

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 244

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 271

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 270

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 265

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 243

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 242

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 240

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 263

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 241

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 239

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 262

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 257

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 237

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 235

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 236

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 234

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 233

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 247

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 231

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 232

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 245

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 230

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 226

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 227

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 228

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 229

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 224

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 222

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 221

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 223

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 225

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 219

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 220

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 216

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 238

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 215

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 214

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 217

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 213

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 212

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 211

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 207

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 209

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 210

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 204

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 203

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 201

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 198

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 206

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 199

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 196

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 195

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 218

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 205

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 200

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 191

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 194

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 190

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 189

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 192

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 202

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 197

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 208

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 187

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 184

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 188

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 183

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 186

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 185

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 182

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 181

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 180

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 179

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 177

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 175

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 172

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 171

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 170

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 167

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 169

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 168

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 166

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 164

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 163

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 162

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 157

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 150

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 160

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 156

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 158

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 151

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 155

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 152

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 153

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 161

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 154

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 178

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 159

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 173

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 149

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 148

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 147

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 174

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 165

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 144

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 146

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 141

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 143

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 140

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 145

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 142

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 139

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 138

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 137

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 135

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 136

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 128

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 129

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 130

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 131

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 134

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 133

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 124

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 123

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 132

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 127

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 125

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 126

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 122

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 121

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 119

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 116

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 115

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 120

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 117

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 118

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 113

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 114

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 111

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 112

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 110

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 108

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 109

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 106

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 105

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 102

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 99

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 100

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 96

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 98

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 104

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 94

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 97

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 93

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 95

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 90

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 107

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 92

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 88

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 89

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 91

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 85

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 86

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 87

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 83

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 84

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 82

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 193

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 103

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 81

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 101

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 80

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 79

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 78

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 77

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 76

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 75

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 73

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 74

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 69

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 71

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 70

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 68

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 72

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 67

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 63

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 64

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 65

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 60

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 62

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 59

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 57

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 58

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 61

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 56

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 55

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 52

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 54

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 53

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 46

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 47

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 51

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 49

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 44

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 43

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 48

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 45

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 66

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 41

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 42

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 40

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 38

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 36

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 34

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 32

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 33

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 37

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 35

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 31

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 29

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 27

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 28

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 25

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 50

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 26

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 24

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 20

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 19

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 23

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 17

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 21

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 18

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 39

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 15

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 30

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 12

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 11

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 13

description: normal monocyte enriched sample


title: Ramos_cap1

type: SRA

city: Vienna

first: Maximilian

middle: Christian

last: von der Linde

state: Vienna

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

country: Austria

institute: Institute of Molecular Pathology

description:
RNA was generated by performing transcription run-on on freshly isolated nuclei
5' and 3'linkers with random 10mers were added to allow PCR deduplication
True-seq barcoded primers for multiplexing were used in the PCR step to generate barcoded libraries
PRO-cap
SR75

library_source: transcriptomic

data_processing:
PRO-cap
Reads were trimmed for standard adapters and low quality (Q<30) 3’-end bases and filtered for a remaining length of at least 20nt (excluding the UMI, if applicable) using cutadapt v2.5.
Alignment to the reference genome was done with Bowtie v1.2.3. The NCBI GRCm38.6 assembly was used as the mouse reference. To this we added the fixated sequence of the recombined VDJ locus as an additional chromosome. Similarly, for human data, the Hg38 assembly was used, with the relevant fixed VDJ sequence added as a chromosome.
Where applicable, the dmr6 assembly of Drosophila melanogaster from Flybase (https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase, release version number 6.27) was used as the spike-in reference and was added to the alignment index. During alignment, up to 3 mismatches were allowed.
To accommodate mapping to the repetitive IgH locus, a high degree of multimapping was allowed (194 potential V segments annotated for GRCm38.6). In the case of alignment with spike-ins, only reads mapping exclusively to either genome were considered.
For PCR deduplication, UMIs were identified (10 nucleotides at the 3' end) and filtered with umi-tools v1.0.0. No sequence differences were allowed in UMIs when collapsing the duplicates.
Multimapping reads were then filtered to identify those specific to the VDJ sequence, taking into account the repetitiveness of the reference IgH locus. Reads mapping to the fixed VDJ sequence were allowed to multimap only to the native IgH locus (mouse chr12:113572929-116009954, human ch14:105836764-106875071). The native loci were defined as the region between the earliest position belonging to an annotated V segment and the latest position belonging to an annotated J segment. Reads with a mapped location outside these areas were rejected. This filtering was implemented in a custom Python script. The qualifying reads were then classified as reads mapping uniquely to the particular VDJ sequence and reads mapping to both the VDJ sequence and to the native IgH region.
Genome browser tracks were created by quantifying and scaling read coverage of the VDJ sequence using bedtools v2.29.0. Reads were split by strand, and strand labels for PROseq were inverted in order to match the strand designations of the respective PROcap reads. For both data types, only the first 5' base of the strand-adjusted reads was used for the tracks. Additionlly, the 5' end of PROseq reads was shifted by 1 base downstream, to compensate for the last base in the mRNA being the exogenous termination base. For normalized tracks, read counts were scaled to RPM (reads per million). Finally, “-“ strand coverage tracks were further scaled by -1, for visualization convenience.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_PROcapseq .
Assembly: NCBI mm9, NCBI HG38, custom IGH genome (see github)
Supplementary files format and content: bigWig of rpm-normalized read densities
Library strategy: PRO-cap

molecule: total RNA

organism:
Drosophila melanogaster
Homo sapiens

source_name: Ramos + S2

extract_protocol:
Cells were harvested and nuclei isolated. Transcription run-on in the presence of 2 biotinylated NTPs (Bio-UTP and Bio-CTP) and unlabeled ATP and GTP. Afterwards Trizol extraction of total RNA
total extraction with Trizol, labeled RNA enrichment .3' and 5' linker attachment. cDNA preparation and barcoding PCR, gel extraction of ~180-350bp library

tag: cell line

value: Ramos + S2

tag: genotype

value: wt

tag: growth protocol

value: full RPMI

tag: treatment

value: unstimulated

tag: sorted


title: blade，accrual，30d，rep3 IP

city: Guiyang

first: wu

middle: lin

last: jun

state: Guizhou

address: Xibei Street

country: China

institute: guizhou university

description:
XHT_F VS XHT_VG_diffPeak_Gene_differential_expression.txt
XHT_FVSXHT_VG_diffPeak_result.txt

data_processing:
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/). Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome raphanus sativus (Version: NA). Peak calling and diff peak analysis were performed by R package exomePeak (https://www.bioconductor.org/packages/3.3/bioc/html/exomePeak.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). HOMER (http://homer.ucsd.edu/homer/motif) was used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: Index of /download_genome/Brassica_Genome_data/Rapsa_Xiang_V1.0
Supplementary files format and content: txt and gz

organism: Raphanus sativus

source_name: blade

growth_protocol: The radish material used in this experiment was XHT, cultivated under the following conditions: daytime temperature of 25°C and 16 hours of light, and nighttime temperature of 23°C and complete darkness.

extract_protocol:
Leaves were collected at 30 and 120 days after sowing, immediately stored in prepared tin foil, immediately immersed in liquid nitrogen for rapid cooling, and then transferred to a freezer at -80°C for long-term storage. For each library, leaves collected from three plants were mixed together and three independent biological replicates were performed for each sample.
RNA libraries for RNA-seq and m6A-seq

treatment_protocol: No processing has taken place

tag: tissue

value: blade

value: diploid


title: blade，accrual，120d，rep3 IP


title: blade，accrual，30d，rep1 IP


title: Ramos_cap2


title: Monocyte-Specific DNA Methylation Sample 10

description: normal monocyte enriched sample


title: blade，accrual，30d，rep2 IP


title: blade，accrual，120d，rep2 IP


title: Monocyte-Specific DNA Methylation Sample 8

description: normal monocyte enriched sample


title: blade，accrual，30d，rep3 input

description: XHT_F VS XHT_VG_Gene_differential_expression.txt


title: blade，accrual，120d，rep1 IP


title: Monocyte-Specific DNA Methylation Sample 7

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 22

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 6

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 14

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 16

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 4

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 5

description: normal monocyte enriched sample


title: blade，accrual，120d，rep3 input


title: Monocyte-Specific DNA Methylation Sample 3

description: normal monocyte enriched sample


title: blade，accrual，30d，rep2 input


title: blade，accrual，120d，rep2 input


title: blade，accrual，30d，rep1 input


title: Monocyte-Specific DNA Methylation Sample 2

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 9

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 1

description: normal monocyte enriched sample


title: Ramos_D3_2_seq

description:
RNA was generated by performing transcription run-on on freshly isolated nuclei
5' and 3'linkers with random 8mers were added to allow PCR deduplication
True-seq barcoded RPI primers for multiplexing were used in the PCR step to generate barcoded libraries
PRO-seq

data_processing:
PRO-seq
Reads were trimmed for standard adapters and low quality (Q<30) 3’-end bases and filtered for a remaining length of at least 20nt (excluding the UMI, if applicable) using cutadapt v2.5.
Alignment to the reference genome was done with Bowtie v1.2.3. The NCBI GRCm38.6 assembly was used as the mouse reference. To this we added the fixated sequence of the recombined VDJ locus as an additional chromosome. Similarly, for human data, the Hg38 assembly was used, with the relevant fixed VDJ sequence added as a chromosome.
Where applicable, the dmr6 assembly of Drosophila melanogaster from Flybase (https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase, release version number 6.27) was used as the spike-in reference and was added to the alignment index. During alignment, up to 3 mismatches were allowed.
To accommodate mapping to the repetitive IgH locus, a high degree of multimapping was allowed (194 potential V segments annotated for GRCm38.6). In the case of alignment with spike-ins, only reads mapping exclusively to either genome were considered.
For PCR deduplication, UMIs were identified (8 nucleotides at the 3' end) and filtered with umi-tools v1.0.0. No sequence differences were allowed in UMIs when collapsing the duplicates.
Multimapping reads were then filtered to identify those specific to the VDJ sequence, taking into account the repetitiveness of the reference IgH locus. Reads mapping to the fixed VDJ sequence were allowed to multimap only to the native IgH locus (mouse chr12:113572929-116009954, human ch14:105836764-106875071). The native loci were defined as the region between the earliest position belonging to an annotated V segment and the latest position belonging to an annotated J segment. Reads with a mapped location outside these areas were rejected. This filtering was implemented in a custom Python script. The qualifying reads were then classified as reads mapping uniquely to the particular VDJ sequence and reads mapping to both the VDJ sequence and to the native IgH region.
Genome browser tracks were created by quantifying and scaling read coverage of the VDJ sequence using bedtools v2.29.0. Reads were split by strand, and strand labels for PROseq were inverted in order to match the strand designations of the respective PROcap reads. For both data types, only the first 5' base of the strand-adjusted reads was used for the tracks. Additionlly, the 5' end of PROseq reads was shifted by 1 base downstream, to compensate for the last base in the mRNA being the exogenous termination base. For normalized tracks, read counts were scaled to RPM (reads per million). Finally, “-“ strand coverage tracks were further scaled by -1, for visualization convenience.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_PROcapseq .
Assembly: NCBI mm9, NCBI HG38, custom IGH genome (see github)
Supplementary files format and content: bigWig of rpm-normalized read densities
Library strategy: PRO-seq

extract_protocol:
Cells were harvested and nuclei isolated. Transcription run-on in the presence of 4 Biotin-11-NTPs. Afterwards Trizol extraction of total RNA
total extraction with trizol, labeled RNA enrichement .3' and 5' linker attachment. cDNA preparation and PCR


title: Ramos_1C4_1_seq


title: blade，accrual，120d，rep1 input


title: Ramos_D3_1_seq


title: AAA.Thrombus-5

city: Cincinnati

first: Tyler

last: Benson

state: OH

address: CVC 3976 231 Albert Sabin Way

institute: University of Cincinnati

data_processing:
Data was analyzed using the bioinformatics software CLC Genomics Workbench version 20.0.3 (Qiagen, Hilden, Germany).
Reads were mapped using the following parameters:  min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Total counts.
Assembly: hg38
Supplementary files format and content: All processed data files are in an xlsx format containing FPKm values for each sample.

molecule: polyA RNA

source_name: AAA Thrombus

extract_protocol:
RNA was isolated from human AAA wall, accompanying thrombi, and control aortic walls tissue with the commercially available NucleoSpin® RNA kit (Macherey-Nagel REF 740955) with several modifications. Tissue was thawed on ice and transferred to BeadBugÔ prefilled tubes (Benchmark Scientific Triple-Pure High Impact Zirco nium Beads Item D1032-15). Tubes were filled with 1 mL QIAzol Lysis Reagent (QIAGEN Cat No. 79306) and homogenized with a BeadBugÔ Microtube Homogenizer (Benchmark Scientific) after which 200 μL of chloroform were added. Samples were vortexed and left to sit at room temperature for 2 – 3 minutes. Samples were then centrifuged at 12,000 X g for 15 minutes at 4°C. The aqueous phase was removed to new tubes and 150 μL isopropyl alcohol was added to each. Following a 10-minute incubation at room temperature, each lysate was loaded onto a NucleoSpin® RNA Column and eluted to RNA.  RNA was quantified with a NanoDrop™ 2000 Spectrophotometer (Thermo Scientific) and samples were stored at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AAA Thrombus

value: AAA


title: AAA.Thrombus-1


title: AAA.Aortic.Wall-5

source_name: Aortic Wall

value: Aortic Wall


title: AAA-Aortic-Wall-3


title: AAA-Aortic-Wall-2


title: Ramos_2B11_1_seq


title: Ramos_VH3-30_KI_2E4_seq


title: Ramos_2B11_2_seq


title: Control-Aortic-Wall-5

value: Control


title: AAA-Aortic-Wall-1


title: Ramos_VH3-30_KI_1G6_seq


title: Control-Aortic-Wall-4


title: Control-Aortic-Wall-3


title: Control-Aortic-Wall-1


title: irAE_controls_5B

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

description: 10x Genomics

library_source: other

data_processing:
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10x Genomics) to demultiplex FASTQ reads, align reads to the human reference genome (GRCh38, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: GRCh38
Supplementary files format and content: combined_pbmc_data.h5ad includes the counts for all demultiplexed cells that passed QC in .h5 format

molecule: other

source_name: PBMCs

extract_protocol:
Tissue samples obtained by biopsy or autopsy were immediately placed in ice-cold HypoThermosol solution (BioLife Solutions, Bothell, WA) and kept on ice during transfer to the research facility. Tissue was then washed twice with cold phosphate buffered saline. Tissue was then dissociated using the human tumor dissociation kit according to the manufacturer’s instructions (Miltenyi Biotic, Bergisch Gladbach, Germany) with modification such that calcium chloride was added to the enzymatic cocktail to a final concentration of 1.25 mM. Tubes containing tissue fragments in the enzymatic cocktail were placed in a heated shaker at 37° C with shaking at 750 RPM for 25 minutes with the machine placed on its side to prevent tissue fragments from settling. Following incubation, the reaction was quenched through the addition of 100 µl human serum. The mixture was further dissociated through manual trituration followed by filtration through 70 µm mesh. Following centrifugation at 350 x g for 12 minutes, the supernatant was removed and RBC lysis was performed (ACK lysing buffer, Lonza, Basel, Switzerland). Following a wash step, cells were resuspended in phenol-free RPMI with 2% (v/v) human AB serum.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMCs

tag: group

value: control


title: Ramos_B18hi_KI_2E4_seq


title: irAE_controls_4C

description: 10x Genomics


title: Ramos_1C4_2_seq


title: Ramos_VH4-59_KI_1E2_seq


title: Ramos_B18hi_KI_1A7_seq


title: Ramos_VH4-59_KI_1F8_seq


title: Ramos_seq1


title: AAA.Thrombus-3


title: Ramos_seq2


title: Ramos_VH3-30_KI_2E4_cap

description:
RNA was generated by performing transcription run-on on freshly isolated nuclei
5' and 3'linkers with random 10mers were added to allow PCR deduplication
True-seq barcoded primers for multiplexing were used in the PCR step to generate barcoded libraries
PRO-cap
PE150 use only read 1


title: Ramos_VH3-30_KI_1G6_cap


title: HCV-X780

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and filtered on low-quality bases using fastp (v0.23.2). To remove noise introduced by sequencing errors, the reads were filtered based on the base quality score. Reads of which more than 40% of the bases had an average phred score below Q15 or which had more than 5 unknown bases were removed. If the resulting reads were shorter than 15 bp, they were removed altogether (both pairs in paired-end reads).
For each samples, trimmed reads were mapped to the human reference genome GRCh38.p13 using a short read aligner based on Burrows-Wheeler Transform (STAR2 v2.7.10) with default settings.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq (v2.0.2). Only unique reads that fall within exon regions were counted, count files that were generated with HTSeq were used as input for downstream analysis.
Assembly: GRCh38.p13
Supplementary files format and content: .tsv counts files

extract_protocol:
For RNA sequencing of peripheral blood CD19+ B cells, all infected cohorts were matched by age, sex, and ethnicity to healthy control individuals. Included patients did not have other liver disease, were not pregnant, and were not on anti(retro)viral therapy. Liver fibrosis was determined by histology or transient elastography (maximum of ≤F2). Peripheral blood mononuclear cells (PBMCs) were isolated from 7 immune active chronic HBV patients, 7 viremic chronic HCV patients, and 7 matched healthy controls (CTRL) and stored at -150°C. Frozen PBMCs were thawed and stained for CD3-PE, CD19-eF450, and Fixable Aqua Dead Cell Stain. CD19+ B cells were isolated from each sample by fluorescence-activated cell sorting using the BD FACSAria II cell sorter. The purities of all samples included in the analysis were higher than 95%.
Sorted B cells were kept in TriPure™ Isolation Reagent (Roche, 11667165001) at -20°C, and RNA was isolated using a PicoPure RNA isolation kit (Arcturus) according to manufacturer's protocol. The concentration, quality and integrity of the RNA samples was analyzed on a Bioanalyzer 2100 (Agilent Technologies), all samples had a RIN value of ≥7.
Ultra-low Input Transcriptomics Workflow (GenomeScan, Leiden, The Netherlands).

value: CD19+ B cells

tag: disease state

value: chronic HCV


title: irAE_controls_1C

description: 10x Genomics


title: Ramos_VH4-59_KI_1E2_cap


title: Ramos_B18hi_KI_2E4_cap


title: Ramos_AIDKO_EmuKO_2B11_K36me3

description:
Cross-linked and sonicated nuclei were lysed and subjected to immunoprecipitation with antibody
Libraries were prepared following standard Illumina protocols
ChIP-seq

library_source: genomic

data_processing:
Reads were trimmed for standard adapters and low quality (Q<30) 3’-end bases and filtered for a remaining length of at least 20nt (excluding the UMI, if applicable) using cutadapt (Martin, 2011). Alignment to the reference genome was done with Bowtie (Langmead et al., 2009).
For human data, the Hg38 assembly was used, with the relevant variable region sequence added as a chromosome. Where applicable, the dmr6 assembly of Drosophila melanogaster from Flybase was used as the spike-in reference and was added to the alignment index. During alignment, up to three mismatches were allowed.
To accommodate mapping to the repetitive IGH/Igh locus, a high degree of multimapping was allowed (194 potential V segments annotated for GRCm38.6). In the case of alignment with spike-ins, only reads mapping exclusively to either genome were considered.
Mutlimapping reads were then filtered to identify those specific to the variable region sequence, taking into account the repetitiveness of the reference IGH/Igh locus. Reads mapping to the fixed variable region sequence were allowed to multimap only to the native IGH/Igh locus (human chr14:105836764-106875071). The native loci were defined as the region between the earliest position belonging to an annotated V segment and the latest position belonging to an annotated J segment.
genome-wide coverage tracks were computed with deeptools bamCoverage 3.3.0 using --ignoreDuplicates --nomalizeUsing CPM --scaleFactor 1.61717/1.25156 for H3K09me3 WT/KD and using --ignoreDuplicates --nomalizeUsing CPM --exactScaling for H3 WT and KD
Reads with a mapped location outside these areas were rejected. This filtering was implemented in a custom Python script. The qualifying reads were then classified as reads mapping uniquely to the particular variable region sequence and reads mapping to both the variable region sequence and to the native IGH/Igh region. Genome browser tracks were created by quantifying and scaling read coverage of the variable region sequence using bedtools (Quinlan and Hall, 2010). For normalized tracks, read counts were scaled to RPM (reads per million), in case of spike-in normalization using the read counts of spike-in genome as normalizer.
Assembly: NCBI HG38, custom IGH genome (see github), drosophila FlyBase DMR6
Supplementary files format and content: bigwig format files showing coverage tracks that can be visualized in genome browser

growth_protocol: Ramos cells cultured in complete RPMI medium, S2 cells cultured in Schneider Drosophila medium

extract_protocol:
ChIPseq were performed after mixing with 10% S2 cells as described without modifications (Pavri et al., 2010). In short, 18x10^6 Ramos and 2x10^6 S2 cells  were pooled and crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, libraries were prepared following the NEB Next Ulta II DNA library kit. Libraries were amplified with the kappa library amplification qCR master mix

tag: chip antibody

value: H3K36me3 (Abcam, ab9050)


title: Ramos_B18hi_KI_1A7_cap


title: Ramos_VH4-59_KI_1F8_cap


title: Ramos_AIDKO_EmuKO_2B11_K4me3

value: H3K4me3 (Abcam, ab8580)


title: HCV-X659


title: Control-Aortic-Wall-2


title: HCV-X314


title: HCV-X275


title: HCV-X490


title: Ramos_AIDKO_EmuKO_1C4_IgG

value: IgG (Life Technologies 10500C)


title: HCV-X247


title: irAE_controls_2A

description: 10x Genomics


title: irAE_controls_3C

description: 10x Genomics


title: Ramos_AIDKO_EmuKO_1C4_K36me3

value: Ramos + S2


title: Ramos_AIDKO_EmuKO_1C4_K27Ac

value: H3K27ac (Abcam, ab4729)


title: HBV-X188

value: chronic HBV


title: Ramos_AIDKO_D3_IgG

value: AID-/-


title: Ramos_AIDKO_EmuKO_2B11_IgG


title: HBV-X108


title: HBV-X175


title: HCV-X406


title: HBV-X165


title: HBV-X125


title: HBV-X117


title: Ramos_AIDKO_D3_K4me3


title: VH-HC432

value: CTRL


title: Ramos_AIDKO_D3_K27Ac


title: VH-HC340


title: GCB_B18hi_AIDKO_1

description:
gen.DNA was purified and used for 2 rounds of PCRs attaching adapters and dual barcoding on 5' and 3' ends of the library
Dual barcoded libraries were multiplexed and sequenced on Illumina platforms with paired-end seq readmode
MutPE-seq

data_processing:
Reads were trimmed for standard adapters with cutadapt. Poor quality (Q<25) 3’ bases were trimmed with trimmomatic by averaging over a sliding window of 5nt. Read pairs were then filtered for minimum remaining length (200nt for read 1, 100nt for read 2) using cutadapt. Read mates were merged down to make combined single-end reads with FLASH allowing 10% mismatch between the mates.
Obvious erroneous mergers were removed by selecting combined reads with lengths within ±30nt of the amplicon length using cutadapt, The remaining combined reads were aligned with Bowtie2, using the “–very-sensitive-local” alignment mode and only the fixed variable region sequence and its immediate vicinity as reference.
Alignments were split into strata by the number of mismatches reported, using a custom Perl script. For each stratum a pile-up was generated with samtools (Li et al., 2009) taking into account only bases with quality of at least 30.
The pileups were then quantified with a custom Python script and the resulting mutation counts were processed and visualized with custom scripts in R (v3.5.1), with the help of additional R packages (ggplot2 , ggrepel, patchwork).
Background mutation profiles were controlled for by subtracting the corresponding mutation frequencies in control samples from the frequencies in the samples of interest, at each position and for each substitution type. Annotation of hot and cold spots was created by means of regex search for the corresponding patterns in the reference sequence.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_MutPE .
Assembly: NCBI mm9, NCBI HG38, custom IGH genome (see github)
Supplementary files format and content: bedGraph format files showing coverage tracks that can be visualized in genome browser
Library strategy: MutPE-seq

organism: Mus musculus

source_name: spleen

extract_protocol:
cells were harvested and gen.DNA prepared by PCI extraction and EtOH precipitation
2 rounds of PCRs were used to add adapter sequences and dual barcoding for paired-end sequencing on Illumina platform

value: spleen

value: GCB

value: Aicdatm1Hon IgHtm1Mnz

value: SRBC injected (d0,d5), harvest d10


title: Ramos_AIDKO_EmuKO_2B11_K27ac


title: priBd3_B18hi_AIDKO_2

value: MACS CD43 depleted primary B cells + S2

value: full RPMI

value: IL4, LPS, RP105


title: VH-HC433

value: PBMCs

value: CD19+ B cells


title: Ramos_AIDKO_EmuKO_1C4_K4me3


title: HBV-X099


title: VH-HC634


title: GCB_B18hi_3


title: GCB_B18hi_2


title: Monocyte-Specific DNA Methylation Sample 176

description: normal monocyte enriched sample

value: monocyte

value: Female

value: Japanese American


title: GCB_B18hi_4


title: C3_8B

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10x Genomics) to demultiplex FASTQ reads, align reads to the human reference genome (GRCh38, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: GRCh38
Supplementary files format and content: combined_tissue_data.h5ad includes the counts for all cells that passed QC in .h5 format
Supplementary files format and content: combined_pbmc_data.h5ad includes the counts for all demultiplexed cells that passed QC in .h5 format
Supplementary files format and content: raw_feature_bc_matrix.h5 files includes the UMI counts for all droplets for each sample in .h5 format
Supplementary files format and content: all_contig_annotations_tcr.csv files include the TCR data for the associated samples
Supplementary files format and content: fbc.csv files contains data for featured barcodes for applicable samples (all PBMC samples)
Supplementary files format and content: hashing_info.csv includes information about which samples correspond to which fbc hashtags in the PBMC samples
Supplementary files format and content: cite_info.csv includes information about the antibodies included in the FBC pool

tag: age

value: not applicable


title: C3_45B

description: 10x Genomics


title: VH-HC437


title: C3_8A

description: 10x Genomics


title: Ramos_AIDKO_D3_K36me3

value: Ramos + S2

value: H3K36me3 (Abcam, ab9050)


title: Ramos_ATAC_merge

description:
Native chromatin  was transposed with transposase 5 enzyme
Libraries were prepared following standard Illumina protocols
ATAC-Seq

data_processing:
ATACSeq
The illumina reads were adapter trimmed on their 3’ ends with cutadapt (version 1.15;  --match-read-wildcards -O 1 -f fastq -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC for read1 and cutadapt --match-read-wildcards -O 1 -f fastq -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for read2).
The paired end trimmed reads larger then 18nt were aligned with bowtie2 (version 2.1.0;  --sensitive   -p 10 -X 5000 -N 0   --trim5 0 --trim3 0) to the human hg38 genome.
The aligned reads were sorted by position with samtools (version 0.1.19).
Strand specific and undirected occupancy profiles were generated with deeptools bamCoverage v2.2.2.
Assembly: NCBI hg38
Supplementary files format and content: bigWig of rpm-normalized read densities

source_name: Ramos

growth_protocol: Ramos cells were cultured in complete RPMI medium

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor modifocations in the tagmentation step where we used a homemade Tn5 enzyme and assembeld the Tn5-adapter tagmentation mix ourselves. However, the adapter sequences and primers used for library amplification are the same as in the Buenrostro et al. protocol.
transposed DNA was amplified with RT-qPCR monitoring to avoid oveamplification and the libraries were purified with AMPure XP beads.

value: Ramos


title: GCB_B18hi_1


title: e_B18hi_2

source_name: ear

value: ear

value: somatic cells


title: C3_45A

description: 10x Genomics


title: GCB_B18hi_AIDKO_2

value: spleen

value: GCB


title: Set2_ADCP1_ChIP_control_input_rep2

city: Beijing

first: Weifeng

last: Zhang

address: Zhongguancun Street

institute: Tsinghua University

data_processing:
Illumina RTA software was used for basecalling.
Reads coverage was normalized to RPKM (Reads Per Kilobase Million)
Assembly: TAIR10 for Arabidopsis
Supplementary files format and content: bw

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis surface-sterilized seeds were sown on 1/2 MS medium and cold-imbibed (4 °C) in darkness for 2 days before being transferred to long-day conditions (day/night cycle of 16/8 h) at 22 °C. Tobacco and tomato plants grown in a 22 °C plant culture room.

extract_protocol:
5 g leaves were cross-linked in 1% formaldehyde for 10 min. Then stopped by adding 0.125 M glycine and washed by PBS. The nuclei were extrected by Honda buffer and washed 3 times by NRBT. Then the nuclei were sonicated 4 times for 10 min (30 s on/off intervals) using the Bioruptor® Pico. The sonicated nuclei were centrifuged at 15000rpm for 15 min, and the supernatant was transferred to new tubes and diluted 10 times with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl). 50 μL diluted supernatant was preserved as input. Then 2 μg anti-GFP antibody (Abcam, ab290) or anti-H3K9me2 antibody (Abcam, ab1220) was added into supernatant and rotate at 4 °C overnight. 50 μL washed Protein G Dynabeads (Invitrogen, 10004D) was added to the sample. After rotating for 4 h, the beads were washed sequentially with Low Salt Buffer, High Salt Buffer, LiCl Buffer, TE Buffer (each buffer for a quick wash, and a 10 min wash). Then add 100 μL 10% Chelex resin (Biorad, 1422842) to elute immune complexes by incubating at 95 °C for 10 min at 1300 rpm. After cooled to RT, 2 μL Protease K (10 mg/mL, Amresco 0706) was added into samples and incubated at 45 °C for 1 h, and then boiled at 95 °C and 1300 rpm for 10 min. Then the elution was purified with phenol-chloroform for sequencing.
The library preparation steps were conducted according to the manual (ABclonal, RK20228). Briefly, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

value: leaf


title: C1_45B

description: 10x Genomics


title: e_B18hi_1

value: SRBC injected (d0,d5), harvest d10


title: C1_8B

description: 10x Genomics


title: priBd3_B18hi_AIDER_2

value: MACS CD43 depleted primary B cells + S2

value: full RPMI


title: VH-HC233

value: PBMCs

value: CTRL


title: C1_8A

description: 10x Genomics


title: C1_45A

description: 10x Genomics


title: priBd3_B18hi_AIDKO_1

value: Aicdatm1Hon IgHtm1Mnz

value: IL4, LPS, RP105


title: M8_45B

description: 10x Genomics


title: M8_45A

description: 10x Genomics


title: VH-HC423

value: CD19+ B cells


title: priBd0_B18hi_AIDER_2


title: Set2_ADCP1-GFP in suvh456_input_rep2

value: ADCP1-GFP insuvh456 transgenic plants


title: Set2_ADCP1-GFP in suvh456_input_rep1

value: ADCP1-GFP in suvh456 transgenic plants


title: tobacco ChIP_control

organism: Nicotiana benthamiana

value: tobacco (Nicotiana benthamiana)


title: priBd3_B18hi_AIDER_1


title: Set2_ADCP1-GFP in Col-0_input_rep2

value: ADCP1-GFP in Col-0 transgenic plants


title: M198_GrB_EMT6

city: Los Angeles

first: Madhuri

last: Wadehra

state: CA

address: 675 Charles Young Dr. South

institute: UCLA

data_processing:
cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina NovaSeq 6000 for PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
The alignment was performed using STAR [2] with mouse reference genome GRCm39. The Ensembl Transcripts release GRCm39.107 GTF was used for gene feature annotation. For normalization of transcripts counts, CPM normalized counts were generated by adding 1.0E-4 followed by counts per million (CPM) normalization.
Assembly: GRCm39
Supplementary files format and content: 24-0521_Raw_Read_Counts.txt
Supplementary files format and content: 24-0521_Add_00001_CPM_Normalized_counts.txt

source_name: Mammary Tumor

extract_protocol:
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit.
The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand.

value: Mammary Tumor

value: Epithelial breast tumor cells

value: WT

value: Granzyme-B


title: M6_45B

description: 10x Genomics

value: not applicable


title: M7_45B

description: 10x Genomics


title: M7_45A

description: 10x Genomics


title: M171_GrB_EMT6


title: priBd0_B18hi_AIDER_1

value: spleen


title: Set2_ADCP1-GFP in Col-0_input_rep1

value: leaf


title: Set2_ADCP1_ChIP_control_rep2


title: GCB_B18hi_seq2

value: GCB

value: in vivo

value: SRBC injected (d0,d5), harvest d12


title: GCB_B18hi_seq1


title: Set2_ADCP1_ChIP_control_input_rep1


title: M199_GrB_EMT6_U


title: M6_45A

description: 10x Genomics

value: PBMCs


title: M189_IgG_EMT6

value: IgG


title: A16-303_A5

description: Adaptive bulk TCRseq data

data_processing:
Adaptive Biotechnologies processed and aligned the raw data with proprietary software
Assembly: GRCh38
Supplementary files format and content: tab-seperated value files that include all relevant info for recovered and constructed TCR sequences
Library strategy: TCR-seq

source_name: Heart tissue

extract_protocol:
Bulk TCRseq data was generated on Formalin-fixed, paraffin-embedded slides. Genomic DNA was extracted using the AllPrep DNA/RNA FFPE Kit instructions (Qiagen)
T-cell receptor β chain (TCR-β) sequencing of the CDR3 region was performed (immunoSEQ ® human T-cell receptor beta [hsTCRB], Adaptive Biotechnologies)

value: Heart tissue

value: M

tag: donor

value: control


title: Set2_ADCP1-GFP in suvh456_ChIP_rep2

value: ADCP1-GFP insuvh456 transgenic plants


title: T01708-11

description: Adaptive bulk TCRseq data

value: F


title: M5_45B

description: 10x Genomics


title: M170_GrB_EMT6

value: Mammary Tumor


title: Set2_ADCP1_ChIP_control_rep1


title: M5_45A

description: 10x Genomics


title: A19-213_A13

description: Adaptive bulk TCRseq data


title: Set2_ADCP1-GFP in Col-0_ChIP_rep2

value: ADCP1-GFP in Col-0 transgenic plants


title: M3_8B

description: 10x Genomics


title: A20-331_A1

description: Adaptive bulk TCRseq data

value: irMyocarditis


title: M143_IgG_EMT6

value: Epithelial breast tumor cells

value: WT


title: M191_IgG_EMT6


title: Set2_ADCP1-GFP in suvh456_ChIP_rep1

value: ADCP1-GFP in suvh456 transgenic plants


title: M3_8A

description: 10x Genomics

value: not applicable


title: M121_IgG_EMT6_U


title: suvh456_H3_ChIP_rep2

value: leaf


title: M3_45B

description: 10x Genomics


title: M3_45A

description: 10x Genomics


title: A19-230_A48

description: Adaptive bulk TCRseq data


title: suvh456_H3_ChIP_rep1


title: Set2_ADCP1-GFP in Col-0_ChIP_rep1


title: Mouse tumor STR22 treatment #4

city: Chicago

first: Dongbo

last: Yang

state: IL

address: 929 E 57th St

institute: University of Chicago

data_processing:
Sequencing: The libraries were sequenced by a NovaSeq 6000 sequencer to generate paired-end 100bp reads.
Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3.
RNA-seq: reads were mapped to the human genome or the mouse genome (UCSC hg19 or mm10, with GENCODE annotation) using RNA STAR 2.7.5b. ChIP-seq: IP and input reads for each sample were mapped to the human genome (UCSC hg19 with GENCODE annotation) using BWA-MEM 0.7.17.1 and the mapped reads were converted to SAM files using samtools 1.2.
RNA-seq: mapped reads from each sample were counted by featureCounts 1.6.4 for per-gene read counts. ChIP-seq: peak calling was performed by Homer 4.11.1 using the IP and input SAM files for each sample (settings for peak calling were included in the submitted peak files).
Assembly: Human (hg19) and mouse (mm10)
Supplementary files format and content: RNA-seq: a tab delimited text file containing a matrix table with raw gene counts for every gene and every sample. ChIP-seq: a peak text files for each sample.

growth_protocol: HeLa cells were maintained in 10% FBS DMEM media and 1% penicillin/streptomycin in 5% CO2. 4T1 cells were maintained in 10% FBS RPMI-1640 media and 1% penicillin/streptomycin in 5% CO2

extract_protocol: RNA-seq and ChIP-seq libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

value: STR22 tail-vein injection

tag: extraction

value: Total RNA was extracted from tumor samples using the Direct-zol RNA MiniPrep Plus kit (Zymo Research, R2072)

tag: library

value: RNA-seq


title: M2_8B

description: 10x Genomics

value: PBMCs


title: A19-230_A5

description: Adaptive bulk TCRseq data

source_name: tumor

value: tumor


title: A18-122_A41

description: Adaptive bulk TCRseq data

value: Heart tissue

value: M


title: M2_8A

description: 10x Genomics


title: suvh456_H3K9me2_ChIP_rep2


title: T03054-11

description: Adaptive bulk TCRseq data

source_name: Normal tissue adjacent to tumor

value: Normal tissue adjacent to tumor


title: suvh456_H3K9me2_ChIP_rep1


title: Mouse tumor STR22 treatment #2


title: Mouse tumor STR22 treatment #1


title: A18-122_A52

description: Adaptive bulk TCRseq data


title: Yn-ADCP1+Yc-HMGA_input_rep2

data_processing:
Illumina RTA software was used for basecalling.
Reads coverage was normalized to RPKM (Reads Per Kilobase Million)
Assembly: TAIR10 for Arabidopsis, Nicotiana benthamiana v2.6.1 for tobacco, S_lycopersicum_chromosomes.4.00 for tomato

extract_protocol:
5 g leaves were cross-linked in 1% formaldehyde for 10 min. Then stopped by adding 0.125 M glycine and washed by PBS. The nuclei were extrected by Honda buffer and washed 3 times by NRBT. Then the nuclei were sonicated 4 times for 10 min (30 s on/off intervals) using the Bioruptor® Pico. The sonicated nuclei were centrifuged at 15000rpm for 15 min, and the supernatant was transferred to new tubes and diluted 10 times with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl). 50 μL diluted supernatant was preserved as input. Then 2 μg anti-GFP antibody (Abcam, ab290), anti-mCherry antibody (Abcam, ab213511), or anti-H3K9me2 antibody (Abcam, ab1220) was added into supernatant and rotate at 4 °C overnight. 50 μL washed Protein G Dynabeads (Invitrogen, 10004D) was added to the sample. After rotating for 4 h, the beads were washed sequentially with Low Salt Buffer, High Salt Buffer, LiCl Buffer, TE Buffer (each buffer for a quick wash, and a 10 min wash). Then add 100 μL 10% Chelex resin (Biorad, 1422842) to elute immune complexes by incubating at 95 °C for 10 min at 1300 rpm. After cooled to RT, 2 μL Protease K (10 mg/mL, Amresco 0706) was added into samples and incubated at 45 °C for 1 h, and then boiled at 95 °C and 1300 rpm for 10 min. Then the elution was purified with phenol-chloroform for sequencing.
The library preparation steps were conducted according to the manual (ABclonal, RK20228). Briefly, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

value: Yn-ADCP1+Yc-HMGA transgenic plants


title: Mouse tumor PBS treatment #5

value: PBS tail-vein injection


title: M1_8B

description: 10x Genomics


title: A18-122_A51

description: Adaptive bulk TCRseq data


title: Yn-ADCP1+Yc-HMGA_ChIP_rep2


title: M2_45A

description: 10x Genomics


title: A20-363_A18

description: Adaptive bulk TCRseq data

value: F


title: Yn-ADCP1+Yc-HMGA_input_rep1


title: Mouse tumor STR22 treatment #5


title: Mouse tumor PBS treatment #4


title: A19-41_A10_Liver

description: Adaptive bulk TCRseq data

value: irMyocarditis


title: M1_8A

description: 10x Genomics


title: A19-41_A33

description: Adaptive bulk TCRseq data


title: Yn-ADCP1+Yc-HMGA_ChIP_rep1


title: Mouse tumor PBS treatment #3


title: mc-HMGA_input_rep2

value: mc-HMGA transgenic plants


title: M2_45B

description: 10x Genomics


title: Mouse tumor STR22 treatment #3


title: M1_45B

description: 10x Genomics


title: A19-395_A53-1

description: Adaptive bulk TCRseq data


title: A19-41_A10_Tumor

description: Adaptive bulk TCRseq data


title: Mouse tumor PBS treatment #2


title: Peripheral blood cells, healthy control, a 15-year girl with heart failure before heart transplantation, scRNAseq

city: Tianjin

first: Kuan

last: Li

state: Tianjin

address: Jingu road 890

institute: Tianjin Key Laboratory of Pulmonary Regenerative Medicine

description:
10x Genomics
normal_blood

data_processing:
The raw sequencing data of PBMCs were processed by Cell Ranger (version 6.1.1)
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: barcodes, features and matrix files

source_name: Peripheral blood

extract_protocol:
For each participant, 5mL venous blood was collected in a BD Vacutainer EDTA Tube (BD, Cat#: 367861). The samples were density gradient centrifuged to obtain peripheral blood cells using the Ficoll-Paque medium (PMID:33564978). Lung tissues were minced and digested to prepare single-cell suspension. Single-cell suspension with the concentration of 7-12X10^5 cells/mL. For single-cell suspensions of lung tissues, the cell viabilities were 56-75%. For single-cell suspensions of peripheral blood cells, cell viabilities were higher than 80%. Each single-cell suspension was used to constructing a single-cell RNA library according to 10x Genomics® Cell Preparation Guide (PMID:35724763;34521850).
The single-cell RNA-seq raw data were aligned and counted against the human reference genome (GRCh38) using Cell Ranger (version 4.0.0) to obtain gene-cell matrices. After removing doublet cells with DoubletFinder (version 2.0.3), the matrices were submitted to Seurat package (version 4.1.1) to achieve quality control, batch effect removal, dimension reduction and clustering analysis. Quality control: total RNA counts between 200 and 6000, and mitochondrial gene percentage <10%. The top 2,000 most variable genes were obtained for dimensional reduction by “FindVariableFeatures”, “ScaleData” and “RunPCA” function. After batch effect removal with Harmony package (version 0.1.0), “FindNeighbors”, “FindClusters” and ‘RunTSNE’ were performed to identify the cell clusters. Finally, the two-dimensional profiles were visualized by t-Distributed Stochastic Neighbor Embedding (t-SNE). The cell types were identified based on canonical marker genes (PMID:35724763).

value: Peripheral blood

value: female

tag: subject status


title: Mouse tumor PBS treatment #1


title: mc-HMGA_ChIP_rep2


title: mc-HMGA_input_rep1


title: P7_3

city: Harbin

first: Sikai

last: Wang

address: Baojian Road

institute: Second Affiliated Hospital of Harbin Medical University

data_processing:
CLC Genomic Workbench v 11.0.1
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: spinal cord

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: spinal cord


title: Peripheral blood cells, a 10-year girl with ARDS at the point of  ICU check out, scRNAseq

description:
10x Genomics
ICU_check_out_blood


title: A17-341_A27

description: Adaptive bulk TCRseq data


title: M1_45A

description: 10x Genomics

value: not applicable


title: mc-HMGA_ChIP_rep1

value: leaf


title: A17-341_A3

description: Adaptive bulk TCRseq data


title: P7_2


title: P7_1


title: ADCP1-GFP in hmga_input_rep2

value: ADCP1-GFP in hmga transgenic plants


title: Peripheral blood cells, a 10-year girl with ARDS at the point of ECMO weaning off, scRNAseq

description:
10x Genomics
D14_ARDS_B_blood


title: Peripheral blood cells, a 10-year girl with ARDS at the point of  ECMO initiation, scRNAseq

description:
10x Genomics
ARDS_B1_blood


title: A17-341_A2

description: Adaptive bulk TCRseq data


title: ADCP1-GFP in hmga_input_rep1


title: SIC_333_1668_1_heart

description: 10x Genomics

value: male

value: control


title: SIC_319_1590_2_heart

description: 10x Genomics


title: ADCP1-GFP in Col-0_input_rep2

value: ADCP1-GFP in Col-0 transgenic plants


title: P3_3


title: Lung tissue, healthy control, a 3-year boy with metastatic hepatoblastoma, scRNAseq

description:
10x Genomics
normal_child_lung_3

source_name: Lung tissue

value: Lung tissue


title: P3_2


title: SIC_319_1590_1_heart

description: 10x Genomics

value: Heart tissue


title: ADCP1-GFP in Col-0_input_rep1


title: P3_1


title: Lung tissue, healthy control, a 1-year boy with lung sequestration, scRNAseq

description:
10x Genomics
normal_child_lung_1


title: Lung tissue, a 10-year girl with ARDS, scRNAseq

description:
10x Genomics
ARDS_A_lung

value: a 10-year girl with ARDS


title: SIC_317_1583_1_heart

description: 10x Genomics


title: P14_3


title: ADCP1-GFP in hmga_ChIP_rep2


title: SIC_232_702_1_heart

description: 10x Genomics


title: P14_2


title: Replicate 2 hypoxia IP

data_processing:
Sequencing: The libraries were sequenced by a NovaSeq 6000 sequencer to generate paired-end 100bp reads.
Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3.
RNA-seq: reads were mapped to the human genome (UCSC hg19 with GENCODE annotation) using RNA STAR 2.7.5b. ChIP-seq: IP and input reads for each sample were mapped to the human genome (UCSC hg19 with GENCODE annotation) using BWA-MEM 0.7.17.1 and the mapped reads were converted to SAM files using samtools 1.2.
RNA-seq: mapped reads from each sample were counted by featureCounts 1.6.4 for per-gene read counts. ChIP-seq: peak calling was performed by Homer 4.11.1 using the IP and input SAM files for each sample (settings for peak calling were included in the submitted peak files).
Assembly: Human (hg19)
Supplementary files format and content: RNA-seq: a tab delimited text file containing a matrix table with raw gene counts for every gene and every sample. ChIP-seq: a peak text files for each sample.

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in 10% FBS DMEM media and 1% penicillin/streptomycin in 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37 ℃ and then quenched with 125 mM glycine for 1 min. Cells were sheared in buffer containing: 0.1% SDS, 50 mM Tris-HCl (pH 7.6), 1 mM EDTA (pH8.0), 0.002% Triton X-100, supplemented with PMSF (Roche, 10837091001) and protease inhibitor (Roche, 11836170001). Lysates were sonicated with a Bioruptor for a total of 40 cycles (30 sec on/ 30 sec off each cycle). Sonicated lysate was incubated with HIF1ɑ antibody (Novus Biologicals, NB100-479) conjugated with Dynabeads Protein A (Life Technologies, 10001D) + G (Invitrogen, 10003D) overnight at 4 ℃. Beads were washed twice for 5 mins each, first with RIPA buffer (10mM Tris-HCl pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% NaDOC, 1% Triton X-100), then RIPA buffer supplemented with 0.3M NaCl, LiCl buffer (0.21 M LiCl, 0.5% NP-40, 0.5% NaDOC) and finally TE buffer plus 0.2% Triton X-100. Next, beads were washed once with TE buffer for 5 mins. DNA samples were eluted from beads in buffer containing 0.003% SDS, 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA (pH 8.0), 0.1 mg/ml Proteinase K (Fisher Scientific, 25-530-049) for 4 hrs at 65°C. ChIP-DNA was purified by AMPure XP (Beckman Coulter, A63881).
RNA-seq and ChIP-seq libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

value: Vehicle, 1percent oxygen


title: ADCP1-GFP in hmga_ChIP_rep1


title: ADCP1-GFP in Col-0_ChIP_rep2


title: SIC_171_526_1_heart

description: 10x Genomics


title: Replicate 2 normoxia IP

value: Vehicle, normoxia


title: SIC_175_551_1_heart

description: 10x Genomics


title: A7_4


title: Replicate 2 hypoxia with STR22 input

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37 ℃ and then quenched with 125 mM glycine for 1 min. Cells were sheared in buffer containing: 0.1% SDS, 50 mM Tris-HCl (pH 7.6), 1 mM EDTA (pH8.0), 0.002% Triton X-100, supplemented with PMSF (Roche, 10837091001) and protease inhibitor (Roche, 11836170001). Lysates were sonicated with a Bioruptor for a total of 40 cycles (30 sec on/ 30 sec off each cycle). 5% of each lysate was used for input and the rest was used for IP. Elution buffer was added to input samples to match the volume of IP samples. DNA samples were treated by 0.1 mg/ml Proteinase K (Fisher Scientific, 25-530-049) for 4 hrs at 65°C in buffer containing 0.003% SDS, 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA (pH 8.0). ChIP-DNA was purified by AMPure XP (Beckman Coulter, A63881).
RNA-seq and ChIP-seq libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

value: STR22, 1percent oxygen


title: H3_ChIP_rep2


title: ADCP1-GFP in Col-0_ChIP_rep1


title: A7_3


title: SIC_153_463_1_heart

description: 10x Genomics

value: irMyocarditis


title: Replicate 2 hypoxia input


title: SIC_217_661_1_heart

description: 10x Genomics


title: A7_1


title: H3K9me2_ChIP_rep2


title: A7_2


title: SIC_258_787_2_heart

description: 10x Genomics


title: H3_ChIP_rep1


title: Replicate 2 normoxia input


title: Replicate 1 hypoxia with STR22 IP


title: H3K9me2_ChIP_rep1


title: A3_4


title: SIC_182_561_1_heart

description: 10x Genomics


title: Replicate 1 hypoxia IP


title: A3_3


title: Replicate 2 hypoxia with STR22 IP


title: SIC_237_662_1_heart

description: 10x Genomics


title: P14_1


title: OA4

city: shanghai

first: ling

last: yang

address: Kong-Jiang Road 1665 in Shanghai

institute: Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to rat genome assembly Rnor6 (ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ensembl.org/pub/release-89/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.89.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0).
Assembly: Rnor6
Supplementary files format and content: File include Count and  FPKM values for each sample

organism: Rattus norvegicus

source_name: synovium tissue

growth_protocol: 3-month-old male SPF rats were treated with regard for alleviation of suffering according to the principles of the 3R, and were housed at temperature, 12-hour light/dark cycle, humidity.

extract_protocol:
Each rat was feeed for four weeks after treatment until euthanasia and be extracted with its synovial tissue.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Intraperitoneal injection with 3% sodium pentobarbital(0.1 mL/100 g) . Then, for injection models(KOA group), we injected 0.1ml of MIA (10 mg/kg) at the right knee joint spaces, then, flexion and extension were performed at joints to ensure uniform distribution of MIA within the joint spaces.

value: synovium tissue

value: MIA-induced KOA group

value: intra-articular injection of MIA


title: Replicate 1 normoxia IP


title: A3_2

value: spinal cord


title: OA3


title: SIC_264_1040_1_heart

description: 10x Genomics


title: Replicate 1 hypoxia with STR22 input


title: OA2


title: SIC_182_560_2_heart

description: 10x Genomics


title: A3_1


title: A14_4


title: Replicate 1 hypoxia input


title: SIC_164_494_1_heart

description: 10x Genomics


title: Replicate 1 normoxia input


title: A14_2


title: OA1


title: NC4

value: NC group

value: no treatment


title: Hypoxia with STR22 replicate 2

extract_protocol:
Total RNA was extracted from cell culture samples using the RNeasy Plus Mini Kit (Qiagen).
RNA-seq and ChIP-seq libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.


title: A14_3


title: Hypoxia with STR22 replicate 3


title: A14_1


title: NC2


title: Hypoxia with STR22 replicate 1


title: SIC_232_702_2_heart

description: 10x Genomics

value: female


title: NC3


title: SIC_177_539_1_heart

description: 10x Genomics


title: SIC_197_620_1_heart

description: 10x Genomics

value: male


title: SIC_48_172_1_heart

description: 10x Genomics


title: GCB_B18hi_cap

data_processing:
PRO-cap
Reads were trimmed for standard adapters and low quality (Q<30) 3’-end bases and filtered for a remaining length of at least 20nt (excluding the UMI, if applicable) using cutadapt v2.5.
Alignment to the reference genome was done with Bowtie v1.2.3. The NCBI GRCm38.6 assembly was used as the mouse reference. To this we added the fixated sequence of the recombined VDJ locus as an additional chromosome. Similarly, for human data, the Hg38 assembly was used, with the relevant fixed VDJ sequence added as a chromosome.
Where applicable, the dmr6 assembly of Drosophila melanogaster from Flybase (https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase, release version number 6.27) was used as the spike-in reference and was added to the alignment index. During alignment, up to 3 mismatches were allowed.
To accommodate mapping to the repetitive IgH locus, a high degree of multimapping was allowed (194 potential V segments annotated for GRCm38.6). In the case of alignment with spike-ins, only reads mapping exclusively to either genome were considered.
For PCR deduplication, UMIs were identified (10 nucleotides at the 3' end) and filtered with umi-tools v1.0.0. No sequence differences were allowed in UMIs when collapsing the duplicates.
Multimapping reads were then filtered to identify those specific to the VDJ sequence, taking into account the repetitiveness of the reference IgH locus. Reads mapping to the fixed VDJ sequence were allowed to multimap only to the native IgH locus (mouse chr12:113572929-116009954, human ch14:105836764-106875071). The native loci were defined as the region between the earliest position belonging to an annotated V segment and the latest position belonging to an annotated J segment. Reads with a mapped location outside these areas were rejected. This filtering was implemented in a custom Python script. The qualifying reads were then classified as reads mapping uniquely to the particular VDJ sequence and reads mapping to both the VDJ sequence and to the native IgH region.
Genome browser tracks were created by quantifying and scaling read coverage of the VDJ sequence using bedtools v2.29.0. Reads were split by strand, and strand labels for PROseq were inverted in order to match the strand designations of the respective PROcap reads. For both data types, only the first 5' base of the strand-adjusted reads was used for the tracks. Additionlly, the 5' end of PROseq reads was shifted by 1 base downstream, to compensate for the last base in the mRNA being the exogenous termination base. For normalized tracks, read counts were scaled to RPM (reads per million). Finally, “-“ strand coverage tracks were further scaled by -1, for visualization convenience.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_PROcapseq .
Assembly: NCBI mm9, NCBI HG38, custom IGH genome (see github)
Supplementary files format and content: bigWig of rpm-normalized read densities
Library strategy: PRO-cap

extract_protocol:
Cells were harvested and nuclei isolated. Transcription run-on in the presence of 2 biotinylated NTPs (Bio-UTP and Bio-CTP) and unlabeled ATP and GTP. Afterwards Trizol extraction of total RNA
total extraction with Trizol, labeled RNA enrichment .3' and 5' linker attachment. cDNA preparation and barcoding PCR, gel extraction of ~180-350bp library

value: spleen

tag: cell type

value: GCB

value: in vivo

value: SRBC injected (d0,d5), harvest d12


title: Hypoxia replicate 2


title: tomato ChIP_control

organism: Solanum lycopersicum

value: leaf

value: tomato (MicroTom)


title: SIC_264_1040_2_heart

description: 10x Genomics

extract_protocol:
Tissue samples obtained by biopsy or autopsy were immediately placed in ice-cold HypoThermosol solution (BioLife Solutions, Bothell, WA) and kept on ice during transfer to the research facility. Tissue was then washed twice with cold phosphate buffered saline. Tissue was then dissociated using the human tumor dissociation kit according to the manufacturer’s instructions (Miltenyi Biotic, Bergisch Gladbach, Germany) with modification such that calcium chloride was added to the enzymatic cocktail to a final concentration of 1.25 mM. Tubes containing tissue fragments in the enzymatic cocktail were placed in a heated shaker at 37° C with shaking at 750 RPM for 25 minutes with the machine placed on its side to prevent tissue fragments from settling. Following incubation, the reaction was quenched through the addition of 100 µl human serum. The mixture was further dissociated through manual trituration followed by filtration through 70 µm mesh. Following centrifugation at 350 x g for 12 minutes, the supernatant was removed and RBC lysis was performed (ACK lysing buffer, Lonza, Basel, Switzerland). Following a wash step, cells were resuspended in phenol-free RPMI with 2% (v/v) human AB serum.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart tissue

tag: Sex


title: tomato AtADCP1_ChIP_rep2

value: AtADCP1-GFP in tomato transgenic plants


title: Hypoxia replicate 1

value: Vehicle, 1percent oxygen


title: tomato AtADCP1_ChIP_rep1


title: Normoxia replicate 3

value: Vehicle, normoxia


title: SIC_258_787_1_heart

description: 10x Genomics

value: irMyocarditis


title: SIC_199_631_1_heart

description: 10x Genomics


title: tomato H3K9me2_ChIP_rep2


title: tomato H3K9me2_ChIP_rep1


title: Normoxia replicate 2


title: SIC_177_539_2_heart

description: 10x Genomics


title: Normoxia replicate 1