title: genomic DNA from eutopic endometrium Sample_268

source_name: endometrium sample 268


title: genomic DNA from eutopic endometrium Sample_265

status: Public on Sep 12 2023

type: genomic

city: Herston

first: Sally

last: Mortlock

state: Queensland

address: AWaGHR Centre, School of Public Health, The University of Queensland

department: School of Public Health

country: Australia

institute: University of Queensland

description:
genomic DNA from eutopic endometrium
Control eutopic endometrium sample

hyb_protocol: All DNA samples were adjusted to the same volume and concentration for sodium bisulfite conversion followed by DNAm analysis on the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina scan protocol was performed at the University of Southern California Epigenome Center.

data_processing:
Background correction with dye-bias, signal intensity normalization and Beta value generation performed using the SeSAME R package. Samples with a low overall intensity signal (median unmethylated or methylated signal <9), a detection p-value >0.05 in more than 1% of DNAm sites were removed. Probes with a detection p-value >0.05 in more than 10% of samples and probes not overlapping between batches were removed. Probes were masked based on the SeSAME package. 759,345 DNAm sites for 984 samples remained.
Normalized Beta and Normalized M-value

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: endometrium sample 265

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from endometrial samples

tag: gender

value: Female

tag: sample type

value: endometrium

tag: disease state

value: Control

tag: cycle phase

value: PE

tag: plate

tag: terminus

tag: batch

tag: euro

value: EUR

tag: recruiment

tag: age


title: genomic DNA from eutopic endometrium Sample_266

description:
genomic DNA from eutopic endometrium
Endometriosis eutopic endometrium sample

source_name: endometrium sample 266

value: Endometriosis

value: MSE


title: genomic DNA from eutopic endometrium Sample_267

source_name: endometrium sample 267


title: genomic DNA from eutopic endometrium Sample_459

source_name: endometrium sample 459


title: genomic DNA from eutopic endometrium Sample_263

source_name: endometrium sample 263


title: genomic DNA from eutopic endometrium Sample_270

source_name: endometrium sample 270


title: genomic DNA from eutopic endometrium Sample_264

source_name: endometrium sample 264

value: SE


title: genomic DNA from eutopic endometrium Sample_261

source_name: endometrium sample 261


title: genomic DNA from eutopic endometrium Sample_262

source_name: endometrium sample 262


title: genomic DNA from eutopic endometrium Sample_260

source_name: endometrium sample 260

value: ESE


title: genomic DNA from eutopic endometrium Sample_259

source_name: endometrium sample 259


title: genomic DNA from eutopic endometrium Sample_255

source_name: endometrium sample 255


title: genomic DNA from eutopic endometrium Sample_256

source_name: endometrium sample 256


title: genomic DNA from eutopic endometrium Sample_257

source_name: endometrium sample 257


title: genomic DNA from eutopic endometrium Sample_301

source_name: endometrium sample 301


title: genomic DNA from eutopic endometrium Sample_254

source_name: endometrium sample 254


title: genomic DNA from eutopic endometrium Sample_252

source_name: endometrium sample 252


title: genomic DNA from eutopic endometrium Sample_253

source_name: endometrium sample 253


title: genomic DNA from eutopic endometrium Sample_258

source_name: endometrium sample 258


title: genomic DNA from eutopic endometrium Sample_250

source_name: endometrium sample 250


title: genomic DNA from eutopic endometrium Sample_248

source_name: endometrium sample 248


title: genomic DNA from eutopic endometrium Sample_249

source_name: endometrium sample 249


title: genomic DNA from eutopic endometrium Sample_244

source_name: endometrium sample 244


title: genomic DNA from eutopic endometrium Sample_243

source_name: endometrium sample 243


title: genomic DNA from eutopic endometrium Sample_245

source_name: endometrium sample 245


title: genomic DNA from eutopic endometrium Sample_240

source_name: endometrium sample 240


title: genomic DNA from eutopic endometrium Sample_241

source_name: endometrium sample 241


title: genomic DNA from eutopic endometrium Sample_247

source_name: endometrium sample 247

value: LSE


title: genomic DNA from eutopic endometrium Sample_242

source_name: endometrium sample 242


title: genomic DNA from eutopic endometrium Sample_288

source_name: endometrium sample 288


title: genomic DNA from eutopic endometrium Sample_246

source_name: endometrium sample 246


title: genomic DNA from eutopic endometrium Sample_239

source_name: endometrium sample 239


title: genomic DNA from eutopic endometrium Sample_238

source_name: endometrium sample 238


title: genomic DNA from eutopic endometrium Sample_237

source_name: endometrium sample 237


title: genomic DNA from eutopic endometrium Sample_236

source_name: endometrium sample 236


title: genomic DNA from eutopic endometrium Sample_251

source_name: endometrium sample 251


title: genomic DNA from eutopic endometrium Sample_235

source_name: endometrium sample 235


title: genomic DNA from eutopic endometrium Sample_234

source_name: endometrium sample 234


title: genomic DNA from eutopic endometrium Sample_233

source_name: endometrium sample 233


title: genomic DNA from eutopic endometrium Sample_302

source_name: endometrium sample 302


title: genomic DNA from eutopic endometrium Sample_232

source_name: endometrium sample 232


title: genomic DNA from eutopic endometrium Sample_231

source_name: endometrium sample 231


title: genomic DNA from eutopic endometrium Sample_229

source_name: endometrium sample 229


title: genomic DNA from eutopic endometrium Sample_230

source_name: endometrium sample 230


title: genomic DNA from eutopic endometrium Sample_227

source_name: endometrium sample 227


title: genomic DNA from eutopic endometrium Sample_225

source_name: endometrium sample 225


title: genomic DNA from eutopic endometrium Sample_226

source_name: endometrium sample 226


title: genomic DNA from eutopic endometrium Sample_224

source_name: endometrium sample 224


title: genomic DNA from eutopic endometrium Sample_223

source_name: endometrium sample 223


title: genomic DNA from eutopic endometrium Sample_222

source_name: endometrium sample 222


title: genomic DNA from eutopic endometrium Sample_221

source_name: endometrium sample 221

value: Menstrual


title: genomic DNA from eutopic endometrium Sample_219

source_name: endometrium sample 219


title: genomic DNA from eutopic endometrium Sample_220

source_name: endometrium sample 220


title: genomic DNA from eutopic endometrium Sample_981

source_name: endometrium sample 981


title: genomic DNA from eutopic endometrium Sample_982

source_name: endometrium sample 982


title: genomic DNA from eutopic endometrium Sample_984

source_name: endometrium sample 984


title: genomic DNA from eutopic endometrium Sample_980

source_name: endometrium sample 980


title: genomic DNA from eutopic endometrium Sample_218

source_name: endometrium sample 218


title: genomic DNA from eutopic endometrium Sample_983

source_name: endometrium sample 983


title: genomic DNA from eutopic endometrium Sample_977

source_name: endometrium sample 977


title: genomic DNA from eutopic endometrium Sample_978

source_name: endometrium sample 978


title: genomic DNA from eutopic endometrium Sample_975

source_name: endometrium sample 975


title: genomic DNA from eutopic endometrium Sample_976

source_name: endometrium sample 976


title: genomic DNA from eutopic endometrium Sample_979

source_name: endometrium sample 979


title: genomic DNA from eutopic endometrium Sample_974

source_name: endometrium sample 974


title: genomic DNA from eutopic endometrium Sample_973

source_name: endometrium sample 973


title: genomic DNA from eutopic endometrium Sample_971

source_name: endometrium sample 971


title: genomic DNA from eutopic endometrium Sample_967

source_name: endometrium sample 967


title: genomic DNA from eutopic endometrium Sample_972

source_name: endometrium sample 972


title: genomic DNA from eutopic endometrium Sample_970

source_name: endometrium sample 970


title: genomic DNA from eutopic endometrium Sample_969

source_name: endometrium sample 969


title: genomic DNA from eutopic endometrium Sample_964

source_name: endometrium sample 964


title: genomic DNA from eutopic endometrium Sample_966

source_name: endometrium sample 966


title: genomic DNA from eutopic endometrium Sample_965

source_name: endometrium sample 965


title: genomic DNA from eutopic endometrium Sample_962

source_name: endometrium sample 962


title: genomic DNA from eutopic endometrium Sample_961

source_name: endometrium sample 961


title: genomic DNA from eutopic endometrium Sample_963

source_name: endometrium sample 963


title: genomic DNA from eutopic endometrium Sample_960

source_name: endometrium sample 960


title: genomic DNA from eutopic endometrium Sample_959

source_name: endometrium sample 959


title: genomic DNA from eutopic endometrium Sample_958

source_name: endometrium sample 958


title: genomic DNA from eutopic endometrium Sample_956

source_name: endometrium sample 956


title: genomic DNA from eutopic endometrium Sample_957

source_name: endometrium sample 957


title: genomic DNA from eutopic endometrium Sample_955

source_name: endometrium sample 955


title: genomic DNA from eutopic endometrium Sample_953

source_name: endometrium sample 953


title: genomic DNA from eutopic endometrium Sample_954

source_name: endometrium sample 954


title: genomic DNA from eutopic endometrium Sample_952

source_name: endometrium sample 952


title: genomic DNA from eutopic endometrium Sample_951

source_name: endometrium sample 951


title: genomic DNA from eutopic endometrium Sample_950

source_name: endometrium sample 950


title: genomic DNA from eutopic endometrium Sample_269

source_name: endometrium sample 269


title: genomic DNA from eutopic endometrium Sample_949

source_name: endometrium sample 949


title: genomic DNA from eutopic endometrium Sample_947

source_name: endometrium sample 947


title: genomic DNA from eutopic endometrium Sample_948

source_name: endometrium sample 948


title: genomic DNA from eutopic endometrium Sample_946

source_name: endometrium sample 946


title: genomic DNA from eutopic endometrium Sample_228

source_name: endometrium sample 228


title: genomic DNA from eutopic endometrium Sample_945

source_name: endometrium sample 945


title: genomic DNA from eutopic endometrium Sample_944

source_name: endometrium sample 944


title: genomic DNA from eutopic endometrium Sample_943

source_name: endometrium sample 943


title: genomic DNA from eutopic endometrium Sample_942

source_name: endometrium sample 942


title: genomic DNA from eutopic endometrium Sample_940

source_name: endometrium sample 940


title: genomic DNA from eutopic endometrium Sample_941

source_name: endometrium sample 941


title: genomic DNA from eutopic endometrium Sample_939

source_name: endometrium sample 939


title: genomic DNA from eutopic endometrium Sample_938

source_name: endometrium sample 938


title: genomic DNA from eutopic endometrium Sample_937

source_name: endometrium sample 937


title: genomic DNA from eutopic endometrium Sample_936

source_name: endometrium sample 936


title: genomic DNA from eutopic endometrium Sample_935

source_name: endometrium sample 935


title: genomic DNA from eutopic endometrium Sample_934

source_name: endometrium sample 934


title: genomic DNA from eutopic endometrium Sample_933

source_name: endometrium sample 933


title: genomic DNA from eutopic endometrium Sample_931

source_name: endometrium sample 931


title: genomic DNA from eutopic endometrium Sample_932

source_name: endometrium sample 932


title: genomic DNA from eutopic endometrium Sample_930

source_name: endometrium sample 930


title: genomic DNA from eutopic endometrium Sample_928

source_name: endometrium sample 928


title: genomic DNA from eutopic endometrium Sample_927

source_name: endometrium sample 927


title: genomic DNA from eutopic endometrium Sample_929

source_name: endometrium sample 929


title: genomic DNA from eutopic endometrium Sample_926

source_name: endometrium sample 926


title: genomic DNA from eutopic endometrium Sample_925

source_name: endometrium sample 925


title: genomic DNA from eutopic endometrium Sample_924

source_name: endometrium sample 924


title: genomic DNA from eutopic endometrium Sample_922

source_name: endometrium sample 922


title: genomic DNA from eutopic endometrium Sample_923

source_name: endometrium sample 923


title: genomic DNA from eutopic endometrium Sample_921

source_name: endometrium sample 921


title: genomic DNA from eutopic endometrium Sample_920

source_name: endometrium sample 920


title: genomic DNA from eutopic endometrium Sample_919

source_name: endometrium sample 919


title: genomic DNA from eutopic endometrium Sample_918

source_name: endometrium sample 918


title: genomic DNA from eutopic endometrium Sample_914

source_name: endometrium sample 914


title: genomic DNA from eutopic endometrium Sample_913

source_name: endometrium sample 913


title: genomic DNA from eutopic endometrium Sample_912

source_name: endometrium sample 912


title: genomic DNA from eutopic endometrium Sample_915

source_name: endometrium sample 915


title: genomic DNA from eutopic endometrium Sample_917

source_name: endometrium sample 917


title: genomic DNA from eutopic endometrium Sample_916

source_name: endometrium sample 916


title: genomic DNA from eutopic endometrium Sample_911

source_name: endometrium sample 911


title: genomic DNA from eutopic endometrium Sample_910

source_name: endometrium sample 910


title: genomic DNA from eutopic endometrium Sample_909

source_name: endometrium sample 909


title: genomic DNA from eutopic endometrium Sample_908

source_name: endometrium sample 908


title: genomic DNA from eutopic endometrium Sample_907

source_name: endometrium sample 907


title: genomic DNA from eutopic endometrium Sample_906

source_name: endometrium sample 906


title: genomic DNA from eutopic endometrium Sample_905

source_name: endometrium sample 905


title: genomic DNA from eutopic endometrium Sample_904

source_name: endometrium sample 904


title: genomic DNA from eutopic endometrium Sample_903

source_name: endometrium sample 903


title: genomic DNA from eutopic endometrium Sample_902

source_name: endometrium sample 902


title: genomic DNA from eutopic endometrium Sample_900

source_name: endometrium sample 900


title: genomic DNA from eutopic endometrium Sample_216

source_name: endometrium sample 216


title: genomic DNA from eutopic endometrium Sample_217

source_name: endometrium sample 217


title: genomic DNA from eutopic endometrium Sample_214

source_name: endometrium sample 214


title: genomic DNA from eutopic endometrium Sample_215

source_name: endometrium sample 215


title: genomic DNA from eutopic endometrium Sample_901

source_name: endometrium sample 901


title: genomic DNA from eutopic endometrium Sample_213

source_name: endometrium sample 213


title: genomic DNA from eutopic endometrium Sample_212

source_name: endometrium sample 212


title: genomic DNA from eutopic endometrium Sample_211

source_name: endometrium sample 211


title: genomic DNA from eutopic endometrium Sample_210

source_name: endometrium sample 210


title: genomic DNA from eutopic endometrium Sample_209

source_name: endometrium sample 209


title: genomic DNA from eutopic endometrium Sample_208

source_name: endometrium sample 208


title: genomic DNA from eutopic endometrium Sample_207

source_name: endometrium sample 207


title: genomic DNA from eutopic endometrium Sample_206

source_name: endometrium sample 206


title: genomic DNA from eutopic endometrium Sample_205

source_name: endometrium sample 205


title: genomic DNA from eutopic endometrium Sample_204

source_name: endometrium sample 204


title: genomic DNA from eutopic endometrium Sample_202

source_name: endometrium sample 202


title: genomic DNA from eutopic endometrium Sample_201

source_name: endometrium sample 201


title: genomic DNA from eutopic endometrium Sample_200

source_name: endometrium sample 200


title: genomic DNA from eutopic endometrium Sample_198

source_name: endometrium sample 198


title: genomic DNA from eutopic endometrium Sample_203

source_name: endometrium sample 203


title: genomic DNA from eutopic endometrium Sample_197

source_name: endometrium sample 197


title: genomic DNA from eutopic endometrium Sample_199

source_name: endometrium sample 199


title: genomic DNA from eutopic endometrium Sample_196

source_name: endometrium sample 196


title: genomic DNA from eutopic endometrium Sample_195

source_name: endometrium sample 195


title: genomic DNA from eutopic endometrium Sample_194

source_name: endometrium sample 194


title: genomic DNA from eutopic endometrium Sample_193

source_name: endometrium sample 193


title: genomic DNA from eutopic endometrium Sample_192

source_name: endometrium sample 192


title: genomic DNA from eutopic endometrium Sample_191

source_name: endometrium sample 191


title: genomic DNA from eutopic endometrium Sample_190

source_name: endometrium sample 190


title: genomic DNA from eutopic endometrium Sample_189

source_name: endometrium sample 189


title: genomic DNA from eutopic endometrium Sample_188

source_name: endometrium sample 188


title: genomic DNA from eutopic endometrium Sample_187

source_name: endometrium sample 187


title: genomic DNA from eutopic endometrium Sample_184

source_name: endometrium sample 184


title: genomic DNA from eutopic endometrium Sample_185

source_name: endometrium sample 185


title: genomic DNA from eutopic endometrium Sample_183

source_name: endometrium sample 183


title: genomic DNA from eutopic endometrium Sample_182

source_name: endometrium sample 182


title: genomic DNA from eutopic endometrium Sample_181

source_name: endometrium sample 181


title: genomic DNA from eutopic endometrium Sample_180

source_name: endometrium sample 180


title: genomic DNA from eutopic endometrium Sample_179

source_name: endometrium sample 179


title: genomic DNA from eutopic endometrium Sample_178

source_name: endometrium sample 178


title: genomic DNA from eutopic endometrium Sample_177

source_name: endometrium sample 177


title: genomic DNA from eutopic endometrium Sample_176

source_name: endometrium sample 176


title: genomic DNA from eutopic endometrium Sample_175

source_name: endometrium sample 175


title: genomic DNA from eutopic endometrium Sample_186

source_name: endometrium sample 186


title: genomic DNA from eutopic endometrium Sample_174

source_name: endometrium sample 174


title: genomic DNA from eutopic endometrium Sample_173

source_name: endometrium sample 173


title: genomic DNA from eutopic endometrium Sample_172

source_name: endometrium sample 172


title: genomic DNA from eutopic endometrium Sample_169

source_name: endometrium sample 169


title: genomic DNA from eutopic endometrium Sample_171

source_name: endometrium sample 171


title: genomic DNA from eutopic endometrium Sample_170

source_name: endometrium sample 170


title: genomic DNA from eutopic endometrium Sample_168

source_name: endometrium sample 168


title: genomic DNA from eutopic endometrium Sample_166

source_name: endometrium sample 166


title: genomic DNA from eutopic endometrium Sample_167

source_name: endometrium sample 167


title: genomic DNA from eutopic endometrium Sample_165

source_name: endometrium sample 165


title: genomic DNA from eutopic endometrium Sample_163

source_name: endometrium sample 163


title: genomic DNA from eutopic endometrium Sample_162

source_name: endometrium sample 162


title: genomic DNA from eutopic endometrium Sample_164

source_name: endometrium sample 164


title: genomic DNA from eutopic endometrium Sample_161

source_name: endometrium sample 161


title: genomic DNA from eutopic endometrium Sample_160

source_name: endometrium sample 160


title: genomic DNA from eutopic endometrium Sample_159

source_name: endometrium sample 159


title: genomic DNA from eutopic endometrium Sample_158

source_name: endometrium sample 158


title: genomic DNA from eutopic endometrium Sample_157

source_name: endometrium sample 157


title: genomic DNA from eutopic endometrium Sample_154

source_name: endometrium sample 154


title: genomic DNA from eutopic endometrium Sample_156

source_name: endometrium sample 156


title: genomic DNA from eutopic endometrium Sample_155

source_name: endometrium sample 155


title: genomic DNA from eutopic endometrium Sample_153

source_name: endometrium sample 153


title: genomic DNA from eutopic endometrium Sample_151

source_name: endometrium sample 151


title: genomic DNA from eutopic endometrium Sample_152

source_name: endometrium sample 152


title: genomic DNA from eutopic endometrium Sample_150

source_name: endometrium sample 150


title: genomic DNA from eutopic endometrium Sample_149

source_name: endometrium sample 149


title: genomic DNA from eutopic endometrium Sample_148

source_name: endometrium sample 148


title: genomic DNA from eutopic endometrium Sample_147

source_name: endometrium sample 147


title: genomic DNA from eutopic endometrium Sample_146

source_name: endometrium sample 146


title: genomic DNA from eutopic endometrium Sample_144

source_name: endometrium sample 144


title: genomic DNA from eutopic endometrium Sample_145

source_name: endometrium sample 145


title: genomic DNA from eutopic endometrium Sample_143

source_name: endometrium sample 143


title: genomic DNA from eutopic endometrium Sample_142

source_name: endometrium sample 142


title: genomic DNA from eutopic endometrium Sample_140

source_name: endometrium sample 140


title: genomic DNA from eutopic endometrium Sample_139

source_name: endometrium sample 139


title: genomic DNA from eutopic endometrium Sample_138

source_name: endometrium sample 138


title: genomic DNA from eutopic endometrium Sample_141

source_name: endometrium sample 141


title: genomic DNA from eutopic endometrium Sample_762

source_name: endometrium sample 762


title: genomic DNA from eutopic endometrium Sample_753

source_name: endometrium sample 753


title: genomic DNA from eutopic endometrium Sample_769

source_name: endometrium sample 769


title: genomic DNA from eutopic endometrium Sample_784

source_name: endometrium sample 784


title: genomic DNA from eutopic endometrium Sample_137

source_name: endometrium sample 137


title: genomic DNA from eutopic endometrium Sample_756

source_name: endometrium sample 756


title: genomic DNA from eutopic endometrium Sample_136

source_name: endometrium sample 136


title: genomic DNA from eutopic endometrium Sample_968

source_name: endometrium sample 968


title: genomic DNA from eutopic endometrium Sample_134

source_name: endometrium sample 134


title: genomic DNA from eutopic endometrium Sample_135

source_name: endometrium sample 135


title: genomic DNA from eutopic endometrium Sample_133

source_name: endometrium sample 133


title: genomic DNA from eutopic endometrium Sample_129

source_name: endometrium sample 129


title: genomic DNA from eutopic endometrium Sample_130

source_name: endometrium sample 130


title: genomic DNA from eutopic endometrium Sample_128

source_name: endometrium sample 128


title: genomic DNA from eutopic endometrium Sample_131

source_name: endometrium sample 131


title: genomic DNA from eutopic endometrium Sample_132

source_name: endometrium sample 132


title: genomic DNA from eutopic endometrium Sample_125

source_name: endometrium sample 125


title: genomic DNA from eutopic endometrium Sample_123

source_name: endometrium sample 123


title: genomic DNA from eutopic endometrium Sample_127

source_name: endometrium sample 127


title: genomic DNA from eutopic endometrium Sample_126

source_name: endometrium sample 126


title: genomic DNA from eutopic endometrium Sample_124

source_name: endometrium sample 124


title: genomic DNA from eutopic endometrium Sample_120

source_name: endometrium sample 120


title: genomic DNA from eutopic endometrium Sample_116

source_name: endometrium sample 116


title: genomic DNA from eutopic endometrium Sample_121

source_name: endometrium sample 121


title: genomic DNA from eutopic endometrium Sample_122

source_name: endometrium sample 122


title: genomic DNA from eutopic endometrium Sample_119

source_name: endometrium sample 119


title: genomic DNA from eutopic endometrium Sample_118

source_name: endometrium sample 118


title: genomic DNA from eutopic endometrium Sample_117

source_name: endometrium sample 117


title: genomic DNA from eutopic endometrium Sample_115

source_name: endometrium sample 115


title: genomic DNA from eutopic endometrium Sample_112

source_name: endometrium sample 112


title: genomic DNA from eutopic endometrium Sample_113

source_name: endometrium sample 113


title: genomic DNA from eutopic endometrium Sample_109

source_name: endometrium sample 109


title: genomic DNA from eutopic endometrium Sample_108

source_name: endometrium sample 108


title: genomic DNA from eutopic endometrium Sample_107

source_name: endometrium sample 107


title: genomic DNA from eutopic endometrium Sample_104

source_name: endometrium sample 104


title: genomic DNA from eutopic endometrium Sample_100

source_name: endometrium sample 100


title: genomic DNA from eutopic endometrium Sample_102

source_name: endometrium sample 102


title: genomic DNA from eutopic endometrium Sample_103

source_name: endometrium sample 103


title: genomic DNA from eutopic endometrium Sample_105

source_name: endometrium sample 105


title: genomic DNA from eutopic endometrium Sample_101

source_name: endometrium sample 101


title: genomic DNA from eutopic endometrium Sample_99

source_name: endometrium sample 99


title: genomic DNA from eutopic endometrium Sample_98

source_name: endometrium sample 98


title: genomic DNA from eutopic endometrium Sample_95

source_name: endometrium sample 95


title: genomic DNA from eutopic endometrium Sample_97

source_name: endometrium sample 97


title: genomic DNA from eutopic endometrium Sample_94

source_name: endometrium sample 94


title: genomic DNA from eutopic endometrium Sample_93

source_name: endometrium sample 93


title: genomic DNA from eutopic endometrium Sample_90

source_name: endometrium sample 90


title: genomic DNA from eutopic endometrium Sample_89

source_name: endometrium sample 89


title: genomic DNA from eutopic endometrium Sample_83

source_name: endometrium sample 83


title: genomic DNA from eutopic endometrium Sample_86

source_name: endometrium sample 86


title: genomic DNA from eutopic endometrium Sample_85

source_name: endometrium sample 85


title: genomic DNA from eutopic endometrium Sample_79

source_name: endometrium sample 79


title: genomic DNA from eutopic endometrium Sample_78

source_name: endometrium sample 78


title: genomic DNA from eutopic endometrium Sample_80

source_name: endometrium sample 80


title: genomic DNA from eutopic endometrium Sample_77

source_name: endometrium sample 77


title: genomic DNA from eutopic endometrium Sample_75

source_name: endometrium sample 75


title: genomic DNA from eutopic endometrium Sample_76

source_name: endometrium sample 76


title: genomic DNA from eutopic endometrium Sample_74

source_name: endometrium sample 74


title: genomic DNA from eutopic endometrium Sample_73

source_name: endometrium sample 73


title: genomic DNA from eutopic endometrium Sample_88

source_name: endometrium sample 88


title: genomic DNA from eutopic endometrium Sample_69

source_name: endometrium sample 69


title: genomic DNA from eutopic endometrium Sample_71

source_name: endometrium sample 71


title: genomic DNA from eutopic endometrium Sample_67

source_name: endometrium sample 67


title: genomic DNA from eutopic endometrium Sample_66

source_name: endometrium sample 66


title: genomic DNA from eutopic endometrium Sample_65

source_name: endometrium sample 65


title: genomic DNA from eutopic endometrium Sample_64

source_name: endometrium sample 64


title: genomic DNA from eutopic endometrium Sample_63

source_name: endometrium sample 63


title: genomic DNA from eutopic endometrium Sample_60

source_name: endometrium sample 60


title: genomic DNA from eutopic endometrium Sample_58

source_name: endometrium sample 58


title: genomic DNA from eutopic endometrium Sample_114

source_name: endometrium sample 114


title: genomic_DNAmethylation_PM256

status: Public on Mar 12 2025

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to the standard Illumina protocol

scan_protocol: HiScan according to the standard Illumina settings

data_processing: minfi preprocessRaw function, betas extracted

label_protocol: Standard Illumina protocol

extract_protocol: DNA salt extraction & bisulfite conversion

tag: tissue

value: Villi

tag: sentrix

tag: Sex

value: M

tag: ga


title: genomic DNA from eutopic endometrium Sample_56

source_name: endometrium sample 56


title: genomic DNA from eutopic endometrium Sample_111

source_name: endometrium sample 111


title: genomic DNA from eutopic endometrium Sample_55

source_name: endometrium sample 55


title: genomic DNA from eutopic endometrium Sample_106

source_name: endometrium sample 106


title: genomic DNA from eutopic endometrium Sample_110

source_name: endometrium sample 110


title: genomic DNA from eutopic endometrium Sample_96

source_name: endometrium sample 96


title: genomic DNA from eutopic endometrium Sample_54

source_name: endometrium sample 54


title: genomic DNA from eutopic endometrium Sample_53

source_name: endometrium sample 53


title: genomic DNA from eutopic endometrium Sample_52

source_name: endometrium sample 52


title: vehicle, 5 months, male, rep 4

status: Public on Feb 11 2025

type: SRA

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

library_source: transcriptomic

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: mm10
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

molecule: polyA RNA

organism: Mus musculus

source_name: liver

growth_protocol: This study was approved by the Institutional Animal Care and Use Committee at Sanford Burnham Prebys MDI. C57BL6 mice were purchased from Jackson Labs and Charles River and group housed under specific pathogen free conditions with ad libitum access to water and food (Teklad 2018).

extract_protocol:
Fresh liver was lysed in Trizol (Ambion 15596026), and RNA was isolated with chloroform according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 10 mg/kg HDM201 (Novartis) suspended in phosphate-buffered methylcellulose according to the manufacturer’s instructions (0.5% methylcellulose in phosphate buffer, pH6.8, 50mM) by daily oral gavage in the morning. Mice were monitored daily and weighed every 2-3 days during treatment. After 14 days of treatment, mice were euthanized by CO2 asphyxiation in the morning

value: liver

value: 5 months

value: male

tag: genotype

tag: treatment

value: Vehicle


title: genomic DNA from eutopic endometrium Sample_51

source_name: endometrium sample 51

value: Female


title: genomic DNA from eutopic endometrium Sample_50

source_name: endometrium sample 50

value: endometrium


title: genomic DNA from eutopic endometrium Sample_47

source_name: endometrium sample 47

value: Control


title: genomic DNA from eutopic endometrium Sample_48

source_name: endometrium sample 48


title: genomic DNA from eutopic endometrium Sample_87

source_name: endometrium sample 87

value: PE


title: genomic DNA from eutopic endometrium Sample_46

source_name: endometrium sample 46

value: EUR


title: genomic DNA from eutopic endometrium Sample_45

source_name: endometrium sample 45

value: Endometriosis


title: genomic DNA from eutopic endometrium Sample_44

source_name: endometrium sample 44


title: genomic DNA from eutopic endometrium Sample_42

source_name: endometrium sample 42


title: genomic DNA from eutopic endometrium Sample_39

source_name: endometrium sample 39


title: genomic DNA from eutopic endometrium Sample_41

source_name: endometrium sample 41


title: genomic DNA from eutopic endometrium Sample_37

source_name: endometrium sample 37


title: genomic DNA from eutopic endometrium Sample_38

source_name: endometrium sample 38


title: genomic DNA from eutopic endometrium Sample_36

source_name: endometrium sample 36


title: genomic DNA from eutopic endometrium Sample_72

source_name: endometrium sample 72


title: genomic DNA from eutopic endometrium Sample_35

source_name: endometrium sample 35


title: genomic DNA from eutopic endometrium Sample_34

source_name: endometrium sample 34

value: MSE


title: genomic DNA from eutopic endometrium Sample_68

source_name: endometrium sample 68


title: genomic DNA from eutopic endometrium Sample_33

source_name: endometrium sample 33


title: genomic DNA from eutopic endometrium Sample_32

source_name: endometrium sample 32


title: genomic DNA from eutopic endometrium Sample_29

source_name: endometrium sample 29


title: genomic DNA from eutopic endometrium Sample_30

source_name: endometrium sample 30


title: genomic DNA from eutopic endometrium Sample_31

source_name: endometrium sample 31


title: genomic DNA from eutopic endometrium Sample_28

source_name: endometrium sample 28


title: genomic DNA from eutopic endometrium Sample_26

source_name: endometrium sample 26


title: genomic DNA from eutopic endometrium Sample_24

source_name: endometrium sample 24


title: genomic DNA from eutopic endometrium Sample_23

source_name: endometrium sample 23


title: genomic DNA from eutopic endometrium Sample_25

source_name: endometrium sample 25


title: genomic DNA from eutopic endometrium Sample_59

source_name: endometrium sample 59


title: genomic DNA from eutopic endometrium Sample_22

source_name: endometrium sample 22

value: SE


title: genomic DNA from eutopic endometrium Sample_20

source_name: endometrium sample 20


title: genomic DNA from eutopic endometrium Sample_19

source_name: endometrium sample 19


title: genomic DNA from eutopic endometrium Sample_17

source_name: endometrium sample 17


title: genomic DNA from eutopic endometrium Sample_18

source_name: endometrium sample 18


title: genomic DNA from eutopic endometrium Sample_16

source_name: endometrium sample 16


title: genomic DNA from eutopic endometrium Sample_15

source_name: endometrium sample 15


title: genomic DNA from eutopic endometrium Sample_13

source_name: endometrium sample 13


title: genomic DNA from eutopic endometrium Sample_11

source_name: endometrium sample 11


title: genomic DNA from eutopic endometrium Sample_10

source_name: endometrium sample 10


title: genomic DNA from eutopic endometrium Sample_9

source_name: endometrium sample 9


title: genomic DNA from eutopic endometrium Sample_7

source_name: endometrium sample 7


title: genomic DNA from eutopic endometrium Sample_5

source_name: endometrium sample 5


title: genomic DNA from eutopic endometrium Sample_8

source_name: endometrium sample 8


title: genomic DNA from eutopic endometrium Sample_6

source_name: endometrium sample 6


title: genomic DNA from eutopic endometrium Sample_4

source_name: endometrium sample 4


title: genomic DNA from eutopic endometrium Sample_3

source_name: endometrium sample 3

value: ESE


title: genomic DNA from eutopic endometrium Sample_2

source_name: endometrium sample 2


title: genomic DNA from eutopic endometrium Sample_1

source_name: endometrium sample 1


title: Aged Brain, Vehicle

status: Public on Aug 16 2023

description:
Control
10x Genomics Gene Expression Flex

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cellranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

molecule: total RNA

organism: Mus

source_name: Brain

extract_protocol:
Freshly collected brains were fresh frozen in liquid nitrogen and stored at -80 C until tissues were sent for analysis. Fixed, single cell suspension were prepared from flash frozen mouse brain tissue using the Chromium Next GEM Single Cell Fixed RNA Preparation kit (10x Genomics) according to the user guide (CG000553, Rev B). Minced tissues were fixed for 24 hrs at 4C. Cell dissociation was performed using the gentleMACS Octo Dissociator (Miltenyi).
Libraries were constructed using the single-plex Chromium Fixed RNA Profiling kit (CG000477, Rev C). Probes were incubated for 20 hrs at 42C and 9 cycles were performed for the indexing PCR.

treatment_protocol: 20-month old mice were treated with the Bax inhibitor, BAI1,3 times a week for three months. Mice were sacrificed and tissues were fresh frozen and stored at -80 C until they were sent for analysis

value: Brain

value: 20-month old

value: WT

tag: strain


title: Aged Brain, BAI1

description:
BAI1-treated
10x Genomics Gene Expression Flex


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Proliferating: Prolif_BAK_BAX_rep2

data_processing:
Real Time Analysis 3.4.4 software used for basecalling.
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary_files_format_and_content: Raw count matrix contains raw counts for each sample and each gene

source_name: human lung

growth_protocol: MRC5 fibroblasts and IMR90 fibroblasts were grown in Dulbecco's Modified Eagle's Medium supplemented with 10% FBD, 100 units/ml penicillin, 100 ug/ml streptomycin and 2mM L-glutamine and maintained at 37 C with 5% CO2. MRC5 fibroblasts were cultured in atmospheric oxygen conditions and IMR90 fibroblasts were cultured under low oxygen (3%) conditions.

extract_protocol:
Cells were scrapped on ice, pellets were collected and RNA was harvested using RNeasy Mini Kit (Qiagen, 74106) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Senescence was induced by exposing cells to 20 Gy X-ray irradiation.

tag: cell type

value: Human primary lung fibroblasts MRC5

value: Infected with LentiCRISPR v2 hBAK and LentiCRISPR v2 hBAX

value: Not irradiated


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Proliferating: Prolif_BAK_BAX_rep3


title: Human primary lung fibroblasts MRC5 Empty CRISPR Senescent: IR_pLenti_rep2

value: Infected with LentiCRISPR v2-puro

value: Cells were induced to senesce by X-ray irradiation with 20 Gy


title: Human primary lung fibroblasts MRC5 Empty CRISPR Senescent: IR_pLenti_rep1


title: Human primary lung fibroblasts MRC5 Empty CRISPR Proliferating: Prolif_pLenti_rep3


title: Human primary lung fibroblasts MRC5 Empty CRISPR Proliferating: Prolif_pLenti_rep1


title: genomic DNA from eutopic endometrium Sample_27

source_name: endometrium sample 27

tag: gender

value: Female

tag: sample type


title: genomic DNA from eutopic endometrium Sample_21

source_name: endometrium sample 21

value: endometrium

tag: disease state

tag: cycle phase


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP+mtDNA: Parkin_Sen_CCCP_mtDNA_rep2

value: Human primary lung fibroblasts IMR90

value: Infected with LZRS-YFP_Parkin

value: Cells were transfected with 5ug of mtDNA

value: Cells were treated with 12uM of CCCP


title: genomic DNA from eutopic endometrium Sample_14

source_name: endometrium sample 14

value: Control

tag: plate

tag: terminus

value: EUR


title: genomic DNA from eutopic endometrium Sample_12

source_name: endometrium sample 12

value: Endometriosis

value: PE

tag: batch

tag: euro


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP+mtDNA: Parkin_Sen_CCCP_mtDNA_rep1


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP: Parkin_Sen_CCCP_rep3


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP: Parkin_Sen_CCCP_rep2


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP: Parkin_Sen_CCCP_rep1


title: Human primary lung fibroblasts IMR90- Senescence Parkin: Parkin_Sen_rep3


title: Human primary lung fibroblasts IMR90- Senescence Parkin: Parkin_Sen_rep2


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Senescent: IR_BAK_BAX_rep3


title: Human primary lung fibroblasts IMR90- Senescence Parkin: Parkin_Sen_rep1


title: Human primary lung fibroblasts IMR90- Proliferating Parkin: Parkin_Prol_rep3

value: No irradiated


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Senescent: IR_BAK_BAX_rep2


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Senescent: IR_BAK_BAX_rep1


title: Human primary lung fibroblasts IMR90- Proliferating Parkin: Parkin_Prol_rep1


title: Human primary lung fibroblasts IMR90- Proliferating Parkin: Parkin_Prol_rep2


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Proliferating: Prolif_BAK_BAX_rep1


title: Human primary lung fibroblasts MRC5 Empty CRISPR Senescent: IR_pLenti_rep3


title: genomic_DNAmethylation_QF0151_vc_R1

status: Public on Aug 08 2023

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridised to the Illumina Infinium  MethylationEPIC Beadchips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using an HiSCAN with standard recommended Illumina scanner settings.

data_processing:
See original publication
Beta values with dasen + noob normalization, filtered for quality probes.

label: Cy5 and Cy3

extract_protocol: V-NORM and V-SSRI samples: 1.5-2 cm3 samples of chorionic villi were taken from each of four distinct cotyledons (sites) from below the surface of the fetal-facing side of the placental disc. The samples were washed thoroughly to remove blood, and any thick vessels were removed. Samples were frozen at -20°C until use. DNA was then extracted from all four cotyledon samples using a salting-out DNA extraction procedure, and extracted DNA from the four sites was pooled in equimolar proportions to provide a representative sample of each placenta. The second sampling process involved the QF-2011 placentas, which were processed in Brisbane, Australia within 60 minutes of delivery, and eight sites (1 cm3 each) representing different cotyledons were sampled across the fetal-facing side of each placenta. These samples were snap frozen in liquid nitrogen and subsequently shipped frozen to Montreal, Canada. Samples were pooled and ground while snap frozen over liquid nitrogen. DNA was extracted using a commercial kit  from pooled samples in Montreal, before shipping to Vancouver on dry ice for DNAme processing.

tag: cohort

value: NIH Batch 1

value: FALSE

value: European/Caucasian

tag: syncytiotrophoblast

tag: cytotrophoblast

tag: stromal

tag: endothelial

tag: hofbauer

tag: nrbc


title: genomic_DNAmethylation_M0085_vc

tag: sentrix

tag: Sex

value: Male


title: genomic_DNAmethylation_QF0350_vc_R1


title: genomic_DNAmethylation_M0028_vc


title: genomic_DNAmethylation_QF0240_vc


title: genomic_DNAmethylation_QF0232_vc


title: genomic_DNAmethylation_QF0302_vc


title: genomic_DNAmethylation_QF0130_vc


title: genomic_DNAmethylation_M0035_vc


title: genomic_DNAmethylation_M0078_vc


title: genomic_DNAmethylation_M0050_vc


title: genomic_DNAmethylation_QF0180_vc_R2


title: genomic_DNAmethylation_QF0252_vc


title: genomic_DNAmethylation_QF0291_vc


title: genomic_DNAmethylation_M0109_vc_R1


title: genomic_DNAmethylation_M0204_vc


title: genomic_DNAmethylation_M0067_vc


title: genomic_DNAmethylation_M0205_vc


title: genomic_DNAmethylation_QF0344_vc


title: genomic_DNAmethylation_M0208_vc


title: Human primary lung fibroblasts MRC5 Empty CRISPR Proliferating: Prolif_pLenti_rep2

tag: cell type

value: Human primary lung fibroblasts MRC5

tag: treatment

value: Infected with LentiCRISPR v2-puro

value: Not irradiated


title: genomic_DNAmethylation_QF0161_vc

value: Female


title: genomic_DNAmethylation_QF0148_vc_R2

value: TRUE


title: genomic_DNAmethylation_QF0137_vc_R1


title: genomic_DNAmethylation_QF0197_vc


title: genomic_DNAmethylation_M0076_vc


title: genomic_DNAmethylation_M0033_vc


title: genomic_DNAmethylation_M0002_vc


title: genomic_DNAmethylation_M0109_vc_R2


title: genomic_DNAmethylation_QF0139_vc


title: genomic_DNAmethylation_QF0371_vc_R2


title: genomic_DNAmethylation_QF0235_vc


title: genomic_DNAmethylation_QF0222_vc


title: genomic_DNAmethylation_M0029_vc


title: genomic_DNAmethylation_QF0283_vc


title: genomic_DNAmethylation_QF0362_vc


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP+mtDNA: Parkin_Sen_CCCP_mtDNA_rep3

value: Human primary lung fibroblasts IMR90

value: Infected with LZRS-YFP_Parkin

value: Cells were induced to senesce by X-ray irradiation with 20 Gy


title: genomic_DNAmethylation_M0101_vc


title: genomic_DNAmethylation_M0206_vc


title: genomic_DNAmethylation_M0112_vc


title: genomic_DNAmethylation_QF0311_vc


title: genomic_DNAmethylation_QF0148_vc_R1


title: genomic_DNAmethylation_QF0191_vc


title: genomic_DNAmethylation_M0015_vc


title: genomic_DNAmethylation_QF0151_vc_R2


title: genomic_DNAmethylation_QF0316_vc


title: genomic_DNAmethylation_QF0371_vc_R1


title: genomic_DNAmethylation_QF0188_vc


title: genomic_DNAmethylation_QF0315_vc


title: genomic_DNAmethylation_QF0314_vc


title: genomic_DNAmethylation_QF0323_vc


title: genomic_DNAmethylation_TO-27_vc

value: V-SSRI

value: East Asian


title: genomic_DNAmethylation_TO-81_vc

value: Black


title: genomic_DNAmethylation_TO-60_vc


title: genomic_DNAmethylation_TO-34_vc


title: genomic_DNAmethylation_TO-23_vc


title: genomic_DNAmethylation_TO-54_vc


title: genomic_DNAmethylation_TO-43_vc

value: Other(including mixed)


title: genomic_DNAmethylation_TO-48_vc


title: genomic_DNAmethylation_TO-35_vc


title: genomic_DNAmethylation_TO-41_vc


title: genomic_DNAmethylation_TO-28_vc


title: genomic_DNAmethylation_TO-12_vc


title: genomic_DNAmethylation_TO-79_vc


title: genomic_DNAmethylation_TO-56_vc


title: genomic_DNAmethylation_TO-61_vc


title: genomic_DNAmethylation_PM77_vc_R3

value: V-NORM

value: Unknown


title: genomic_DNAmethylation_TO-65_vc

value: NIH Batch 1

value: FALSE


title: genomic_DNAmethylation_TO-50_vc

value: European/Caucasian


title: genomic_DNAmethylation_TO-53_vc


title: genomic_DNAmethylation_TO-69_vc

value: Male


title: genomic_DNAmethylation_TO-51_vc


title: genomic_DNAmethylation_TO-38_vc


title: genomic DNA from eutopic endometrium Sample_91

source_name: endometrium sample 91

tag: gender

tag: sample type

value: endometrium

tag: disease state

value: Control

value: PE

value: EUR

tag: recruiment

tag: age


title: genomic_DNAmethylation_TO-80_vc

tag: batch


title: genomic_DNAmethylation_TO-64_vc

tag: cohort


title: genomic_DNAmethylation_TO-58_vc

tag: syncytiotrophoblast


title: genomic_DNAmethylation_TO-22_vc

value: Female

tag: cytotrophoblast


title: genomic_DNAmethylation_TO-30_vc

tag: stromal


title: genomic_DNAmethylation_TO-37_vc

tag: endothelial


title: genomic_DNAmethylation_TO-14_vc

tag: hofbauer


title: genomic_DNAmethylation_QF0159_vc

tag: nrbc


title: genomic_DNAmethylation_QF0322_vc

tag: sentrix


title: genomic_DNAmethylation_M0105_vc

tag: Sex


title: genomic_DNAmethylation_M0062_vc


title: genomic_DNAmethylation_QF0154_vc


title: genomic_DNAmethylation_QF0123_vc


title: genomic_DNAmethylation_M0072_vc


title: genomic_DNAmethylation_QF0239_vc


title: genomic_DNAmethylation_M0202_vc


title: genomic_DNAmethylation_QF0299_vc


title: genomic_DNAmethylation_TO-33_vc


title: genomic_DNAmethylation_QF0307_vc


title: genomic_DNAmethylation_M0051_vc


title: genomic_DNAmethylation_M0056_vc


title: genomic_DNAmethylation_QF0199_vc


title: genomic_DNAmethylation_M0017_vc


title: genomic_DNAmethylation_QF0306_vc


title: genomic DNA from eutopic endometrium Sample_62

source_name: endometrium sample 62

tag: cycle phase

value: MSE

tag: plate

tag: terminus

tag: euro


title: genomic_DNAmethylation_QF0360_vc


title: genomic_DNAmethylation_M0079_vc


title: genomic DNA from eutopic endometrium Sample_61

source_name: endometrium sample 61

tag: gender

tag: sample type

tag: disease state

value: Endometriosis

value: LSE


title: genomic_DNAmethylation_QF0153_vc

tag: batch


title: genomic_DNAmethylation_PM77_vc_R2

tag: cohort

value: TRUE


title: genomic_DNAmethylation_M0053_vc

tag: syncytiotrophoblast


title: genomic_DNAmethylation_M0102_vc

tag: cytotrophoblast


title: genomic_DNAmethylation_QF0280_vc

value: East Asian

tag: stromal


title: genomic_DNAmethylation_QF0178_vc

tag: endothelial


title: genomic_DNAmethylation_M0075_vc

tag: hofbauer


title: genomic_DNAmethylation_QF0128_vc

value: Black

tag: nrbc


title: genomic_DNAmethylation_QF0350_vc_R2

tag: sentrix


title: genomic_DNAmethylation_QF0347_vc

tag: Sex


title: genomic_DNAmethylation_M0003_vc


title: genomic_DNAmethylation_QF0140_vc


title: genomic_DNAmethylation_M0034_vc


title: genomic_DNAmethylation_M0063_vc


title: genomic_DNAmethylation_QF0180_vc_R1


title: genomic_DNAmethylation_M0070_vc


title: genomic_DNAmethylation_QF0198_vc


title: genomic_DNAmethylation_M0210_vc


title: genomic_DNAmethylation_QF0304_vc


title: genomic_DNAmethylation_QF0297_vc_R2


title: genomic_DNAmethylation_M0087_vc


title: genomic_DNAmethylation_QF0137_vc_R2


title: genomic_DNAmethylation_QF0189_vc


title: genomic_DNAmethylation_QF0332_vc


title: genomic_DNAmethylation_QF0343_vc


title: genomic_DNAmethylation_M0071_vc


title: genomic_DNAmethylation_QF0146_vc


title: genomic_DNAmethylation_QF0317_vc


title: genomic_DNAmethylation_M0068_vc


title: genomic_DNAmethylation_M0065_vc


title: genomic DNA from eutopic endometrium Sample_49

source_name: endometrium sample 49

tag: cycle phase

tag: recruiment

tag: age


title: genomic_DNAmethylation_QF0167_vc


title: genomic_DNAmethylation_QF0327_vc


title: genomic_DNAmethylation_QF0297_vc_R1


title: genomic_DNAmethylation_M0207_vc


title: genomic_DNAmethylation_QF0170_vc


title: genomic_DNAmethylation_TO-16_vc

value: V-SSRI


title: genomic_DNAmethylation_QF0290_vc


title: genomic_DNAmethylation_TO-19_vc


title: genomic_DNAmethylation_TO-29_vc


title: genomic_DNAmethylation_TO-67_vc


title: genomic_DNAmethylation_TO-44_vc


title: genomic_DNAmethylation_TO-73_vc


title: genomic_DNAmethylation_TO-77_vc

value: Other(including mixed)


title: genomic_DNAmethylation_TO-45_vc

value: NIH Batch 1


title: genomic_DNAmethylation_TO-32_vc

value: FALSE


title: genomic_DNAmethylation_TO-49_vc

value: European/Caucasian


title: genomic_DNAmethylation_TO-52_vc

value: Male


title: genomic_DNAmethylation_TO-66_vc


title: genomic_DNAmethylation_TO-83_vc


title: genomic_DNAmethylation_TO-40_vc


title: genomic_DNAmethylation_TO-63_vc

value: Unknown


title: genomic_DNAmethylation_TO-57_vc


title: genomic_DNAmethylation_TO-59_vc


title: genomic_DNAmethylation_TO-75_vc


title: genomic_DNAmethylation_TO-62_vc


title: genomic_DNAmethylation_TO-17_vc


title: genomic_DNAmethylation_TO-76_vc


title: genomic_DNAmethylation_TO-55_vc


title: genomic_DNAmethylation_TO-15_vc


title: genomic_DNAmethylation_TO-26_vc


title: genomic_DNAmethylation_TO-18_vc


title: genomic_DNAmethylation_TO-13_vc


title: genomic_DNAmethylation_TO-47_vc


title: genomic_DNAmethylation_TO-46_vc


title: genomic_DNAmethylation_TO-36_vc


title: genomic_DNAmethylation_TO-82_vc


title: genomic_DNAmethylation_TO-24_vc


title: genomic_DNAmethylation_TO-42_vc


title: genomic_DNAmethylation_PM77_vc_R1

value: V-NORM


title: genomic_DNAmethylation_TO-31_vc


title: genomic_DNAmethylation_PM374_vc

value: NIH Batch 2


title: genomic_DNAmethylation_PM366_vc_R2


title: genomic_DNAmethylation_TO-68_vc


title: genomic_DNAmethylation_PM375_vc

value: Mixed


title: genomic_DNAmethylation_PM77_vc


title: genomic_DNAmethylation_PM366_vc_R1

value: Female


title: genomic_DNAmethylation_PM381_vc


title: genomic_DNAmethylation_PM359_vc


title: genomic_DNAmethylation_PM373_vc


title: genomic_DNAmethylation_PM372_vc


title: genomic_DNAmethylation_PM367_vc


title: genomic_DNAmethylation_PM370_vc


title: genomic_DNAmethylation_PM369_vc


title: genomic_DNAmethylation_PM139_vc


title: genomic_DNAmethylation_PM379_vc


title: genomic_DNAmethylation_PM371_vc


title: genomic_DNAmethylation_PM362_vc


title: genomic_DNAmethylation_PM365_vc


title: genomic_DNAmethylation_PM364_vc


title: genomic_DNAmethylation_PM376_vc


title: genomic_DNAmethylation_PM368_vc


title: genomic_DNAmethylation_PM354_vc

value: NIH Batch 3


title: genomic_DNAmethylation_PM219_vc


title: genomic_DNAmethylation_PM378_vc


title: genomic_DNAmethylation_PM357_vc


title: genomic_DNAmethylation_PM167_vc


title: genomic_DNAmethylation_PM180_vc


title: genomic_DNAmethylation_M0201_vcN


title: genomic_DNAmethylation_QF0136_vcN


title: genomic_DNAmethylation_QF0194_vcN


title: genomic_DNAmethylation_PM77_vc_R


title: genomic_DNAmethylation_PM352_vc


title: genomic_DNAmethylation_QF0230_vcN


title: genomic_DNAmethylation_PM220_vc


title: genomic_DNAmethylation_QF0365_vcN


title: genomic_DNAmethylation_QF0368_vcN


title: genomic_DNAmethylation_PM151_vc


title: genomic_DNAmethylation_M0023_vcN


title: genomic_DNAmethylation_QF0150_vcN


title: genomic_DNAmethylation_PM202_vc


title: genomic_DNAmethylation_QF0357_vcN


title: genomic_DNAmethylation_PM353_vc


title: genomic_DNAmethylation_PM353_vc_R


title: genomic_DNAmethylation_PM212_vc


title: genomic_DNAmethylation_PM178_vc


title: genomic_DNAmethylation_PM184_vc


title: genomic_DNAmethylation_QF0185_vcN


title: genomic_DNAmethylation_PM187_vc


title: genomic_DNAmethylation_PM355_vc


title: genomic_DNAmethylation_QF0325_vcN


title: genomic_DNAmethylation_PM139_vc_R


title: Embryonic stage16 Hand-GFP+ cells from wild type Drosophila [Hrt24_25hr]

status: Public on Aug 07 2023

city: Baltimore

first: Hangnoh

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Single cell RNA-Seq of Drosophila embryonic heart (25hr)

data_processing:
CASAVA version 1.8.2 (Illumina, San Diego, CA) was used for basecalling.
We used Cell Ranger pipeline version 3.0.2 (10X Genomics, Pleasanton, CA) for demultiplexing of raw reads, aligning them to the reference genome, filtering and counting of the mapped reads.
The supplementary file (count matrix) was generated using Seurat package (Stuart*, Butler*, et al., 2019. PMID: 31178118)
Genome_build: Drosophila BDGP Release 6
Supplementary_files_format_and_content: Combined_Count_Matrix.tsv.gz

organism: Drosophila melanogaster

source_name: Embryonic heart

growth_protocol: Hand-GFP+ wild type files were maintained at 25°C on standard diet and one-week-old flies were collected. Flies were put in a collection cage and juice plates were changed 3 times before egg collection. Eggs were collected at 1h intervals at 25°C, and then transferred to 18°C for development. Samples were collected at the indicated time points.

extract_protocol:
Collected embryos were washed thoroughly with ice-cold 1X phosphate buffered saline (PBS) and then dechorionated in fresh 4-5% bleach (sodium hypochlorite solution; Sigma) for 3 min at room temperature. Dechorionated embryos were extensively rinsed with H2O. Then embryos (~150 mg) were transferred to a Dounce homogenizer (15 ml Tissue Grinder; Dounce). A 5 ml suspension of embryos (Schneider medium) was subjected to mechanical disruption using the Dounce homogenizer, achieved by five strokes using a pestle. Homogenized samples were transferred to 15 ml centrifuge tubes. Collagenase (Type I) (20 U/ml; Worthington), 100 U total, was added to the Schneider medium with the embryos and incubated at room temperature for 10 min. Next, 10 μl of ethylenediaminetetraacetid acid (EDTA) (0.5 M; final concentration of 1 mM) and 0.5 ml 2.5% Trypsin were added to the 5 ml cell solution to digest the samples for 20 min at room temperature. The trypsin reaction was stop by adding 20% fetal bovine serum (FBS) and cells were filtered out using a 70 μm mesh. The cells were then pelleted by centrifugation (1000xg, 5 min, 4°C) and resuspended in 2 ml pre-chilled artificial hemolymph. Isolated embryonic cells were sorted by flow cytometry (BD Influx cell sorter).
The library preparation (Single Cell 3’ Reagent Kits v3, 10x Genomics, CA, USA) and sequencing were performed using Illumina HiSeq by Novogene Corporation Inc (Sacramento, CA).
Single-cell RNA-Seq (Single Cell 3’ Reagent Kits v3, 10x Genomics, CA, USA)

tag: developmental stage

value: Stage 16

tag: tissue

value: Embryonic heart


title: Embryonic stage14-late Hand-GFP+ cells from wild type Drosophila [Hrt22_23hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (22hr)

value: Stage 14-late


title: Embryonic stage15 Hand-GFP+ cells from wild type Drosophila [Hrt23_24hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (23hr)

value: Stage 15


title: Embryonic stage13 Hand-GFP+ cells from wild type Drosophila [Hrt18_19hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (18hr)

value: Stage 13


title: scRNAseq, mouse, Brain, MCAo, rep2

status: Public on Jul 15 2023

city: Munich

first: Louis

last: Kuemmerle

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Centre Munich

data_processing:
The 10X Genomics core computational software Cellranger v.3.0.2 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment. (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
For QC, filtering, normalization, and doublet exclusion the scanpy python package v.1.6.1, anndata v0.7.5 and scrublet v.0.2.3 were used.
Genome_build: mm10
Supplementary_files_format_and_content: anndata (annotated data matrix) object saved in h5ad-file format (sc_adata_oct22m.h5ad, sc_adata_march22h.h5ad) as generated and used in the code at https://github.com/erturklab/skull_immune. The files contain the raw, preprocessed, normalized and annotated count data of all single cell experiments.
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.

extract_protocol:
The bones were dissected from the body and the muscles and connective tissue were meticulously cleared off. The bone marrow inside was flushed out to the collection tube with the help of a syringe and further dissection of the bone was performed by fine pincers. The remaining bone was cut in to small  pieces and added to the cell mix. This mixture was shortly vortexed with 37C warmed DMEM with 10% heat inactivated FBS and filtered with 70 μm. The brain was isolated from the calvaria and the rest of the body, then, the cortex was separated and the leptomeninges was removed from the surface, the final sample consisted of the injured region. The sample was placed in 5 ml of trypsin enzyme with 0.05% concentration and incubated in a pre-heated 37 °C water bath for 2 minutes.Following this, the reaction was stopped with 10 ml of 37°C pre-warmed DMEM with 10% heat inactivated FBS, the cells were dissociated by gentle trituration with a 1000μl and 200μl pipette and filtered through 70 μm Falcon™ Cell Strainers. For meningeal cell isolation; after the brain was removed, the meningeal dura layer that was attached to the calvaria bone, was plucked carefully using fine tipped dissection pincers under a dissection microscope. Leptomeninges was not isolated and therefore is not included in this study. The dissected meninges was placed in 37°C pre-warmed DMEM with 10% heat inactivated FBS solution, shredded with a fine scalpel, gently titrating with a 200μl pipette and filtered through a 70 μm Falcon™ Cell Strainers.Samples were centrifuged at 4 °C, with 1000 rpm, for 5 minutes.The supernatant of all samples was then discarded and remaining precipitate was put into small 1.5 ml Eppendorf tubes after resuspension with DMEM.
10x single-cell protocol

value: Brain

tag: strain

tag: genotype

value: wildtype

tag: treatment

value: MCAo


title: Embryonic stage14-early Hand-GFP+ cells from wild type Drosophila [Hrt21_22hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (21hr)

value: Stage 14-early


title: scRNAseq, mouse, Brain, Naive, rep1

value: Naive


title: scRNAseq, mouse, Brain, Sham, rep1

value: Sham


title: scRNAseq, mouse, Brain, MCAo, rep1


title: Embryonic stage13 Hand-GFP+ cells from wild type Drosophila [Hrt20_21hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (20hr)


title: S-2P- B cell v2M6 Rep2 - ADT

status: Public on Jul 07 2023

city: Bethesda

first: Susan

last: Moir

address: 9000 Rockville Pike, 10/6A02

department: NIAID

institute: NIH

description: 10x Genomics

data_processing:
The GEX and ADT libraries were mapped to the GRCh38 human reference genome using CellRanger version 6.0.1. Data were further processed using Seurat version 4.1.0 running in R v4.1.0.
B cell receptor V(D)J data processing, B cell receptor (BCR) V(D)J repertoire data processing and analysis were carried out using tools in the Immcantation framework (www.immcantation.org). V(D)J genes were re-assigned from CellRanger output using IgBLAST v.1.15.0. Cells with multiple IGH V(D)J sequences were assigned to the most abundant IGH V(D)J sequence by UMI count. Following V(D)J gene annotation, non-functional sequences were removed from further analysis, and functional V(D)J sequences were assigned into clonal groups using Change-O v.1.0.0. Then, the immune repertoire information was added into Seurat object as meta data integrated to the transcriptome information at a per-cell level.
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, antibody feature reference csv files

extract_protocol:
B cells of three vaccinees were isolated from thawed cryopreserved peripheral blood mononuclear cells (PBMC) by negative magnetic bead-based selection using a B cell enrichment cocktail (StemCell Technologies). The isolated B cells were stained with PE-Cy7-conjugated anti-human CD19 (ThermoFisher, cat# 25-0198-42) and APC-H7-conjugated anti-human CD20 (BD Biosciences, cat# 560734). SARS-CoV-2-specific B cells were identified using biotinylated spike protein (S-2P) tetramerized with PE-Cy5.5-labeled streptavidin (SA) (ThermoFisher, cat# SA1018) at a molar ratio of 4:1. Three B cell populations were sorted, (1) CD20+S-2P+ B cell, (2) CD20+S-2P-  B cell, and (3) CD20- B cell (plasmablast) populations, using a BD FACSAria Fusion instrument (BD Biosciences).
Isolated B cells from different donors were pooled evenly before cell sorting. Cells from each donor were demultiplexed in silico using donor-specific single nucleotide polymorphism (SNP) information collected during data analysis. Multiple cell pools were prepared, such that cells from the same donors but different time points were in different pools. After cell sorting, cell pools from v2D28 and v2M6 timepoints were Fc blocked (Human TruStain FcX, BioLegend), CITE-seq and hashtag stained with custom TotalSeq-C cocktail antibodies, (including RBD and S1 oligo-tagged tetramers, and washed 3x with staining buffer (2% BSA in PBS). Due to the lower frequency of S-2P+ B cells at earlier time points, pools from v1D14 to v2D14 timepoints were CITE-seq and hashtag (HTO) stained before cell sorting to avoid cell loss during washes. No RBD and S1 oligo-tagged tetramers could be added due to technical reasons. Final cell pools were suspended in 0.04% BSA in PBS and then counted before being immediately processed by the single cell partitioning step. Cell pools were mixed with a reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using the 10x Chromium Single Cell Immune Profiling Next GEM v2 Chemistry Kit (10x Genomics, Pleasanton, CA). The RT step was conducted using a C1000 touch Thermo Cycler (BioRad, Hercules, CA). Single-cell gene expression (GEX), cell surface protein (ADT) and B cell receptor (BCR) libraries were prepared as instructed by 10x Genomics Single Cell Immune Profiling kit v.2 user guide. A total of 84 libraries were quality control tested using a TapeStation 4200 (Agilent, Santa Clara, CA) and quantified using the KAPA Library Quantification kit (Roche, Wilmington, MA). These libraries were then pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the sequencing parameters recommended by the 10x Genomics user guide. The minimum sequencing depths were 50,000 read pairs/cell for the GEX library, 5,000 read pairs/cell for the BCR library, and 5,000 read pairs/cell for the ADT library. Sequencing saturation of the libraries was 80% for the GEX and 10% for the BCR and ADT libraries.

tag: cell type

value: S-2P- B cell

tag: timepoint


title: S-2P- B cell v2M6 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2M6 Rep2 - GEX

description: 10x Genomics


title: S-2P- B cell v2M6 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2M6 Rep1 - ADT

description: 10x Genomics


title: S-2P- B cell v2M6 Rep1 - GEX

description: 10x Genomics


title: genomic_DNAmethylation_TO-25_vc

tag: cohort

value: V-SSRI

tag: batch

value: NIH Batch 1

value: FALSE

value: Male

value: European/Caucasian

tag: syncytiotrophoblast

tag: cytotrophoblast


title: S-2P+ B cell v2M6 Rep2 - VDJ

description: 10x Genomics

value: S-2P+ B cell


title: S-2P+ B cell v2M6 Rep2 - ADT

description: 10x Genomics


title: S-2P+ B cell v2M6 Rep1 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2M6 Rep1 - GEX

description: 10x Genomics


title: S-2P+ B cell v2M6 Rep2 - GEX

description: 10x Genomics


title: S-2P+ B cell v2M6 Rep1 - ADT

description: 10x Genomics


title: Plasmablast v1D14 Rep2 - VDJ

description: 10x Genomics

value: Plasmablast


title: Plasmablast v1D14 Rep2 - ADT

description: 10x Genomics


title: Plasmablast v1D14 Rep2 - GEX

description: 10x Genomics


title: Plasmablast v1D14 Rep1 - ADT

description: 10x Genomics


title: Plasmablast v1D14 Rep1 - VDJ

description: 10x Genomics


title: Plasmablast v1D14 Rep1 - GEX

description: 10x Genomics


title: S-2P- B cell v1D14 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v1D14 Rep2 - ADT

description: 10x Genomics


title: S-2P- B cell v1D14 Rep2 - GEX

description: 10x Genomics


title: S-2P- B cell v1D14 Rep1 - ADT

description: 10x Genomics


title: S-2P- B cell v1D14 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v1D14 Rep1 - GEX

description: 10x Genomics


title: S-2P+ B cell v1D14 - VDJ

description: 10x Genomics


title: S-2P+ B cell v1D14 - ADT

description: 10x Genomics


title: Plasmablast v2D6 Rep2 - ADT

description: 10x Genomics


title: S-2P+ B cell v1D14 - GEX

description: 10x Genomics


title: Plasmablast v2D6 Rep2 - VDJ

description: 10x Genomics


title: Plasmablast v2D6 Rep2 - GEX

description: 10x Genomics


title: Plasmablast v2D6 Rep1 - GEX

description: 10x Genomics


title: Plasmablast v2D6 Rep1 - VDJ

description: 10x Genomics


title: Plasmablast v2D6 Rep1 - ADT

description: 10x Genomics


title: S-2P- B cell v2D6 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D6 Rep2 - ADT

description: 10x Genomics


title: S-2P- B cell v2D6 Rep1 - ADT

description: 10x Genomics


title: S-2P- B cell v2D6 Rep1 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D6 Rep2 - ADT

description: 10x Genomics


title: S-2P- B cell v2D6 Rep1 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D6 Rep1 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D6 Rep2 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D6 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D6 Rep2 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D6 Rep1 - GEX

description: 10x Genomics


title: Plasmablast v2D9 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D6 Rep2 - GEX

description: 10x Genomics


title: Plasmablast v2D9 - GEX

description: 10x Genomics


title: Plasmablast v2D9 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D9 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D9 Rep2 - ADT

description: 10x Genomics


title: S-2P- B cell v2D9 Rep2 - GEX

description: 10x Genomics


title: S-2P- B cell v2D9 Rep1 - ADT

description: 10x Genomics


title: S-2P- B cell v2D9 Rep1 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep2 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep2 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep2 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep1 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep1 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D9 Rep1 - GEX

description: 10x Genomics


title: S-2P- B cell v2D9 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D14 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D14 Rep2 - ADT

description: 10x Genomics


title: S-2P- B cell v2D14 Rep2 - GEX

description: 10x Genomics


title: S-2P- B cell v2D14 Rep1 - ADT

description: 10x Genomics


title: S-2P- B cell v2D14 Rep1 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D14 Rep1 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D14 Rep2 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D14 Rep1 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D14 Rep2 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D14 Rep1 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D14 Rep1 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D14 Rep2 - ADT

description: 10x Genomics


title: S-2P- B cell v2D28 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D28 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep2 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep2 - VDJ

description: 10x Genomics


title: S-2P- B cell v2D28 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep2 - GEX

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep1 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep1 - VDJ

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep1 - GEX

description: 10x Genomics


title: IPSI 24h

status: Public on Jun 29 2023

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

country: Sweden

institute: Lund University

description: high output 150 cycle kit, Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 single index

data_processing:
The cells from the sequenced data were counted with cell ranger v.5 set to default for contra- or IPSI - 1h, -12h or -24h samples. The individual .h5 - files were aggregated in cell ranger aggr
Assembly: mm10
Supplementary files format and content: Cell Ranger Aggr matrix. Aggregated Cell ranger file with all the conditions in the experiments, e.g,, 1h, 12h or 24h contra- or IPSI-lateral single cells from mouse brain cortex.
Supplementary files format and content: Order of files and cell indentifying suffixes in the matrix:
Supplementary files format and content: 1: Contra 1h
Supplementary files format and content: 2: IPSI 1h
Supplementary files format and content: 3: Contra 12h
Supplementary files format and content: 4: IPSI 12h
Supplementary files format and content: 5: Contra 24h
Supplementary files format and content: 6: IPSI 24h

source_name: brain

extract_protocol:
Brain cortex from stroke (penumbra or stroke tissue ,IPSI) or contra (nonstroke corresponding brain cortex tissue area)
According to the 10x Library & Gel Bead Kit v3 single index or Library & Gel Bead Kit v3.1 dual index protocols, respectively

value: brain

value: male

value: Endothelial cells, Astrocytes, Oligodendrocytes, Microglia, Immune cells, Pericytes, Neuronal progenitors

value: RGS5::GFP het

tag: time

value: IPSI (stroke)


title: Contra 24h

value: Contra (stroke)


title: IPSI 12h

description: S2, Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3.1 dual index


title: Contra 1h

description: S2, Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 single index


title: Contra 12h


title: IPSI 1h


title: brain aged Stroke Day 14 replicate1 (female)

status: Public on Jun 14 2023

city: New York

first: Josef

last: Anrather

state: NY

address: 407 East 61st Street

department: BMRI

institute: Weill Cornell Medical College

description: Drop-seq

data_processing:
Demultiplexed fastq files were cleaned of reads not passing the Illumina Passing Filter with fastq_illumina_filter (version 0.1) and processed with the Drop-seq Tools (version 2.3.0) pipeline
Count matrices were processed with the R package Seurat (version 4,1), data were integrated across samples with the R package Harmony (version 0.1.1).
Assembly: mm10
Supplementary files format and content: comma-separated matrix and metadata files

extract_protocol:
Brain single cell suspensions were obtained by enzymatic digestion with papain (Neural Tissue Dissociation Kit (P), #130-092-628, Miltenyi Biotec) following the manufacturer's instructions. Four to five hemispheres were pooled for each experiment. In order to increase cell viability and to preserve the transcriptional state during the generation of single-cell suspensions, Brilliant Blue G (BBG, P2X7 receptor antagonist, 1M, Sigma), actinomycin D (RNA polymerase inhibitor, 5g/ml, Sigma) and AP-5 (25 nM, NMDA receptor blocker, Tocris) were added to the dissociation solution. Next, cell suspension was filtered through a 70 m filter, resuspended in 30% Percoll (GE Healthcare)-HBSS containing 1M BBG, and spun for 10 minutes at 700 g. After gradient centrifugation, the myelin layer was removed, and the cell pellet was resuspended in 2%FBS-PBS buffer and filtered through a 40 m filter. Isolated cells were washed and resuspended in 100 l of blocking buffer per hemisphere to proceed for FACS staining and cell sorting.
For isolation of peripheral leukocytes, mice were anesthetized with pentobarbital (100 mg/Kg, i.p.) and 0.5 ml of blood was drawn from the heart and transfer into tubes containing sodium heparin (20 Units). BBG (1M) and actinomycin D (5g/ml) inhibitors were added during the isolation procedure. For each experiment the blood from two mice (1 ml total blood) was pooled and erythrocytes were lysed. After erythrolysis, blood cells were resuspended in MACS buffer (PBS supplemented with 2% FBS, 2 mM EDTA; 300 μl/107 cells), incubated with a biotinylated Ter-119 antibody (Biolegend) and purified with anti-biotin microbeads according to the manufacturer's instructions (Miltenyi Biotec). Afterward, cells were washed and resuspended in 0.01% BSA-PBS at a concentration of 105 leukocytes /ml.

value: 17-20 month old

value: female

value: Sorted CD45high, microglia, endothelial cells

value: Stroke

tag: time point

value: Day 14


title: brain aged Stroke Day 2 replicate2 (female)

description: Drop-seq

tag: Sex

value: Day 2


title: brain aged Sham Day 2 replicate1 (female)

description: Drop-seq

value: Sham


title: brain aged Stroke Day 2 replicate1 (female)

description: Drop-seq


title: brain aged Stroke Day 2 replicate1 (male)

description: Drop-seq


title: brain aged Sham Day 2 replicate1 (male)

description: Drop-seq


title: brain young Stroke Day 14 replicate4 (male)

description: Drop-seq

value: 8-10 week old


title: brain young Stroke Day 14 replicate3 (male)

description: Drop-seq


title: brain young Stroke Day 14 replicate2 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate4 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate3 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate2 (male)

description: Drop-seq


title: brain young Stroke Day 2 replicate1 (male)

description: Drop-seq


title: brain young Sham Day 2 replicate3 (male)

description: Drop-seq


title: brain young Stroke Day 14 replicate1 (male)

description: Drop-seq


title: brain young Sham Day 2 replicate2 (male)

description: Drop-seq


title: MCAO-brain, scRNAseq

city: Shanghai

first: Yueman

last: Zhang

address: 160 Pujian Rd

country: China

institute: Department of Anesthesiology,  Renji Hospital, School of Medicine Shanghai Jiao Tong University, China

description: BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 30%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: TXT file contain counts and barcodes for each sample

growth_protocol: Male C57/BL6 mice were purchased from Shanghai SLAC Laboratory Animals and were housed under standard laboratory conditions (22°C and a 12‐hour light‐dark cycle with free access to food and water).

extract_protocol:
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice treated middle cerebral artery occlusion (MCAO) means they were anesthetized with 3% isoflurane in 67%:30% N2O/ O2 (induction), until they were unresponsive to the tail pinch test and were then fitted with a nose cone providing 1.5% isoflurane for anesthesia maintenance. A monofilament was introduced into the common carotid artery, advanced to the origin of the middle cerebral artery, and left in position for 60 minutes until reperfusion.Sham-operated animals underwent the same anesthesia and surgical procedures except MCAO.

value: Brain

value: MCAO


title: brain young Sham Day 2 replicate4 (male)

description: Drop-seq


title: brain young Sham Day 2 replicate1 (male)

description: Drop-seq


title: IP02

status: Public on Jun 01 2023

city: Seoul

first: Sejin

last: Oh

address: 81 Irwon-ro Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: scRNA-seq

data_processing:
Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.
The 10x sequencing data was mapped to human reference genome (GRCh38; official Cell Ranger reference) for generating raw gene expression matrix.
Assembly: hg38
Supplementary files format and content: MTX

source_name: Skin

extract_protocol:
the keloid tissue was washed in phosphate-buffered saline (PBS). Excised keloids were immersed in physiological saline and immediately transferred to the lab. After sample was minced into small pieces with scalpel in a petri-dish, prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) was used to digest at 37ºC for 60 min. The debris were filtered out with a 70-μm cell strainer (#352340, Corning). The remaining tissue were transferred into dissociation solution containing 0.25% Trypsin for a second round of dissociation. Subsequently, the live cells were resuspended in PBS-0.04% bovine serum albumin. Cells were pelleted by centrifuging at 500 x g for 5min.
To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 9,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.

tag: pathology

value: Keloid

tag: location

value: Chest

tag: gender

value: Female


title: sham-brain,  scRNAseq

description: BD Rhapsody

value: sham surgey


title: IC02

description: scRNA-seq


title: AP02

description: scRNA-seq

value: Back


title: AC01

description: scRNA-seq

value: Male


title: AC02

description: scRNA-seq


title: AP01

description: scRNA-seq


title: C9-4_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

status: Public on May 23 2023

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N. Fifth Street

institute: TGen

description:
C7_NonStimulated_FTD27_1_V7_Sattler_IPSC_microglia_S40
genecounts_Stim_Master.csv

data_processing:
base calling was performed using Illumina' bcl2fastq software
adapter trimming was performed using cutadapt to remove the first 3 bases from end of R2, as specifed by Takara Bio
reads were aligned to the human genome using STAR v.2.7.10a with default options
alignment (BAM) fies from STAR were converted into gene counts tables using featureCounts v. 1.6.4 with default options
Assembly: GRCh38
Supplementary files format and content: raw gene counts tables from featureCounts

source_name: cell line

growth_protocol:
IPSCs were differentiated into microglia following an established protocol (McQuade et al., 2018). Briefly, iPSCs were maintained in mTeSR Plus Kit (Stemcell Technologies # 05825) in 10cm dishes. At DIV -1 of HPCs differentiation, five to seven day old iPSCs cultures were then used to generate cluster of differentiating 43 positive (CD43+) hematopoietic progenitor cells (HPCs) following a 12 day commercially available kit (STEMdiff Hematopoietic Kit; Stemcell Technologies # 05310). IPSCs were cleaned and 1/3 dish was gently dissociated with dispase (Stemcell Technologies # 07923) for 12-15 minutes at 37°C. IPSCs were then collected and spun down at 500rpm for 1-2 minutes and resuspended in 2mL of mTeSR Plus media with 20 µM ROCK inhibitor Y-27632 (Stemcell Technologies # 72304). Matrigel, hESC-Qualified Matrix (Corning # 354277) coated six well plates were used to start the HPC differentiation. Using a 5mL serological pipette, one drop or two drops of iPSCs were seeded per well into matrigel. Then, next day, on DIV 0 of HPCs differentiation, wells with 80 small colonies per well were selected to start HPCs differentiation. IPSCs were fed following the manufacturer’s instructions. On DIV 12 of HPCs differentiation, only the non-adherent HPCs were transferred to a new six well plate to start microglia differentiation (DIV 12/0).
Matrigel, GFR (growth factor reduced) Membrane Matrix (Corning # 356231) coated six well plates were prepared to start microglia differentiation (DIV12/0). HPCs were differentiated into microglia for 28 days using serum free media conditions. HPCs in suspension were collected and spun down at 300 xG for 6 minutes and resuspended into microglia basal media (MBM, 2mL/well) containing: DMEM/F12 no phenol (Gibco # 11-039-021), 2% Insulin Transferin Selenite (Gibco # 41400045), 2% B27 (Gibco # 17504-044), 0.5% N2 (Gibco # 17502-048), 1% Glutamax (Gibco # 35050-061), 1% NEAA (Gibco # 11140-050), 1% Pen/Strep (Gibco # 15140-122), 400μM 1-Thioglycerol (Sigma # M1753), 5μg/mL human insulin (Sigma # I2643) and supplemented with 3 growth factors (GFs): 100ng/mL human recombinant interleukin-34 (IL-34; Peprotech # 200-34), 25ng/mL macrophage colony-stimulating factor (M-CSF; Gibco # PHC9501) and 50ng/mL transforming growth factor β1 (TGFβ1; Miltenyi Biotec # 130-108-969) (MBM + 3GFs); cytokines and growth factors known to be essential for the development of microglia (Butovsky et al., 2014, Greter et al., 2012, Wang et al., 2012, Abud et al., 2017, Pandya et al., 2017, Abutbul et al., 2012, Chen et al., 2002, Elmore et al., 2014). Microglia differentiation starts (DIV 12/0) once the HPCs are transferred and plated at a density of 200 000 cells per well of a six well. Cells will predominantly grow in suspension. On DIV 2, 4, 6, 8 and 10 of microglia differentiation, 1mL of MBM + 3GFs media was added to each well. On DIV 12, a partial media change was done. IPSC-MGs from one six well plate were spun down at 300 xG for 6 minutes and resuspended into MBM + 3 GFs and split back into the same six well plate. On DIV 14, 16, 18, 20, 22, 24, 1mL media was added per well. On DIV 25, MBM + 3GFs was changed to maturation media composed of MBM supplemented with the 5 growth factors (MBM +5 GFs): 100ng/mL IL34, 25ng/mL M-CSF and 50ng/ml TGFβ1, 100ng/mL cluster of differentiation 200 (CD200; Novoprotein # C31150UG) and100ng/mL fracktaline chemokine C-X3-C motif ligand 1 (CX3CL1; Peprotech # 300-31) (MBM + 5 GFs). The presence of CD200 and CX3CL1 in the culture media, both glial and neuronal molecules are critical for microglia maturation and maintenance of an in vivo-like microglia resting state phenotype in an in vitro setting (Barclay et al., 2002, Kim et al., 2011, Kierdorf and Prinz, 2013) (Figure 1A). At DIV 28, IPSC-MG reached maturation. 1mL of MBM + 5GFs media was added to the cultures every other day. Mature cells were used for experimentation within 10 days (DIV 28-DIV38).
For cortical neuron differentiation, 70% confluent iPS cells maintained in mTeSR Plus media on 10 cm dishes were used for embryoid bodies (EBs) formation. The cells were cultured in low attachment six well plates (Greiner bio-one # 657970) using WiCell Medium containing: DMEM/F12 (Gibco #11330057), 25% knock out serum replacement (Gibco # 10828-028), 1.3% L-glutamine (Gibco # 35050-061), 1.3% NEAA (Gibco # 11140-050), 0.1mM 2-Mercaptoethanol (Sigma# M3148) and placed on a shaker in the incubator for 8 days to allow EBs formation. EBs were then resuspended in Forebrain Neural Induction Media (FB-NIM) containing: DMEM/F12, 1% N2 supplement (Gibco # 17502-048), 1% NEAA, 2ug/mL heparin (Sigma # H3149), 10 μg/mL bFGF (Stemcell Technologies # 78003) and plated on to T25 flasks coated with basement membrane matrigel (Corning # 356234) to allow formation of neuronal rosettes. Neuronal rosettes were maintained in FB-NIM for the next 10 days and then, collected and maintained in suspension on a shaker with half FB-NIM media changes every other day to allow for neurosphere growth. Neurospheres were maintained for 20 days in FB-NIM and then resuspended using forebrain neuronal differentiation media (FB-DM) containing:  Neurobasal Medium (Corning # 21103-049), 2% B27 (Gibco # 17504-044), 10 ug/mL BDNF (Stem cell technologies # 78005), 10 ug/mL GDNF (Stem cell technologies # 78058), 1μg/mL laminin (Life technologies # 23017-015), 3.3 μg/mL cAMP (Stem cell technologies # 73884), 3.52 μg/mL Ascorbic acid (Stem cell technologies # 72132 ), 0.5mM L-glutamine and 1% NEAA and then plated on to T25 flasks. iPSC cortical neurons were harvested on DIV 65-72 for RNA sequencing analysis.

extract_protocol:
RNA was isolated with RNeasy Mini Kit (QIAGEN-74104) following the manufacturer’s instructions. RNA samples were measured for quantity with Quant-iT Ribogreen RNA Assay (Thermo Fisher, Cat. No. R11490) and quality with Agilent High Sensitivity RNA ScreenTape and buffer (Agilent, Cat. No. 5067-5579 & 5067-5580).
For each RNA sample, an indexed, Illumina-compatible, double-stranded cDNA whole transcriptome library was synthesized from 1 μg of total whole transcriptome library was synthesized from 1 μg of total Prep Kit – HI Mammalian (Takara Bio, Cat. No. 634876) and SMARTer RNA Unique Dual Index Kit (Takara Bio, Cat. No. 634418). Library preparation included ribosomal RNA depletion, RNA fragmentation (94◦ C for 3 min), cDNA synthesis, and a 12-cycle unique dual indexing enrichment PCR.

treatment_protocol: On DIV 28-30 iPSC-MG from 4 C9orf72 ALS/FTD patient lines and 5 control lines were plated on to 4 chambers glass slides as described above. For LPS stimulation - One hour after plating, iPSC-MGs were treated for 6 h with LPS (100ng/mL). All iPSC-MG were then collected and sent for RNA sequencing analysis. For Aβ (1-40) stimulation - iPSC-MGs were treated for 2 h with vehicle (DMSO) or 1µM Aβ (1-40) TAMRA (human Aβ, AnaSpec # AS-60488; (Paolicelli et al., 2017)) prepared in microglia basal media with growth factors. All iPSC-MGs were collected at 2 hours and sent for RNA sequencing analysis.

value: cell line

tag: cell line

value: iPSC

value: iPSC- microglia

value: vehicle treatment, 2h


title: C9-7_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
C10_AB_1to40_stimulated_092_5_V10_Sattler_IPSC_microglia_S43
genecounts_Stim_Master.csv

tag: tissue

value: 1uM Ab (1-40) TAMRA treatment, 2 h


title: C9-3_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
A4_NonStimulated_FTD16_15_C9_v5_Sattler_IPSC_microglia_S24
genecounts_Stim_Master.csv


title: C9-7_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
C9_NonStimulated_092_5_V9_Sattler_IPSC_microglia_S42
genecounts_Stim_Master.csv


title: C9-4_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
C8_AB_1to40_stimulated_FTD27_1_V8_Sattler_IPSC_microglia_S41
genecounts_Stim_Master.csv


title: Control-7_Ab, iPSC-MG, control, day 28-30/40-42

description:
C6_AB_1to40_stimulated_Healthy_Control_V6_Sattler_IPSC_microglia_S39
genecounts_Stim_Master.csv

value: Control


title: C9-1_Ab_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
NonStimulated_CSOBUU_C9_v7_Sattler_IPSC_microglia_S14
genecounts_Stim_Master.csv


title: C9-1_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
AB_1to40_stimulated_CSOBUU_C9_v8_Sattler_IPSC_microglia_S15
genecounts_Stim_Master.csv


title: Control-7_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
C5_NonStimulated_Healthy_Control_V5_Sattler_IPSC_microglia_S38
genecounts_Stim_Master.csv


title: Control-5_Ab, iPSC-MG, control, day 28-30/40-42

description:
C4_AB_1to40_stimulated_CS14_V4_Sattler_IPSC_microglia_S37
genecounts_Stim_Master.csv


title: Control-5_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
C3_NonStimulated_CS14_V3_Sattler_IPSC_microglia_S36
genecounts_Stim_Master.csv


title: Control-6_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_JH082_Control_v1_Sattler_IPSC_microglia_S9
genecounts_Stim_Master.csv


title: Control-6_Ab, iPSC-MG, control, day 28-30/40-42

description:
AB_1to40_stimulated_JH082_Control_v2_Sattler_IPSC_microglia_S10
genecounts_Stim_Master.csv


title: Control-2_Ab, iPSC-MG, control, day 28-30/40-42

description:
AB_1to40_stimulated_CS03_Control_v4_Sattler_IPSC_microglia_S5
genecounts_Stim_Master.csv


title: Control-2_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_CS03_Control_v3_Sattler_IPSC_microglia_S4
genecounts_Stim_Master.csv


title: Control-1_Ab, iPSC-MG, control, day 28-30/40-42

description:
C2_AB_1to40_stimulated_CS83_V2_Sattler_IPSC_microglia_S35
genecounts_Stim_Master.csv


title: Control-1_Ab_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
C1_NonStimulated_CS83_V1_Sattler_IPSC_microglia_S34
genecounts_Stim_Master.csv


title: C9-4_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
B5_NonStimulated_FTD27_1_V5_Sattler_IPSC_microglia_S30
genecounts_Stim_Master.csv

value: vehicle treatment, 6h


title: C9-3_LPS, iPSC-MG, C9orf72, day 28-30/40-42

description:
A2_LPS_stimulated_FTD16_15_C9_v14_Sattler_IPSC_microglia_S22
genecounts_Stim_Master.csv

value: 100ng/mL LPS treatment, 6 h


title: C9-3_Ab, iPSC-MG, C9orf72, day 28-30/40-42

description:
A5_AB_1to40_stimulated_FTD16_15_C9_v6_Sattler_IPSC_microglia_S25
genecounts_Stim_Master.csv


title: C9-3_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
A1_NonStimulated_FTD16_15_C9_v13_Sattler_IPSC_microglia_S21
genecounts_Stim_Master.csv


title: C9-1_LPS_matched_vehicle, iPSC-MG, C9orf72, day 28-30/40-42

description:
NonStimulated_CSOBUU_C9_v10_Sattler_IPSC_microglia_S11
genecounts_Stim_Master.csv


title: C9-1_LPS, iPSC-MG, C9orf72, day 28-30/40-42

description:
LPS_stimulated_CSOBUU_C9_v11_Sattler_IPSC_microglia_S12
genecounts_Stim_Master.csv


title: Control-7_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
B1_NonStimulated_Healthy_Control_V1_Sattler_IPSC_microglia_S26
genecounts_Stim_Master.csv


title: Control-7_LPS, iPSC-MG, control, day 28-30/40-42

description:
B2_LPS_stimulated_Healthy_Control_V2_Sattler_IPSC_microglia_S27
genecounts_Stim_Master.csv


title: Control-5_LPS, iPSC-MG, control, day 28-30/40-42

description:
B4_LPS_stimulated_CS14_V4_Sattler_IPSC_microglia_S29
genecounts_Stim_Master.csv


title: Control-6_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_JH082_Control_v4_Sattler_IPSC_microglia_S6
genecounts_Stim_Master.csv


title: Control-5_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
B3_NonStimulated_CS14_V3_Sattler_IPSC_microglia_S28
genecounts_Stim_Master.csv


title: Control-2_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_CS03_Control_v1_Sattler_IPSC_microglia_S1
genecounts_Stim_Master.csv


title: Control-2_LPS, iPSC-MG, control, day 28-30/40-42

description:
LPS_stimulated_CS03_Control_v2_Sattler_IPSC_microglia_S2
genecounts_Stim_Master.csv


title: Control-1_LPS_matched_vehicle, iPSC-MG, control, day 28-30/40-42

description:
NonStimulated_CS83_CONTROL_v7_Sattler_IPSC_microglia_S13
genecounts_Stim_Master.csv


title: Control-1_LPS, iPSC-MG, control, day 28-30/40-42

description:
LPS_stimulated_CS83_CONTROL_v8_Sattler_IPSC_microglia_S14
genecounts_Stim_Master.csv


title: Cortical-12, iPSC cortical neurons, day 65-72

description:
CS83_p33_20_CNs_S34
genecounts_Master.csv

value: iPSC-cortical neurons

value: no treatment, only differentiated cells


title: Cortical-11, iPSC cortical neurons, day 65-72

description:
CS0YJY_p23_19_CNs_S26
genecounts_Master.csv

value: Sporadic ALS


title: Cortical-10_1, iPSC cortical neurons, day 65-72

description:
CS1HKR_p23_17_CNs_S33
genecounts_Master.csv


title: Cortical-9, iPSC cortical neurons, day 65-72

description:
Progranulin_16_CNs_S29
genecounts_Master.csv

value: Mutant Progranulin


title: Cortical-10_2, iPSC cortical neurons, day 65-72

description:
CS1HKR_p24_18_CNs_S17
genecounts_Master.csv


title: Cortical-7, iPSC cortical neurons, day 65-72

description:
078_p30_14_CNs_S21
genecounts_Master.csv


title: Cortical-8, iPSC cortical neurons, day 65-72

description:
092_5_p25_15_CNs_S22
genecounts_Master.csv


title: Cortical-6, iPSC cortical neurons, day 65-72

description:
FTD_26pt5_p39_13_CNs_S23
genecounts_Master.csv


title: Cortical-5_3, iPSC cortical neurons, day 65-72

description:
FTD_27_1_p35_10_CNs_2_S4
genecounts_Master.csv


title: Cortical-5_1, iPSC cortical neurons, day 65-72

description:
FTD_27pt1_p33_11_CNs_S27
genecounts_Master.csv


title: Cortical-5_2, iPSC cortical neurons, day 65-72

description:
FTD_27pt1_p36_12_CNs_S31
genecounts_Master.csv


title: Cortical-4_2, iPSC cortical neurons, day 65-72

description:
034_p29_9_CNs_S18
genecounts_Master.csv


title: Cortical-4_1, iPSC cortical neurons, day 65-72

description:
034_p21_8_CNs_S16
genecounts_Master.csv


title: Cortical-3_2, iPSC cortical neurons, day 65-72

description:
JH082_p30_6_CNs_S25
genecounts_Master.csv


title: Cortical-2_3, iPSC cortical neurons, day 65-72

description:
CS03_p26_3_CNs_S24
genecounts_Master.csv


title: Cortical-3_1, iPSC cortical neurons, day 65-72

description:
JH082_p19_7_CNs_S32
genecounts_Master.csv


title: Cortical-2_2, iPSC cortical neurons, day 65-72

description:
CS03_p21_d68_5_CNs_S19
genecounts_Master.csv


title: Cortical-2_1, iPSC cortical neurons, day 65-72

description:
CS03_p21_4_CNs_S20
genecounts_Master.csv


title: Cortical-1_1, iPSC cortical neurons, day 65-72

description:
CS25_p24_1_CNs_S30
genecounts_Master.csv


title: C9-6, iPSC-MG, C9orf72, day 28/40

description:
CS1HKR_p25_20_Microglia_S10
genecounts_Master.csv


title: Cortical-1_2, iPSC cortical neurons, day 65-72

description:
CS25_p31_2_CNs_S28
genecounts_Master.csv


title: C9-7, iPSC-MG, C9orf72, day 28/40

description:
092_5_p24_2_Microglia_S14
genecounts_Master.csv


title: C9-4, iPSC-MG, C9orf72, day 28/40

description:
FTD_27pt1_p33_8_Microglia_S2
genecounts_Master.csv


title: C9-5, iPSC-MG, C9orf72, day 28/40

description:
FTD_26pt5_p40_7_Microglia_S6
genecounts_Master.csv


title: C9-3, iPSC-MG, C9orf72, day 28/40

description:
FTD_16_15_p20_26_Microglia_S13
genecounts_Master.csv


title: C9-1, iPSC-MG, C9orf72, day 28/40

description:
CSO_BUU_p25_25_Microglia_S12
genecounts_Master.csv


title: C9-2, iPSC-MG, C9orf72, day 28/40

description:
CS5_MNZ_p24_24_Microglia_S8
genecounts_Master.csv


title: Control-6, iPSC-MG, control, day 28/40

description:
JH082_p28_1_Microglia_S11
genecounts_Master.csv


title: Control-2_2, iPSC-MG, control, day 28/40

description:
CS03_p23_5_Microglia_S9
genecounts_Master.csv


title: Control-2_1, iPSC-MG, control, day 28/40

description:
CS03_p23_21_Microglia_S3
genecounts_Master.csv


title: Control-5, iPSC-MG, control, day 28/40

description:
CS14_p23_6_Microglia_S1
genecounts_Master.csv


title: Control-1, iPSC-MG, control, day 28/40

description:
CS83_p34_22_Microglia_S5
genecounts_Master.csv