title: genomic DNA from venous blood 230

description:
SV069M.1.1
Normal venous blood sample

source_name: venous blood 230

tag: parity

tag: gestational age

tag: cohort


title: genomic DNA from venous blood 236

status: Public on Jun 08 2023

type: genomic

city: GAINESVILLE

first: Edward

last: Quinn

state: FL

address: 2033 Mowry Road

department: Anthropology

country: USA

institute: University of Florida

description:
SV069b.b.1.1 - eq100
Normal venous blood sample

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

scan_protocol: Arrays were imaged using the Illumina iScan using standard recommended Illumina scanner settings

data_processing:
SeSame R package
Average Beta after noob normalization

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: venous blood 236

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from venous blood using the QIAmp DNA Blood Mini Kit (Qiagen, Germantown, Maryland). The protocol was performed in two parts. Steps one through seven were performed at HEAL Africa Hospital to kill infectious agents and stabilize DNA prior to shipment to the University of Florida. Steps 8-11 were done at the University of Florida but modified them slightly - two AW1 washes and two AW2 washes were done instead of one wash each. We eluted three times in 45 ul TE buffer each time.

tag: gender

value: Female

tag: tissue

tag: age

tag: birthweight

tag: dyad

tag: maternal age

tag: delivery mode

value: vaginal

tag: maternal alcohol

value: No

value: Multigravida

tag: general trauma

tag: sexual trauma

tag: war trauma

tag: chronic stress

value: Sexual Violence Ward

tag: replicate

value: FALSE

tag: replicate id

tag: dna methylation age

tag: age acceleration


title: genomic DNA from venous blood 234

description:
SV067M.1.1
Normal venous blood sample

source_name: venous blood 234

value: caesarean section

tag: parity

value: Primigravida

tag: gestational age

tag: cohort


title: genomic DNA from venous blood 229

description:
SV055bb.1 - eq100
Normal venous blood sample

source_name: venous blood 229

tag: gender

value: Male

tag: tissue

tag: age


title: genomic DNA from venous blood 226

description:
SV026b.b.1.1
Normal venous blood sample

source_name: venous blood 226

tag: birthweight

tag: dyad

tag: maternal age


title: genomic DNA from venous blood 224

description:
SV060M.2.1
Normal venous blood sample

source_name: venous blood 224

tag: delivery mode

tag: maternal alcohol

tag: general trauma


title: genomic DNA from venous blood 227

description:
SV028M.2.1
Normal venous blood sample

source_name: venous blood 227

tag: sexual trauma

tag: war trauma

tag: chronic stress


title: genomic DNA from venous blood 228

description:
SV006M.1
Normal venous blood sample

source_name: venous blood 228

tag: replicate

tag: replicate id

tag: dna methylation age


title: genomic DNA from venous blood 223

description:
SV072M.1.1
Normal venous blood sample

source_name: venous blood 223

tag: parity

tag: gestational age

tag: age acceleration


title: genomic DNA from venous blood 222

description:
SV072b.b.2.1
Normal venous blood sample

source_name: venous blood 222

tag: gender

tag: tissue

tag: cohort


title: genomic DNA from venous blood 219

description:
SV014b.b.1.1
Normal venous blood sample

source_name: venous blood 219

tag: age

tag: birthweight

tag: dyad


title: genomic DNA from venous blood 238

description:
SV064M.2.1
Normal venous blood sample

source_name: venous blood 238

tag: maternal age

tag: delivery mode

tag: maternal alcohol


title: genomic DNA from venous blood 218

description:
SV005bb.2.1a
Normal venous blood sample

source_name: venous blood 218

tag: general trauma

tag: sexual trauma

tag: war trauma


title: genomic DNA from venous blood 217

description:
SV005M.1.1
Normal venous blood sample

source_name: venous blood 217

tag: chronic stress

tag: replicate

tag: replicate id


title: genomic DNA from venous blood 221

description:
SV073M.1.1
Normal venous blood sample

source_name: venous blood 221

tag: parity

tag: gestational age

tag: dna methylation age


title: genomic DNA from venous blood 209

description:
SV011M.1.1 - eq100
Normal venous blood sample

source_name: venous blood 209

tag: gender

tag: tissue

value: TRUE

tag: age acceleration


title: genomic DNA from venous blood 210

description:
SV011M.1.1 - eq101
Normal venous blood sample

source_name: venous blood 210

tag: age

tag: birthweight

tag: cohort


title: genomic DNA from venous blood 213

description:
SV061bb.2.1 - eq100
Normal venous blood sample

source_name: venous blood 213

tag: dyad

tag: maternal age

tag: delivery mode


title: genomic DNA from venous blood 211

description:
SV051M.1 - eq100
Normal venous blood sample

source_name: venous blood 211

tag: maternal alcohol

tag: general trauma

tag: sexual trauma


title: genomic DNA from venous blood 216

description:
SV021bb.2.1 - eq100
Normal venous blood sample

source_name: venous blood 216

tag: war trauma

tag: chronic stress

tag: replicate


title: genomic DNA from venous blood 208

description:
SV007M.1.1 - eq101
Normal venous blood sample

source_name: venous blood 208

value: Yes

tag: parity

tag: gestational age

tag: replicate id


title: genomic DNA from venous blood 212

description:
SV051M.1 - eq101
Normal venous blood sample

source_name: venous blood 212

tag: gender

tag: tissue

tag: dna methylation age


title: genomic DNA from venous blood 215

description:
SV058M.1.1 - eq101
Normal venous blood sample

source_name: venous blood 215

tag: age

tag: birthweight

tag: age acceleration


title: genomic DNA from venous blood 207

description:
SV007M.1 - eq100
Normal venous blood sample

source_name: venous blood 207

tag: dyad

tag: maternal age

tag: cohort


title: genomic DNA from venous blood 206

description:
C76M.1.2
Normal venous blood sample

source_name: venous blood 206

tag: delivery mode

tag: maternal alcohol

tag: general trauma

value: General Maternity Ward


title: genomic DNA from venous blood 205

description:
C087bb1
Normal venous blood sample

source_name: venous blood 205

tag: sexual trauma

tag: war trauma

tag: chronic stress


title: genomic DNA from venous blood 204

description:
C087M
Normal venous blood sample

source_name: venous blood 204

tag: parity

tag: gestational age

tag: replicate


title: genomic DNA from venous blood 202

description:
C75M.2.1
Normal venous blood sample

source_name: venous blood 202

tag: gender

tag: tissue

tag: replicate id


title: genomic DNA from venous blood 225

description:
SV031b.b.1.1
Normal venous blood sample

source_name: venous blood 225

tag: age

tag: birthweight

tag: dna methylation age


title: genomic DNA from venous blood 201

description:
C081bb.1.1.
Normal venous blood sample

source_name: venous blood 201

tag: dyad

tag: maternal age

tag: age acceleration


title: genomic DNA from venous blood 203

description:
C075bb.1.1.
Normal venous blood sample

source_name: venous blood 203

tag: delivery mode

tag: maternal alcohol

tag: cohort


title: genomic DNA from venous blood 197

description:
C67bb2.1
Normal venous blood sample

source_name: venous blood 197

tag: general trauma

tag: sexual trauma

tag: war trauma


title: genomic DNA from venous blood 200

description:
C81M.2.1
Normal venous blood sample

source_name: venous blood 200

tag: parity

tag: gestational age

tag: chronic stress


title: genomic DNA from venous blood 199

description:
C76bb.1.1
Normal venous blood sample

source_name: venous blood 199

tag: gender

tag: tissue

tag: replicate


title: genomic DNA from venous blood 220

description:
SV019M.2.1 - eq101
Normal venous blood sample

source_name: venous blood 220

tag: age

tag: birthweight

tag: replicate id


title: genomic DNA from venous blood 198

description:
C085M
Normal venous blood sample

source_name: venous blood 198

tag: dyad

tag: maternal age

tag: dna methylation age


title: genomic DNA from venous blood 196

description:
C10M.1.1
Normal venous blood sample

source_name: venous blood 196

tag: delivery mode

tag: maternal alcohol

tag: age acceleration


title: genomic DNA from venous blood 195

description:
C88bb.2.1
Normal venous blood sample

source_name: venous blood 195

tag: general trauma

tag: sexual trauma

tag: cohort


title: genomic DNA from venous blood 214

description:
SV061bb.2.1 - eq101
Normal venous blood sample

source_name: venous blood 214

tag: parity

tag: gestational age

tag: war trauma


title: genomic DNA from venous blood 193

description:
C10bb.1.1
Normal venous blood sample

source_name: venous blood 193

tag: gender

tag: tissue

tag: chronic stress


title: genomic DNA from venous blood 194

description:
C088M
Normal venous blood sample

source_name: venous blood 194

tag: age

tag: birthweight

tag: replicate


title: genomic DNA from venous blood 190

description:
C28bb.1.1
Normal venous blood sample

source_name: venous blood 190

tag: dyad

tag: maternal age

tag: replicate id


title: genomic DNA from venous blood 192

description:
C67M.1.1
Normal venous blood sample

source_name: venous blood 192

tag: delivery mode

tag: maternal alcohol

tag: dna methylation age


title: genomic DNA from venous blood 189

description:
C26M1.1
Normal venous blood sample

source_name: venous blood 189

tag: general trauma

tag: sexual trauma

tag: age acceleration


title: genomic DNA from venous blood 191

description:
C085bb
Normal venous blood sample

source_name: venous blood 191

tag: parity

tag: gestational age

tag: cohort


title: genomic DNA from venous blood 186

description:
C033bb.1.1
Normal venous blood sample

source_name: venous blood 186

tag: gender

tag: tissue

tag: war trauma


title: genomic DNA from venous blood 185

description:
C090M.2.1.
Normal venous blood sample

source_name: venous blood 185

tag: age

tag: birthweight

tag: chronic stress


title: genomic DNA from venous blood 188

description:
C004bb.2.1
Normal venous blood sample

source_name: venous blood 188

tag: dyad

tag: maternal age

tag: replicate


title: genomic DNA from venous blood 187

description:
C54M.1.1
Normal venous blood sample

source_name: venous blood 187

tag: delivery mode

tag: maternal alcohol

tag: replicate id


title: genomic DNA from venous blood 184

description:
C012bb.1.1.TECHREP
Normal venous blood sample

source_name: venous blood 184

tag: general trauma

tag: sexual trauma

tag: dna methylation age


title: genomic DNA from venous blood 182

description:
C79bb2.1
Normal venous blood sample

source_name: venous blood 182

tag: parity

tag: gestational age

tag: age acceleration


title: genomic DNA from venous blood 181

description:
C79M.1.1
Normal venous blood sample

source_name: venous blood 181

tag: gender

tag: tissue

tag: cohort


title: genomic DNA from venous blood 179

description:
C44M.2.1
Normal venous blood sample

source_name: venous blood 179

tag: age

tag: birthweight

tag: war trauma


title: genomic DNA from venous blood 178

description:
C32b.b.1.1
Normal venous blood sample

source_name: venous blood 178

tag: dyad

tag: maternal age

tag: chronic stress


title: genomic DNA from venous blood 183

description:
C17M.1.1
Normal venous blood sample

source_name: venous blood 183

tag: delivery mode

tag: maternal alcohol

tag: replicate


title: genomic DNA from venous blood 175

description:
C032M.1.1.
Normal venous blood sample

source_name: venous blood 175

tag: general trauma

tag: sexual trauma

tag: replicate id


title: genomic DNA from venous blood 176

description:
C44bb1.1
Normal venous blood sample

source_name: venous blood 176

tag: parity

tag: gestational age

tag: dna methylation age


title: genomic DNA from venous blood 173

description:
C19bb.2.1
Normal venous blood sample

source_name: venous blood 173

tag: gender

tag: tissue

tag: age acceleration


title: genomic DNA from venous blood 180

description:
C51b.b.1.1
Normal venous blood sample

source_name: venous blood 180

tag: age

tag: birthweight

tag: cohort


title: genomic DNA from venous blood 172

description:
C070M.1.1.
Normal venous blood sample

source_name: venous blood 172

tag: dyad

tag: maternal age

tag: war trauma


title: genomic DNA from venous blood 171

description:
C92bb.2.1
Normal venous blood sample

source_name: venous blood 171

tag: delivery mode

tag: maternal alcohol

tag: chronic stress


title: genomic DNA from venous blood 170

description:
C083M
Normal venous blood sample

source_name: venous blood 170

tag: general trauma

tag: sexual trauma

tag: replicate


title: genomic DNA from venous blood 169

description:
C083bb
Normal venous blood sample

source_name: venous blood 169

tag: parity

tag: gestational age

tag: replicate id


title: genomic DNA from venous blood 168

description:
C092M.2.1.
Normal venous blood sample

source_name: venous blood 168

tag: gender

tag: tissue

tag: dna methylation age


title: genomic DNA from venous blood 167

description:
C70bb.1.1
Normal venous blood sample

source_name: venous blood 167

tag: age

tag: birthweight

tag: age acceleration


title: genomic DNA from venous blood 166

description:
C047bb.2.1.b
Normal venous blood sample

source_name: venous blood 166

tag: dyad

tag: maternal age

tag: cohort


title: genomic DNA from venous blood 163

description:
C098bb.1.1.
Normal venous blood sample

source_name: venous blood 163

tag: delivery mode

tag: maternal alcohol

tag: war trauma


title: genomic DNA from venous blood 165

description:
C047M
Normal venous blood sample

source_name: venous blood 165

tag: general trauma

tag: sexual trauma

tag: chronic stress


title: genomic DNA from venous blood 161

description:
C086bb
Normal venous blood sample

source_name: venous blood 161

tag: parity

tag: gestational age

tag: replicate


title: genomic DNA from venous blood 160

description:
C086M
Normal venous blood sample

source_name: venous blood 160

tag: gender

tag: tissue

tag: replicate id


title: genomic DNA from venous blood 159

description:
C21bb.1.1
Normal venous blood sample

source_name: venous blood 159

tag: age

tag: birthweight

tag: dna methylation age


title: genomic DNA from venous blood 162

description:
C46M.2.1
Normal venous blood sample

source_name: venous blood 162

tag: dyad

tag: maternal age

tag: age acceleration


title: genomic DNA from venous blood 158

description:
C21M.1.1
Normal venous blood sample

source_name: venous blood 158

tag: delivery mode

tag: maternal alcohol

tag: cohort


title: genomic DNA from venous blood 157

description:
C046bb
Normal venous blood sample

source_name: venous blood 157

tag: general trauma

tag: sexual trauma

tag: war trauma


title: genomic DNA from venous blood 156

description:
C101bb.1.1
Normal venous blood sample

source_name: venous blood 156

tag: parity

tag: gestational age

tag: chronic stress


title: genomic DNA from venous blood 153

description:
C39M.1.1
Normal venous blood sample

source_name: venous blood 153

tag: gender

tag: tissue

tag: replicate


title: genomic DNA from venous blood 177

description:
C51M.1.1
Normal venous blood sample

source_name: venous blood 177

tag: age

tag: birthweight

tag: replicate id


title: genomic DNA from venous blood 154

description:
C39bb2.1a
Normal venous blood sample

source_name: venous blood 154

tag: dyad

tag: maternal age

tag: dna methylation age


title: genomic DNA from venous blood 174

description:
C19M.1.2
Normal venous blood sample

source_name: venous blood 174

tag: delivery mode

tag: maternal alcohol

tag: age acceleration


title: genomic DNA from venous blood 150

description:
C18bb.1.1
Normal venous blood sample

source_name: venous blood 150

tag: general trauma

tag: sexual trauma

tag: cohort


title: genomic DNA from venous blood 149

description:
C66M.1.1
Normal venous blood sample

source_name: venous blood 149

tag: parity

tag: gestational age

tag: war trauma


title: genomic DNA from venous blood 151

description:
C101M.1.1
Normal venous blood sample

source_name: venous blood 151

tag: gender

tag: tissue

tag: chronic stress


title: genomic DNA from venous blood 148

description:
C61M.1.1
Normal venous blood sample

source_name: venous blood 148

tag: age

tag: birthweight

tag: replicate


title: genomic DNA from venous blood 145

description:
C020bb.1.1.TECHREP
Normal venous blood sample

source_name: venous blood 145

tag: dyad

tag: maternal age

tag: replicate id


title: genomic DNA from venous blood 146

description:
C062M.1.1.TECHREP
Normal venous blood sample

source_name: venous blood 146

tag: delivery mode

tag: maternal alcohol

tag: dna methylation age


title: genomic DNA from venous blood 147

description:
C2bb.1.1
Normal venous blood sample

source_name: venous blood 147

tag: general trauma

tag: sexual trauma

tag: age acceleration


title: genomic DNA from venous blood 143

description:
C62bb.1.1
Normal venous blood sample

source_name: venous blood 143

tag: parity

tag: gestational age

tag: cohort


title: genomic DNA from venous blood 144

description:
C20M.1.1
Normal venous blood sample

source_name: venous blood 144

tag: gender

tag: tissue

tag: war trauma


title: genomic DNA from venous blood 164

description:
C98M.2.1
Normal venous blood sample

source_name: venous blood 164

tag: age

tag: birthweight

tag: chronic stress


title: genomic DNA from venous blood 141

description:
C061bb.1.1.
Normal venous blood sample

source_name: venous blood 141

tag: dyad

tag: maternal age

tag: replicate


title: genomic DNA from venous blood 140

description:
C58bb.1.1
Normal venous blood sample

source_name: venous blood 140

tag: delivery mode

tag: maternal alcohol

tag: replicate id


title: genomic DNA from venous blood 142

description:
C001M.1.1.TECHREP
Normal venous blood sample

source_name: venous blood 142

tag: general trauma

tag: sexual trauma

tag: dna methylation age


title: genomic DNA from venous blood 138

description:
C74bb.1.1
Normal venous blood sample

source_name: venous blood 138

tag: parity

tag: gestational age

tag: age acceleration


title: genomic DNA from venous blood 136

description:
C006bb.1.2.
Normal venous blood sample

source_name: venous blood 136

tag: gender

tag: tissue

tag: cohort


title: genomic DNA from venous blood 135

description:
C48M.2.1
Normal venous blood sample

source_name: venous blood 135

tag: age

tag: birthweight

tag: war trauma


title: genomic DNA from venous blood 155

description:
C18M.1.2
Normal venous blood sample

source_name: venous blood 155

tag: dyad

tag: maternal age

tag: chronic stress


title: genomic DNA from venous blood 134

description:
C048bb.1.2.
Normal venous blood sample

source_name: venous blood 134

tag: delivery mode

tag: maternal alcohol

tag: replicate


title: genomic DNA from venous blood 131

description:
C77bb.1.1
Normal venous blood sample

source_name: venous blood 131

tag: general trauma

tag: sexual trauma

tag: replicate id


title: genomic DNA from venous blood 130

description:
C77M.1.2
Normal venous blood sample

source_name: venous blood 130

tag: parity

tag: gestational age

tag: dna methylation age


title: genomic DNA from venous blood 132

description:
C50M.1.1
Normal venous blood sample

source_name: venous blood 132

tag: gender

tag: tissue

tag: age acceleration


title: genomic DNA from venous blood 125

description:
C50b.b.1.1
Normal venous blood sample

source_name: venous blood 125

tag: age

tag: birthweight

tag: cohort


title: genomic DNA from venous blood 127

description:
C5bb.1.2
Normal venous blood sample

source_name: venous blood 127

tag: dyad

tag: maternal age

tag: war trauma


title: genomic DNA from venous blood 128

description:
C5M.2.1
Normal venous blood sample

source_name: venous blood 128

tag: delivery mode

tag: maternal alcohol

tag: chronic stress


title: genomic DNA from venous blood 129

description:
C99bb.2.1
Normal venous blood sample

source_name: venous blood 129

tag: general trauma

tag: sexual trauma

tag: replicate


title: genomic DNA from venous blood 152

description:
C66bb2.1
Normal venous blood sample

source_name: venous blood 152

tag: parity

tag: gestational age

tag: replicate id


title: genomic DNA from venous blood 124

description:
C012bb.1.1.
Normal venous blood sample

source_name: venous blood 124

tag: gender

tag: tissue

tag: dna methylation age


title: genomic DNA from venous blood 122

description:
C24bb.1.1
Normal venous blood sample

source_name: venous blood 122

tag: age

tag: birthweight

tag: age acceleration


title: genomic DNA from venous blood 123

description:
C094M.1.2.
Normal venous blood sample

source_name: venous blood 123

tag: dyad

tag: maternal age

tag: cohort


title: genomic DNA from venous blood 126

description:
C99M.2.1
Normal venous blood sample

source_name: venous blood 126

tag: delivery mode

tag: maternal alcohol

tag: war trauma


title: genomic DNA from venous blood 120

description:
C094bb.1.1.
Normal venous blood sample

source_name: venous blood 120

tag: general trauma

tag: sexual trauma

tag: chronic stress


title: genomic DNA from venous blood 119

description:
C029M.1.1.
Normal venous blood sample

source_name: venous blood 119

tag: parity

tag: gestational age

tag: replicate


title: genomic DNA from venous blood 121

description:
C24M.1.1
Normal venous blood sample

source_name: venous blood 121

tag: gender

tag: tissue

tag: replicate id


title: genomic DNA from venous blood 137

description:
C6M.2.1
Normal venous blood sample

source_name: venous blood 137

tag: age

tag: birthweight

tag: dna methylation age


title: genomic DNA from venous blood 116

description:
C69bb.1.1
Normal venous blood sample

source_name: venous blood 116

tag: dyad

tag: maternal age

tag: age acceleration


title: genomic DNA from venous blood 113

description:
C38M1.1
Normal venous blood sample

source_name: venous blood 113

tag: delivery mode

tag: maternal alcohol

tag: cohort


title: genomic DNA from venous blood 115

description:
C52M.1.1
Normal venous blood sample

source_name: venous blood 115

tag: general trauma

tag: sexual trauma

tag: war trauma


title: genomic DNA from venous blood 117

description:
C012M.1.2.
Normal venous blood sample

source_name: venous blood 117

tag: parity

tag: gestational age

tag: chronic stress


title: genomic DNA from venous blood 133

description:
C74M.1.1
Normal venous blood sample

source_name: venous blood 133

tag: gender

tag: tissue

tag: replicate


title: genomic DNA from venous blood 111

description:
C084M
Normal venous blood sample

source_name: venous blood 111

tag: age

tag: birthweight

tag: replicate id


title: genomic DNA from venous blood 109

description:
C69M.1.1
Normal venous blood sample

source_name: venous blood 109

tag: dyad

tag: maternal age

tag: dna methylation age


title: genomic DNA from venous blood 110

description:
C52b.b.1.1
Normal venous blood sample

source_name: venous blood 110

tag: delivery mode

tag: maternal alcohol

tag: age acceleration


title: genomic DNA from venous blood 139

description:
C58M.1.2
Normal venous blood sample

source_name: venous blood 139

tag: general trauma

tag: sexual trauma

tag: cohort


title: genomic DNA from venous blood 108

description:
C97M.2.1
Normal venous blood sample

source_name: venous blood 108

tag: parity

tag: gestational age

tag: war trauma


title: genomic DNA from venous blood 107

description:
C031bb.1.1.
Normal venous blood sample

source_name: venous blood 107

tag: gender

tag: tissue

tag: chronic stress


title: genomic DNA from venous blood 114

description:
C38bb1.1
Normal venous blood sample

source_name: venous blood 114

tag: age

tag: birthweight

tag: replicate


title: genomic DNA from venous blood 106

description:
C29M.2.1
Normal venous blood sample

source_name: venous blood 106

tag: dyad

tag: maternal age

tag: replicate id


title: genomic DNA from venous blood 105

description:
C7bb2.1
Normal venous blood sample

source_name: venous blood 105

tag: delivery mode

tag: maternal alcohol

tag: dna methylation age


title: genomic DNA from venous blood 103

description:
C68bb.1.1
Normal venous blood sample

source_name: venous blood 103

tag: general trauma

tag: sexual trauma

tag: age acceleration


title: genomic DNA from venous blood 100

description:
C71M.1.1
Normal venous blood sample

source_name: venous blood 100

tag: parity

tag: gestational age

tag: cohort


title: genomic DNA from venous blood 99

description:
C100bb
Normal venous blood sample

source_name: venous blood 99

tag: gender

tag: tissue

tag: war trauma


title: genomic DNA from venous blood 118

description:
C29bb.1.1
Normal venous blood sample

source_name: venous blood 118

tag: age

tag: birthweight

tag: chronic stress


title: genomic DNA from venous blood 102

description:
C30M.1.1
Normal venous blood sample

source_name: venous blood 102

tag: dyad

tag: maternal age

tag: replicate


title: genomic DNA from venous blood 98

description:
C64bb.1.1
Normal venous blood sample

source_name: venous blood 98

tag: delivery mode

tag: maternal alcohol

tag: replicate id


title: genomic DNA from venous blood 96

description:
C71bb.1.1
Normal venous blood sample

source_name: venous blood 96

tag: general trauma

tag: sexual trauma

tag: dna methylation age


title: genomic DNA from venous blood 92

description:
C063M.1.1.
Normal venous blood sample

source_name: venous blood 92

tag: parity

tag: gestational age

tag: age acceleration


title: genomic DNA from venous blood 112

description:
C084bb
Normal venous blood sample

source_name: venous blood 112

tag: gender

tag: tissue

tag: cohort


title: genomic DNA from venous blood 104

description:
C78M.1.1
Normal venous blood sample

source_name: venous blood 104

tag: age

tag: birthweight

tag: war trauma


title: genomic DNA from venous blood 97

description:
C064M.1.1.
Normal venous blood sample

source_name: venous blood 97

tag: dyad

tag: maternal age

tag: chronic stress


title: genomic DNA from venous blood 95

description:
C100M.1.1.
Normal venous blood sample

source_name: venous blood 95

tag: delivery mode

tag: maternal alcohol

tag: replicate


title: genomic DNA from venous blood 93

description:
C023bb.1.1.
Normal venous blood sample

source_name: venous blood 93

tag: general trauma

tag: sexual trauma

tag: replicate id


title: genomic DNA from venous blood 94

description:
C040M.1.1.
Normal venous blood sample

source_name: venous blood 94

tag: parity

tag: gestational age

tag: dna methylation age


title: genomic DNA from venous blood 91

description:
C40bb.2.1
Normal venous blood sample

source_name: venous blood 91

tag: gender

tag: tissue

tag: age acceleration


title: genomic DNA from venous blood 89

description:
C63bb.1.1
Normal venous blood sample

source_name: venous blood 89

tag: age

tag: birthweight

tag: cohort


title: genomic DNA from venous blood 88

description:
C23M.2.1
Normal venous blood sample

source_name: venous blood 88

tag: dyad

tag: maternal age

tag: war trauma


title: genomic DNA from venous blood 86

description:
C27bb1.1
Normal venous blood sample

source_name: venous blood 86

tag: delivery mode

tag: maternal alcohol

tag: chronic stress


title: genomic DNA from venous blood 90

description:
C93M.2.1
Normal venous blood sample

source_name: venous blood 90

tag: general trauma

tag: sexual trauma

tag: replicate


title: genomic DNA from venous blood 85

description:
C41M.2.1
Normal venous blood sample

source_name: venous blood 85

tag: parity

tag: gestational age

tag: replicate id


title: genomic DNA from venous blood 83

description:
C15M.2.1
Normal venous blood sample

source_name: venous blood 83

tag: gender

tag: tissue

tag: dna methylation age


title: genomic DNA from venous blood 84

description:
C96bb.2.1
Normal venous blood sample

source_name: venous blood 84

tag: age

tag: birthweight

tag: age acceleration


title: genomic DNA from venous blood 81

description:
C082M
Normal venous blood sample

source_name: venous blood 81

tag: dyad

tag: maternal age

tag: cohort


title: genomic DNA from venous blood 80

description:
C15bb.2.1
Normal venous blood sample

source_name: venous blood 80

tag: delivery mode

tag: maternal alcohol

tag: war trauma


title: genomic DNA from venous blood 79

description:
C034M.1.1.
Normal venous blood sample

source_name: venous blood 79

tag: general trauma

tag: sexual trauma

tag: chronic stress


title: genomic DNA from venous blood 101

description:
C55bb.1.1
Normal venous blood sample

source_name: venous blood 101

tag: parity

tag: gestational age

tag: replicate


title: genomic DNA from venous blood 78

description:
C103M.1.1.
Normal venous blood sample

source_name: venous blood 78

tag: gender

tag: tissue

tag: replicate id


title: genomic DNA from venous blood 87

description:
C093bb.2.1.
Normal venous blood sample

source_name: venous blood 87

tag: age

tag: birthweight

tag: dna methylation age


title: genomic DNA from venous blood 73

description:
C9bb.1.1
Normal venous blood sample

source_name: venous blood 73

tag: dyad

tag: maternal age

tag: age acceleration


title: genomic DNA from venous blood 62

description:
C95M.2.1
Normal venous blood sample

source_name: venous blood 62

tag: delivery mode

tag: maternal alcohol

tag: cohort


title: genomic DNA from venous blood 67

description:
C35M1.1
Normal venous blood sample

source_name: venous blood 67

tag: general trauma

tag: sexual trauma

tag: war trauma


title: genomic DNA from venous blood 75

description:
C56bb.1.1
Normal venous blood sample

source_name: venous blood 75

tag: parity

tag: gestational age

tag: chronic stress


title: genomic DNA from venous blood 68

description:
C11.bb.2.1
Normal venous blood sample

source_name: venous blood 68

tag: gender

tag: tissue

tag: replicate


title: genomic DNA from venous blood 60

description:
C42M.1.1
Normal venous blood sample

source_name: venous blood 60

tag: age

tag: birthweight

tag: replicate id


title: genomic DNA from venous blood 72

description:
C9M.1.1
Normal venous blood sample

source_name: venous blood 72

tag: dyad

tag: maternal age

tag: dna methylation age


title: genomic DNA from venous blood 74

description:
C089M.1.1.
Normal venous blood sample

source_name: venous blood 74

tag: delivery mode

tag: maternal alcohol

tag: age acceleration


title: genomic DNA from venous blood 69

description:
C22M1.1
Normal venous blood sample

source_name: venous blood 69

tag: general trauma

tag: sexual trauma

tag: cohort


title: genomic DNA from venous blood 71

description:
C089bb.1.1.
Normal venous blood sample

source_name: venous blood 71

tag: parity

tag: gestational age

tag: war trauma


title: genomic DNA from venous blood 70

description:
C35bb1.1
Normal venous blood sample

source_name: venous blood 70

tag: gender

tag: tissue

tag: chronic stress


title: genomic DNA from venous blood 82

description:
C57bb.1.1
Normal venous blood sample

source_name: venous blood 82

tag: age

tag: birthweight

tag: replicate


title: genomic DNA from venous blood 76

description:
C056M.1.1.
Normal venous blood sample

source_name: venous blood 76

tag: dyad

tag: maternal age

tag: replicate id


title: genomic DNA from venous blood 57

description:
C42bb.1.1
Normal venous blood sample

source_name: venous blood 57

tag: delivery mode

tag: maternal alcohol

tag: dna methylation age


title: genomic DNA from venous blood 54

description:
C091bb.2.1.
Normal venous blood sample

source_name: venous blood 54

tag: general trauma

tag: sexual trauma

tag: age acceleration


title: genomic DNA from venous blood 56

description:
C3bb.1.1
Normal venous blood sample

source_name: venous blood 56

tag: parity

tag: gestational age

tag: cohort


title: genomic DNA from venous blood 59

description:
C43bb.1.1
Normal venous blood sample

source_name: venous blood 59

tag: gender

tag: tissue

tag: war trauma


title: genomic DNA from venous blood 58

description:
C43M.2.1
Normal venous blood sample

source_name: venous blood 58

tag: age

tag: birthweight

tag: chronic stress


title: genomic DNA from venous blood 52

description:
C59bb.1.1
Normal venous blood sample

source_name: venous blood 52

tag: dyad

tag: maternal age

tag: replicate


title: genomic DNA from venous blood 51

description:
C8M1.1
Normal venous blood sample

source_name: venous blood 51

tag: delivery mode

tag: maternal alcohol

tag: replicate id


title: genomic DNA from venous blood 77

description:
C103bb.2.1.
Normal venous blood sample

source_name: venous blood 77

tag: general trauma

tag: sexual trauma

tag: dna methylation age


title: genomic DNA from venous blood 50

description:
C008bb.1.1
Normal venous blood sample

source_name: venous blood 50

tag: parity

tag: gestational age

tag: age acceleration


title: genomic DNA from venous blood 55

description:
C59M.1.1
Normal venous blood sample

source_name: venous blood 55

tag: gender

tag: tissue

tag: cohort


title: genomic DNA from venous blood 53

description:
C003M.1.1
Normal venous blood sample

source_name: venous blood 53

tag: age

tag: birthweight

tag: war trauma


title: genomic DNA from venous blood 66

description:
C22bb1.1
Normal venous blood sample

source_name: venous blood 66

tag: dyad

tag: maternal age

tag: chronic stress


title: genomic DNA from venous blood 63

description:
C014M
Normal venous blood sample

source_name: venous blood 63

tag: delivery mode

tag: maternal alcohol

tag: replicate


title: genomic DNA from venous blood 65

description:
C11M.1.1
Normal venous blood sample

source_name: venous blood 65

tag: general trauma

tag: sexual trauma

tag: replicate id


title: genomic DNA from venous blood 64

description:
C049bb.1.2.
Normal venous blood sample

source_name: venous blood 64

tag: parity

tag: gestational age

tag: dna methylation age


title: genomic DNA from venous blood 61

description:
C95bb.2.1
Normal venous blood sample

source_name: venous blood 61

tag: gender

tag: tissue

tag: age acceleration


title: genomic DNA from venous blood 48

description:
C37M1.1
Normal venous blood sample

source_name: venous blood 48

tag: age

tag: birthweight

tag: cohort


title: genomic DNA from venous blood 49

description:
C091M.1.1.
Normal venous blood sample

source_name: venous blood 49

tag: dyad

tag: maternal age

tag: war trauma


title: genomic DNA from venous blood 43

description:
C37bb1.1
Normal venous blood sample

source_name: venous blood 43

tag: delivery mode

tag: maternal alcohol

tag: chronic stress


title: genomic DNA from venous blood 47

description:
C102bb.2.1.
Normal venous blood sample

source_name: venous blood 47

tag: general trauma

tag: sexual trauma

tag: replicate


title: genomic DNA from venous blood 46

description:
C65M.1.1
Normal venous blood sample

source_name: venous blood 46

tag: parity

tag: gestational age

tag: replicate id


title: genomic DNA from venous blood 41

description:
C053bb.1.1.
Normal venous blood sample

source_name: venous blood 41

tag: gender

tag: tissue

tag: dna methylation age


title: genomic DNA from venous blood 42

description:
C53M.2.1
Normal venous blood sample

source_name: venous blood 42

tag: age

tag: birthweight

tag: age acceleration


title: genomic DNA from venous blood 44

description:
C102M.2.1.
Normal venous blood sample

source_name: venous blood 44

tag: dyad

tag: maternal age

tag: cohort


title: genomic DNA from venous blood 34

description:
C96M.2.1
Normal venous blood sample

source_name: venous blood 34

tag: delivery mode

tag: maternal alcohol

tag: war trauma


title: genomic DNA from venous blood 40

description:
C97bb.2.1
Normal venous blood sample

source_name: venous blood 40

tag: general trauma

tag: sexual trauma

tag: chronic stress


title: genomic DNA from venous blood 32

description:
C62M.1.1
Normal venous blood sample

source_name: venous blood 32

tag: parity

tag: gestational age

tag: replicate


title: genomic DNA from venous blood 33

description:
C68M.2.1
Normal venous blood sample

source_name: venous blood 33

tag: gender

tag: tissue

tag: replicate id


title: genomic DNA from venous blood 39

description:
C55M.1.1
Normal venous blood sample

source_name: venous blood 39

tag: age

tag: birthweight

tag: dna methylation age


title: genomic DNA from venous blood 36

description:
C80M2.1
Normal venous blood sample

source_name: venous blood 36

tag: dyad

tag: maternal age

tag: age acceleration


title: genomic DNA from venous blood 37

description:
C82b.b.1.1
Normal venous blood sample

source_name: venous blood 37

tag: delivery mode

tag: maternal alcohol

tag: cohort


title: genomic DNA from venous blood 30

description:
C91bb.1.2
Normal venous blood sample

source_name: venous blood 30

tag: general trauma

tag: sexual trauma

tag: war trauma


title: genomic DNA from venous blood 29

description:
C54bb.1.1
Normal venous blood sample

source_name: venous blood 29

tag: parity

tag: gestational age

tag: chronic stress


title: genomic DNA from venous blood 31

description:
C57M.2.1
Normal venous blood sample

source_name: venous blood 31

tag: gender

tag: tissue

tag: replicate


title: genomic DNA from venous blood 26

description:
C17bb.2.1
Normal venous blood sample

source_name: venous blood 26

tag: age

tag: birthweight

tag: replicate id


title: genomic DNA from venous blood 28

description:
C31M.2.1
Normal venous blood sample

source_name: venous blood 28

tag: dyad

tag: maternal age

tag: dna methylation age


title: genomic DNA from venous blood 24

description:
C28M.2.1
Normal venous blood sample

source_name: venous blood 24

tag: delivery mode

tag: maternal alcohol

tag: age acceleration


title: genomic DNA from venous blood 45

description:
C65bb.1.1
Normal venous blood sample

source_name: venous blood 45

tag: general trauma

tag: sexual trauma

tag: cohort


title: genomic DNA from venous blood 22

description:
C26bb1.1
Normal venous blood sample

source_name: venous blood 22

tag: parity

tag: gestational age

tag: war trauma


title: genomic DNA from venous blood 23

description:
C27M.2.1
Normal venous blood sample

source_name: venous blood 23

tag: gender

tag: tissue

tag: chronic stress


title: genomic DNA from venous blood 20

description:
C14b.b.1.1
Normal venous blood sample

source_name: venous blood 20

tag: age

tag: birthweight

tag: replicate


title: genomic DNA from venous blood 21

description:
C41bb1.1
Normal venous blood sample

source_name: venous blood 21

tag: dyad

tag: maternal age

tag: replicate id


title: genomic DNA from venous blood 35

description:
C80bb2.1
Normal venous blood sample

source_name: venous blood 35

tag: delivery mode

tag: maternal alcohol

tag: dna methylation age


title: genomic DNA from venous blood 19

description:
C13M.1.1
Normal venous blood sample

source_name: venous blood 19

tag: general trauma

tag: sexual trauma

tag: age acceleration


title: genomic DNA from venous blood 38

description:
C90bb.2.1
Normal venous blood sample

source_name: venous blood 38

tag: parity

tag: gestational age

tag: cohort


title: genomic DNA from venous blood 17

description:
C4M.2.1
Normal venous blood sample

source_name: venous blood 17

tag: gender

tag: tissue

tag: war trauma


title: genomic DNA from venous blood 16

description:
C33M.1.1
Normal venous blood sample

source_name: venous blood 16

tag: age

tag: birthweight

tag: chronic stress


title: genomic DNA from venous blood 14

description:
C20bb.1.1_250
Normal venous blood sample

source_name: venous blood 14

tag: dyad

tag: maternal age

tag: replicate


title: genomic DNA from venous blood 18

description:
C13bb.2.1
Normal venous blood sample

source_name: venous blood 18

tag: delivery mode

tag: maternal alcohol

tag: replicate id


title: genomic DNA from venous blood 13

description:
C2M.1.1_250
Normal venous blood sample

source_name: venous blood 13

tag: general trauma

tag: sexual trauma

tag: dna methylation age


title: genomic DNA from venous blood 12

description:
C34bb.1.1_clean
Normal venous blood sample

source_name: venous blood 12

tag: parity

tag: gestational age

tag: age acceleration


title: genomic DNA from venous blood 6

description:
C49M.1.2
Normal venous blood sample

source_name: venous blood 6

tag: gender

tag: tissue

tag: cohort


title: genomic DNA from venous blood 9

description:
C49M.1.2_clean
Normal venous blood sample

source_name: venous blood 9

tag: age

tag: birthweight

tag: war trauma


title: genomic DNA from venous blood 10

description:
C49M.1.2_400
Normal venous blood sample

source_name: venous blood 10

tag: dyad

tag: maternal age

tag: chronic stress


title: genomic DNA from venous blood 8

description:
C89M2.1
Normal venous blood sample

source_name: venous blood 8

tag: delivery mode

tag: maternal alcohol

tag: replicate


title: genomic DNA from venous blood 7

description:
C89bb.2.1
Normal venous blood sample

source_name: venous blood 7

tag: general trauma

tag: sexual trauma

tag: replicate id


title: genomic DNA from venous blood 5

description:
C49bb.2.1
Normal venous blood sample

source_name: venous blood 5

tag: parity

tag: gestational age

tag: dna methylation age


title: genomic DNA from venous blood 3

description:
C25b.b.1.1
Normal venous blood sample

source_name: venous blood 3

tag: gender

tag: tissue

tag: age acceleration


title: genomic DNA from venous blood 11

description:
C7M.1.1_clean
Normal venous blood sample

source_name: venous blood 11

tag: age

tag: birthweight

tag: cohort


title: genomic DNA from venous blood 2

description:
C1M.1.1
Normal venous blood sample

source_name: venous blood 2

tag: dyad

tag: maternal age

tag: war trauma


title: genomic DNA from venous blood 27

description:
C6.bb.2.1a
Normal venous blood sample

source_name: venous blood 27

tag: delivery mode

tag: maternal alcohol

tag: chronic stress


title: genomic DNA from venous blood 1

description:
C1bb.1.1
Normal venous blood sample

source_name: venous blood 1

tag: general trauma

tag: sexual trauma

tag: replicate


title: genomic DNA from venous blood 4

description:
C25M1.1
Normal venous blood sample

source_name: venous blood 4

tag: parity

tag: gestational age

tag: replicate id


title: genomic DNA from venous blood 25

description:
C30bb.1.1
Normal venous blood sample

source_name: venous blood 25

tag: gender

tag: tissue

tag: dna methylation age


title: TnpB3_NT_ChIP-seq_paired_raw_rep1

status: Public on Jun 01 2023

type: SRA

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

library_source: genomic

data_processing:
ChIP-seq single- and paired-end reads were trimmed and mapped to an E. coli BL21(DE3) reference genome (GenBank accession CP001509.3) using fastp (Chen et al., 2018) and Bowtie2 (Langmead et al., 2012) with default parameters, respectively. Two genomic lacZ/lacI regions and flanking regions, which are partially identical to plasmid-encoded sequences, were masked in all alignments (genomic coordinates 335,600-337,101 and 748,601-750,390). In the ChIP-seq analysis of Cas9 and Cas12a, another plasmid-like genomic sequence was masked (genomic coordinates: 4,121,275-4,121,400). Mapped reads were sorted and indexed using the SAMtools software package (Li et al., 2009) (samtools sort and samtools index commands, respectively). For all data sets, the command samtools view was used to eliminate multi-mapping reads with a MAPQ-score <10 (-bq 10 option). Alignments were normalised by RPKM (Reads Per Kilobase per Million mapped reads) and converted to 1 bp-bin bigwig files using the deepTools2 (Ramirez et al., 2016) command bamCoverage (--normalizeUsing RPKM -bs 1 parameters). After normalization, genome-mapping reads were visualised in IGV (Robinson et al., 2011). The Bedtools software package (bedtools makewindows -w 1000 and bedtools map -o max) (Quinlan et al., 2010) and IGV were used to generate all genome-wide views. Maximum read coverage values were plotted in 1-kb bins across the genome, as described previously (Cooper et al., 2018). Peaks were called on pre-normalised alignments using MACS3 (Zhang et al., 2008), with the parameters -g 4500000 --nomodel --extsize 400 -q 0.05 -B, with respect to non-immunoprecipitated control samples of TnpB and Cas9 (-n option). The peak summit coordinates in the MACS3 output  summits.bed file were extended to encompass a 200-bp window using the following Bedtools command: bedtools slop -l 100 -r 99. Sequence motifs were identified using MEME ChIP (Bailey et al., 2009) with default parameters.
Assembly: CP001509.3
Supplementary files format and content: bigWig (.bw) files represent normalized files, generated using deepTools2 bamCoverage
Supplementary files format and content: .bed files were generated using MACS3 and represent peak calls and summit enrichment values
Supplementary files format and content: .xlsx file contains number of raw and uniquely mapped reads

organism: Escherichia coli BL21(DE3)

source_name: Solid cell culture

growth_protocol: E. coli transformations were performed using a single plasmid encoding a catalytically inactive effector and ωRNA or gRNA. The E. coli growth protocol generally followed the ChIP-seq protocol that was previously described (Hoffmann, Kim, Beh et al. 2022). In brief, after 16 h incubation at 37 °C on LB-agar plates with antibiotics but no IPTG induction, colonies were scraped and resuspended in 1 ml of fresh LB. The optical density at 600 nm was measured, and approximately 4.0 × 10^8 cells (equivalent to 1 ml of OD600 = 0.25) were spread onto two LB-agar plates containing antibiotics and supplemented with 0.05 mM IPTG. We chose to culture cells on solid LB-agar to reduce any competition-induced effects of culturing in liquid LB media. Plates were incubated at 37°C for 24 h, during which time a bacterial lawn formed.

extract_protocol:
IPTG-induced E. coli cells were scraped and spread onto the wall of a 50 ml conical tube in a thin layer, to allow for efficient resuspension and crosslinking in the next step. Crosslinking and immunoprecipitation generally followed our previous ChIP-seq study (Hoffmann, Kim, Beh et al., 2022), based on previously established protocols (Bonocora and Wade, 2015; Davis et al. 2011). 1 ml of 37% formaldehyde (Fisher Scientific) was added to a separate tube containing 40 ml of LB medium (~1% final concentration), and the solution was mixed immediately by inverting. This solution was added to the conical tube containing the scraped cells, and the cells were fully resuspended in the LB-formaldehyde solution by vigorous vortexing at room temperature. Crosslinking was performed by gently shaking at room temperature for 20 min. To stop crosslinking, 4.6 ml of 2.5 M glycine (~0.25 M final concentration) were added, followed by 10 min incubation with gentle shaking. Cells were pelleted at 4 °C by spinning at 4,000 x g for 8 min. The following steps were performed on ice, using buffers that had been sterile-filtered through a 0.22 µm filter. The supernatant was discarded and pellets were fully resuspended in 40 ml TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl) by vortexing. After another spin at 4,000 x g for 8 min at 4°C, the supernatant was removed and the pellet again resuspended in 40 ml TBS buffer. Next, the OD600 was measured for a 1:1 mixture of the cell suspension and fresh TBS buffer, and a standardised volume equivalent to 40 ml of OD600 = 0.6 was aliquoted into new 50 ml conical tubes. A final 8 min spin at 4,000 x g and 4 °C was performed, cells were pelleted, and the supernatant was discarded. Residual liquid was removed by briefly inverting the tube, and cell pellets were flash frozen using liquid nitrogen and stored at -80 °C or kept on ice for the subsequent steps. Bovine serum albumin (GoldBio) was dissolved in 1X PBS buffer (Gibco) and sterile-filtered to generate a 5 mg/ml BSA solution. For each sample, 25 µl of Dynabeads Protein G (Thermo Fisher) slurry (hereafter referred to as ‘beads’ or ‘magnetic beads’) were prepared for immunoprecipitation. Beads from up to 250 µl of the initial slurry were processed together in a single tube, and washes were performed at room temperature, as follows: The slurry was transferred to a 1.5 ml tube and placed onto a magnetic rack until the beads had fully settled. The supernatant was removed carefully, 1 ml BSA solution was added, and beads were fully resuspended by vortexing, followed by rotating for 30 seconds. This was repeated for three more washes. Finally, beads were resuspended in 25 µl (× n samples) of BSA solution, followed by addition of 4 µl (× n samples) of monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich). The suspension was moved to 4 °C and rotated for >3 h to conjugate antibodies to magnetic beads. While conjugation was proceeding, crosslinked cell pellets were thawed on ice, resuspended in FA Lysis Buffer 150 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 150 mM NaCl) with protease inhibitor cocktail (Sigma-Aldrich) and transferred to a 1 ml milliTUBE AFA Fiber (Covaris). Samples were sonicated on a M220 Focused-ultrasonicator (Covaris) with the following SonoLab 7.2 settings: min. temp. 4°C, set point 6 °C, max. temp. 8°C, peak power 75.0, duty factor 10, cycles/bursts 200, 17.5 min sonication time. After sonication, samples were cleared of cell debris by centrifugation at 20,000 x g and 4 °C for 20 min. The pellet was discarded, and the supernatant (~1 ml) was transferred into a fresh tube and kept on ice for immunoprecipitation. For non-inmunoprecipitated input control samples, 10 µl (~1%) of the sheared cleared lysate were transferred into a separate 1.5 ml tube, flash-frozen in liquid nitrogen, and stored at -80 °C. After >3 h, the conjugation mixture of magnetic beads and antibody was washed four times as described above, but at 4 °C. Next, the beads were resuspended in 30 µl (× n samples) FA Lysis Buffer 150 with protease inhibitor, and 31 µl of resuspended antibody-conjugated beads were mixed with each sample of sheared cell lysate. Samples were rotated overnight for 12–16 h at 4 °C for immunoprecipitation of FLAG-tagged proteins. The next day, tubes containing beads were placed on a magnetic rack and the supernatant was discarded. Then, six bead washes were performed at room temperature as follows, using 1 ml of each buffer followed by sample rotation for 1.5 min: (1) Two washes with FA Lysis Buffer 150 (without protease inhibitor); (2) one wash with FA Lysis Buffer 500 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); (3) one wash with ChIP Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); and (4) two washes with TE Buffer 10/1 (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were then placed on a magnetic rack, the supernatant was removed, and beads were resuspended in 200 µl of ChIP Elution Buffer (1% (w/v) SDS, 0.1 M NaHCO3), freshly made on the day of the washes. To release protein-DNA complexes from beads, the suspensions were incubated at 65 °C for 1.25 h with gentle vortexing every 15 min to resuspend settled beads. During this incubation, the non-immunoprecipitated input samples were thawed, and 190 µl of ChIP Elution Buffer was added, followed by the addition of 10 µl of 5 M NaCl. After the 1.25 h incubation of the immunoprecipitated samples was complete, tubes were placed back onto a magnetic rack, and the supernatant containing eluted protein-DNA complexes was transferred to a new tube. 9.75 µl of 5 M NaCl were added to ~195 µl of eluate, and samples (both immunoprecipitated and non-immunoprecipitated controls) were incubated at 65°C overnight (without shaking) to reverse-crosslink proteins and DNA. The next day, samples were mixed with 1 µl of 10 mg/ml RNase A (Thermo Fisher) and incubated for 1 h at 37 °C, followed by addition of 2.8 µl of 20 mg/ml Proteinase K (Fisher Scientific) and 1 h incubation at 55 °C. After the addition of 1 ml of buffer PB (QIAGEN recipe), samples were purified using QIAquick spin columns (QIAGEN) and eluted in 40 ul TE Buffer 10/0.1 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
For ChIP-seq, Illumina libraries were generated for immunoprecipitated and input samples using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sample concentrations for ChIP-seq were determined using the DeNovix dsDNA Ultra High Sensitivity Kit. Starting DNA amounts were standardised such that an approximately equal mass of all input and immunoprecipitated DNA was used for library preparation. After adapter ligation, a single PCR amplification was performed to add Illumina barcodes, and ~450 bp-sized DNA fragments were selected using a two-sided AMPure XP bead (Beckman Coulter) size selection, as follows: The volume of barcoded immunoprecipitated and input DNA was brought up to 50 µl with TE Buffer 10/0.1; in the first size selection step, 0.55X AMPure beads (27.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the supernatant was discarded and the AMPure beads were kept; in the second size selection step, 0.35X AMPure beads (17.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the AMPure beads were discarded and the supernatant was kept. The concentration of DNA was determined for pooling using the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were sequenced in either single- or paired-end mode on the Illumina MiniSeq and NextSeq platform. For each ChIP-seq sample, >2,000,000 raw reads (including genomic and plasmid-mapping reads) were obtained.

treatment_protocol: IscB, TnpB, Cas9, and Cas12a proteins were heterologously expressed in E. coli BL21(DE3) upon induction with 0.05 mM IPTG.

tag: strain

tag: chip antibody

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

tag: epitope tag_on_sample_protein

tag: induction parameters

tag: flag-tagged protein

tag: targeting condition

value: non-targeting (NT)

tag: biological replicate_#


title: TnpB3_targeting_ChIP-seq_paired_raw_rep1

value: targeting


title: Input_TnpB3_targeting_ChIP-seq_paired_raw

value: none (non-immunoprecipitated control sample)


title: IscB_NT_ChIP-seq_paired_raw_rep1

value: IscB


title: IscB_NT_ChIP-seq_paired_raw_rep2


title: genomic DNA from venous blood 15

description:
C78bb.1.1_250
Normal venous blood sample

source_name: venous blood 15

tag: age

tag: birthweight

tag: dyad

tag: maternal age

tag: delivery mode

tag: maternal alcohol

tag: war trauma

tag: chronic stress

tag: cohort

tag: age acceleration


title: IscB_targeting_ChIP-seq_paired_raw_rep1

tag: strain


title: Cas12a_NT_ChIP-seq_paired_raw_rep1

tag: chip antibody


title: Cas12a_targeting_ChIP-seq_paired_raw_rep2

tag: epitope tag_on_sample_protein


title: Cas12a_targeting_ChIP-seq_paired_raw_rep1

tag: induction parameters


title: Cas12a_NT_ChIP-seq_paired_raw_rep2

tag: flag-tagged protein


title: TnpB3_targeting_ChIP-seq_paired_raw_rep2

tag: targeting condition


title: Cas9_NT_ChIP-seq_paired_raw_rep2

tag: biological replicate_#


title: Cas9_NT_ChIP-seq_paired_raw_rep1


title: TnpB3_NT_ChIP-seq_paired_raw_rep2


title: Input_Cas9_targeting_ChIP-seq_paired_raw


title: Cas9_targeting_ChIP-seq_paired_raw_rep1


title: RTK05 - Targeting biol rep 2 ChIP

status: Public on Mar 09 2023

data_processing:
ChIP-seq data were processed using CoBRA v2.0 with modifications as follows. Each experimental condition (TnsC with TTN-targeting gRNA or TnsC with non-targeting [NT] gRNA) was processed with three biological replicate ChIP samples and one corresponding non-immunoprecipitated input sample. Reads were aligned to the hg38 human reference genome using BWA-MEM with default settings. Reads were sorted and indexed using SAMtools, and multi-mapping reads with a MAPQ score < 1 were removed using the samtools view command. Peaks were called using MACS2 v2.2.6. The callpeak function was executed in paired-end mode with the following parameters: -g 2.7e9 -q 0.0001 --keep-dup auto --nomodel. Input samples were used as controls for peak calling. Bedgraph files for each sample with pileup information in signal per million reads (SPMR) were generated with the --SPMR and -B subcommands of MACS2 callpeak and were converted to bigwig files using bedGraphToBigWig. Reads mapping to the Y chromosome or the mitochondrial genome were removed prior to downstream analysis.
A consensus list of peaks for each experimental condition was identified using bedtools v2.30.0. First, peak files for the three replicates were concatenated and sorted and overlapping peaks were merged. Then, peaks appearing in fewer than three replicates were removed. Blacklisted regions of the genome defined by the ENCODE Consortium were also removed. The consensus lists for the conditions were then intersected to identify peaks exclusive to either condition or peaks shared by both conditions.
Assembly: hg38
Supplementary files format and content: bigWig (.bw) files were generated using bedGraphToBigWig from bedGraph files with pileup information for each sample.
Supplementary files format and content: .narrowPeak files were generated using MACS2 and contain peak calls and summit enrichment values for each sample.
Supplementary files format and content: Consensus .bed files were generated by overlapping .narrowPeak files between replicates and removing ENCODE blacklisted regions.

growth_protocol: For ChIP-seq analysis experiments, HEK293T cells were seeded at approximately 1,500,000 cells per well in a 10 cm dish coated with poly-D-lysine 24 hours prior to transfection. Cells were co-transfected with the following eCAST-1 components: 1.5 ug p3xFLAG-TnsC, 1.5 ug pTniQ, 1.5 ug pCas6, 7.5 ug pCas7, 1.5 ug pCas8, and 3 ug of either a targeting (TTN crRNA 1) or non-targeting crRNA.

extract_protocol:
72 hours after transfection, cells were washed with DPBS with no calcium or magnesium (Fisher Scientific), harvested using TrypLE (Fisher Scientific), and neutralized with culture media. The resuspended cells were pelleted by centrifugation at 300 x g for 5 minutes, and the supernatant was aspirated. Pellets were resuspended in 1% freshly made formaldehyde (Thermo Fisher Scientific) in DPBS and shaken gently for 10 minutes. Fixation was quenched by adding 2.5 M glycine, for a final concentration of 125 mM glycine, and shaking cells gently for 5 minutes. Cells were pelleted as described above, washed with cold DPBS, pelleted, resuspended in DPBS and 1x cOmplete EDTA-free protease inhibitors (Millipore Sigma), pelleted, flash frozen in liquid nitrogen, and stored at -80 °C. On the day of sonication, the cross-linked pellets were resuspended in 1 mL of Lysis Buffer 1 (50 mM HEPES-KOH, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and 1X protease inhibitors and rotated for 10 minutes. Cells were pelleted at 1350 g for 5 minutes. Pellets were resuspended in 1 mL of Lysis Buffer 2 (10 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and 1X protease inhibitors and rotated for 10 minutes before being pelleted at 1350 g for 5 minutes. Pellets were resuspended in 900 uL of Lysis Buffer 3 (10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine), 100 uL of 10% Triton X-100, and 1X protease inhibitors. All steps took place at 4 °C. The resuspended cells were transferred to 1 ml milliTUBE AFA Fiber (Covaris) and sonicated on M220 Focused-ultrasonicator (Covaris) under the following SonoLab 7.2 settings:  minimum temperature 4°C, set point 6 °C, maximum temperature 7 °C, Peak Power 75.0, Duty Factor 10.0, Cycles/Burst 200, sonication time 490 seconds. Sonicated cell lysate was centrifuged at 20,000 g for 10 minutes at 4 °C. The supernatant was transferred to a new tube, and 5% was saved as the input sample. The remaining supernatant was incubated with Dynabeads Protein G (Thermo Fisher Scientific) that were bound to the monoclonal anti-Flag M2 antibody (Sigma-Aldrich) the day before sonication by overnight rotating at 4 °C, and the lysate-Dynabead mixture was rotated overnight at 4 °C. The samples were washed three times each with low salt buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 1 mM EDTA, 50 mM Tris HCl), high salt buffer (550 mM NaCl, 0.1% SDS, 1% Triton X-100, 1 mM EDTA, 50 mM Tris HCl), and LiCl buffer (150 mM LiCl, 0.5% Na-deoxycholate, 0.1% SDS, 1% Nonidet P-40, 1 mM EDTA, 50 mM Tris HCl) on a magnetic stand at 4 °C. The samples were washed with 1 mL of TE buffer (1 mM EDTA, 10 mM Tris HCl) with 50 mM NaCl and centrifuged at 960 g for 3 minutes at 4 °C. The supernatant was carefully aspirated with a pipette. 210 uL of elution buffer (1% SDS, 50 mM Tris HCl, 10 mM EDTA, 200 mM NaCl) was added to samples and incubated for 30 minutes at 65 °C. Samples were centrifuged for 1 minute at 16,000 g at room temperature, and 200 uL of supernatant was incubated overnight at 65 °C. The input sample was diluted in 150 uL of elution buffer and also incubated overnight at 65 °C. 0.5 uL of 10 mg/mL RNase was added, and samples were incubated for 1 hour at 37 °C. 2 uL of 20 mg/mL Proteinase K were added, and samples were incubated for 1 hour at 55 °C. The DNA was recovered by the QiaQUICK PCR Purification Kit (Qiagen) and DNA was eluted in 50 uL of water for downstream analysis.
Sample DNA concentration was determined by the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were generated using the NEBNext Ultra II Dna Library Prep Kit for Illumina (NEB). Sample concentrations were normalized such that 12 ng of DNA in each condition was used for library preparation. The concentration of DNA was determined for pooling using the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were sequenced in paired-end mode on the Illumina NextSeq platforms with automated demultiplexing and adaptor trimming. For each ChIP-seq sample, 75-bp paired end reads were obtained and between 9.5 and 18.9 million uniquely mapped fragments were analyzed.

treatment_protocol: eCAST-1 effector proteins Cas6, Cas7, Cas8, TniQ, and 3xFLAG-TnsC were transfected as plasmids into HEK293T cells, along with a plasmid expressing either a targeting (TTN) or non-targeting crRNA.

tag: cell line

value: Monoclonal ANTI-FLAG M2 antibody (Sigma-Aldrich, cat. number:F1804)

tag: sample type

value: ChIP

tag: condition

value: Targeting

tag: protein

tag: replicate


title: RTK03 - Nontargeting biol rep 3 ChIP

value: Nontargeting


title: Chd4KO_4_Chd-666

status: Public on May 31 2023

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

library_source: transcriptomic

data_processing:
The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the mm10 UCSC reference genome using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses performed with DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: mm10
Supplementary files format and content: preprocessed_tpm

molecule: total RNA

organism: Mus musculus

source_name: Pancreatic beta cells

extract_protocol:
RNA was isolated from FACS-purified β cells using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher). The DNAse treated RNA was analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number above 8.0 were used for cDNA synthesis and library preparation.
cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). A dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. The average size of the library insert was approximately 300-400 bp

tag: tissue

value: Pancreatic beta cells

tag: cell type

value: beta cell

tag: genotype


title: Chd4KO_3_Chd-664


title: Cas9_targeting_ChIP-seq_paired_raw_rep2


title: Chd4KO_1_Chd-565


title: RTK08 - Targeting biol rep 1 input

value: Input


title: RTK07 - Nontargeting biol rep 1 input


title: RTK04 - Targeting biol rep 1 ChIP


title: RTK06 - Targeting biol rep 3 ChIP


title: IscB_targeting_ChIP-seq_paired_raw_rep2


title: RTK01 - Nontargeting biol rep 1 ChIP


title: AV157_Rep_3

status: Public on Nov 01 2022

city: Pittsburgh

first: Arjumand

last: Ghazi

state: Pennzylvania

address: 4401 Penn Avenue

institute: University of Pittsburgh

data_processing:
Data was processed using CLC Genomic Workbench RNA-Seq workflow
Genome_build: WBcel235

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were maintained on nematode growth medium (NGM) plates seeded with E. coli (OP50), at 20 °C.

extract_protocol:
Animals were picked as L4's then on Day 1 of adulhood, the animals were collected and washed with M9 three times. The TRIzol was added to the rinsed pellet and stored at -80°C. The samples were then freeze thawed 6 times and the RNA was harvested using the TRIzol method. RNA was checked for quality and concentration using the Agilent Tapestation and Qubit Fluorometry.
The library was prepared using the NEBNext Poly(A) mRNA Magnetic Isolation module and NEBNext Multiplex Oligos for Illumina. The DNA libraries were checked for quality and quantified using Tapestation D1000 and Qubit High Sensitivity.

value: whole animal


title: RTK02 - Nontargeting biol rep 2 ChIP


title: AV157_Rep_1


title: TY4986_Rep_3


title: TY4986_Rep_2


title: AV157_Rep_2


title: TY4986_Rep_1


title: AV477_Rep_2


title: N2_Rep_3


title: AV477_Rep_3


title: AV477_Rep_1


title: N2_Rep_2


title: Chd4KO_2_Chd-636


title: N2_Rep_1


title: HMC3 cells, APA Reference library, Replicate 2

status: Public on Oct 08 2022

city: seattle

first: Samantha

last: Koplik

email: skoplik@uw.edu, kopliksam@gmail.com

state: Washington

address: 185 Stevens Way

department: Electrical and Computer Engineering

institute: University of Washington

description: apa_100_variants_rev2_20220621_hmc3_v3_umi_mut_0.csv

data_processing:
The open-source adaptor trimming software package cutadapt v1.15 was used to trim adapters off read 1. Read 1 was then aligned and mapped to the known respective library sequences.
The sequence upstream of the proximal PAS CSE was used to map cleaved mRNA back to the full UTR sequence (allowing for ≤ 2 substitution errors). Reads were searched 5’ to 3’ across for the site of polyadenylation as sequencing reads were long enough to precisely locate cut sites for all proximal isoforms
The site of polyadenylation was identified by searching for a consecutive run of 20 A’s (allowing for ≤ 2 substitution errors). A read was considered distally cleaved if no polyadenylation site was found in read 1.
Mapped reads were collapsed over UMIs in read 2. The final unique-UMI counts were pooled across 2 biological replicates.
Estimated the log odds ratio (LOR) of each variant’s proximal isoform abundance with respect to the wildtype abundance. These isoform abundances were calculated by summing all cleavage probabilities mapping to cut sites +0 to +50 nt downstream of the CSE
Assembly: custom library array sequences
Supplementary files format and content: csv files for each cell line containing  logit measured and predicted (with APARENT2) scores for each sequence. Includes both individual replicate scores and pooled replicate scores

growth_protocol: HEK293T cells (ATCC CRL-3216) were maintained in DMEM (Gibco), SK-N-SH cells (ATCC HTB-11) in MEM (Gibco), and HMC3 cells (ATCC CRL-3304) in EMEM (ATCC), all supplemented with 10% fetal bovine serum (Cytiva) and 1% penicillin/streptomycin (Gibco). Cells were cultured at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested 36-48 h post-transfection. Cells were detached with TrypLE (Gibco), washed with PBS, and lysed. One to 5% of cells were set aside for flow cytometry to confirm transfection efficiency. Total RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase I digestion. mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
The resulting mRNAs were reverse transcribed with SuperScript IV Reverse Transcriptase (Thermo Fisher) to generate cDNA. Polyadenylated mRNA was reverse transcribed with an anchored polyT primer containing Illumina adaptor sequences, a unique molecular identifier(UMI), and unique index sequences for each sample (P7-index-PE2-UMI-T18VN). RNA hydrolysis was performed on cDNA and samples were purified using DNA Clean & Concentrator-5 (Zymo). Library cDNA was then amplified with KAPA HiFi HotStart ReadyMix (Roche) using a library-specific forward primer containing additional Illumina adaptor sequences (P5-PE1) and reverse primer matching the adaptor sequence added during RT. Amplification was conducted and monitored with qPCR and stopped early to minimize PCR biases. Samples were size selected to keep fragments >=  100nt using KAPA Pure Beads (Roche). Sample size distributions were analyzed using Tapestation High Sensitivity D1000 (Agilent).

treatment_protocol: HEK293T, SK-N-SH, and HMC3 cells were transfected with variant or reference plasmid libraries using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's instructions. Media were replaced 5 h post-transfection.

value: Human microglial

value: WT

tag: library transfected

value: APA REF 100


title: HMC3 cells, APA Variant library, Replicate 1

value: APA VAR 100


title: HMC3 cells, APA Reference library, Replicate 1


title: SK-N-SH cells, APA Reference library, Replicate 2

description: apa_100_variants_rev2_20220621_sknsh_v3_umi_mut_0.csv

source_name: SK-N-SH

value: SK-N-SH

value: Human neuroblastoma


title: HMC3 cells, APA Variant library, Replicate 2


title: SK-N-SH cells, APA Reference library, Replicate 1


title: SK-N-SH cells, APA Variant library, Replicate 1


title: SK-N-SH cells, APA Variant library, Replicate 2


title: HEK293T cells, APA Reference library, Replicate 2

description: apa_100_variants_rev2_20220621_hek293_v3_umi_mut_0.csv

value: Human embryonic kidney


title: HEK293T cells, APA Variant library, Replicate 2


title: HEK293T cells, APA Reference library, Replicate 1


title: HEK293T cells, APA Variant library, Replicate 1


title: Obese Patient8

status: Public on Mar 15 2022

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
BaseCall performed with CASAVA v1.8.2
Reads were aligned to the hg19 version of the human genome as reference using STAR v2.6.1d after removal of contaminants  (rDNA, tRNA, mtrDNA) using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the hg19-Ensembl Transcript release 75 and normalized by log2 (x+1) transformation
Normalized counts were used to determine differential gene expression between Patients and Controls (as reference) gene specific analysis (GSA)
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain raw counts

source_name: Circulating MDSC

extract_protocol:
Total RNA was extracted from enriched cells (from 0.3x106 to 4x106 PE-CD66b+ PBMC) by using phenol method with Qiazol followed by miRNeasy Mini Kit (both from Qiagen, Germany). The concentration of RNA was tested by Qubit RNA HS Assay kit in the Qubit fluorometer (Invitrogen, Thermo Fisher Scientific) and RNA integrity was assessed using RNA 6000 Pico Kit on the Agilent Bio Analyzer 2100
Paired-end libraries (2 x 75) were prepared (600ng per sample) using the TruSeq Stranded mRNA Library Prep kit

value: Circulating MDSC

tag: race/ethnicity

value: African American

tag: bmi

tag: %granulocytic mdsc

tag: age (years)

tag: gender

value: Female


title: Obese Patient6


title: Obese Patient5

value: Caucasian

value: Male


title: Obese Patient3


title: Obese Patient4


title: Control5


title: Obese Patient1


title: Obese Patient2


title: Control4


title: Control1


title: Control3


title: Control2


title: PID2046_Day22.23

status: Public on Feb 16 2022

city: Stanford

first: Madeleine

last: Scott

state: CA

address: 729 Lagunita Dr

institute: Stanford

data_processing:
Illumina ? For basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using kallisto (v0.46.0) quant
quantified raw reads from kallisto count were normalized using DESeq2
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited raw gene counts per sample

source_name: blood

extract_protocol:
Blood was taken directly before (Baseline = BL) or after vaccination
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

tag: age

tag: day

tag: Sex

value: Included


title: PID2046_Day28


title: PID2046_Day7


title: PID2046_Day21


title: PID2046_Day1.2


title: PID2001_Day28


title: PID2046_BL

value: BL


title: PID2001_Day21


title: PID2001_Day7


title: PID2001_Day22.23


title: PID2000_Day28


title: PID2001_BL


title: PID2001_Day1.2

value: Removed


title: Obese Patient7


title: PID2000_Day7


title: PID2000_Day22.23


title: PID2000_Day1.2


title: PID2000_Day21


title: PID2043_Day28


title: PID2043_Day22.23


title: PID2043_Day21


title: PID2043_Day7


title: PID2043_BL


title: PID2043_Day1.2


title: PID2038_Day28


title: PID2038_Day22


title: PID2038_Day7


title: PID2038_Day21


title: PID2038_BL


title: PID2036_Day28


title: PID2036_Day7


title: PID2036_Day22.23


title: PID2036_Day1.2


title: PID2036_Day21


title: PID2049_Day21


title: PID2000_BL


title: PID2049_Day22.23


title: PID2049_Day28


title: PID2036_BL


title: PID2049_Day7


title: PID2050_Day28


title: PID2050_Day7


title: PID2050_Day22.23


title: PID2050_Day21


title: PID2050_BL


title: PID2031_Day28


title: PID2031_Day21


title: PID2031_Day22.23


title: PID2031_Day7


title: PID2055_Day28


title: PID2031_Day1.2


title: PID2031_BL


title: PID2055_Day22.23


title: PID2055_Day21


title: PID2055_Day7


title: PID2051_Day22.23


title: PID2055_BL


title: PID2055_Day1.2


title: PID2051_Day28


title: PID2051_Day21


title: PID2049_Day2


title: PID2051_Day7


title: PID2049_Day1


title: PID2051_Day2


title: PID2051_BL


title: PID2011_Day22.23


title: PID2049_BL


title: PID2011_BL


title: PID2051_Day1


title: PID2011_Day7


title: PID2011_Day1.2


title: PID2011_Day21


title: PID2054_Day28


title: PID2054_Day21


title: PID2054_BL


title: PID2054_Day22.23


title: PID2020_Day28


title: PID2054_Day1.2


title: PID2020_Day21


title: PID2020_Day7


title: PID2020_Day22.23


title: PID2054_Day7


title: PID2020_Day1.2


title: PID2030_Day28


title: PID2020_BL


title: PID2030_Day7


title: PID2009_Day21


title: PID2030_Day1.2


title: PID2030_BL


title: PID2009_Day7


title: PID2056_Day22.23


title: PID2009_BL


title: PID2009_Day1.2


title: PID2056_Day7


title: PID2056_Day28


title: PID2034_Day28


title: PID2034_Day22.23


title: PID2056_BL


title: PID2047_Day28


title: PID2034_BL


title: PID2034_Day7


title: PID2047_Day7


title: PID2047_Day2


title: PID2047_Day22.23


title: PID2040_Day28


title: PID2047_Day1


title: PID2047_BL


title: PID2047_Day21


title: PID2040_Day22.23


title: PID2030_Day22.23


title: PID2040_Day7


title: PID2040_BL


title: PID2052_Day22.23


title: PID2052_Day21


title: PID2056_Day1.2


title: PID2052_Day7


title: PID2034_Day21


title: PID2052_Day1.2


title: PID2012_Day21


title: PID2012_Day7


title: PID2012_BL


title: PID2052_BL


title: PID2040_Day21


title: PID2048_Day22.23


title: PID2048_Day28


title: PID2048_Day21


title: PID2056_Day21


title: PID2044_Day21


title: PID2048_BL


title: PID2044_Day22.23


title: PID2044_Day28


title: PID2048_Day1.2


title: PID2044_Day7


title: PID2048_Day7


title: PID2012_Day28


title: PID2044_Day1.2


title: PID2052_Day28


title: PID2040_Day1.2


title: PID2044_BL


title: PID2027_Day22.23


title: PID2027_Day21


title: PID2027_Day7


title: PID2012_Day22.23


title: PID2027_Day1.2


title: PID2007_Day22.23


title: PID2007_Day28


title: PID2007_Day21


title: PID2007_Day1.2


title: PID2042_Day28


title: PID2027_BL


title: PID2007_BL


title: PID2042_Day1.2


title: PID2018_Day22.23


title: PID2018_Day21


title: PID2007_Day7


title: PID2042_BL


title: PID2018_BL


title: PID2042_Day21


title: PID2045_Day28


title: PID2045_Day22.23


title: PID2045_Day21


title: PID2018_Day1.2


title: PID2045_Day1.2


title: PID2045_Day7


title: PID2045_BL


title: PID2013_Day21


title: PID2013_Day7


title: PID2013_BL


title: PID2013_Day1.2


title: PID2042_Day22.23


title: PID2042_Day7


title: PID2028_Day28


title: PID2028_Day21


title: PID2018_Day28


title: PID2028_Day1.2


title: PID2028_Day7


title: PID2028_Day22.23


title: PID2028_BL


title: PID2053_Day28


title: PID2053_Day21


title: PID2053_Day7


title: PID2053_Day1.2


title: PID2053_Day22.23


title: PID2013_Day28


title: T_cell_Pt_8

status: Public on Nov 17 2021

city: Avon

first: Beiyan

last: Zhou

state: Connecticut

address: 263 Farmington Ave, Immunology

department: Immunology

institute: UCONN Health

description: Sample 8

data_processing:
The libraries were sequenced on Illumina® MiniSeq™ System
The bcl files were de-multiplexed using  bacl2fastq v2.20.0.422.
Reads in fastq files were aligned to GRCh38 human reference genome and transcriptome with Hisat2.
TPMs were calculated from aligned reads using StringTie.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel spreadsheet (.xlsx), matrix of TMPs in each sample

source_name: CD8+ T cell from PBMC of Patient 8

extract_protocol:
CD8+ T cells in peripheral blood lymphocytes  from 8 patients were isolated using fluorescence activated cell sorting (FACS).
Libraries of T cell RNA samples from 8 melanoma and lung cancer patients were prepared using Collibri™ 3’ mRNA Library Prep Kit for Illumina®. The libraries were pooled and prepared for sequencing following the “Standard Normalization Method” within the Illumina® MiniSeq System Denature and Dilute Libraries Guide.

value: peripheral blood

value: CD8+ T cell

tag: disease

value: melanoma


title: T_cell_Pt_7

description: Sample 7

source_name: CD8+ T cell from PBMC of Patient 7


title: PID2053_BL


title: T_cell_Pt_6

description: Sample 6

source_name: CD8+ T cell from PBMC of Patient 6


title: T_cell_Pt_4

description: Sample 4

source_name: CD8+ T cell from PBMC of Patient 4

value: Lung cancer


title: T_cell_Pt_2

description: Sample 2

source_name: CD8+ T cell from PBMC of Patient 2


title: T_cell_Pt_3

description: Sample 3

source_name: CD8+ T cell from PBMC of Patient 3


title: T_cell_Pt_5

description: Sample 5

source_name: CD8+ T cell from PBMC of Patient 5


title: T_cell_Pt_1

description: Sample 1

source_name: CD8+ T cell from PBMC of Patient 1


title: CD8TIL.Pt15

status: Public on Nov 16 2021

data_processing:
The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on a HiSeq 2500 with 150 cycle sequencing (asymmetric reads per 10x Genomics).
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger v3.1.0 (10X Genomics), which usesbcl2fastq v2.17.1.14for FASTQ files generation.
FASTQ files were aligned to GRCh38 human reference genome and transcriptome using the CellRanger v3.1.0 software pipeline with default parameters
UMIs were calculated by CellRanger v3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Market Exchange Format (MEX) matrices (.mtx) containing the UMI counts for each cell;  TSV files (.tsv) with genes and barcode sequences corresponding to row and column indices of the MEX file, respectively

source_name: CD8 T cells from melanoma tumor

extract_protocol:
CD8+ T cells in peripheral blood lymphocytes and  tumor-infiltrating lymphocytes from 2 melanoma patients were isolated using fluorescence activated cell sorting (FACS). Further processing on sorted cells was conducted using  Chromium Single Cell 5' Gene Expression kit (10x Genomics).
Single-cell gel beads in emulsion (GEMs) macrophages were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium Single Cell 5' Gene Expression (10x Genomics) according to manufacturer's protocol.

value: tumor

tag: disease state

value: CD8+ T cells


title: CD8TIL.Pt14


title: CD8PBL.Pt14

source_name: CD8 T cells from peripheral blood


title: T_cell_Pt_26

data_processing:
The libraries were sequenced on Illumina NovaSeq 6000 System
The bcl files were de-multiplexed using  bacl2fastq v2.20.0.422.
Reads in fastq files were aligned to GRCh38 human reference genome and transcriptome with Hisat2.
TPMs were calculated from aligned reads using StringTie.
TPMs of individual samples were pooled into a matrix using R
Genome_build: GRCh38
Supplementary_files_format_and_content: excel spreadsheet (.xlsx), matrix of TMPs in each sample

source_name: CD8+ T cell from PBMC of Patient 26

extract_protocol:
CD8+ T cells in peripheral blood lymphocytes  from 28 patients were isolated using fluorescence activated cell sorting (FACS).
Libraries of T cell RNA samples from 28 melanoma patients were prepared using NovaSeq 6000 S2 Reagent Kit v1.5. The libraries were pooled and prepared for sequencing following the “Standard Normalization Method” within the Illumina Novaseq 6000 System Denature and Dilute Libraries Guide.

tag: io status

value: R

value: M


title: T_cell_Pt_24

source_name: CD8+ T cell from PBMC of Patient 24

value: NR


title: T_cell_Pt_21

source_name: CD8+ T cell from PBMC of Patient 21


title: T_cell_Pt_27

source_name: CD8+ T cell from PBMC of Patient 27

value: F


title: T_cell_Pt_23

source_name: CD8+ T cell from PBMC of Patient 23


title: T_cell_Pt_28

source_name: CD8+ T cell from PBMC of Patient 28


title: CD8TIL.Pt8

data_processing:
The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on a HiSeq 2500 with 150 cycle sequencing (asymmetric reads per 10x Genomics).
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger v1.3 (10X Genomics), which usesbcl2fastq v2.17.1.14for FASTQ files generation.
FASTQ files were aligned to GRCh38 human reference genome and transcriptome using the CellRanger v3.0 software pipeline with default parameters
UMIs were calculated by CellRanger v3.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Market Exchange Format (MEX) matrices (.mtx) containing the UMI counts for each cell;  TSV files (.tsv) with genes and barcode sequences corresponding to row and column indices of the MEX file, respectively

extract_protocol:
CD8+ T cells in peripheral blood lymphocytes and  tumor-infiltrating lymphocytes from 8 melanoma patients were isolated using fluorescence activated cell sorting (FACS). Further processing on sorted cells was conducted using  Chromium™ Single Cell 3' Reagent Kit v2 (10x Genomics).
Single-cell gel beads in emulsion (GEMs) macrophages were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v2 (10x Genomics) according to manufacturer's protocol.

value: CD8 T cells


title: T_cell_Pt_22

source_name: CD8+ T cell from PBMC of Patient 22


title: T_cell_Pt_25

source_name: CD8+ T cell from PBMC of Patient 25


title: T_cell_Pt_18

source_name: CD8+ T cell from PBMC of Patient 18


title: ATF1 #5

status: Public on Nov 18 2021

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description: intracranial mesenchymal tumor tissue

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.28.4) in R. The detection p-value for each sample was computed. All samples had detection p values less than 0.002. Functional normalization with NOOB background correction and dye-bias normalization was performed.

source_name: intracranial mesenchymal tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25).  Genomic DNA was extracted from these punches using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered.  No ex vivo culture or xenografting was performed.

tag: patient sex

value: female

tag: patient age at dx (yrs)

tag: fusion type

tag: tumor location

value: tentorium


title: T_cell_Pt_20

source_name: CD8+ T cell from PBMC of Patient 20

tag: cell type

tag: tissue


title: CD8PBL.Pt8


title: CD8PBL.Pt7


title: T_cell_Pt_19

source_name: CD8+ T cell from PBMC of Patient 19


title: T_cell_Pt_16

source_name: CD8+ T cell from PBMC of Patient 16


title: ATF1 #7

description: intracranial mesenchymal tumor tissue

value: male

value: CP angle


title: CREM #2

description: intracranial mesenchymal tumor tissue

value: lateral ventricle


title: CREM #4

description: intracranial mesenchymal tumor tissue

value: falx


title: CD8TIL.Pt7


title: CD8PBL.Pt6

value: peripheral blood


title: T_cell_Pt_13

source_name: CD8+ T cell from PBMC of Patient 13


title: T_cell_Pt_17

source_name: CD8+ T cell from PBMC of Patient 17


title: CREB1 #6

description: intracranial mesenchymal tumor tissue

value: cerebral convexity


title: ATF1 #8

description: intracranial mesenchymal tumor tissue


title: CD8TIL.Pt4

source_name: CD8 T cells from melanoma tumor


title: CREB1 #4

description: intracranial mesenchymal tumor tissue


title: CREM #3

description: intracranial mesenchymal tumor tissue


title: CD8TIL.Pt6


title: T_cell_Pt_11

source_name: CD8+ T cell from PBMC of Patient 11


title: CREB1 #5

description: intracranial mesenchymal tumor tissue


title: ATF1 #1

description: intracranial mesenchymal tumor tissue


title: T_cell_Pt_15

source_name: CD8+ T cell from PBMC of Patient 15


title: T_cell_Pt_14

source_name: CD8+ T cell from PBMC of Patient 14


title: CREM #1

description: intracranial mesenchymal tumor tissue

value: spinal cord


title: CREB1 #3

description: intracranial mesenchymal tumor tissue


title: T_cell_Pt_9

source_name: CD8+ T cell from PBMC of Patient 9


title: CD8TIL.Pt5


title: CD8PBL.Pt5

source_name: CD8 T cells from peripheral blood


title: T_cell_Pt_12

source_name: CD8+ T cell from PBMC of Patient 12


title: T_cell_Pt_7

source_name: CD8+ T cell from PBMC of Patient 7


title: CD8TIL.Pt2


title: CREB1 #1

description: intracranial mesenchymal tumor tissue


title: CD8TIL.Pt3


title: CD8PBL.Pt4


title: CD8PBL.Pt3


title: ATF1 #4

description: intracranial mesenchymal tumor tissue


title: T_cell_Pt_6

source_name: CD8+ T cell from PBMC of Patient 6


title: T_cell_Pt_10

source_name: CD8+ T cell from PBMC of Patient 10


title: CREB1 #2

description: intracranial mesenchymal tumor tissue


title: T_cell_Pt_5

source_name: CD8+ T cell from PBMC of Patient 5


title: T_cell_Pt_8

source_name: CD8+ T cell from PBMC of Patient 8


title: T_cell_Pt_3

source_name: CD8+ T cell from PBMC of Patient 3


title: ATF1 #2

description: intracranial mesenchymal tumor tissue

source_name: intracranial mesenchymal tumor tissue


title: FUS #1

description: intracranial mesenchymal tumor tissue

value: FUS-CREM


title: CD8PBL.Pt1


title: T_cell_Pt_4

source_name: CD8+ T cell from PBMC of Patient 4


title: T_cell_Pt_2

source_name: CD8+ T cell from PBMC of Patient 2


title: CD8PBL.Pt2


title: ATF1 #6

description: intracranial mesenchymal tumor tissue


title: ATF1 #3

description: intracranial mesenchymal tumor tissue


title: CHiC_HL-E125-Pendel-72-GFPp

status: Public on Nov 04 2021

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing:
Library strategy: Capture Hi-C
Sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v6.1.0. The pipeline was set up with Bowtie2 v2.3.4.2 for short read mapping.  In case replicates were available, they were combined before the processing with the HiCUP pipeline. Juicer command line tools v1.7.6 was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing. For binning and normalization, only the genomic region chr13: 54,000,001-57,300,000 was considered.  Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb resolution. Subtraction maps were produced from the KR normalized maps and scaled together across their subdiagonals. cHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 99-th  percentile were truncated for visualization purposes.
In order to obtain more fine-grained interaction profiles for selected loci, we defined 10kb viewpoint regions and generated virtual Capture-C-like profiles based on the filtered, unique read-pairs that were also used for the cHiC maps. A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region, while the other read mapped outside of it. The reads outside of the viewpoint were counted per restriction fragment and read counts were binned afterwards to 1 kb bins. In case a fragment was overlapping more than one bin, the read count was distributed proportionally. Afterwards, the each binned profiles wasere smoothed by averaging over a running window of 5 bins and scaled by 10^3 / sum of all its counts on chr5. The viewpoint and a window ± 5kb around it were not considered for the computation of the scaling factor. The profiles were generated with custom Java code using htsjdk v2.12.0  (https://samtools.github.io/htsjdk/). Virtual Capture-C viepoint: Shh promoter (chr5:28,789,001-28,799,000)

source_name: Embryonic Limb Bud

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status.

extract_protocol:
Tissues were homogenized in typsin-EDTA solution, fixes with 2% FA at room temperature, 10 min and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor). Upon PBS wash, samples were frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared and adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

value: Embryonic Limb Bud

tag: cell population

value: GFP+

tag: genotype


title: CD8TIL.Pt1

source_name: CD8 T cells from melanoma tumor

value: tumor


title: CHiC_HL-E125-WT-36-GFPp


title: CREB1 #7

description: intracranial mesenchymal tumor tissue


title: CHiC_HL-E125-WT-36-GFPn

value: GFP-


title: T_cell_Pt_1

source_name: CD8+ T cell from PBMC of Patient 1

value: CD8+ T cells

value: R

value: M


title: CHiC_HL-E125-Pendel-72-GFPn


title: 9862-2_7_hSS_90_Activated

status: Public on Oct 20 2021

city: Los Angeles

first: Aaron

last: Gordon

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

institute: UCLA

data_processing:
Paired end reads were mapped using STAR to hg38 with Gencode v25 annotations.
Gene expression levels were quantified using rsem (v1.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw counts

source_name: human subpalial spheroids

growth_protocol: hCS and hSS differentiations from hiPSCs grown on MEF feeders were performed as previously described (Birey et al., 2017; Sloan et al., 2018).

extract_protocol:
RNA was extracted from hSS and hCS using the Quick-RNA Miniprep kit (Zymo Research, R1054).
For library construction, non-stranded cDNA libraries were constructed using poly(A) mRNA enrichment and the NEBNext Ultra™ II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, E7770S).

tag: iPSc line

value: TS

tag: region

value: hSS

tag: differntiation

tag: differentiation day

tag: genetic ancestry pc1

tag: genetic ancestry pc2

tag: activation with kcl

value: Activated

tag: reprogramming method

value: Episomal


title: 7643-32_7_hSS_90_Activated

tag: Sex

value: F


title: 9862-2_7_hSS_90_Baseline

value: Baseline


title: 8858-1_7_hSS_90_Activated

value: CTRL


title: ATAC-seq_HD1 (714) Lin-CD34+ cells

status: Public on Oct 23 2021

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

data_processing:
Equal molar concentrations of uniquely indexed samples were pooled together. Pooled libraries were sequenced using a NextSeq500 150-cycle flow cell (Illumina).
Reads were aligned to the mouse (mm10) or human (hg38) genomes, and peaks were called using the cellranger-atac count pipeline.
Individual samples were merged using the cellranger-atac pipeline to generate the peak-barcode matrix and TF-barcode matrix.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: A sparse matrix with the number of reads in each peak for each cell, a sparse matrix with the transcription factor (TF) activity for each cell, and a fragment file with the number of reads in each peaks for each cell

source_name: Stem and Progenitor cells from a healthy donor

extract_protocol:
The scATAC Low Cell Input Nuclei Isolation protocol (10X Genomics) was used to isolate nuclei from FACS-purified cells. The trypan blue exclusion assay was performed to check for intact nuclei.
The remaining extracted nuclei were used for the consecutive steps of the scATAC-seq library preparation protocol following 10X Genomics guidelines.

value: bone marrow hematopoietic cells

tag: treatment


title: 8858-1_7_hSS_90_Baseline


title: 2242-1_7_hSS_90_Activated


title: 7643-32_7_hSS_90_Baseline


title: 8858-1_8_hSS_119_Activated


title: 2242-1_7_hSS_90_Baseline


title: 1205-4_8_hCS_119_Baseline

source_name: human cortical spheroids

value: hCS


title: 8858-1_8_hSS_119_Baseline


title: 1205-4_8_hCS_119_Activated


title: 8303-4_6_hSS_101_Activated

value: Sendai


title: 9862-2_6_hSS_101_Baseline


title: 7643-32_6_hSS_101_Activated


title: 8858-1_6_hSS_101_Activated


title: 8303-4_6_hSS_101_Baseline


title: 1205-4_6_hSS_101_Baseline


title: 9862-2_2_hSS_75_Baseline


title: 1205-4_6_hSS_101_Activated


title: 8858-1_6_hSS_101_Baseline


title: 8303-4_2_hSS_75_Baseline


title: 0524-1_2_hSS_75_Baseline


title: 7643-32_2_hSS_75_Baseline


title: 1205-4_2_hSS_75_Baseline


title: 8303-4_3_hSS_40_Baseline


title: 9862-2_3_hSS_40_Baseline


title: 0524-1_3_hSS_40_Baseline


title: 9862-2_6_hSS_101_Activated


title: 1205-4_3_hSS_40_Baseline


title: 7643-32_3_hSS_40_Baseline


title: 7643-32_6_hSS_101_Baseline


title: 9862-2_4_hSS_53_Baseline


title: 2242-1_4_hCS_53_Baseline


title: 8303-4_4_hCS_53_Baseline


title: 8858-1_4_hCS_53_Baseline


title: 2242-1_4_hSS_53_Baseline


title: 8303-4_4_hSS_53_Baseline


title: 8858-1_4_hSS_53_Baseline


title: 1205-4_10_hCS_94_Activated


title: 7643-32_4_hSS_53_Baseline


title: 1208-2_10_hCS_94_Activated


title: 8119-1_10_hCS_94_Activated


title: 1205-4_10_hCS_94_Baseline


title: 1208-2_10_hSS_94_Activated


title: 1205-4_10_hSS_94_Activated


title: 8119-1_10_hCS_94_Baseline


title: 1205-4_10_hSS_94_Baseline


title: 1208-2_10_hSS_94_Baseline


title: 1205-4_9_hCS_129_Baseline


title: 1205-4_9_hCS_129_Activated


title: 1205-4_9_hSS_129_Activated


title: 1205-4_9_hSS_129_Baseline


title: 9862-2_4_hCS_53_Baseline


title: 9862-2_1_hCS_65_Baseline_2


title: 9862-2_1_hCS_65_Baseline_1


title: 7643-32_1_hSS_65_Baseline_1


title: 8303-4_1_hCS_65_Baseline


title: 8858-1_1_hCS_65_Baseline


title: 1205-4_1_hCS_65_Baseline


title: 8303-4_1_hSS_65_Baseline


title: 7643-32_1_hSS_65_Baseline_2


title: 1205-4_1_hSS_65_Baseline


title: 7643-32_7_hCS_121_Activated


title: 7643-32_7_hCS_121_Baseline


title: 8303-4_7_hCS_121_Activated


title: 8303-4_7_hCS_121_Baseline


title: 9862-2_7_hCS_121_Activated


title: 9862-2_7_hCS_121_Baseline


title: 2242-1_7_hCS_121_Baseline


title: 8858-1_7_hCS_121_Activated


title: 7643-32_7_hSS_121_Activated


title: 2242-1_7_hCS_121_Activated


title: 8858-1_1_hSS_65_Baseline


title: 7643-32_7_hSS_121_Baseline


title: 2242-1_7_hSS_121_Activated


title: 9862-2_7_hSS_121_Activated


title: 8858-1_7_hCS_121_Baseline


title: 8303-4_5_hCS_125_Activated


title: 8858-1_7_hSS_121_Activated


title: 8858-1_7_hSS_121_Baseline


title: 2242-1_7_hSS_121_Baseline


title: 9862-2_5_hCS_125_Activated


title: 8858-1_5_hCS_125_Activated


title: 8858-1_5_hCS_125_Baseline


title: 8303-4_5_hCS_125_Baseline


title: 2242-1_5_hCS_125_Baseline


title: 2242-1_5_hCS_125_Activated


title: 2242-1_5_hSS_125_Baseline


title: 8303-4_5_hSS_125_Activated


title: 8303-4_5_hSS_125_Baseline


title: 8858-1_5_hSS_125_Activated


title: 2242-1_5_hSS_125_Activated