title: OQ_204

source_name: OQ tissue from cancer patient CUB-204 with grade nan ER+ PgR+ HER2- ILC


title: TU_204

status: Public on Jun 18 2025

type: other

city: Chicago

first: Saya

last: Dennis

state: IL

address: 680 N. Lake Shore Dr.

department: Preventive Medicine

country: USA

institute: Northwestern University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe R software (version 1.20.0)

label: Cy3, Cy5

molecule: other

organism: Homo sapiens

source_name: TU tissue from cancer patient CUB-204 with grade nan ER+ PgR+ HER2- ILC

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue was homogenized and extracted using QIAGEN’s AllPrep DNA/RNA Kit. DNA quality was assessed using a NanoDrop 1000 Spectrophotometer.

tag: tissue

value: TU


title: CUB_298

source_name: CUB tissue from cancer patient CUB-298 with grade III ER- PgR- HER2+ IDC

value: CUB


title: TU_289

source_name: TU tissue from cancer patient CUB-289 with grade III ER- PgR- HER2- IDC


title: CUB_023

source_name: CUB tissue from cancer patient CUB-023 with grade nan ER+ PgR+ HER2- ILC


title: TU_023

source_name: TU tissue from cancer patient CUB-023 with grade nan ER+ PgR+ HER2- ILC


title: TU_194

source_name: TU tissue from cancer patient CUB-194 with grade III ER+ PgR+ HER2- ---------


title: OQ_194

source_name: OQ tissue from cancer patient CUB-194 with grade III ER+ PgR+ HER2- ---------

value: OQ


title: TU_011

source_name: TU tissue from cancer patient CUB-011 with grade II ER- PgR- HER2+ IDC


title: CUB_215

source_name: CUB tissue from cancer patient CUB-215 with grade III ER+ PgR+ HER2- IDC


title: OQ_014

source_name: OQ tissue from cancer patient CUB-014 with grade III ER- PgR- HER2- IDC


title: TU_068

source_name: TU tissue from cancer patient CUB-068 with grade I ER+ PgR+ HER2- IDC


title: TU_014

source_name: TU tissue from cancer patient CUB-014 with grade III ER- PgR- HER2- IDC


title: OQ_215

source_name: OQ tissue from cancer patient CUB-215 with grade III ER+ PgR+ HER2- IDC


title: CUB_014

source_name: CUB tissue from cancer patient CUB-014 with grade III ER- PgR- HER2- IDC


title: TU_314

source_name: TU tissue from cancer patient CUB-314 with grade II ER+ PgR- HER2- IDC


title: TU_215

source_name: TU tissue from cancer patient CUB-215 with grade III ER+ PgR+ HER2- IDC


title: CUB_314

source_name: CUB tissue from cancer patient CUB-314 with grade II ER+ PgR- HER2- IDC


title: CUB_157

source_name: CUB tissue from cancer patient CUB-157 with grade II ER- PgR- HER2- IDC


title: OQ_006

source_name: OQ tissue from cancer patient CUB-006 with grade III ER- PgR- HER2+ IDC


title: CUB_290

source_name: CUB tissue from cancer patient CUB-290 with grade III ER- PgR- HER2+ IDC


title: OQ_290

source_name: OQ tissue from cancer patient CUB-290 with grade III ER- PgR- HER2+ IDC


title: TU_322

source_name: TU tissue from cancer patient CUB-322 with grade III ER- PgR- HER2- IDC


title: TU_290

source_name: TU tissue from cancer patient CUB-290 with grade III ER- PgR- HER2+ IDC


title: TU_135

source_name: TU tissue from cancer patient CUB-135 with grade III ER- PgR- HER2- IDC


title: OQ_322

source_name: OQ tissue from cancer patient CUB-322 with grade III ER- PgR- HER2- IDC


title: OQ_023

source_name: OQ tissue from cancer patient CUB-023 with grade nan ER+ PgR+ HER2- ILC


title: CUB_194

source_name: CUB tissue from cancer patient CUB-194 with grade III ER+ PgR+ HER2- ---------


title: TU_019

source_name: TU tissue from cancer patient CUB-019 with grade I ER- PgR- HER2+ IDC


title: TU_320

source_name: TU tissue from cancer patient CUB-320 with grade III ER- PgR- HER2- IDC


title: TU_045

source_name: TU tissue from cancer patient CUB-045 with grade III ER- PgR- HER2+ IDC


title: CUB_322

source_name: CUB tissue from cancer patient CUB-322 with grade III ER- PgR- HER2- IDC


title: TU_100

source_name: TU tissue from cancer patient CUB-100 with grade II ER+ PgR+ HER2- IDC


title: TU_006

source_name: TU tissue from cancer patient CUB-006 with grade III ER- PgR- HER2+ IDC


title: TU_035

source_name: TU tissue from cancer patient CUB-035 with grade III ER- PgR- HER2- IDC


title: OQ_304

source_name: OQ tissue from cancer patient CUB-304 with grade III ER- PgR- HER2+ IDC


title: CUB_100

source_name: CUB tissue from cancer patient CUB-100 with grade II ER+ PgR+ HER2- IDC


title: OQ_314

source_name: OQ tissue from cancer patient CUB-314 with grade II ER+ PgR- HER2- IDC


title: CUB_181

source_name: CUB tissue from cancer patient CUB-181 with grade III ER- PgR- HER2+ IDC


title: OQ_035

source_name: OQ tissue from cancer patient CUB-035 with grade III ER- PgR- HER2- IDC


title: OQ_045

source_name: OQ tissue from cancer patient CUB-045 with grade III ER- PgR- HER2+ IDC


title: CUB_283

source_name: CUB tissue from cancer patient CUB-283 with grade II ER+ PgR+ HER2- IDC


title: CUB_035

source_name: CUB tissue from cancer patient CUB-035 with grade III ER- PgR- HER2- IDC


title: CUB_321

source_name: CUB tissue from cancer patient CUB-321 with grade II ER- PgR- HER2+ IDC


title: CUB_045

source_name: CUB tissue from cancer patient CUB-045 with grade III ER- PgR- HER2+ IDC


title: CUB_176

source_name: CUB tissue from cancer patient CUB-176 with grade III ER- PgR- HER2- --------


title: TU_037

source_name: TU tissue from cancer patient CUB-037 with grade nan ER+ PgR+ HER2- ILC


title: TU_031

source_name: TU tissue from cancer patient CUB-031 with grade III ER+ PgR¬± HER2- IDC


title: CUB_031

source_name: CUB tissue from cancer patient CUB-031 with grade III ER+ PgR¬± HER2- IDC


title: CUB_204

source_name: CUB tissue from cancer patient CUB-204 with grade nan ER+ PgR+ HER2- ILC


title: CUB_037

source_name: CUB tissue from cancer patient CUB-037 with grade nan ER+ PgR+ HER2- ILC


title: TU_176

source_name: TU tissue from cancer patient CUB-176 with grade III ER- PgR- HER2- --------


title: OQ_037

source_name: OQ tissue from cancer patient CUB-037 with grade nan ER+ PgR+ HER2- ILC


title: TU_114

source_name: TU tissue from cancer patient CUB-114 with grade nan ER+ PgR+ HER2nan DCIS


title: OQ_114

source_name: OQ tissue from cancer patient CUB-114 with grade nan ER+ PgR+ HER2nan DCIS


title: CUB_142

source_name: CUB tissue from cancer patient CUB-142 with grade II ER+ PgR+ HER2- IDC


title: OQ_176

source_name: OQ tissue from cancer patient CUB-176 with grade III ER- PgR- HER2- --------


title: CUB_304

source_name: CUB tissue from cancer patient CUB-304 with grade III ER- PgR- HER2+ IDC


title: TU_304

source_name: TU tissue from cancer patient CUB-304 with grade III ER- PgR- HER2+ IDC


title: TU_154

source_name: TU tissue from cancer patient CUB-154 with grade II ER+ PgR+ HER2- IDC


title: TU_142

source_name: TU tissue from cancer patient CUB-142 with grade II ER+ PgR+ HER2- IDC


title: OQ_100

source_name: OQ tissue from cancer patient CUB-100 with grade II ER+ PgR+ HER2- IDC


title: TU_260

source_name: TU tissue from cancer patient CUB-260 with grade III ER- PgR- HER2- IDC


title: TU_039

source_name: TU tissue from cancer patient CUB-039 with grade III ER- PgR- HER2- IDC


title: OQ_142

source_name: OQ tissue from cancer patient CUB-142 with grade II ER+ PgR+ HER2- IDC


title: TU_080

source_name: TU tissue from cancer patient CUB-080 with grade III ER- PgR- HER2- IDC


title: CUB_114

source_name: CUB tissue from cancer patient CUB-114 with grade nan ER+ PgR+ HER2nan DCIS


title: OQ_283

source_name: OQ tissue from cancer patient CUB-283 with grade II ER+ PgR+ HER2- IDC


title: TU_283

source_name: TU tissue from cancer patient CUB-283 with grade II ER+ PgR+ HER2- IDC


title: CUB_080

source_name: CUB tissue from cancer patient CUB-080 with grade III ER- PgR- HER2- IDC


title: OQ_080

source_name: OQ tissue from cancer patient CUB-080 with grade III ER- PgR- HER2- IDC


title: OQ_031

source_name: OQ tissue from cancer patient CUB-031 with grade III ER+ PgR¬± HER2- IDC


title: CUB_039

source_name: CUB tissue from cancer patient CUB-039 with grade III ER- PgR- HER2- IDC


title: OQ_213

source_name: OQ tissue from cancer patient CUB-213 with grade III ER+ PgR- HER2- IDC


title: OQ_043

source_name: OQ tissue from cancer patient CUB-043 with grade III ER- PgR- HER2- IDC


title: OQ_039

source_name: OQ tissue from cancer patient CUB-039 with grade III ER- PgR- HER2- IDC


title: TU_213

source_name: TU tissue from cancer patient CUB-213 with grade III ER+ PgR- HER2- IDC


title: CUB_213

source_name: CUB tissue from cancer patient CUB-213 with grade III ER+ PgR- HER2- IDC


title: TU_141

source_name: TU tissue from cancer patient CUB-141 with grade II ER- PgR- HER2- IDC


title: TU_043

source_name: TU tissue from cancer patient CUB-043 with grade III ER- PgR- HER2- IDC


title: TU_167

source_name: TU tissue from cancer patient CUB-167 with grade III ER+ PgR+ HER2- IDC


title: CUB_141

source_name: CUB tissue from cancer patient CUB-141 with grade II ER- PgR- HER2- IDC


title: OQ_134

source_name: OQ tissue from cancer patient CUB-134 with grade nan ER+ PgR+ HER2- ILC


title: TU_085

source_name: TU tissue from cancer patient CUB-085 with grade III ER- PgR- HER2- IDC


title: CUB_134

source_name: CUB tissue from cancer patient CUB-134 with grade nan ER+ PgR+ HER2- ILC


title: OQ_303

source_name: OQ tissue from cancer patient CUB-303 with grade III ER- PgR- HER2- IDC


title: TU_134

source_name: TU tissue from cancer patient CUB-134 with grade nan ER+ PgR+ HER2- ILC


title: OQ_056

source_name: OQ tissue from cancer patient CUB-056 with grade nan ER- PgR- HER2nan DCIS


title: CUB_289

source_name: CUB tissue from cancer patient CUB-289 with grade III ER- PgR- HER2- IDC


title: OQ_289

source_name: OQ tissue from cancer patient CUB-289 with grade III ER- PgR- HER2- IDC


title: TU_056

source_name: TU tissue from cancer patient CUB-056 with grade nan ER- PgR- HER2nan DCIS


title: OQ_320

source_name: OQ tissue from cancer patient CUB-320 with grade III ER- PgR- HER2- IDC


title: TU_107

source_name: TU tissue from cancer patient CUB-107 with grade nan ER+ PgR+ HER2- ILC


title: OQ_182

source_name: OQ tissue from cancer patient CUB-182 with grade nan ER+ PgR+ HER2- ILC


title: CUB_043

source_name: CUB tissue from cancer patient CUB-043 with grade III ER- PgR- HER2- IDC


title: CUB_265

source_name: CUB tissue from cancer patient CUB-265 with grade I ER+ PgR+ HER2- IDC


title: TU_303

source_name: TU tissue from cancer patient CUB-303 with grade III ER- PgR- HER2- IDC


title: CUB_192

source_name: CUB tissue from cancer patient CUB-192 with grade II ER+ PgR+ HER2- IDC


title: OQ_107

source_name: OQ tissue from cancer patient CUB-107 with grade nan ER+ PgR+ HER2- ILC


title: TU_182

source_name: TU tissue from cancer patient CUB-182 with grade nan ER+ PgR+ HER2- ILC


title: OQ_034

source_name: OQ tissue from cancer patient CUB-034 with grade II ER+ PgR+ HER2- IDC


title: TU_034

source_name: TU tissue from cancer patient CUB-034 with grade II ER+ PgR+ HER2- IDC


title: TU_265

source_name: TU tissue from cancer patient CUB-265 with grade I ER+ PgR+ HER2- IDC


title: TU_192

source_name: TU tissue from cancer patient CUB-192 with grade II ER+ PgR+ HER2- IDC


title: CUB_182

source_name: CUB tissue from cancer patient CUB-182 with grade nan ER+ PgR+ HER2- ILC


title: CUB_291

source_name: CUB tissue from cancer patient CUB-291 with grade II ER+ PgR+ HER2- IDC


title: CUB_034

source_name: CUB tissue from cancer patient CUB-034 with grade II ER+ PgR+ HER2- IDC


title: CUB_107

source_name: CUB tissue from cancer patient CUB-107 with grade nan ER+ PgR+ HER2- ILC


title: CUB_189

source_name: CUB tissue from cancer patient CUB-189 with grade nan ER+ PgR+ HER2- ILC


title: TU_291

source_name: TU tissue from cancer patient CUB-291 with grade II ER+ PgR+ HER2- IDC


title: OQ_128

source_name: OQ tissue from cancer patient CUB-128 with grade nan ER+ PgR+ HER2- ILC


title: OQ_141

source_name: OQ tissue from cancer patient CUB-141 with grade II ER- PgR- HER2- IDC


title: OQ_291

source_name: OQ tissue from cancer patient CUB-291 with grade II ER+ PgR+ HER2- IDC


title: CUB_320

source_name: CUB tissue from cancer patient CUB-320 with grade III ER- PgR- HER2- IDC


title: CUB_051

source_name: CUB tissue from cancer patient CUB-051 with grade III ER- PgR- HER2- IDC


title: TU_128

source_name: TU tissue from cancer patient CUB-128 with grade nan ER+ PgR+ HER2- ILC


title: TU_051

source_name: TU tissue from cancer patient CUB-051 with grade III ER- PgR- HER2- IDC


title: CUB_186

source_name: CUB tissue from cancer patient CUB-186 with grade nan ER+ PgR+ HER2- ILC


title: OQ_051

source_name: OQ tissue from cancer patient CUB-051 with grade III ER- PgR- HER2- IDC


title: CUB_303

source_name: CUB tissue from cancer patient CUB-303 with grade III ER- PgR- HER2- IDC


title: TU_138

source_name: TU tissue from cancer patient CUB-138 with grade II ER+ PgR¬± HER2- IDC


title: OQ_138

source_name: OQ tissue from cancer patient CUB-138 with grade II ER+ PgR¬± HER2- IDC


title: CUB_056

source_name: CUB tissue from cancer patient CUB-056 with grade nan ER- PgR- HER2nan DCIS


title: CUB_138

source_name: CUB tissue from cancer patient CUB-138 with grade II ER+ PgR¬± HER2- IDC


title: OQ_265

source_name: OQ tissue from cancer patient CUB-265 with grade I ER+ PgR+ HER2- IDC


title: CUB_059

source_name: CUB tissue from cancer patient CUB-059 with grade nan ER+ PgR+ HER2+ ILC


title: OQ_059

source_name: OQ tissue from cancer patient CUB-059 with grade nan ER+ PgR+ HER2+ ILC


title: TU_059

source_name: TU tissue from cancer patient CUB-059 with grade nan ER+ PgR+ HER2+ ILC


title: OQ_192

source_name: OQ tissue from cancer patient CUB-192 with grade II ER+ PgR+ HER2- IDC


title: OQ_316

source_name: OQ tissue from cancer patient CUB-316 with grade III ER- PgR- HER2- IDC


title: TU_008

source_name: TU tissue from cancer patient CUB-008 with grade II ER+ PgR+ HER2- IDC


title: OQ_008

source_name: OQ tissue from cancer patient CUB-008 with grade II ER+ PgR+ HER2- IDC


title: CUB_008

source_name: CUB tissue from cancer patient CUB-008 with grade II ER+ PgR+ HER2- IDC


title: HDB_K107249

source_name: HDB tissue from healthy donor K107249

value: HDB


title: OQ_086

source_name: OQ tissue from cancer patient CUB-086 with grade III ER+ PgR+ HER2- IDC


title: HDB_K106955

source_name: HDB tissue from healthy donor K106955


title: CUB_128

source_name: CUB tissue from cancer patient CUB-128 with grade nan ER+ PgR+ HER2- ILC


title: HDB_K105872

source_name: HDB tissue from healthy donor K105872


title: HDB_K105266

source_name: HDB tissue from healthy donor K105266


title: HDB_K106562

source_name: HDB tissue from healthy donor K106562


title: HDB_K102457

source_name: HDB tissue from healthy donor K102457


title: HDB_K107071

source_name: HDB tissue from healthy donor K107071


title: CUB_195

source_name: CUB tissue from cancer patient CUB-195 with grade III ER- PgR- HER2- IDC


title: HDB_K106959

source_name: HDB tissue from healthy donor K106959


title: HDB_K106017

source_name: HDB tissue from healthy donor K106017


title: HDB_K105655

source_name: HDB tissue from healthy donor K105655


title: HDB_K106029

source_name: HDB tissue from healthy donor K106029


title: HDB_K105456

source_name: HDB tissue from healthy donor K105456


title: TU_086

source_name: TU tissue from cancer patient CUB-086 with grade III ER+ PgR+ HER2- IDC


title: HDB_K106716

source_name: HDB tissue from healthy donor K106716


title: HDB_K105076

source_name: HDB tissue from healthy donor K105076


title: OQ_058

source_name: OQ tissue from cancer patient CUB-058 with grade II ER+ PgR+ HER2- IDC


title: HDB_K107069

source_name: HDB tissue from healthy donor K107069


title: TU_195

source_name: TU tissue from cancer patient CUB-195 with grade III ER- PgR- HER2- IDC


title: HDB_K105634

source_name: HDB tissue from healthy donor K105634


title: CUB_086

source_name: CUB tissue from cancer patient CUB-086 with grade III ER+ PgR+ HER2- IDC


title: HDB_K106027

source_name: HDB tissue from healthy donor K106027


title: HDB_K106091

source_name: HDB tissue from healthy donor K106091


title: HDB_K106578

source_name: HDB tissue from healthy donor K106578


title: HDB_K105346

source_name: HDB tissue from healthy donor K105346


title: HDB_K105861

source_name: HDB tissue from healthy donor K105861


title: HDB_K106188

source_name: HDB tissue from healthy donor K106188


title: HDB_K107252

source_name: HDB tissue from healthy donor K107252


title: HDB_K107208

source_name: HDB tissue from healthy donor K107208


title: HDB_K106453

source_name: HDB tissue from healthy donor K106453


title: HDB_K106968

source_name: HDB tissue from healthy donor K106968


title: HDB_K106021

source_name: HDB tissue from healthy donor K106021


title: HDB_K105631

source_name: HDB tissue from healthy donor K105631


title: HDB_K106630

source_name: HDB tissue from healthy donor K106630


title: HDB_K105562

source_name: HDB tissue from healthy donor K105562


title: HDB_K107253

source_name: HDB tissue from healthy donor K107253


title: HDB_K105077

source_name: HDB tissue from healthy donor K105077


title: HDB_K107175

source_name: HDB tissue from healthy donor K107175


title: HDB_K105056

source_name: HDB tissue from healthy donor K105056


title: HDB_K105865

source_name: HDB tissue from healthy donor K105865


title: HDB_K106821

source_name: HDB tissue from healthy donor K106821


title: HDB_K106833

source_name: HDB tissue from healthy donor K106833


title: HDB_K106526

source_name: HDB tissue from healthy donor K106526


title: HDB_K107246

source_name: HDB tissue from healthy donor K107246


title: HDB_K106179

source_name: HDB tissue from healthy donor K106179


title: HDB_K107245

source_name: HDB tissue from healthy donor K107245


title: HDB_K106203

source_name: HDB tissue from healthy donor K106203


title: HDB_K106233

source_name: HDB tissue from healthy donor K106233


title: HDB_K105569

source_name: HDB tissue from healthy donor K105569


title: HDB_K107262

source_name: HDB tissue from healthy donor K107262


title: HDB_K106413

source_name: HDB tissue from healthy donor K106413


title: HDB_K105563

source_name: HDB tissue from healthy donor K105563


title: HDB_K106427

source_name: HDB tissue from healthy donor K106427


title: HDB_K107255

source_name: HDB tissue from healthy donor K107255


title: HDB_K105341

source_name: HDB tissue from healthy donor K105341


title: HDB_K105651

source_name: HDB tissue from healthy donor K105651


title: HDB_K105143

source_name: HDB tissue from healthy donor K105143


title: HDB_K106841

source_name: HDB tissue from healthy donor K106841


title: HDB_K107105

source_name: HDB tissue from healthy donor K107105


title: HDB_K107250

source_name: HDB tissue from healthy donor K107250


title: HDB_K105801

source_name: HDB tissue from healthy donor K105801


title: HDB_K105462

source_name: HDB tissue from healthy donor K105462


title: HDB_K104914

source_name: HDB tissue from healthy donor K104914


title: HDB_K104839

source_name: HDB tissue from healthy donor K104839


title: HDB_K107271

source_name: HDB tissue from healthy donor K107271


title: HDB_K106772

source_name: HDB tissue from healthy donor K106772


title: HDB_K105268

source_name: HDB tissue from healthy donor K105268


title: HDB_K105678

source_name: HDB tissue from healthy donor K105678


title: HDB_K107256

source_name: HDB tissue from healthy donor K107256


title: HDB_K106962

source_name: HDB tissue from healthy donor K106962


title: HDB_K105078

source_name: HDB tissue from healthy donor K105078


title: HDB_K107048

source_name: HDB tissue from healthy donor K107048


title: HDB_K107100

source_name: HDB tissue from healthy donor K107100


title: HDB_K105115

source_name: HDB tissue from healthy donor K105115


title: HDB_K105215

source_name: HDB tissue from healthy donor K105215


title: HDB_K107268

source_name: HDB tissue from healthy donor K107268


title: HDB_K105855

source_name: HDB tissue from healthy donor K105855


title: HDB_K106933

source_name: HDB tissue from healthy donor K106933


title: HDB_K104750

source_name: HDB tissue from healthy donor K104750


title: HDB_K106626

source_name: HDB tissue from healthy donor K106626


title: HDB_K107272

source_name: HDB tissue from healthy donor K107272


title: HDB_K106341

source_name: HDB tissue from healthy donor K106341


title: HDB_K106234

source_name: HDB tissue from healthy donor K106234


title: HDB_K107096

source_name: HDB tissue from healthy donor K107096


title: HDB_K106582

source_name: HDB tissue from healthy donor K106582


title: HDB_K107104

source_name: HDB tissue from healthy donor K107104


title: HDB_K105799

source_name: HDB tissue from healthy donor K105799


title: HDB_K105109

source_name: HDB tissue from healthy donor K105109


title: HDB_K105189

source_name: HDB tissue from healthy donor K105189


title: HDB_K105454

source_name: HDB tissue from healthy donor K105454


title: HDB_K107026

source_name: HDB tissue from healthy donor K107026


title: HDB_K106161

source_name: HDB tissue from healthy donor K106161


title: HDB_K102418

source_name: HDB tissue from healthy donor K102418


title: HDB_K105722

source_name: HDB tissue from healthy donor K105722


title: HDB_K107270

source_name: HDB tissue from healthy donor K107270


title: HDB_K106463

source_name: HDB tissue from healthy donor K106463


title: HDB_K106013

source_name: HDB tissue from healthy donor K106013


title: HDB_K105914

source_name: HDB tissue from healthy donor K105914


title: HDB_K106681

source_name: HDB tissue from healthy donor K106681


title: HDB_K106106

source_name: HDB tissue from healthy donor K106106


title: HDB_K105099

source_name: HDB tissue from healthy donor K105099


title: HDB_K105814

source_name: HDB tissue from healthy donor K105814


title: HDB_K102432

source_name: HDB tissue from healthy donor K102432


title: HDB_K106710

source_name: HDB tissue from healthy donor K106710


title: HDB_K102503

source_name: HDB tissue from healthy donor K102503


title: HDB_K107001

source_name: HDB tissue from healthy donor K107001


title: HDB_K106356

source_name: HDB tissue from healthy donor K106356


title: HDB_K107215

source_name: HDB tissue from healthy donor K107215


title: HDB_K107254

source_name: HDB tissue from healthy donor K107254


title: HDB_K105165

source_name: HDB tissue from healthy donor K105165


title: HDB_K105848

source_name: HDB tissue from healthy donor K105848


title: HDB_K105994

source_name: HDB tissue from healthy donor K105994


title: HDB_K107257

source_name: HDB tissue from healthy donor K107257


title: HDB_K106697

source_name: HDB tissue from healthy donor K106697


title: HDB_K107247

source_name: HDB tissue from healthy donor K107247


title: HDB_K107241

source_name: HDB tissue from healthy donor K107241


title: HDB_K105498

source_name: HDB tissue from healthy donor K105498


title: HDB_K107273

source_name: HDB tissue from healthy donor K107273


title: HDB_K106316

source_name: HDB tissue from healthy donor K106316


title: HDB_K105308

source_name: HDB tissue from healthy donor K105308


title: HDB_K106649

source_name: HDB tissue from healthy donor K106649


title: HDB_K104888

source_name: HDB tissue from healthy donor K104888


title: HDB_K107258

source_name: HDB tissue from healthy donor K107258


title: HDB_K105118

source_name: HDB tissue from healthy donor K105118


title: HDB_K106830

source_name: HDB tissue from healthy donor K106830


title: HDB_K107209

source_name: HDB tissue from healthy donor K107209


title: HDB_K105851

source_name: HDB tissue from healthy donor K105851


title: HDB_K104708

source_name: HDB tissue from healthy donor K104708


title: HDB_K105513

source_name: HDB tissue from healthy donor K105513


title: HDB_K107267

source_name: HDB tissue from healthy donor K107267


title: HDB_K105728

source_name: HDB tissue from healthy donor K105728


title: HDB_K104613

source_name: HDB tissue from healthy donor K104613


title: HDB_K104944

source_name: HDB tissue from healthy donor K104944


title: HDB_K106738

source_name: HDB tissue from healthy donor K106738


title: HDB_K104349

source_name: HDB tissue from healthy donor K104349


title: HDB_K105059

source_name: HDB tissue from healthy donor K105059


title: HDB_K107261

source_name: HDB tissue from healthy donor K107261


title: HDB_K105342

source_name: HDB tissue from healthy donor K105342


title: HDB_K106953

source_name: HDB tissue from healthy donor K106953


title: HDB_K106982

source_name: HDB tissue from healthy donor K106982


title: HDB_K105893

source_name: HDB tissue from healthy donor K105893


title: HDB_K104510

source_name: HDB tissue from healthy donor K104510


title: HDB_K105581

source_name: HDB tissue from healthy donor K105581


title: HDB_K105281

source_name: HDB tissue from healthy donor K105281


title: HDB_K104364

source_name: HDB tissue from healthy donor K104364


title: HDB_K107264

source_name: HDB tissue from healthy donor K107264


title: HDB_K105338

source_name: HDB tissue from healthy donor K105338


title: HDB_K106399

source_name: HDB tissue from healthy donor K106399


title: HDB_K104562

source_name: HDB tissue from healthy donor K104562


title: HDB_K107265

source_name: HDB tissue from healthy donor K107265


title: HDB_K107259

source_name: HDB tissue from healthy donor K107259


title: HDB_K104497

source_name: HDB tissue from healthy donor K104497


title: HDB_K107269

source_name: HDB tissue from healthy donor K107269


title: HDB_K105811

source_name: HDB tissue from healthy donor K105811


title: HDB_K107263

source_name: HDB tissue from healthy donor K107263


title: HDB_K105263

source_name: HDB tissue from healthy donor K105263


title: HDB_K105707

source_name: HDB tissue from healthy donor K105707


title: HDB_K107251

source_name: HDB tissue from healthy donor K107251


title: HDB_K106813

source_name: HDB tissue from healthy donor K106813


title: HDB_K106769

source_name: HDB tissue from healthy donor K106769


title: HDB_K105705

source_name: HDB tissue from healthy donor K105705


title: HDB_K106331

source_name: HDB tissue from healthy donor K106331


title: HDB_K107260

source_name: HDB tissue from healthy donor K107260


title: HDB_K106230

source_name: HDB tissue from healthy donor K106230


title: HDB_K105314

source_name: HDB tissue from healthy donor K105314


title: HDB_K107266

source_name: HDB tissue from healthy donor K107266


title: HDB_K106843

source_name: HDB tissue from healthy donor K106843


title: HDB_K107115

source_name: HDB tissue from healthy donor K107115


title: HDB_K105037

source_name: HDB tissue from healthy donor K105037


title: HDB_K105845

source_name: HDB tissue from healthy donor K105845


title: HDB_K105703

source_name: HDB tissue from healthy donor K105703


title: HDB_K107248

source_name: HDB tissue from healthy donor K107248


title: HDB_K106199

source_name: HDB tissue from healthy donor K106199


title: HDB_K105559

source_name: HDB tissue from healthy donor K105559


title: HDB_K105506

source_name: HDB tissue from healthy donor K105506


title: HDB_K107070

source_name: HDB tissue from healthy donor K107070


title: HDB_K106472

source_name: HDB tissue from healthy donor K106472


title: HDB_K105116

source_name: HDB tissue from healthy donor K105116


title: HDB_K106839

source_name: HDB tissue from healthy donor K106839


title: HDB_K104865

source_name: HDB tissue from healthy donor K104865


title: HDB_K106745

source_name: HDB tissue from healthy donor K106745


title: HDB_K104729

source_name: HDB tissue from healthy donor K104729


title: HDB_K106028

source_name: HDB tissue from healthy donor K106028


title: HDB_K105903

source_name: HDB tissue from healthy donor K105903


title: HDB_K107274

source_name: HDB tissue from healthy donor K107274


title: HDB_K104370

source_name: HDB tissue from healthy donor K104370


title: HDB_K105022

source_name: HDB tissue from healthy donor K105022


title: Sample 64_skin construct, inflamed, 48 hours, AC100

type: RNA

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

description: Total RNA from skin construct

hyb_protocol: standard protocol

scan_protocol: The iScan System (Illumina) was used to read the BeadChips

data_processing:
Methylation data were obtained in the form of Intensity Data (IDAT) files and processed using the ChAMP package in R (version 4.3.2). Following data import, quality control was performed using Multidimensional Scaling (MDS) and density plots to assess data distribution and identify outliers. Methylation data normalization was carried out with the Beta Mixture Quantile dilation (BMIQ) method, followed by batch effect correction using the ComBat method (accounting for 'Run', 'Slide', and 'Array').
The default ChAMP filtering options were applied: probes with a detection p-value above 0.01 were filtered out and probes with a beadcount <3 in at least 5% of samples were filtered out. Only CpGs were kept in the analysis; the probes with SNPs as identified in Zhou's Nucleic Acids Research Paper 2016 were filtered, as well as probes aligning to multiple locations as identified in Nortlund et al. and those located on X,Y chromosomes. All values <= 0 were replaced with the smallest positive value and all values >= 0 were replaced with the largest value below 1.
The processed_data.txt contains Average Beta
The signal_intensities.txt contains unmethylated and methylated signal intensities

label: cy3, cy5

molecule: total RNA

label_protocol: standard protocol

growth_protocol: Fibroblasts and keratinocytes were cocultured in a collagen matrix for 14 days, until the fibroblasts were embedded in the collagen matrix, and the keratinocytes over them

extract_protocol: standard protocol

treatment_protocol:
After 14 days, half of the constructs were perfused with TNF-α to mimic an inflammatory state
Electrostimulation is tested on normal and inflamed samples, to have unstimulated and stimulated samples, at 1 and 5V in direct current (DC), and in alternate current, at 10 and 100 Hz. Each condition was tested in three replicates, and sampling was done at three timepoints (baseline, 1 h and 48 h) following stimulation.

tag: cell line

value: HaCaT

tag: Sex

value: Male

tag: disease state

value: inflamed

tag: time

value: 48 hours

tag: electrical stimulus


title: Sample 62_skin construct, inflamed, 48 hours, AC100

description: Total RNA from skin construct


title: Sample 61_skin construct, inflamed, 1 hour, AC100

description: Total RNA from skin construct

source_name: skin construct, inflamed, 1 hour, AC100

value: 1 hour


title: Sample 63_skin construct, inflamed, 48 hours, AC100

description: Total RNA from skin construct


title: Sample 57_skin construct, inflamed, 48 hours, AC10

description: Total RNA from skin construct


title: Sample 54_skin construct, inflamed, 1 hour, AC10

description: Total RNA from skin construct

source_name: skin construct, inflamed, 1 hour, AC10


title: Sample 53_skin construct, inflamed, 1 hour, AC10

description: Total RNA from skin construct


title: Sample 55_skin construct, inflamed, 1 hour, AC10

description: Total RNA from skin construct


title: Sample 51_skin construct, inflamed, 48 hours, DC5

description: Total RNA from skin construct

source_name: skin construct, inflamed, 48 hours, DC5


title: Sample 56_skin construct, inflamed, 48 hours, AC10

description: Total RNA from skin construct


title: Sample 50_skin construct, inflamed, 48 hours, DC5

description: Total RNA from skin construct


title: Sample 44_skin construct, inflamed, 48 hours, DC1

description: Total RNA from skin construct

source_name: skin construct, inflamed, 48 hours, DC1


title: Sample 48_skin construct, inflamed, 1 hour, DC5

description: Total RNA from skin construct

source_name: skin construct, inflamed, 1 hour, DC5


title: Sample 42_skin construct, inflamed, 1 hour, DC1

description: Total RNA from skin construct

source_name: skin construct, inflamed, 1 hour, DC1


title: Sample 40_skin construct, inflamed, 48 hours, NO

description: Total RNA from skin construct

source_name: skin construct, inflamed, 48 hours, NO

value: NO


title: Sample 36_skin construct, inflamed, 1 hour, NO

description: Total RNA from skin construct

source_name: skin construct, inflamed, 1 hour, NO


title: Sample 35_skin construct, inflamed, 0 hours, NO

description: Total RNA from skin construct

source_name: skin construct, inflamed, 0 hours, NO

value: 0 hours


title: Sample 38_skin construct, inflamed, 48 hours, NO

description: Total RNA from skin construct


title: Sample 30_skin construct, physio, 48 hours, AC100

description: Total RNA from skin construct

source_name: skin construct, physio, 48 hours, AC100

value: physiological


title: Sample 33_skin construct, inflamed, 0 hours, NO

description: Total RNA from skin construct


title: Sample 29_skin construct, physio, 1 hour, AC100

description: Total RNA from skin construct

source_name: skin construct, physio, 1 hour, AC100


title: Sample 60_skin construct, inflamed, 1 hour, AC100

description: Total RNA from skin construct


title: Sample 37_skin construct, inflamed, 1 hour, NO

description: Total RNA from skin construct


title: Sample 28_skin construct, physio, 1 hour, AC100

description: Total RNA from skin construct


title: Sample 27_skin construct, physio, 1 hour, AC100

description: Total RNA from skin construct


title: Sample 26_skin construct, physio, 48 hours, AC10

description: Total RNA from skin construct

source_name: skin construct, physio, 48 hours, AC10


title: Sample 24_skin construct, physio, 48 hours, AC10

description: Total RNA from skin construct


title: Sample 22_skin construct, physio, 1 hour, AC10

description: Total RNA from skin construct

source_name: skin construct, physio, 1 hour, AC10


title: Sample 23_skin construct, physio, 1 hour, AC10

description: Total RNA from skin construct


title: Sample 19_skin construct, physio, 48 hours, DC5

description: Total RNA from skin construct

source_name: skin construct, physio, 48 hours, DC5


title: Sample 18_skin construct, physio, 48 hours, DC5

description: Total RNA from skin construct


title: Sample 16_skin construct, physio, 1 hour, DC5

description: Total RNA from skin construct

source_name: skin construct, physio, 1 hour, DC5


title: Sample 47_skin construct, inflamed, 1 hour, DC5

description: Total RNA from skin construct


title: Sample 21_skin construct, physio, 1 hour, AC10

description: Total RNA from skin construct


title: Sample 43_skin construct, inflamed, 1 hour, DC1

description: Total RNA from skin construct


title: Sample 41_skin construct, inflamed, 1 hour, DC1

description: Total RNA from skin construct


title: Sample 13_skin construct, physio, 48 hours, DC1

description: Total RNA from skin construct

source_name: skin construct, physio, 48 hours, DC1


title: Sample 14_skin construct, physio, 48 hours, DC1

description: Total RNA from skin construct


title: Sample 11_skin construct, physio, 1 hour, DC1

description: Total RNA from skin construct

source_name: skin construct, physio, 1 hour, DC1


title: Sample 10_skin construct, physio, 1 hour, DC1

description: Total RNA from skin construct


title: Sample 39_skin construct, inflamed, 48 hours, NO

description: Total RNA from skin construct


title: Sample 32_skin construct, physio, 48 hours, AC100

description: Total RNA from skin construct


title: Sample 8_skin construct, physio, 48 hours, NO

description: Total RNA from skin construct

source_name: skin construct, physio, 48 hours, NO


title: Sample 7_skin construct, physio, 48 hours, NO

description: Total RNA from skin construct


title: Sample 5_skin construct, physio, 1 hour, NO

description: Total RNA from skin construct

source_name: skin construct, physio, 1 hour, NO


title: Sample 2_skin construct, physio, 0 hours, NO

description: Total RNA from skin construct

source_name: skin construct, physio, 0 hours, NO


title: Sample 3_skin construct, physio, 0 hours, NO

description: Total RNA from skin construct


title: Sample 1_skin construct, physio, 0 hours, NO

description: Total RNA from skin construct


title: Sample 4_skin construct, physio, 1 hour, NO

description: Total RNA from skin construct


title: Sample 25_skin construct, physio, 48 hours, AC10

description: Total RNA from skin construct


title: PAO1-WT biol rep 2

type: SRA

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description: Library name: sample 10

library_source: transcriptomic

data_processing:
the raw reads were mapped to the Psph genome (NC_005777.3) or PAO1 genome(NC_002516.2) using hisat2 (version 2.1.0)
Differentially expressed genes (DEGs) were identified by DESeq2 (p-value < 0.05 and |log2 Fold Change| > 1 of Psph strains in KB and P. aeruginosa strains in LB, and p-value < 0.05 and -1<log2 Fold Change > log2(1.5) of Psph strains in MM
Assembly: 1448A/PAO1
Supplementary files format and content: csv file includes log2FC, padj and gene information for each sample(compare with corresponding WT)

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa

growth_protocol: P. savastanoi  bacteria were routinely cultured at 28°C in King’ B broth with shaking at 220 rpm . And P. aeruginosa  bacteria were routinely cultured at 37°C in LB (Luria-Bertani) broth with shaking at 220 rpm.

extract_protocol:
1mL of stationary phase (OD600= 2-2.5) bacterial culture, 3mL of mid-log-phase culture (WT and ∆vimR strains) cultured in MM for 6 hours, and 1mL of PAO1-WT and PA3565 overexpressing strains in logarithmic phase(OD600=0.6-1.0) were collected and centrifuged (12,000rpm, 4℃). Subsequent RNA extraction and purification were performed using RNeasy mini kit (Qiagen) and treated with DNaseI (NEB).
After removing rRNA using the MICROBExpress kit (Ambion), cDNA Libraries were constructed using mRNA according to NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina). It was then sequenced using the HiSeq 2000 system (Illumina) platform. All RNA-seq experiments were performed for two biological replicates.

treatment_protocol: P. savastanoi  bacteria were cultured until they reached an optical density at 600 nm (OD600) of 2.0 to 2.5. P. aeruginosa  bacteria were culturerd until they reached an optical density at 600 nm (OD600) of 0.6 to 1.0.

value: Pseudomonas aeruginosa

tag: cell type

value: Gram-negative bacteria

tag: treatment

value: cultured in LB


title: PAO1-WT  biol rep 1

description: Library name: sample 9


title: p-PA3565 biol rep 2

description: Library name: sample 12


title: Sample 20_skin construct, physio, 48 hours, DC5

description: Total RNA from skin construct


title: Sample 12_skin construct, physio, 48 hours, DC1

description: Total RNA from skin construct


title: p-PA3565  biol rep 1

description: Library name: sample 11


title: huEC_3mock_ang

city: ulsan

first: JooChan

last: Lee

state: Gyeongsangbuk-do

address: 0, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, Republic of Korea

country: South Korea

institute: UNIST

description:
Library name: SAMPLE9
huECs treated with Ang II (1 μM, 24h), replicate 3

data_processing:
Raw reads were quality-checked and trimmed. Alignment was done using STAR (v2.7.11b) to the human genome (GRCh38).
Transcript quantification was performed using RSEM (v0.5.1).
Differential expression was analyzed with DESeq2 (v1.42.1),
GO enrichment analysis was conducted using ClusterProfiler (v4.10.1)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files include read counts and normalized expression values (TMM+CPM)
Supplementary files format and content: CSV files contain DESeq2 results with log2FC and adjusted p-values.

source_name: huEC

growth_protocol: huECs were cultured in EGM-2 medium (Lonza) at 37°C in a 5% CO₂ incubator until ~80% confluence before lentiviral transduction.

extract_protocol:
Total RNA was extracted from human endothelial cells using Qiagen RNeasy Mini Kit, including on-column DNase I digestion, according to the manufacturer's instructions.
Libraries were prepared using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina, optimized for single-end 3′ tag-based sequencing.

treatment_protocol: Cells were treated with 1 μM Angiotensin II for 24 hours before RNA extraction.

value: huEC

value: human endothelial cells

tag: genotype

value: WT

value: Angiotensin II

tag: batch


title: huEC_2ptpov_ang

description:
Library name: SAMPLE7
PTP4A1-overexpressing huECs treated with Ang II (1 μM, 24h), replicate 2

value: PTP4A1 overexpression


title: huEC_4mock_ang

description:
Library name: SAMPLE13
huECs treated with Ang II (1 μM, 24h), replicate 4


title: huEC_4mock_no

description:
Library name: SAMPLE14
huECs (1 μM, 24h), replicate 4

value: untreated


title: huEC_2mock_no

description:
Library name: SAMPLE6
huECs (1 μM, 24h), replicate 2


title: huEC_2mock_ang

description:
Library name: SAMPLE5
huECs treated with Ang II (1 μM, 24h), replicate 2


title: huEC_3mock_no

description:
Library name: SAMPLE10
huECs (1 μM, 24h), replicate 3


title: huEC_3ptpov_ang

description:
Library name: SAMPLE11
PTP4A1-overexpressing huECs treated with Ang II (1 μM, 24h), replicate 3


title: huEC_2ptpov_no

description:
Library name: SAMPLE8
PTP4A1-overexpressing huECs, replicate 2


title: huEC_1ptpov_ang

description:
Library name: SAMPLE3
PTP4A1-overexpressing huECs treated with Ang II (1 μM, 24h), replicate 1


title: huEC_1ptpov_no

description:
Library name: SAMPLE4
PTP4A1-overexpressing huECs, replicate 1


title: Sample 6_skin construct, physio, 48 hours, NO

description: Total RNA from skin construct

value: HaCaT


title: huEC_1mock_no

description:
Library name: SAMPLE2
huECs (1 μM, 24h), replicate 1


title: huEC_1mock_ang

description:
Library name: SAMPLE1
huECs treated with Ang II (1 μM, 24h), replicate 1


title: K562 Replicate 1

city: New York

first: Marko

last: Jovanovic

state: New York

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Columbia University

description: Library name: Sample 1

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8
RPM (ATCAGCACTTA) sequence was trimmed using Cutadapt v3.4 from both 5’ and 3’ read ends
The barcodes of trimmed reads were identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline)
RNA read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to the human (hg38) genome using STAR aligner. Only reads that mapped uniquely to the genome were kept for further analysis.
Clusters of barcodes were filtered for repeat UMIs, out-of-order barcodes, and PCR duplicates
Reads from the remaining clusters were split into bam files based on user defined cutoffs for the minimum number of oligos per bead, the maximum number of oligos per bead, and the proportion of oligos with the same ID
Bigwig files were generated from individual antibody DNA alignment files using deeptools v3.5.5
Assembly: hg38
Supplementary files format and content: Bigwig

extract_protocol:
For each experiment, 10 million cells were lysed in 1 mL RIPA buffer (50mM HEPES pH 7.4, 100mM NaCl, 1% NP-40, 0.5% Na-Deoxycholate, 0.1% SDS) supplemented with 20 μL Protease Inhibitor Cocktail (Sigma, #P8340-5mL), 10 μL of Turbo DNase (Invitrogen, #AM2238), 1X Manganese/Calcium mix (2.5 mM MnCl2, 0.5 mM CaCl2), and 5 μL of RiboLock RNase Inhibitor (Thermo Fisher, #EO0382)). Samples were incubated on ice for 10 minutes to allow lysis to proceed. After lysis, cells were sonicated at 3-4 W of power for 3 minutes (pulses 0.7 s on, 3.3 s off) using the Branson sonicator and then incubated at 37°C for 10 minutes to allow for DNase digestion. DNase reaction was quenched with addition of 0.25 M EDTA/EGTA mix for a final concentration of 10 mM EDTA/EGTA. RNase If (NEB, #M0243L) was then added at a 1:500 dilution and samples were incubated at 37°C for 10 minutes to allow partial fragmentation of RNA to obtain RNAs of approximately ~300-400 bp in length. RNase reaction was quenched with addition of 500 μL ice cold RIPA buffer supplemented with 20 μL Protease Inhibitor Cocktail and 5 μL of RiboLock RNase Inhibitor, followed by incubation on ice for 3 minutes. Lysates were then cleared by centrifugation at 15000 x g at 4°C for 2 minutes. The supernatant was transferred to new tubes and diluted in additional RIPA buffer such that the final volume corresponded to 1 mL lysate for every 100 μL of Protein G beads used. Lysate was then combined with the labeled antibody-bead pool and 1 M biotin was added to a final concentration of 10 mM as to quench any disassociated streptavidin-coupled oligos. Beads were left rotating overnight at 4°C on a HulaMixer. Following immunoprecipitation, beads were washed twice with RIPA buffer, twice with high salt wash buffer (50 mM HEPES pH 7.4, 1 M NaCl, 1% NP-40, 0.5% Na-Deoxycholate, 0.1% SDS), and twice with Tween buffer (50 mM HEPES pH 7.4, 0.1% Tween-20).
After split-and-pool barcoding, beads were aliquoted into 5% aliquots for library preparation and sequencing. RNA in each aliquot was degraded by incubating with RNase H (NEB, #M0297L) and RNase cocktail (Invitrogen, #AM2286) at 37°C for 20 minutes. 3’ ends of the resulting cDNA were ligated to attach dsDNA oligos containing library amplification sequences using a “splint” ligation as previously described (Quinodoz et al 2021)31. The “splint” ligation reaction was performed with 1X Instant Sticky End Master Mix (NEB #M0370) at 24°C for 1 hour with shaking at 1400 rpm on a ThermoMixer. Barcoded cDNA and biotinylated oligo tags were then eluted from beads by boiling in NLS elution buffer (20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsarcosine, 2.5 mM TCEP) for 6 minutes at 91°C, with shaking at 1350 rpm. Biotinylated oligo tags were first captured by diluting the eluant in 1X oligo binding buffer (0.5X PBST, 5 mM Tris pH 8.0, 0.5 mM EDTA, 1M NaCl) and subsequently binding to MyOne Streptavidin C1 Dynabeads (Invitrogen, #65001) at room temperature for 30 minutes. Beads were placed on a magnet and the supernatant, containing cDNA, was moved to a separate tube. Biotinylated oligo tags were amplified on-bead using 2X Q5 Hot-Start Mastermix (NEB #M0494) with primers that add the indexed full Illumina adaptor sequences.

value: Human lymphoblastic cells


title: K562 Replicate 2

description: Library name: Sample 2


title: HUVECs_9d_control_3

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

description: Library name: HUVECs_9d_control_3

data_processing:
An average of 37x10⁶ raw sequencing reads were obtained in BAM format and converted to FASTQ files using samtools fastq (v1.21). Initial quality assessment of raw FASTQ files was performed with FastQC (v0.12.1). Reads were trimmed for quality and adapter sequences using Trim Galore (v0.6.10) with a Phred score cutoff of 30 and a minimum read length of 30 bp.
Reads (~36x10⁶ per sample) were aligned to the human genome GRCh38 release 95 primary assembly using STAR (v2.7.11b), with genome indices and transcript annotations based on Ensembl release 95 in a two-pass mapping, reporting only reads that mapped exactly once to the reference genome (-outFilterMultimapNmax 1), with gene counts performed during alignment using the option –quantMode GeneCounts
RSeQC (v4.0.0) infer_experiment.py allowed for the determination of the column from which gene counts should be obtained from STAR output, while RSeQC (v4.0.0) read_distribution.py was used to calculate how mapped reads were distributed over genome features. Further post-aligment quality control was done with Qualimap (v2.2.2a) (qualimap bamqc, qualimap rnaseq). Quality control results were summarized with MultiQC (v1.28).
Assembly: human genome and transcripts from Ensembl GRCh38 release 95 primary assembly
Supplementary files format and content: all_samples_counts_tnf.txt: File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner; Columns: Ensembl Gene ID,  sampleIDs with raw counts (all integer numbers)

source_name: Umbilical Cord

growth_protocol: HUVECs were grown on gelatin pre-coated cell culture dishes in M199-based medium supplemented with 20% FBS, 0.4% endothelial cell growth supplement with heparin (ECGS/H), 2 mM L-glutamine, 0.1% penicillin, 0.1% streptomycin and 0.25 μg/mL fungizone in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using the PeqGOLD Total RNA kit (VWR) and stored at -80°C
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation assay (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the 2100 Bioanalyzer High-Resolution Automated Electrophoresis instrument (Agilent, Santa Clara, CA, USA). RNA-seq libraries were prepared with the NEBNext® Poly(A) mRNA Magnetic Isolation Module E7490 and the NEBNext® Ultra™ II Directional RNA sample preparation kit E7760 (New England Biolabs, Inc., Ipswich, MA, USA). NGS library concentrations were quantified with the Qubit 2.0 assay and the size distribution was assessed using the 2100 Bioanalyzer instrument. Before sequencing, sample-specific NGS libraries were diluted and pooled in equimolar amounts. Expression profiling libraries were sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA, USA) following a 100-base-pair, paired-end recipe.

treatment_protocol: HUVECs were treated for the indicated time-points (5h = 5h treatment before isolation; 9d = 6d continous treatment followed by 3d recovery period in growth medium before isolation) with 10ng/ml TNFα. Control samples were not exposed no TNFα and collected at the same time as their stimulated counterparts.

value: Umbilical Cord

value: HUVEC

value: Endothelial Cells

value: control


title: HUVECs_5h_TNF_3

description: Library name: HUVECs_5h_TNF_3

value: TNF


title: HUVECs_9d_control_1

description: Library name: HUVECs_9d_control_1


title: HUVECs_9d_control_2

description: Library name: HUVECs_9d_control_2


title: HUVECs_9d_TNF_2

description: Library name: HUVECs_9d_TNF_2


title: HUVECs_9d_TNF_3

description: Library name: HUVECs_9d_TNF_3


title: HUVECs_9d_TNF_1

description: Library name: HUVECs_9d_TNF_1


title: huEC_3ptpov_no

description:
Library name: SAMPLE12
PTP4A1-overexpressing huECs, replicate 3


title: HUVECs_5h_TNF_2

description: Library name: HUVECs_5h_TNF_2


title: HUVECs_5h_control_3

description: Library name: HUVECs_5h_control_3


title: HUVECs_5h_control_2

description: Library name: HUVECs_5h_control_2


title: HUVECs_5h_TNF_1

description: Library name: HUVECs_5h_TNF_1


title: HUVECs_5h_control_1

description: Library name: HUVECs_5h_control_1


title: LN flare + LSep.04

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

description: Library name: L23

data_processing:
Mapping by hisat2 (2.0.5) to reference hg38
Quantification by featureCounts (1.5.0-p3)
Assembly: hg38
Supplementary files format and content: tab delimited text file with Ensembl ID, gene symbol and raw counts

source_name: kidney

growth_protocol: HRGECs (ScienCell, Carlsbad, CA,#4000, lot 31804) were cultured according to manufacturer’s protocol in fibronectin-coated flasks in complete growth media (Endothelial cell medium (ECM), #1001, ScienCell) supplemented with 5% fetal bovine serum (0025, ScienCell), 1% EC growth supplement (#1052, ScienCell) and 1% penicillin/streptomycin solution (#0503, ScienCell)) and incubated at 37˚C with 5% CO2 and sub-cultured upon reaching 90% confluency in 100 mm dishes. HRGECs were used at passage 3-4 for these studies.

extract_protocol:
To isolate RNA from cell cultures, the RNeasy Mini Kit (Qiagen, Hilden, Germany, #74104) was used. Cells were directly lysed by adding Buffer RLT while scraping the cells. RNA was then isolated according to the manufacturer’s protocol. RNA was immediately placed on ice for subsequent analysis. RNA purity and concentration were assessed using a Nanodrop spectrophotometer, ensuring an OD 260/280 ratio ≥ 2.0 and an OD 260/230 ratio ≥ 2.0 for RNA sequencing quality.
Libray preparation and sequencing conducted by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: Cells cultured as above were washed three times in ECM (#1001-b, ScienCell) then cultured with 3 mL/dish of either:  No Tx (ECM only, n = 3), 10% healthy control serum (HC, n = 5), 10% LN remission serum, or 10% LN flare serum (n=5) +/-  5 µM L-Sepiapterin (L-Sep, PTC Therapeutics, Warren, NJ, USA, #PTC923) . Cells cultured with 5 µM L-Sep were first cultured in L-Sep for one hour, then serum was added. All cultures were then incubated at 5% CO2 and 37°C for another 3 hours.

value: kidney

value: Human Renal Glomerular Endothelial Cells (Sciencell #4000)

value: Renal endothelial

value: LN flare serum + L-Sep


title: LN flare.05

description: Library name: L19

value: LN flare serum


title: LN flare + LSep.03

description: Library name: L22


title: LN flare.02

description: Library name: L16


title: LN flare.01

description: Library name: L15


title: LN flare.03

description: Library name: L17


title: LN remission.05

description: Library name: L14

value: LN remission serum


title: LN flare.04

description: Library name: L18


title: LN flare + LSep.02

description: Library name: L21


title: Healthy Control.05

description: Library name: L9

value: Healthy Control serum


title: LN remission.01

description: Library name: L10


title: LN remission.04

description: Library name: L13


title: LN remission.02

description: Library name: L11


title: Healthy Control.04

description: Library name: L8


title: Healthy Control.03

description: Library name: L7


title: Healthy Control.01

description: Library name: L5


title: Xpb in KO

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

country: France

institute: IGBMC

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA and bcl2fastq.
Reads were mapped onto the mm10 assembly of Mus musculus genome using bowtie2 version 2.2.6 (-- phred33 --end-to-end --no-mixed --no-discordant -I 10 -X 700 --mm --very-sensitive). Af- ter alignment, reads were filtered using samtools view version 1.7 with the following parameters: -f 2 -F 1804 -q 10. Then duplicate reads were tagged using MarkDuplicates version 2.18.4 from Picard tool’s suite.
The tool makeUCSCfile from HOMER with the following parameters -norm 3963942
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: ES cells

extract_protocol:
Cut and Tag experiments were carried out on 200 000 live cells using CUT&Tag-IT™ Assay Kit (Active motif, Catalog No. 53165 for TBP and Taf4, and No. 53160 for Xpb) according to the manufacture’s manual. 10 000 drosophila nuclei (or 5%) (Active motif, Catalog No. 53173 for TBP and Taf4 and No. 53168 for XPB) were added as spikes to each sample at the same time as Concanavalin A Beads.
Libraries were prepared according to the Active motif CUT&Tag-IT™ Assay Kit manufacture’s manual (Catalog No. 53165 and No. 53160) using Nextera™-Compatible Multiplex Primers (Active motif, Catalog No. 53155).

value: ES cells

value: no doxycycline


title: Taf4 in KO


title: Xpb in Taf13 expressing

value: doxycycline


title: Healthy Control.02

description: Library name: L6


title: 2018023, cortex, PU.1+, snRNAseq

city: San Francisco

first: Xianhua

last: Piao

state: CA

institute: University of California, San Francisco

description:
Library name: 2018023cx-olig
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the 10X Cell Ranger software v6.0.2
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: brain

extract_protocol:
Fresh frozen postmortem human tissues were lysed, ultracentrifuged in sucrose cushion, and FACS-enriched for target nuclei population.
Library was performed accoding to manufacter's instructions (10X Chromium Single Cell 3' Reagent Kits v3.1), targeting 5,000 cells/nuclei per library.

value: brain

value: PU.1+ nuclei


title: LN flare + LSep.05

description: Library name: L24


title: 2018023, cortex, OLIG2+, snRNAseq

description:
Library name: 2018023cx-mglia
10x Genomics

value: OLIG2+ nuclei


title: TBP in KO.


title: Taf4 in Taf13 expressing


title: TBP in Taf13 expressing


title: LN flare + LSep.01

description: Library name: L20


title: 2018023, periventricle, PU.1+, snRNAseq

description:
Library name: 2018023lv-mglia
10x Genomics


title: 2018023, cortex, unenriched, snRNAseq

description:
Library name: 2018023cx-all
10x Genomics

value: unenriched nuclei


title: 2018023, periventricle,OLIG2+, snRNAseq

description:
Library name: 2018023lv-olig
10x Genomics


title: KO3

data_processing:
Image analysis and base calling were performed using RTA version 2.7.7 and bcl2fastq version 2.20.0.422.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10. Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 102 and “union” mode.
Assembly: mm10
Supplementary files format and content: Tab-separated text file with raw read counts per Ensembl Gene.

extract_protocol:
Total RNA isolation was performed using Tri Reagent (Molecular Research Center, TR118) according to manufacturer’s instruction.
RNA-Seq libraries were generated from 800 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.


title: 3XHA-Taf13 expressing cells 3

value: no treatment


title: 2018023, periventricle, unenriched, snRNAseq

description:
Library name: 2018023lv-all
10x Genomics


title: 2018003, cortex, PU.1+, snRNAseq

description:
Library name: 2018003cx-mglia
10x Genomics


title: 2018003, cortex, OLIG2+, snRNAseq

description:
Library name: 2018003cx-olig
10x Genomics


title: KO1


title: 3XHA-Taf13 expressing cells 2


title: 2018003, periventricle,OLIG2+, snRNAseq

description:
Library name: 2018003lv-olig
10x Genomics


title: 3XHA-Taf13 expressing cells 1


title: 2018003, periventricle, PU.1+, snRNAseq,rep2

description:
Library name: 2018003lv-mglia2
10x Genomics


title: PolII in KO

data_processing:
Image analysis and base calling were performed using RTA and bcl2fastq.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.1.2 with the following parameters --no-unal -m 1 --seedlen 40 --best --strata --chunkmbs 1024 --sam --tryhard.
Wig and BigWig files were generated using Homer (Heinz et al. 2010) makeUCSCfile v4.11.0 with default parameters except for “-norm 2e7 -fragLength 200”.
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with 0,4 % PFA for sonicated chromatin and with 1% PFA for MNase digested chromatin. Cells were sonicated on E220 Focused-ultrasonicator (Covaris) either MNase digested according protocol described in (Chromatin Immunoprecipitation Assay Using Micrococcal Nucleases in Mammalian Cells. T. Yamakawa , K. Itakura. J Vis Exp. 2019 May 10:(147). doi: 10.3791/59375). Precipitated chromatin was de cross-linked and DNA was purified with phenol-chloroform.
ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 0.1 to 7 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (10 + 4 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: no doxycycling


title: 2018003, periventricle, PU.1+, snRNAseq, rep1

description:
Library name: 2018003lv-mglia
10x Genomics


title: PolII in 3XHA-Taf13 expressing cells


title: Taf1 in KO


title: 2018003, periventricle, unenriched, snRNAseq

description:
Library name: 2018003lv-all
10x Genomics


title: 2014028, periventricle, PU.1+, snRNAseq

description:
Library name: 2014028lv-mglia
10x Genomics


title: 2014028, periventricle, OLIG2+, snRNAseq

description:
Library name: 2014028lv-olig
10x Genomics


title: Taf1 in Taf13 expressing cells


title: H3K27ac in 3XHA-Taf13 expressing cells


title: H3K27ac in KO


title: 2014028, periventricle, unenriched, snRNAseq

description:
Library name: 2014028lv-all
10x Genomics


title: 2014028, cortex, OLIG2+, snRNAseq

description:
Library name: 2014028cx-olig
10x Genomics


title: 2014028, cortex, unenriched, snRNAseq

description:
Library name: 2014028cx-all
10x Genomics


title: TBP in 3XHA-Taf13 expressing cells


title: 2014028, cortex, PU.1+, snRNAseq

description:
Library name: 2014028cx-mglia
10x Genomics


title: KO2


title: 2024002, whole, PU.1+, snRNAseq

description:
Library name: 2024002wh-mglia
10x Genomics


title: 2018003, cortex, unenriched, snRNAseq

description:
Library name: 2018003cx-all
10x Genomics


title: 2023002, whole, OLIG2+, snRNAseq

description:
Library name: 2023002wh-olig
10x Genomics


title: IgG_WT_B1

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

description: Library name: Sample 1

data_processing:
CUT&Tag and CUTAC read mapping and processing Libraries were demultiplexed using demuxFQ (flags: -c -d -i -e -t 1 -r 0.01 -R -l 9). FASTQC- version 0.11.8 was used to assess the read quality and bases with a quality score below 20 were trimmed from both reads using cutadapt (cutadapt -q 20). For CUTAC libraries, reads greater than 120bp in length were removed alignment. Reads were aligned to the hg38 reference genome using bwa mem with default parameters. Sorted bam files with duplicates removed were generated with SAMtools (version 1.15.1), and converted to bigwig using deepTools bamCoverage (parameters: --normalizeUsing CPM, --binSize 10, 5 or 3 with 12nt smoothing function). Statistical comparisons between WT and mutants were performed by two-sided t-test, using cpm signal summed over 1kb regions. Sample size for CUT&Tag; 4C-seq data was analysed using the pipe4C pipeline (https://github.com/deLaatLab/pipe4C) in R (version 4.3.0) Read 1 sequencing reads were used as input for the pipe4C pipeline and all reads mapped to the viewpoint chromosome were scaled to 1 million reads. An average running mean window size was set at 21 fragment ends. 4C plots were generated using peakC74 (https://github.com/deWitLab/peakC) where two biological replicates were used as input into the peakC program and subsequently plotted with ggplot2 in R. Biological replicates were processed on the same day and sequenced on the same flow cell. Samples for comparison were sequenced together in a single run.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: myelogenous leukemia

growth_protocol: K562 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2. Cell cultures were routinely checked for mycoplasma infection.

extract_protocol: Sequencing libraries were generated by mixing 25 uL NEBNext High Fidelity 2X PCR Master Mix (M0541, New England Biolabs), 2 uL of P5 indexing primer (10 mM), 2 uL of P7 indexing primer (10 mM) with 21 uL of purified DNA in a PCR reaction under the following conditions: 72 ºC for 5 min, 98 ºC for 30 sec followed by n cycles of 98 ºC 10 sec, 63 ºC for 10 sec, and a final extension at 72 ºC for 1 min. For BG4 and SG4 libraries n=8 cycles were used, for all other CUT&Tag libraries n=10 was used. Libraries were purified using Ampure XP beads (A63882, Beckman Coulter Life Sciences) by incubation with 0.4X ratio of beads for 15 min, followed by supernatant incubation with 1.4X ratio of beads for 15 min. Beads were washed twice with 800 mL 80% ethanol and eluted in 25 uL of 10mM Tris-HCl pH 8.0. Library size distribution was analysed on a Tapestation 2200 (Agilent Technologies) and library concentrations were quantified by NEBNext Library Quant Kit for Illumina (E7630, New England BioLabs). Individual libraries were pooled for optimal read balancing and sequenced paired end with NextSeq 2000 P2 or P3 Reagents 100 Cycles v3 (20046811, 20040559, Illumina, Inc.) on the NextSeq 2000 platform (Illumina, Inc.). Dynabeads MyOne Streptavidin T1 beads (65601, Thermo Fisher Scientific) were incubated with Concanavalin A (C2272, biotin conjugate, Sigma-Aldrich) in ratio of 10 mg/mL beads to 1.15 mg/mL Concanavalin A at 22 ºC for 30 min at 400 rpm on a thermoshaker (Eppendorf). Volume sufficient for 10 µL beads per reaction was prepared. Beads were washed with 1 mL of binding buffer (20mM HEPES pH 7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and resuspended in volume of binding buffer sufficient for 10 uL beads per reaction. Cells were fixed in 0.1% formaldehyde (28906, Thermo Fisher Scientific) in 1X PBS for 2 min at room temperature and quenched with 0.075M glycine. Cells were centrifuged at 1300xg 4 ºC for 4 min and resuspended in wash buffer (20mM HEPES pH 7.5, 150mM KCl, 0.5mM spermidine (S0266, Sigma-Aldrich), one tablet protease inhibitor (11873580001, Roche cOmplete, EDTA-free)) at 500 cells/mL. 10 uL beads were incubated with 100 uL of cell suspension at 25 ºC for 10 min at 600 rpm, washed twice with 100 uL wash buffer and resuspended in 50 uL of antibody buffer (2mM EDTA, 0.1% BSA (A8577, Sigma-Aldrich), 0.05% digitonin (300410, Merck Millipore) in wash buffer). Primary antibody was added and incubated at 4 ºC at 600rpm overnight. Primary antibodies used include; BG4 scFv (made in house) at 0.5 mM per reaction, SG4 (made in house) at 1 mM per reaction, anti-H3K4me1 antibody (710795, Thermo Fisher Scientific), anti-H3K27ac antibody (ab4729, Abcam), anti-Ser5 phosphorylated Rpb1 antibody (#13523, Cell Signaling Technology), anti-GATA1 antibody (ab181544, Abcam), anti-BRG1 antibody (ab110641, Abcam), anti-P300 antibody (sc-48343, Santa Cruz Biotechnology), Normal Rabbit IgG (2729, Cell Signaling Technology)). Cells were washed twice with 100 uL dig wash buffer (0.05% digitonin in wash buffer) and resuspended in 50 uL of dig-wash buffer. Secondary antibody was then added and incubated at 25 ºC at 600 rpm for 1 hr. For BG4 and SG4 samples, 2 uL of rabbit anti-FLAG antibody (#2368, Cell Signaling Technology) was added, for all other rabbit primary antibodies 0.5 uL of Guinea Pig anti-rabbit IgG antibody (ABIN101961, antibodies-online.com) was added, and for mouse primary antibodies 0.5 uL of Rabbit Anti-mouse IgG H&L (ab46540, Abcam) was added per reaction. Cells were then washed three times with 500 uL dig-wash buffer and resuspended in 50 uL dig-300 buffer (20mM 20mM HEPES pH 7.5, 300mM KCl, 0.5mM spermidine, 0.01% digitonin, one tablet protease inhibitor). pA-Tn5 (2 mM, made in house) was added in 1:250 dilution to each sample and incubated at 25 ºC at 600 rpm for 1 hr. Cells were washed three times with 500 uL dig-300 buffer and resuspended in 300 uL tagmentation buffer (10mM MgCl2 in dig-300 buffer) and incubated at 37 ºC at 600 rpm for 1 hr. Cells were then washed twice with 500 uL TAPS wash buffer (10 mM TAPS (J63268.AE, Thermo Fisher Scientific) and resuspended in 100 uL of proteinase K solution (0.5 mg/mL Proteinase K (EO0491, Thermo Fisher Scientific), 0.5% SDS in 10mM Tris-HCl pH 8.0). Samples were vortexed on full and incubated at 55 ºC for 1 hr at 800 rpm. DNA was extracted using DNA Clean & Concentrator 5 (D4013, Zymo Research) following the manufacturer’s instructions, DNA was eluted in 25 uL DNA elution buffer.

value: myelogenous leukemia

value: K562 aWT

value: IgG


title: 2024002, whole, OLIG2+, snRNAseq

description:
Library name: 2024002wh-olig
10x Genomics


title: IgG_WT_B2

description: Library name: Sample 2


title: 2023002, whole, PU.1+, snRNAseq

description:
Library name: 2023002wh-mglia
10x Genomics


title: NR4A2/IL12 rep 1

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

description: Library name: KM-005

data_processing: Raw FASTQ files were processed adapter trimming using Trim Galore! (v0.6.10), followed by quality control with FastQC (v0.12.1). Reads are aligned to the GRCh38 genome using STAR (v2.7.10a), and gene quantification is performed with Salmon (v1.10.1). Results are summarized with MultiQC (v1.14).

source_name: T cells

extract_protocol:
Total quantity of extracted RNA from purified human CAR T cells was measured using Qubit RNA HS (Thermo Fisher Scientific). A total of 125 ng good-quality RNA was used for library preparation following manufacturer’s instructions (QuantSeq 3’ mRNA-Seq V2, Lexogen).
Libraries were constructed using an oligodT primer and a random forward primer containing the Illumina Read2 linker and the Illumina Read1 linker, respectively. Following this, the library was amplified using PCR primers incorporating sample indices and the Illumina clustering sequences. Indexed libraries were pooled and sequenced using a NextSeq2000 (Illumina) to generate 5 – 15 million single-end 100 bp reads per sample.

value: T cells


title: NR4A2/GFP rep 2

description: Library name: KM-004


title: 2023001, whole, unenriched, snRNAseq,rep3

description:
Library name: 2023001wh-all3
10x Genomics


title: TBP in KO


title: 2023001, whole, unenriched, snRNAseq,rep2

description:
Library name: 2023001wh-all2
10x Genomics


title: Mock rep 2

description: Library name: KM-002


title: NR4A2/GFP rep 1

description: Library name: KM-003


title: 2023001, whole, unenriched, snRNAseq,rep1

description:
Library name: 2023001wh-all1
10x Genomics


title: H3K4Me3 in KO


title: leaves, OX5-3-RNA-seq

city: guangzhou

first: qi

last: guo

address: Wushan Street five road No. 483

country: China

institute: South China Agricultural University

data_processing:
Illumina Casava software used for basecalling.
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%)
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
The KEGG PATHWAY enrichment of DEGs was implemented by the hypergeometric test. KEGG terms with q<0.05 were considered to be significantly enriched. genome build
Assembly: soybean leaves
Supplementary files format and content: tab-delimited text files include raw counts for each Sample .
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

source_name: leaves

extract_protocol:
RNA was extracted from the sample by using Trizol Reagent (Invitrogen) , and then the RNA sample was strictly controlled.RNA purity was detected by NanoPhotometer® spectrophotometer (Thermo Fisher). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina NR604-01/02,

value: leaves

tag: line


title: BEAS2B, 30w, PET, rep2

city: Bellaterra

first: Alba

last: Hernández

state: Barcelona

address: Campus UAB, s/n

department: Genetics and Microbiology

country: Spain

institute: Universitat Autònoma de Barcelona

description: Library name: Sample13

data_processing:
Illumina packages: RTA (Real Time Analysis) and bcl2fastq
Sequence reads were trimmed for adaptor sequence/low quality sequence using Rfastp 1.12.0 (parameters- cutLowQualFront/cutLowQualTail: TRUE minReadLength: 20)
Trimmed sequences reas were mapped to hg38 using align function from Rsubread 2.16.1 (parameters- type: rna)
Read counts were performed using featureCounts function from Rsubread 2.16.1 (parameters- annot.inbuilt: hg38 isPairedEnd: TRUE maxMOp: 15)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: lung

growth_protocol: BEAS2B cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% non-essential aminoacids and 2.5 µg/mL Plasmocin. Cells were maintained in T-75 flasks in a humidified incubator at 37°C with 5% CO₂ and 95% air. Subculturing was performed when cells reached approximately 80% confluence, using trypsin for detachment.

extract_protocol:
Cells were extracted on 70-80% confluence with TRI® Reagent according to the manufacturer’s instructions. DNA contamination was removed using RNase-free DNase I.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold kit following manufacter's protocol.

treatment_protocol: BEAS-2B cells were exposed to 50 µg/mL of PET-NPLs replacing the cell culture medium every 3-4 days with new fresh medium containing the selected concentration of PET-NPLs. Data was collected after 24 hours, 15 weeks or 30 weeks of exposure.

value: lung

value: bronchial epithelial

value: PET-NPLs for 30w


title: leaves, OX5-4-RNA-seq


title: 2024002, whole, unenriched, snRNAseq

description:
Library name: 2024002wh-all
10x Genomics


title: BEAS2B, 30w, PET, rep3

description: Library name: Sample14


title: leaves, OX5-1-RNA-seq


title: leaves, WT-4-RNA-seq

value: WT


title: leaves, OX5-2-RNA-seq


title: BEAS2B, 30w, PET, rep1

description: Library name: Sample12


title: BEAS2B, 30w, Negative control, rep3

description: Library name: Sample11


title: NR4A2/IL12 rep 2

description: Library name: KM-006


title: leaves, WT-3-RNA-seq


title: BEAS2B, 30w, Negative control, rep2

description: Library name: Sample10


title: BEAS2B, 15w, PET, rep2

description: Library name: Sample8

value: PET-NPLs for 15w


title: leaves, WT-2-RNA-seq


title: BEAS2B, 30w, Negative control, rep1

description: Library name: Sample9


title: BEAS2B, 15w, PET, rep1

description: Library name: Sample7


title: leaves, WT-1-RNA-seq


title: 2023002, whole, unenriched, snRNAseq

description:
Library name: 2023002wh-all
10x Genomics


title: BEAS2B, 15w, Negative control, rep1

description: Library name: Sample5


title: Mock rep 1

description: Library name: KM-001


title: BEAS2B, 30w, PET, rep4

description: Library name: Sample15


title: Enriched NO enteric ganglioid.CD24+GFP+.1

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

description:
Library name: Sample7
PP121_GFPplus_S82_r2.bam

data_processing:
Reads were aligned using STAR (2.7) to the human genome (hg38).
featureCounts (v1.6.2) was then used to measure gene counts across samples.
DESeq2 was used to calculate log-fold changes
GRCh38
Assembly: Processed data is provided as (.txt) files containing  sample transcript abundance (tmp normalization) and a (.txt) raw gene count matrix.
Supplementary files format and content: counts, normalized counts, and differential expression analysis

source_name: hPSC-derived ENS culture

growth_protocol: NOS1::GFP reporter H9 hPSC lines were grown on E8 medium.  A previously established 12-day protocol was used to induce enteric neural crest (ENC) (Barber et al., 2019; Fattahi et al., 2016). ENC crestospheres were formed during D12–D15 by removing ENC induction crest medium C on D12 and detaching the ENC monolayers using accutase (30 min, 37 C, 5% CO2), and re-suspended the ENC cells in NC-C medium [FGF2 (10 ng ml-1), CHIR 99021 (3 μM), N2 supplement (10 μl ml-1), B27 supplement (20 μl ml-1), glutagro (10 μl ml-1), and MEM NEAAs (10 μl ml-1) in neurobasal medium] and transferred them to ultra-low-attachment plates to form free-floating 3D enteric crestospheres. On D14, cells were fed with fresh medium. On D15, enteric crestospheres medium was switched to ENC medium [GDNF (10 ng ml-1), ascorbic acid (100 μM), N2 supplement (10 μl ml-1), B27 supplement (20 μl ml-1), glutagro (10 μl ml-1), and MEM NEAAs (10 μl ml-1) in neurobasal medium]. Feeding continued every other day with ENC medium until D30-D40, after which, feeding frequency could be reduced to once or twice per week but at a higher volume. For PP121 treated sample, cells ere treated D15-D20 with PP121.

extract_protocol:
RNA-seq libraries were prepared using QuantSeq (per manufacturers instructions).
BulkRNA sequencing: The libraries were sequenced on a 2x 35 bp PE run on a NextSeq 550 instrument (Illumina).

treatment_protocol: RNA was collected and isolated using the PureLink RNA Isolation kit (Thermo).

value: hPSC-derived ENS culture

value: neural


title: Enriched NO enteric ganglioid.CD24+GFP+.2

description:
Library name: Sample8
PP121_GFPplus_S94_r6.bam


title: BEAS2B, 24h, PET, rep2

description: Library name: Sample4

value: PET-NPLs for 24h


title: BEAS2B, 24h, PET, rep1

description: Library name: Sample3


title: Control enteric ganglioid.CD24+GFP+.1

description:
Library name: Sample3
cntrl_GFPplus_S79_r1.bam


title: BEAS2B, 24h, Negative control, rep2

description: Library name: Sample2


title: BEAS2B, 24h, Negative control, rep1

description: Library name: Sample1


title: Control enteric ganglioid.CD24+GFP+.2

description:
Library name: Sample4
cntrl_GFPplus_S85_r3.bam


title: Control enteric ganglioid.CD24+GFP-.2

description:
Library name: Sample2
cntrl_GFP._S92_r5.bam


title: CART19-CD28_ Day15 biorep3

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 1st St SW

institute: Mayo Clinic

description: Library name: 27_2_C360_CAR19-CD28_D15_R

data_processing:
Differentially expressed genes in UTD versus BBζ D8, D15 and 28ζ D8, D15 was analyzed using the “limma” (v3.58.1) R package after removing lowly expressed genes and voom transformation.
Assembly: genome reference consortium human build 38 patch release 13 (GRCh38.p13) downloaded from NCBI
Supplementary files format and content: voom_normalized_data.xlsx

source_name: cells from normal donor

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
cDNA libraries were prepared using 100 ng of total RNA according to the manufacturer's instructions for the QuantSeq 3' mRNA-Seq Library Kit (Lexogen, Greenland, NH, USA)

value: cells from normal donor

value: T cell

value: Activated through CAR


title: WTC11 hiPSC-PC_3

city: Seoul

first: Yoo Jin

last: Shin

address: 222, Banpo-daero, Seocho-gu,

department: Transplantation Research Center

institute: College of Medicine, The Catholic University of Korea

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: WTC11 hiPSC-PC

growth_protocol: iPSC-ECs were maintained in STEMdiff™ Endothelial Expansion Medium. iPSC-PCs were cultured in DMEM/F12 containing Glutamax and 1X B27, supplemented with 100 ng/ml BMP7, 100 ng/ml Activin A, 50 ng/ml VEGF, 3 μM CHIR99021, and 0.1 μM RA. All cell types were cultured in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: hiPSC-ECs and hiPSC-PCs were treated with 20 μg/mL of A4GALT siRNA-HLNP for 24 hours.

value: WTC11 hiPSC-PC

value: iPSC-derived podocyte


title: CART19-4-1BB_ Day15 biorep2

description: Library name: 22_C359_CAR19-4-1BB_D15


title: CART19-CD28_ Day15 biorep2

description: Library name: 26_2_C359_CAR19-CD28_D15_R


title: WTC11 hiPSC-PC_1


title: Control enteric ganglioid.CD24+GFP-.1

description:
Library name: Sample1
cntrl_GFP._S80_r1.bam


title: WTC11 hiPSC-EC_3

source_name: WTC11 hiPSC-EC

value: WTC11 hiPSC-EC

value: iPSC-derived endothelial cell


title: WTC11 hiPSC-PC_2


title: WTC11 hiPSC-EC_2


title: H3K4Me3 in 3XHA-Taf13 expressing cells

value: ES cells

value: doxycycline


title: CART19-4-1BB_ Day15 biorep3

description: Library name: 23_C360_CAR19-4-1BB_D15


title: BEAS2B, 15w, Negative control, rep2

description: Library name: Sample6

value: lung


title: Enriched NO enteric ganglioid.CD24+GFP-.1

description:
Library name: Sample5
PP121_GFP._S83_r2.bam


title: CART19-CD28_ Day15 biorep1

description: Library name: 25_C344_CAR19-CD28_D15


title: Untransduced control T cells_ Day15 biorep2

description: Library name: 19_C359_UTD_D15


title: Untransduced control T cells_ Day15 biorep1

description: Library name: 18_C344_UTD_D15


title: CART19-4-1BB_ Day15 biorep1

description: Library name: 21_C344_CAR19-4-1BB_D15


title: CART19-CD28_ Day8 biorep2

description: Library name: 15_C359_CAR19-CD28_D8

value: Activated through TCR


title: Enriched NO enteric ganglioid.CD24+GFP-.2

description:
Library name: Sample6
PP121_GFP._S95_r6.bam


title: GLA-KO+siRNA-HLNP hiPSC-PC_1

source_name: GLA-KO hiPSC-PC

value: GLA-KO hiPSC-PC

value: GLA-knock out

value: A4GALT siRNA-HLNP


title: CART19-CD28_ Day8 biorep3

description: Library name: 16_C360_CAR19-CD28_D8


title: CART19-4-1BB_ Day8 biorep3

description: Library name: 12_C360_CAR19-4-1BB_D8


title: GLA-KO+siRNA-HLNP hiPSC-EC_2

source_name: GLA-KO hiPSC-EC

value: GLA-KO hiPSC-EC


title: GLA-KO+siRNA-HLNP hiPSC-PC_3


title: GLA-KO+siRNA-HLNP hiPSC-EC_1


title: GLA-KO+siRNA-HLNP hiPSC-EC_3


title: CART19-4-1BB_ Day8 biorep2

description: Library name: 11_C359_CAR19-4-1BB_D8


title: CART19-4-1BB_ Day8 biorep1

description: Library name: 10_C344_CART19-4-1BB_D8


title: GLA-KO hiPSC-PC_3


title: Untransduced control T cells_ Day8 biorep3

description: Library name: 08_C360_UTD_D8


title: WTC11 hiPSC-EC_1

value: WT


title: GLA-KO hiPSC-PC_2


title: GLA-KO hiPSC-EC_3


title: Untransduced control T cells_ Day8 biorep2

description: Library name: 07_C359_UTD_D8


title: GLA-KO hiPSC-EC_2


title: Untransduced control T cells_ Day8 biorep1

description: Library name: 06_C344_UTD_D8


title: T cells D0_ not activated biorep3

description: Library name: 04_C360_T_cell_D0

value: not activated


title: T cells D0_ not activated biorep2

description: Library name: 03_C359_T_cell_D0

value: cells from normal donor


title: GLA-KO hiPSC-EC_1


title: CART19-CD28_ Day8 biorep1

description: Library name: 14_C344_CAR19-CD28_D8

value: T cell


title: GLA-KO hiPSC-PC_1


title: T cells D0_ not activated biorep1

description: Library name: 02_C344_T_cell_D0


title: Placental explants, 7 mM glucose, biol rep 4

city: Leeds

first: Abigail

middle: Rose

last: Byford

address: Clarendon Way

institute: University of Leeds

description:
Library name: 88_7
GLU_7_088

data_processing:
Raw reads of FASTQ format were processed through fastp to remove reads containing adapter sequences, poly-N and low-quality reads.
Error scores, such as Q20 and Q30, were used as a cut off so that all downstream analyses were based on clean data with high quality.
Reads were then mapped to a reference genome (Homo Sapiens, GRCh38/hg38)  and aligned using STAR. FeatureCounts was used to count the read numbers mapped to each gene.
Assembly: GRCh38/hg38
Supplementary files format and content: read counts for each sample (readcount.txt)
Supplementary files format and content: fpkm values for each sample (fpkm_sample.txt)

source_name: Placenta

growth_protocol: Placental explants were cultured in DMEM-F12 medium, supplemented with 10% fetal bovine serum, 1% penicillin, streptomycin, and glutamine with 5.5 mM glucose.

extract_protocol:
mirVana miRNA isolation kit (Invitrogen)
Novogene next generation sequencing (NGS) RNA Library Prep Set (PT042)

treatment_protocol: Explants were exposed to either constant 5-, 5.5- 7-mM glucose, or fluctuating 5/5.5 mM glucose every 6-18 hours for a total of 48 hours.

value: Placenta

value: 7 mM glucose


title: Human Duodenal Epithelial Organoid, Digesta AuPS25, 24 hours, bio rep 2

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road,

department: Department of Genetics

institute: Rutgers University

description:
Library name: T17
column name in FPKM_All_Samples.csv: T17

data_processing:
kallisto_linux-v0.50.0 was used to align raw sequencing data (fastq) to hg19 reference genome to create H5 files
DESeq2 (v1.46.0) in R (v4.4) was used for differential expression analysis and generation of FPKM table
Assembly: hg19
Supplementary files format and content: csv file including FPKM of all samples

source_name: Intestine

growth_protocol: The duodenum-chip (DC) model was prepared and matured using the 8-day protocol provided by Emulate, Inc.

extract_protocol:
TRIzol extraction, followed by cleanup using Qiagen RNeasy Micro Kit
Library preparation was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: small intestinal digestas of food model (water) with and without AuPS25 were combined with warm de-gassed organoid maintenance media a ratio of 1:11. Media in the epithelial channel inlet reservoirs was replaced with 1.2 mL of digesta-media mixtures, media in the endothelial inlet reservoirs was replaced with fresh warm de-gassed HIMEC media, and all effluent media was aspirated from epithelial and endothelial outlet reservoirs and replaced with 50 µL of organoid maintenance media and HIMEC media

value: Intestine


title: Human Duodenal Epithelial Organoid, Digesta AuPS25, 24 hours, bio rep 3

description:
Library name: T18
column name in FPKM_All_Samples.csv: T18


title: Human Duodenal Epithelial Organoid, Digesta AuPS25, 24 hours, bio rep 1

description:
Library name: T16
column name in FPKM_All_Samples.csv: T16


title: Human Duodenal Epithelial Organoid, Blank Digesta, 24 hours, bio rep 1

description:
Library name: T13
column name in FPKM_All_Samples.csv: T13


title: Placental explants, 5 mM glucose, biol rep 5

description:
Library name: 92_5
GLU_5_092

value: 5 mM glucose


title: Placental explants, 7 mM glucose, biol rep 3

description:
Library name: 83_7
GLU_7_083


title: Placental explants, 7 mM glucose, biol rep 2

description:
Library name: 81_7
GLU_7_081


title: Human Duodenal Epithelial Organoid, Untreated, 24 hours, bio rep 3

description:
Library name: U3
column name in FPKM_All_Samples.csv: U3


title: Placental explants, 7 mM glucose, biol rep 1

description:
Library name: 80_7
GLU_7_080


title: Human Duodenal Epithelial Organoid, Untreated, 24 hours, bio rep 2

description:
Library name: U2
column name in FPKM_All_Samples.csv: U2


title: Placental explants, 5 mM glucose, biol rep 3

description:
Library name: 83_5
GLU_5_083


title: Human Duodenal Epithelial Organoid, Blank Digesta, 24 hours, bio rep 2

description:
Library name: T14
column name in FPKM_All_Samples.csv: T14


title: Placental explants, 5 mM glucose, biol rep 4

description:
Library name: 88_5
GLU_5_088


title: Human Duodenal Epithelial Organoid, Untreated, 24 hours, bio rep 1

description:
Library name: U1
column name in FPKM_All_Samples.csv: U1


title: Placental explants, 5.5 mM glucose, biol rep 3

description:
Library name: 83_5_5
GLU_5_5_083

value: 5.5 mM glucose


title: Placental explants, 7 mM glucose, biol rep 7

description:
Library name: 92_7
GLU_7_092


title: Placental explants, 5 mM glucose, biol rep 2

description:
Library name: 81_5
GLU_5_081


title: Placental explants, 5 mM glucose, biol rep 1

description:
Library name: 80_5
GLU_5_080


title: Placental explants, 5.5 mM glucose, biol rep 5

description:
Library name: 92_5_5
GLU_5_5_092


title: Placental explants, 5.5 mM glucose, biol rep 2

description:
Library name: 81_5_5
GLU_5_5_081


title: Placental explants, 5.5 mM glucose, biol rep 4

description:
Library name: 88_5_5
GLU_5_5_088


title: Human Duodenal Epithelial Orgnaoid, Blank Digesta, 24 hours, bio rep 3

description:
Library name: T15
column name in FPKM_All_Samples.csv: T15


title: Placental explants, 5.5 mM glucose, biol rep 1

description:
Library name: 80_5_5
GLU_5_5_080


title: Placental explants, 5/5.5 mM glucose, biol rep 3

description:
Library name: 83_5_5_5
GLU_5_5_5_083

value: 5/5.5 mM glucose


title: Placental explants, 5/5.5 mM glucose, biol rep 4

description:
Library name: 88_5_5_5
GLU_5_5_5_088


title: Placental explants, 5/5.5 mM glucose, biol rep 5

description:
Library name: 92_5_5_5
GLU_5_5_5_092


title: Placental explants, 5/5.5 mM glucose, biol rep 2

description:
Library name: 81_5_5_5
GLU_5_5_5_081


title: BEL-A_expansion_differentiation_Rhapsody_Pilot_3

city: London

first: Stephan

last: Menzel

address: Rayne Institute, 123 Coldharbour Lane

department: Comprehensive Cancer Centre

institute: King's College London

description: Library name: Pilot_3_HR_EKDL220003921-1a_HL2JFDSX3_L1_1

data_processing:
cDNA/AbSeq library was sequenced with Illumina NovaSeq6000/PE150.
FastQ files were processed with the Rhapsody Targeted Analysis Pipeline (SevenBridges) according to the protocol at https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/products-pdf-folder/software-informatics/rhapsody-sequence-analysis-pipeline/Rhapsody-Sequence-Analysis-Pipeline-UG.pdf, as described in Li, W., et al. (2024). "Analytical Workflows for Single-Cell Multiomic Data Using the BD Rhapsody Platform." Curr Protoc 4(2): e963.
UMI errors derived from library preparation steps or sequencing base deletions were adjusted using distribution-based error correction (DBEC), to create the final molecule count/cell processed data file.
Transcriptomes were analysed with SeqGeq™/v1.7 (BD Biosciences).
Assembly: GRCh38
Supplementary files format and content: molecule counts per cell after dbec correction without normalisation, comma-separated text (Combined_Pilot_3_HR_EKDL220003921-1a_HL2JFDSX3_L1_1_DBEC_MolsPerCell.csv)

source_name: erythroid precursor

growth_protocol: Cells from the human erythroid cell line BEL-A were cultured according to the protocol described in Trakarnsanga K, Griffiths RE, Wilson MC, et al. An immortalized adult human erythroid line facilitates sustainable and scalable generation of functional red cells. Nat Commun. 2017;8(14750):1-7

extract_protocol:
Pooled cells from both harvests were labelled with oligonucleotide-conjugated antibodies for surface markers (‘AbSeq’) CD71, CD36, CD45, CD44, CD34, CD235a and CD49d. About 25,000 cells were captured into single cartridge well on a BD Rhapsody Express Instrument and each provided with a bead containing oligo nucleotide tags for the cell, unique molecular identifiers and a poly-T tail. All steps were carried out according to the manufacturer's instructions at https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD-Rhapsody-Single-Cell-Analysis-System-Instrument.pdf
Subsequent cDNA libraries were amplified and sequenced with Illumina NovaSeq6000/PE150. Reads were mapped to genes with the Rhapsody Targeted Analysis Pipeline (SevenBridges) and transcriptomes analysed with SeqGeq™/v1.7 (BD Biosciences).

treatment_protocol: Cells were harvested during the expansion phase (mostly proerythroblasts) and on day 2 of the differentiation phase (mostly basophilic erythroblasts). The two stages were discernible through a distinct gain of surface GPA during transition between the stages

value: erythroid precursor

value: BEL-A

value: erythroid line

value: expansion and differentiation steps


title: Placental explants, 5/5.5 mM glucose, biol rep 1

description:
Library name: 80_5_5_5
GLU_5_5_5_080


title: epithelium, IgG, rep 1

city: HeFei

first: Liu

last: Shixian

address: No. 81 Meishan Road

institute: Anhui Medical University

data_processing:
Cutadapt was used to filter out unqualified sequences (sequencing adapters, low-quality sequences, etc.) from the raw data
Assembly: hg18
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Library strategy: CUT&Tag

source_name: epithelium

extract_protocol:
Initially, sample preprocessing involved the conversion of samples into cell suspensions, followed by cell collection and enumeration. Subsequent steps included cell washing, primary antibody binding, and subsequent addition of secondary antibodies. Following secondary antibody binding, the product underwent washing and interaction with ChiTagTM transposase.
Sequencing of the library was conducted on the Illumina platform. For qualified libraries, NaOH was utilized to denature the library into single strands. The denatured library was diluted to a specific concentration based on the expected data volume and then introduced to the FlowCell. Hybridization of the denatured and diluted library with adapters on the FlowCell was followed by bridge PCR amplification on the cBot cluster generation platform, culminating in sequencing on the designated platform.

value: epithelium

value: head and neck squamous cell carcinoma cells

tag: group

value: IgG


title: epithelium, HA-PBX2, rep 1


title: epithelium, IgG, rep 2