title: H5-Tub-MGN356

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN356

source_name: Kidney biopsy from human H5-Tub-MGN356


title: H5-Tub-MGN351

status: Public on Jan 24 2018

type: RNA

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

country: USA

institute: University of Michigan

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN351

hyb_protocol: According to manufacturer's protocols.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: Each batch and platform was processed individually with its corresponding BrainArray CDF and normalized by RMA. After individual batch and platform processing, samples were merged by common EntrezGeneIDs, and finally batch corrected using Combat.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Kidney biopsy from human H5-Tub-MGN351

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol.

tag: tissue

value: Tubulointerstitium from kidney biopsy

tag: diagnosis

value: Membranous glomerulonephropathy


title: H5-Tub-SLE357

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE357

source_name: Kidney biopsy from human H5-Tub-SLE357

value: Systemic lupus erythematosus


title: H5-Tub-SLE346

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE346

source_name: Kidney biopsy from human H5-Tub-SLE346


title: H5-Tub-FSGS341

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS341

source_name: Kidney biopsy from human H5-Tub-FSGS341

value: Focal segmental glomerulosclerosis


title: H5-Tub-FSGS347

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS347

source_name: Kidney biopsy from human H5-Tub-FSGS347


title: H5-Tub-FSGS344

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS344

source_name: Kidney biopsy from human H5-Tub-FSGS344


title: H5-Tub-FSGS345

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS345

source_name: Kidney biopsy from human H5-Tub-FSGS345


title: H5-Tub-MGN334

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN334

source_name: Kidney biopsy from human H5-Tub-MGN334


title: H5-Tub-MGN333

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN333

source_name: Kidney biopsy from human H5-Tub-MGN333


title: H7-Glom-DN901

description: Gene Expression data from the glomerular compartment of human H7-Glom-DN901

source_name: Kidney Biopsy from Human H7-Glom-DN901

value: Glomeruli from kidney biopsy

value: Diabetic Nephropathy


title: H7-Tub-TN1185

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-TN1185

source_name: Kidney biopsy from human H7-Tub-TN1185

value: Tumor nephrectomy


title: H5-Tub-SLE338

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE338

source_name: Kidney biopsy from human H5-Tub-SLE338


title: H5-Tub-SLE342

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE342

source_name: Kidney biopsy from human H5-Tub-SLE342


title: H5-Tub-SLE336

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE336

source_name: Kidney biopsy from human H5-Tub-SLE336


title: H5-Tub-SLE343

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE343

source_name: Kidney biopsy from human H5-Tub-SLE343


title: H7-Tub-RPGN1135

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1135

source_name: Kidney biopsy from human H7-Tub-RPGN1135

value: ANCA-associated vasculitis


title: H5-Tub-FSGS328

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS328

source_name: Kidney biopsy from human H5-Tub-FSGS328


title: H7-Glom-DN910

description: Gene Expression data from the glomerular compartment of human H7-Glom-DN910

source_name: Kidney Biopsy from Human H7-Glom-DN910


title: H7-Tub-RPGN1134

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1134

source_name: Kidney biopsy from human H7-Tub-RPGN1134


title: H5-Tub-MGN335

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN335

source_name: Kidney biopsy from human H5-Tub-MGN335


title: H7-Tub-TN1187

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-TN1187

source_name: Kidney biopsy from human H7-Tub-TN1187


title: H5-Tub-MGN337

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN337

source_name: Kidney biopsy from human H5-Tub-MGN337


title: H5-Tub-SLE340

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE340

source_name: Kidney biopsy from human H5-Tub-SLE340


title: H5-Tub-FSGS332

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS332

source_name: Kidney biopsy from human H5-Tub-FSGS332


title: H5-Tub-FSGS327

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS327

source_name: Kidney biopsy from human H5-Tub-FSGS327


title: H5-Tub-MGN324

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN324

source_name: Kidney biopsy from human H5-Tub-MGN324


title: H5-Tub-MGN325

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN325

source_name: Kidney biopsy from human H5-Tub-MGN325


title: H7-Tub-TN1186

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-TN1186

source_name: Kidney biopsy from human H7-Tub-TN1186


title: H5-Tub-MGN331

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN331

source_name: Kidney biopsy from human H5-Tub-MGN331


title: H7-Tub-RPGN1131

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1131

source_name: Kidney biopsy from human H7-Tub-RPGN1131


title: H5-Tub-FSGS339

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS339

source_name: Kidney biopsy from human H5-Tub-FSGS339


title: H5-Tub-SLE329

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE329

source_name: Kidney biopsy from human H5-Tub-SLE329


title: H5-Tub-MGN330

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN330

source_name: Kidney biopsy from human H5-Tub-MGN330


title: H7-Tub-RPGN1130

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1130

source_name: Kidney biopsy from human H7-Tub-RPGN1130


title: H7-Tub-RPGN1129

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1129

source_name: Kidney biopsy from human H7-Tub-RPGN1129


title: H5-Tub-SLE323

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE323

source_name: Kidney biopsy from human H5-Tub-SLE323


title: H5-Tub-MGN321

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN321

source_name: Kidney biopsy from human H5-Tub-MGN321


title: H7-Tub-RPGN1138

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1138

source_name: Kidney biopsy from human H7-Tub-RPGN1138


title: H5-Tub-MGN316

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN316

source_name: Kidney biopsy from human H5-Tub-MGN316


title: H5-Tub-SLE318

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE318

source_name: Kidney biopsy from human H5-Tub-SLE318


title: H5-Tub-FSGS326

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS326

source_name: Kidney biopsy from human H5-Tub-FSGS326


title: H5-Tub-SLE319

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE319

source_name: Kidney biopsy from human H5-Tub-SLE319


title: H7-Tub-RPGN1127

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1127

source_name: Kidney biopsy from human H7-Tub-RPGN1127


title: H5-Tub-MGN322

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN322

source_name: Kidney biopsy from human H5-Tub-MGN322


title: H5-Tub-SLE314

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE314

source_name: Kidney biopsy from human H5-Tub-SLE314


title: H7-Tub-RPGN1128

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1128

source_name: Kidney biopsy from human H7-Tub-RPGN1128


title: H5-Tub-FSGS320

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-FSGS320

source_name: Kidney biopsy from human H5-Tub-FSGS320


title: H5-Tub-MGN315

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN315

source_name: Kidney biopsy from human H5-Tub-MGN315


title: H5-Tub-MGN317

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN317

source_name: Kidney biopsy from human H5-Tub-MGN317


title: H7-Tub-RPGN1121

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1121

source_name: Kidney biopsy from human H7-Tub-RPGN1121


title: H7-Tub-RPGN1120

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1120

source_name: Kidney biopsy from human H7-Tub-RPGN1120


title: H5-Tub-SLE312

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE312

source_name: Kidney biopsy from human H5-Tub-SLE312


title: H5-Tub-SLE313

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE313

source_name: Kidney biopsy from human H5-Tub-SLE313


title: H5-Tub-SLE311

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE311

source_name: Kidney biopsy from human H5-Tub-SLE311


title: H7-Tub-RPGN1123

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1123

source_name: Kidney biopsy from human H7-Tub-RPGN1123


title: H5-Tub-SLE309

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE309

source_name: Kidney biopsy from human H5-Tub-SLE309


title: H5-Tub-SLE310

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE310

source_name: Kidney biopsy from human H5-Tub-SLE310


title: H5-Tub-SLE305

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE305

source_name: Kidney biopsy from human H5-Tub-SLE305


title: H5-Tub-SLE306

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE306

source_name: Kidney biopsy from human H5-Tub-SLE306


title: H7-Tub-RPGN1119

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1119

source_name: Kidney biopsy from human H7-Tub-RPGN1119


title: H5-Tub-SLE307

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE307

source_name: Kidney biopsy from human H5-Tub-SLE307


title: H5-Tub-SLE304

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE304

source_name: Kidney biopsy from human H5-Tub-SLE304


title: H5-Tub-MGN303

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-MGN303

source_name: Kidney biopsy from human H5-Tub-MGN303


title: H7-Tub-RPGN1126

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1126

source_name: Kidney biopsy from human H7-Tub-RPGN1126


title: H7-Tub-RPGN1118

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1118

source_name: Kidney biopsy from human H7-Tub-RPGN1118


title: H5-Tub-SLE302

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE302

source_name: Kidney biopsy from human H5-Tub-SLE302


title: H5-Tub-SLE301

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE301

source_name: Kidney biopsy from human H5-Tub-SLE301


title: H7-Tub-RPGN1122

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1122

source_name: Kidney biopsy from human H7-Tub-RPGN1122


title: H7-Tub-RPGN1113

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1113

source_name: Kidney biopsy from human H7-Tub-RPGN1113


title: H4-Tub-IgA9

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA9

source_name: Kidney biopsy from human H4-Tub-IgA9

value: IgA nephropathy


title: H7-Tub-RPGN1109

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1109

source_name: Kidney biopsy from human H7-Tub-RPGN1109


title: H4-Tub-IgA8

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA8

source_name: Kidney biopsy from human H4-Tub-IgA8


title: H4-Tub-IgA7

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA7

source_name: Kidney biopsy from human H4-Tub-IgA7


title: H4-Tub-IgA3

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA3

source_name: Kidney biopsy from human H4-Tub-IgA3


title: H4-Tub-IgA6

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA6

source_name: Kidney biopsy from human H4-Tub-IgA6


title: H7-Tub-RPGN1106

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1106

source_name: Kidney biopsy from human H7-Tub-RPGN1106


title: H7-Tub-RPGN1107

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1107

source_name: Kidney biopsy from human H7-Tub-RPGN1107


title: H5-Tub-SLE308

description: Gene expression from the tubulointerstitial compartment of human H5-Tub-SLE308

source_name: Kidney biopsy from human H5-Tub-SLE308


title: H4-Tub-IgA5

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA5

source_name: Kidney biopsy from human H4-Tub-IgA5


title: H4-Tub-IgA4

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA4

source_name: Kidney biopsy from human H4-Tub-IgA4


title: H7-Tub-RPGN1102

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1102

source_name: Kidney biopsy from human H7-Tub-RPGN1102


title: H4-Tub-IgA25

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA25

source_name: Kidney biopsy from human H4-Tub-IgA25


title: H4-Tub-IgA27

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA27

source_name: Kidney biopsy from human H4-Tub-IgA27


title: H7-Tub-RPGN1103

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-RPGN1103

source_name: Kidney biopsy from human H7-Tub-RPGN1103


title: H4-Tub-IgA20

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA20

source_name: Kidney biopsy from human H4-Tub-IgA20


title: H4-Tub-IgA21

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA21

source_name: Kidney biopsy from human H4-Tub-IgA21


title: H4-Tub-IgA19

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA19

source_name: Kidney biopsy from human H4-Tub-IgA19


title: H4-Tub-IgA2

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA2

source_name: Kidney biopsy from human H4-Tub-IgA2


title: H4-Tub-IgA26

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA26

source_name: Kidney biopsy from human H4-Tub-IgA26


title: H4-Tub-IgA24

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA24

source_name: Kidney biopsy from human H4-Tub-IgA24


title: H7-Tub-MCD1112

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-MCD1112

source_name: Kidney biopsy from human H7-Tub-MCD1112

value: Minimal change disease


title: H4-Tub-IgA22

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA22

source_name: Kidney biopsy from human H4-Tub-IgA22


title: H4-Tub-IgA13

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA13

source_name: Kidney biopsy from human H4-Tub-IgA13


title: H7-Tub-MCD1163

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-MCD1163

source_name: Kidney biopsy from human H7-Tub-MCD1163


title: H7-Tub-MCD1137

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-MCD1137

source_name: Kidney biopsy from human H7-Tub-MCD1137


title: H7-Tub-MCD1116

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-MCD1116

source_name: Kidney biopsy from human H7-Tub-MCD1116


title: H7-Tub-LD1184

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1184

source_name: Kidney biopsy from human H7-Tub-LD1184


title: H7-Tub-LD1182

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1182

source_name: Kidney biopsy from human H7-Tub-LD1182


title: H3-Tub-TN2

description: Gene expression from the tubulointerstitial compartment of human H3-Tub-TN2

source_name: Kidney biopsy from human H3-Tub-TN2


title: H4-Tub-IgA18

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA18

source_name: Kidney biopsy from human H4-Tub-IgA18


title: H4-Tub-IgA16

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA16

source_name: Kidney biopsy from human H4-Tub-IgA16


title: H7-Tub-LD1183

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1183

source_name: Kidney biopsy from human H7-Tub-LD1183


title: H4-Tub-IgA1

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA1

source_name: Kidney biopsy from human H4-Tub-IgA1


title: H4-Tub-IgA14

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA14

source_name: Kidney biopsy from human H4-Tub-IgA14


title: H3-Tub-MCD9

description: Gene expression from the tubulointerstitial compartment of human H3-Tub-MCD9

source_name: Kidney biopsy from human H3-Tub-MCD9


title: H3-Tub-MCD11

description: Gene expression from the tubulointerstitial compartment of human H3-Tub-MCD11

source_name: Kidney biopsy from human H3-Tub-MCD11


title: H4-Tub-IgA10

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA10

source_name: Kidney biopsy from human H4-Tub-IgA10


title: H4-Tub-IgA23

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA23

source_name: Kidney biopsy from human H4-Tub-IgA23


title: H4-Tub-IgA12

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA12

source_name: Kidney biopsy from human H4-Tub-IgA12


title: H4-Tub-IgA11

description: Gene expression from the tubulointerstitial compartment of human H4-Tub-IgA11

source_name: Kidney biopsy from human H4-Tub-IgA11


title: H7-Tub-LD1177

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1177

source_name: Kidney biopsy from human H7-Tub-LD1177


title: H7-Tub-LD1178

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1178

source_name: Kidney biopsy from human H7-Tub-LD1178


title: H7-Tub-LD1180

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1180

source_name: Kidney biopsy from human H7-Tub-LD1180


title: H7-Tub-LD1174

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1174

source_name: Kidney biopsy from human H7-Tub-LD1174


title: H3-Tub-MCD8

description: Gene expression from the tubulointerstitial compartment of human H3-Tub-MCD8

source_name: Kidney biopsy from human H3-Tub-MCD8


title: H7-Tub-LD1179

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1179

source_name: Kidney biopsy from human H7-Tub-LD1179


title: H7-Tub-LD1175

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1175

source_name: Kidney biopsy from human H7-Tub-LD1175


title: H2-Tub-HT4

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT4

source_name: Kidney biopsy from human H2-Tub-HT4

value: Hypertensive nephropathy


title: H3-Tub-MCD7

description: Gene expression from the tubulointerstitial compartment of human H3-Tub-MCD7

source_name: Kidney biopsy from human H3-Tub-MCD7


title: H3-Tub-TN6

description: Gene expression from the tubulointerstitial compartment of human H3-Tub-TN6

source_name: Kidney biopsy from human H3-Tub-TN6


title: H2-Tub-HT11

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT11

source_name: Kidney biopsy from human H2-Tub-HT11


title: H2-Tub-HT8

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT8

source_name: Kidney biopsy from human H2-Tub-HT8


title: H2-Tub-HT9

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT9

source_name: Kidney biopsy from human H2-Tub-HT9


title: H2-Tub-HT20

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT20

source_name: Kidney biopsy from human H2-Tub-HT20


title: H7-Tub-LD1170

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1170

source_name: Kidney biopsy from human H7-Tub-LD1170


title: H2-Tub-HT7

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT7

source_name: Kidney biopsy from human H2-Tub-HT7


title: H3-Tub-MCD6

description: Gene expression from the tubulointerstitial compartment of human H3-Tub-MCD6

source_name: Kidney biopsy from human H3-Tub-MCD6


title: H2-Tub-HT2

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT2

source_name: Kidney biopsy from human H2-Tub-HT2


title: H2-Tub-HT17

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT17

source_name: Kidney biopsy from human H2-Tub-HT17


title: H2-Tub-HT3

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT3

source_name: Kidney biopsy from human H2-Tub-HT3


title: H7-Tub-LD1171

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1171

source_name: Kidney biopsy from human H7-Tub-LD1171


title: H2-Tub-HT18

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT18

source_name: Kidney biopsy from human H2-Tub-HT18


title: H2-Tub-HT6

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT6

source_name: Kidney biopsy from human H2-Tub-HT6


title: H7-Tub-LD1165

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1165

source_name: Kidney biopsy from human H7-Tub-LD1165


title: H2-Tub-HT16

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT16

source_name: Kidney biopsy from human H2-Tub-HT16


title: H2-Tub-HT19

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT19

source_name: Kidney biopsy from human H2-Tub-HT19


title: H7-Tub-LD1169

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1169

source_name: Kidney biopsy from human H7-Tub-LD1169


title: H2-Tub-HT13

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT13

source_name: Kidney biopsy from human H2-Tub-HT13


title: H2-Tub-HT5

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT5

source_name: Kidney biopsy from human H2-Tub-HT5


title: H2-Tub-HT14

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT14

source_name: Kidney biopsy from human H2-Tub-HT14


title: H7-Tub-LD1168

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1168

source_name: Kidney biopsy from human H7-Tub-LD1168


title: H2-Tub-HT12

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT12

source_name: Kidney biopsy from human H2-Tub-HT12


title: H7-Tub-LD1173

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1173

source_name: Kidney biopsy from human H7-Tub-LD1173


title: H7-Tub-LD1172

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1172

source_name: Kidney biopsy from human H7-Tub-LD1172


title: H2-Tub-HT15

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT15

source_name: Kidney biopsy from human H2-Tub-HT15


title: H2-Tub-HT10

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT10

source_name: Kidney biopsy from human H2-Tub-HT10


title: H7-Tub-FSGS1115

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-FSGS1115

source_name: Kidney biopsy from human H7-Tub-FSGS1115


title: H2-Tub-HT1

description: Gene expression from the tubulointerstitial compartment of human H2-Tub-HT1

source_name: Kidney biopsy from human H2-Tub-HT1


title: H7-Tub-FSGS&MCD1136

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-FSGS&MCD1136

source_name: Kidney biopsy from human H7-Tub-FSGS&MCD1136

value: Focal segmental glomerulosclerosis and minimal change disease


title: H1-Tub-TMD5

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-TMD5

source_name: Kidney biopsy from human H1-Tub-TMD5

value: Thin membrande disease


title: H7-Tub-LD1164

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1164

source_name: Kidney biopsy from human H7-Tub-LD1164


title: H7-Tub-LD1166

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-LD1166

source_name: Kidney biopsy from human H7-Tub-LD1166


title: H1-Tub-TMD3

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-TMD3

source_name: Kidney biopsy from human H1-Tub-TMD3


title: H1-Tub-TMD2

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-TMD2

source_name: Kidney biopsy from human H1-Tub-TMD2


title: H1-Tub-MCD3

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-MCD3

source_name: Kidney biopsy from human H1-Tub-MCD3


title: H7-Tub-DN1133

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-DN1133

source_name: Kidney biopsy from human H7-Tub-DN1133

value: Diabetic nephropathy


title: H7-Tub-DN1139

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-DN1139

source_name: Kidney biopsy from human H7-Tub-DN1139


title: H7-Tub-DN1132

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-DN1132

source_name: Kidney biopsy from human H7-Tub-DN1132


title: H7-Tub-FSGS&MCD1117

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-FSGS&MCD1117

source_name: Kidney biopsy from human H7-Tub-FSGS&MCD1117


title: H1-Tub-MCD2

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-MCD2

source_name: Kidney biopsy from human H1-Tub-MCD2


title: H1-Tub-TMD1

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-TMD1

source_name: Kidney biopsy from human H1-Tub-TMD1


title: H1-Tub-MCD4

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-MCD4

source_name: Kidney biopsy from human H1-Tub-MCD4


title: H1-Tub-TMD6

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-TMD6

source_name: Kidney biopsy from human H1-Tub-TMD6


title: H1-Tub-MCD1

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-MCD1

source_name: Kidney biopsy from human H1-Tub-MCD1


title: H7-Tub-FSGS&MCD1104

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-FSGS&MCD1104

source_name: Kidney biopsy from human H7-Tub-FSGS&MCD1104


title: H7-Tub-FSGS1162

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-FSGS1162

source_name: Kidney biopsy from human H7-Tub-FSGS1162


title: H7-Tub-DN1108

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-DN1108

source_name: Kidney biopsy from human H7-Tub-DN1108


title: H1-Tub-DN7

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN7

source_name: Kidney biopsy from human H1-Tub-DN7


title: H7-Tub-FSGS&MCD1124

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-FSGS&MCD1124

source_name: Kidney biopsy from human H7-Tub-FSGS&MCD1124


title: H1-Tub-DN9

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN9

source_name: Kidney biopsy from human H1-Tub-DN9


title: H7-Tub-DN1110

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-DN1110

source_name: Kidney biopsy from human H7-Tub-DN1110


title: H7-Tub-DN1114

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-DN1114

source_name: Kidney biopsy from human H7-Tub-DN1114


title: H7-Tub-FSGS1125

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-FSGS1125

source_name: Kidney biopsy from human H7-Tub-FSGS1125


title: H1-Tub-TMD4

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-TMD4

source_name: Kidney biopsy from human H1-Tub-TMD4


title: H1-Tub-DN5

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN5

source_name: Kidney biopsy from human H1-Tub-DN5


title: H1-Tub-DN2

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN2

source_name: Kidney biopsy from human H1-Tub-DN2


title: H1-Tub-DN3

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN3

source_name: Kidney biopsy from human H1-Tub-DN3


title: H7-Glom-TN997

description: Gene Expression data from the glomerular compartment of human H7-Glom-TN997

source_name: Kidney Biopsy from Human H7-Glom-TN997

value: Tumor Nephrectomy


title: H7-Tub-DN1101

description: Gene expression from the tubulointerstitial compartment of human H7-Tub-DN1101

source_name: Kidney biopsy from human H7-Tub-DN1101


title: H7-Glom-TN995

description: Gene Expression data from the glomerular compartment of human H7-Glom-TN995

source_name: Kidney Biopsy from Human H7-Glom-TN995


title: H7-Glom-RPGN946

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN946

source_name: Kidney Biopsy from Human H7-Glom-RPGN946

value: ANCA Associated Vasculitis


title: H7-Glom-RPGN942

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN942

source_name: Kidney Biopsy from Human H7-Glom-RPGN942


title: H7-Glom-TN996

description: Gene Expression data from the glomerular compartment of human H7-Glom-TN996

source_name: Kidney Biopsy from Human H7-Glom-TN996


title: H1-Tub-DN10

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN10

source_name: Kidney biopsy from human H1-Tub-DN10


title: H7-Glom-RPGN943

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN943

source_name: Kidney Biopsy from Human H7-Glom-RPGN943


title: H7-Glom-RPGN938

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN938

source_name: Kidney Biopsy from Human H7-Glom-RPGN938


title: H1-Tub-DN1

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN1

source_name: Kidney biopsy from human H1-Tub-DN1


title: H1-Tub-DN8

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN8

source_name: Kidney biopsy from human H1-Tub-DN8


title: H7-Glom-RPGN937

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN937

source_name: Kidney Biopsy from Human H7-Glom-RPGN937


title: H5-Glom-SLE465

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE465

source_name: Kidney Biopsy from Human H5-Glom-SLE465

value: Systemic Lupus Erythematosus


title: H7-Glom-RPGN939

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN939

source_name: Kidney Biopsy from Human H7-Glom-RPGN939


title: H5-Glom-SLE467

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE467

source_name: Kidney Biopsy from Human H5-Glom-SLE467


title: H7-Glom-RPGN934

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN934

source_name: Kidney Biopsy from Human H7-Glom-RPGN934


title: H5-Glom-SLE464

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE464

source_name: Kidney Biopsy from Human H5-Glom-SLE464


title: H7-Glom-RPGN936

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN936

source_name: Kidney Biopsy from Human H7-Glom-RPGN936


title: H1-Tub-DN6

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN6

source_name: Kidney biopsy from human H1-Tub-DN6

value: Tubulointerstitium from kidney biopsy


title: H5-Glom-SLE462

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE462

source_name: Kidney Biopsy from Human H5-Glom-SLE462


title: H5-Glom-SLE463

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE463

source_name: Kidney Biopsy from Human H5-Glom-SLE463


title: H7-Glom-RPGN928

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN928

source_name: Kidney Biopsy from Human H7-Glom-RPGN928


title: H7-Glom-RPGN930

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN930

source_name: Kidney Biopsy from Human H7-Glom-RPGN930


title: H5-Glom-SLE451

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE451

source_name: Kidney Biopsy from Human H5-Glom-SLE451


title: H1-Tub-DN11

description: Gene expression from the tubulointerstitial compartment of human H1-Tub-DN11

source_name: Kidney biopsy from human H1-Tub-DN11


title: H5-Glom-SLE454

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE454

source_name: Kidney Biopsy from Human H5-Glom-SLE454


title: H7-Glom-RPGN925

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN925

source_name: Kidney Biopsy from Human H7-Glom-RPGN925


title: H5-Glom-SLE448

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE448

source_name: Kidney Biopsy from Human H5-Glom-SLE448


title: H5-Glom-SLE450

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE450

source_name: Kidney Biopsy from Human H5-Glom-SLE450


title: H7-Glom-RPGN924

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN924

source_name: Kidney Biopsy from Human H7-Glom-RPGN924


title: H7-Glom-RPGN913

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN913

source_name: Kidney Biopsy from Human H7-Glom-RPGN913


title: H5-Glom-SLE445

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE445

source_name: Kidney Biopsy from Human H5-Glom-SLE445


title: H7-Glom-RPGN929

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN929

source_name: Kidney Biopsy from Human H7-Glom-RPGN929


title: H5-Glom-SLE444

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE444

source_name: Kidney Biopsy from Human H5-Glom-SLE444


title: H5-Glom-SLE442

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE442

source_name: Kidney Biopsy from Human H5-Glom-SLE442


title: H5-Glom-SLE440

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE440

source_name: Kidney Biopsy from Human H5-Glom-SLE440


title: H7-Glom-RPGN909

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN909

source_name: Kidney Biopsy from Human H7-Glom-RPGN909


title: H5-Glom-SLE430

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE430

source_name: Kidney Biopsy from Human H5-Glom-SLE430


title: H5-Glom-SLE423

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE423

source_name: Kidney Biopsy from Human H5-Glom-SLE423


title: H7-Glom-RPGN902

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN902

source_name: Kidney Biopsy from Human H7-Glom-RPGN902


title: H5-Glom-SLE414

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE414

source_name: Kidney Biopsy from Human H5-Glom-SLE414


title: H7-Glom-RPGN906

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN906

source_name: Kidney Biopsy from Human H7-Glom-RPGN906


title: H7-Glom-RPGN908

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN908

source_name: Kidney Biopsy from Human H7-Glom-RPGN908


title: H7-Glom-RPGN911

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN911

source_name: Kidney Biopsy from Human H7-Glom-RPGN911


title: H5-Glom-SLE418

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE418

source_name: Kidney Biopsy from Human H5-Glom-SLE418


title: H5-Glom-SLE419

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE419

source_name: Kidney Biopsy from Human H5-Glom-SLE419


title: H7-Glom-RPGN904

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN904

source_name: Kidney Biopsy from Human H7-Glom-RPGN904


title: H7-Glom-RPGN907

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN907

source_name: Kidney Biopsy from Human H7-Glom-RPGN907


title: H7-Glom-RPGN926

description: Gene Expression data from the glomerular compartment of human H7-Glom-RPGN926

source_name: Kidney Biopsy from Human H7-Glom-RPGN926


title: H5-Glom-SLE413

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE413

source_name: Kidney Biopsy from Human H5-Glom-SLE413


title: H5-Glom-SLE412

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE412

source_name: Kidney Biopsy from Human H5-Glom-SLE412


title: H5-Glom-SLE411

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE411

source_name: Kidney Biopsy from Human H5-Glom-SLE411


title: H5-Glom-SLE438

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE438

source_name: Kidney Biopsy from Human H5-Glom-SLE438


title: H5-Glom-SLE410

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE410

source_name: Kidney Biopsy from Human H5-Glom-SLE410


title: H7-Glom-MCD945

description: Gene Expression data from the glomerular compartment of human H7-Glom-MCD945

source_name: Kidney Biopsy from Human H7-Glom-MCD945

value: Minimal Change Disease


title: H7-Glom-MCD919

description: Gene Expression data from the glomerular compartment of human H7-Glom-MCD919

source_name: Kidney Biopsy from Human H7-Glom-MCD919


title: H7-Glom-LD_993

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_993

source_name: Kidney Biopsy from Human H7-Glom-LD_993


title: H7-Glom-MCD921

description: Gene Expression data from the glomerular compartment of human H7-Glom-MCD921

source_name: Kidney Biopsy from Human H7-Glom-MCD921


title: H7-Glom-LD_994

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_994

source_name: Kidney Biopsy from Human H7-Glom-LD_994


title: H5-Glom-SLE409

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE409

source_name: Kidney Biopsy from Human H5-Glom-SLE409


title: H7-Glom-LD_992

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_992

source_name: Kidney Biopsy from Human H7-Glom-LD_992


title: H5-Glom-SLE408

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE408

source_name: Kidney Biopsy from Human H5-Glom-SLE408


title: H5-Glom-SLE406

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE406

source_name: Kidney Biopsy from Human H5-Glom-SLE406


title: H7-Glom-LD_990

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_990

source_name: Kidney Biopsy from Human H7-Glom-LD_990


title: H5-Glom-SLE407

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE407

source_name: Kidney Biopsy from Human H5-Glom-SLE407


title: H7-Glom-LD_988

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_988

source_name: Kidney Biopsy from Human H7-Glom-LD_988


title: H5-Glom-SLE405

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE405

source_name: Kidney Biopsy from Human H5-Glom-SLE405


title: H7-Glom-MCD973

description: Gene Expression data from the glomerular compartment of human H7-Glom-MCD973

source_name: Kidney Biopsy from Human H7-Glom-MCD973


title: H7-Glom-LD_987

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_987

source_name: Kidney Biopsy from Human H7-Glom-LD_987


title: H7-Glom-LD_989

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_989

source_name: Kidney Biopsy from Human H7-Glom-LD_989


title: H5-Glom-MGN461

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN461

source_name: Kidney Biopsy from Human H5-Glom-MGN461

value: Membranous Glomerulonephropathy


title: H5-Glom-SLE404

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE404

source_name: Kidney Biopsy from Human H5-Glom-SLE404


title: H5-Glom-SLE402

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE402

source_name: Kidney Biopsy from Human H5-Glom-SLE402


title: H5-Glom-SLE401

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE401

source_name: Kidney Biopsy from Human H5-Glom-SLE401


title: H7-Glom-LD_984

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_984

source_name: Kidney Biopsy from Human H7-Glom-LD_984


title: H7-Glom-MCD903

description: Gene Expression data from the glomerular compartment of human H7-Glom-MCD903

source_name: Kidney Biopsy from Human H7-Glom-MCD903


title: H7-Glom-LD_985

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_985

source_name: Kidney Biopsy from Human H7-Glom-LD_985


title: H7-Glom-LD_981

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_981

source_name: Kidney Biopsy from Human H7-Glom-LD_981


title: H5-Glom-MGN456

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN456

source_name: Kidney Biopsy from Human H5-Glom-MGN456


title: H5-Glom-MGN460

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN460

source_name: Kidney Biopsy from Human H5-Glom-MGN460


title: H7-Glom-LD_983

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_983

source_name: Kidney Biopsy from Human H7-Glom-LD_983


title: H7-Glom-LD_980

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_980

source_name: Kidney Biopsy from Human H7-Glom-LD_980


title: H7-Glom-LD_982

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_982

source_name: Kidney Biopsy from Human H7-Glom-LD_982


title: H5-Glom-MGN455

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN455

source_name: Kidney Biopsy from Human H5-Glom-MGN455


title: H5-Glom-MGN453

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN453

source_name: Kidney Biopsy from Human H5-Glom-MGN453


title: H5-Glom-MGN437

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN437

source_name: Kidney Biopsy from Human H5-Glom-MGN437


title: H7-Glom-LD_979

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_979

source_name: Kidney Biopsy from Human H7-Glom-LD_979


title: H7-Glom-LD_978

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_978

source_name: Kidney Biopsy from Human H7-Glom-LD_978


title: H7-Glom-LD_975

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_975

source_name: Kidney Biopsy from Human H7-Glom-LD_975


title: H7-Glom-LD_976

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_976

source_name: Kidney Biopsy from Human H7-Glom-LD_976


title: H5-Glom-MGN439

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN439

source_name: Kidney Biopsy from Human H5-Glom-MGN439


title: H5-Glom-MGN435

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN435

source_name: Kidney Biopsy from Human H5-Glom-MGN435


title: H7-Glom-LD_974

description: Gene Expression data from the glomerular compartment of human H7-Glom-LD_974

source_name: Kidney Biopsy from Human H7-Glom-LD_974


title: H5-Glom-MGN432

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN432

source_name: Kidney Biopsy from Human H5-Glom-MGN432


title: H5-Glom-MGN431

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN431

source_name: Kidney Biopsy from Human H5-Glom-MGN431


title: H7-Glom-FSGS972

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS972

source_name: Kidney Biopsy from Human H7-Glom-FSGS972

value: Focal Segmental Glomerular Sclerosis


title: H7-Glom-FSGS970

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS970

source_name: Kidney Biopsy from Human H7-Glom-FSGS970

value: Glomeruli from kidney biopsy


title: H7-Glom-FSGS927

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS927

source_name: Kidney Biopsy from Human H7-Glom-FSGS927


title: H5-Glom-MGN452

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN452

source_name: Kidney Biopsy from Human H5-Glom-MGN452


title: H7-Glom-FSGS933

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS933

source_name: Kidney Biopsy from Human H7-Glom-FSGS933


title: H7-Glom-FSGS918

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS918

source_name: Kidney Biopsy from Human H7-Glom-FSGS918


title: H5-Glom-MGN421

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN421

source_name: Kidney Biopsy from Human H5-Glom-MGN421


title: H5-Glom-MGN422

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN422

source_name: Kidney Biopsy from Human H5-Glom-MGN422


title: H5-Glom-MGN424

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN424

source_name: Kidney Biopsy from Human H5-Glom-MGN424


title: H7-Glom-FSGS920

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS920

source_name: Kidney Biopsy from Human H7-Glom-FSGS920


title: H5-Glom-SLE466

description: Gene Expression data from the glomerular compartment of human H5-Glom-SLE466

source_name: Kidney Biopsy from Human H5-Glom-SLE466


title: H7-Glom-FSGS917

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS917

source_name: Kidney Biopsy from Human H7-Glom-FSGS917


title: H5-Glom-MGN417

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN417

source_name: Kidney Biopsy from Human H5-Glom-MGN417


title: H5-Glom-MGN415

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN415

source_name: Kidney Biopsy from Human H5-Glom-MGN415


title: H5-Glom-MGN436

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN436

source_name: Kidney Biopsy from Human H5-Glom-MGN436


title: H7-Glom-FSGS912

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS912

source_name: Kidney Biopsy from Human H7-Glom-FSGS912


title: H7-Glom-FSGS915

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS915

source_name: Kidney Biopsy from Human H7-Glom-FSGS915


title: H5-Glom-LD_482

description: Gene Expression data from the glomerular compartment of human H5-Glom-LD_482

source_name: Kidney Biopsy from Human H5-Glom-LD_482


title: H7-Glom-FSGS&MCD940

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS&MCD940

source_name: Kidney Biopsy from Human H7-Glom-FSGS&MCD940

value: Focal Segmental Glomerular Sclerosis/Minimal Change Disease


title: H5-Glom-LD_479

description: Gene Expression data from the glomerular compartment of human H5-Glom-LD_479

source_name: Kidney Biopsy from Human H5-Glom-LD_479


title: H5-Glom-MGN434

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN434

source_name: Kidney Biopsy from Human H5-Glom-MGN434


title: H5-Glom-LD_478

description: Gene Expression data from the glomerular compartment of human H5-Glom-LD_478

source_name: Kidney Biopsy from Human H5-Glom-LD_478


title: H7-Glom-FSGS971

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS971

source_name: Kidney Biopsy from Human H7-Glom-FSGS971


title: H7-Glom-FSGS&MCD922

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS&MCD922

source_name: Kidney Biopsy from Human H7-Glom-FSGS&MCD922


title: H5-Glom-FSGS459

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS459

source_name: Kidney Biopsy from Human H5-Glom-FSGS459


title: H7-Glom-FSGS&MCD923

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS&MCD923

source_name: Kidney Biopsy from Human H7-Glom-FSGS&MCD923


title: H5-Glom-MGN425

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN425

source_name: Kidney Biopsy from Human H5-Glom-MGN425


title: H7-Glom-FSGS&MCD931

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS&MCD931

source_name: Kidney Biopsy from Human H7-Glom-FSGS&MCD931


title: H5-Glom-FSGS458

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS458

source_name: Kidney Biopsy from Human H5-Glom-FSGS458


title: H5-Glom-FSGS457

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS457

source_name: Kidney Biopsy from Human H5-Glom-FSGS457


title: H7-Glom-FSGS&MCD905

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS&MCD905

source_name: Kidney Biopsy from Human H7-Glom-FSGS&MCD905


title: H7-Glom-DN941

description: Gene Expression data from the glomerular compartment of human H7-Glom-DN941

source_name: Kidney Biopsy from Human H7-Glom-DN941

value: Diabetic Nephropathy


title: H5-Glom-FSGS449

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS449

source_name: Kidney Biopsy from Human H5-Glom-FSGS449


title: H5-Glom-FSGS446

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS446

source_name: Kidney Biopsy from Human H5-Glom-FSGS446


title: H7-Glom-DN947

description: Gene Expression data from the glomerular compartment of human H7-Glom-DN947

source_name: Kidney Biopsy from Human H7-Glom-DN947


title: H7-Glom-DN932

description: Gene Expression data from the glomerular compartment of human H7-Glom-DN932

source_name: Kidney Biopsy from Human H7-Glom-DN932


title: H5-Glom-MGN416

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN416

source_name: Kidney Biopsy from Human H5-Glom-MGN416


title: H5-Glom-FSGS441

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS441

source_name: Kidney Biopsy from Human H5-Glom-FSGS441


title: H7-Glom-DN914

description: Gene Expression data from the glomerular compartment of human H7-Glom-DN914

source_name: Kidney Biopsy from Human H7-Glom-DN914


title: H5-Glom-FSGS428

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS428

source_name: Kidney Biopsy from Human H5-Glom-FSGS428


title: H4-Glom-IgA9

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA9

source_name: Kidney Biopsy from Human H4-Glom-IgA9

value: IgA Nephropathy


title: H7-Glom-DN916

description: Gene Expression data from the glomerular compartment of human H7-Glom-DN916

source_name: Kidney Biopsy from Human H7-Glom-DN916


title: H5-Glom-MGN403

description: Gene Expression data from the glomerular compartment of human H5-Glom-MGN403

source_name: Kidney Biopsy from Human H5-Glom-MGN403


title: H7-Glom-FSGS&MCD944

description: Gene Expression data from the glomerular compartment of human H7-Glom-FSGS&MCD944

source_name: Kidney Biopsy from Human H7-Glom-FSGS&MCD944


title: H4-Glom-IgA7

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA7

source_name: Kidney Biopsy from Human H4-Glom-IgA7


title: H4-Glom-IgA8

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA8

source_name: Kidney Biopsy from Human H4-Glom-IgA8


title: H4-Glom-IgA5

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA5

source_name: Kidney Biopsy from Human H4-Glom-IgA5


title: H4-Glom-IgA3

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA3

source_name: Kidney Biopsy from Human H4-Glom-IgA3


title: H4-Glom-IgA27

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA27

source_name: Kidney Biopsy from Human H4-Glom-IgA27


title: H4-Glom-IgA4

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA4

source_name: Kidney Biopsy from Human H4-Glom-IgA4


title: H4-Glom-IgA26

description: Gene Expression data from the glomerular compartment of human Membranous Nephropathy

source_name: Kidney Biopsy from Human H4-Glom-IgA26


title: H4-Glom-IgA25

source_name: Kidney Biopsy from Human H4-Glom-IgA25


title: H4-Glom-IgA22

source_name: Kidney Biopsy from Human H4-Glom-IgA22


title: H4-Glom-IgA23

source_name: Kidney Biopsy from Human H4-Glom-IgA23


title: H4-Glom-IgA21

source_name: Kidney Biopsy from Human H4-Glom-IgA21


title: H4-Glom-IgA20

source_name: Kidney Biopsy from Human H4-Glom-IgA20


title: H4-Glom-IgA18

source_name: Kidney Biopsy from Human H4-Glom-IgA18


title: H4-Glom-IgA24

source_name: Kidney Biopsy from Human H4-Glom-IgA24


title: H4-Glom-IgA14

source_name: Kidney Biopsy from Human H4-Glom-IgA14


title: H4-Glom-IgA2

source_name: Kidney Biopsy from Human H4-Glom-IgA2


title: H4-Glom-IgA17

source_name: Kidney Biopsy from Human H4-Glom-IgA17


title: H4-Glom-IgA19

source_name: Kidney Biopsy from Human H4-Glom-IgA19


title: H4-Glom-IgA16

source_name: Kidney Biopsy from Human H4-Glom-IgA16


title: H4-Glom-IgA15

source_name: Kidney Biopsy from Human H4-Glom-IgA15


title: H4-Glom-IgA11

source_name: Kidney Biopsy from Human H4-Glom-IgA11


title: H4-Glom-IgA12

source_name: Kidney Biopsy from Human H4-Glom-IgA12


title: H3-Glom-TN2

source_name: Kidney Biopsy from Human H3-Glom-TN2


title: H4-Glom-IgA10

source_name: Kidney Biopsy from Human H4-Glom-IgA10


title: H3-Glom-TN4

source_name: Kidney Biopsy from Human H3-Glom-TN4


title: H4-Glom-IgA1

source_name: Kidney Biopsy from Human H4-Glom-IgA1


title: H4-Glom-IgA13

source_name: Kidney Biopsy from Human H4-Glom-IgA13


title: H5-Glom-FSGS433

description: Gene Expression data from the glomerular compartment of human H5-Glom-FSGS433

source_name: Kidney Biopsy from Human H5-Glom-FSGS433


title: H3-Glom-MCD7

source_name: Kidney Biopsy from Human H3-Glom-MCD7


title: H3-Glom-MCD9

source_name: Kidney Biopsy from Human H3-Glom-MCD9


title: H4-Glom-IgA6

description: Gene Expression data from the glomerular compartment of human H4-Glom-IgA6

source_name: Kidney Biopsy from Human H4-Glom-IgA6


title: H3-Glom-MCD10

source_name: Kidney Biopsy from Human H3-Glom-MCD10


title: H3-Glom-MCD12

source_name: Kidney Biopsy from Human H3-Glom-MCD12


title: H2-Glom-HT8

source_name: Kidney Biopsy from Human H2-Glom-HT8

value: Hypertensive Nephropathy


title: H2-Glom-HT7

source_name: Kidney Biopsy from Human H2-Glom-HT7


title: H3-Glom-MCD6

source_name: Kidney Biopsy from Human H3-Glom-MCD6


title: H2-Glom-HT6

source_name: Kidney Biopsy from Human H2-Glom-HT6


title: H2-Glom-HT18

source_name: Kidney Biopsy from Human H2-Glom-HT18


title: H2-Glom-HT16

source_name: Kidney Biopsy from Human H2-Glom-HT16


title: H2-Glom-HT4

source_name: Kidney Biopsy from Human H2-Glom-HT4


title: H2-Glom-HT2

source_name: Kidney Biopsy from Human H2-Glom-HT2


title: H2-Glom-HT15

source_name: Kidney Biopsy from Human H2-Glom-HT15


title: H2-Glom-HT12

source_name: Kidney Biopsy from Human H2-Glom-HT12


title: H2-Glom-HT11

source_name: Kidney Biopsy from Human H2-Glom-HT11


title: RNASeq_YAP-_XV50_rep2

status: Public on Jan 08 2018

type: SRA

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
RNASeq1_count.xlsx
YAP-_XV50_rep2

library_source: transcriptomic

data_processing:
FastQC v0.11.5 with default parameter was used for quality test.
Reads were mapped to hg19 reference genome by STAR v2.5.1 with default parameters. Only uniquely mapped reads were considered for downstream analysis.
ChIP-Seq peak calling was performed by HOMER v4.8 findPeaks command, using input control as background. Option "-style factor" was used for transcription factor peaks (YAP, beta-Catenin, Smad2_3, TEAD4) and "-style histone" was used for Pol II peaks (Ser7P) .
RNA-Seq gene expression was quantified by HOMER analyzeRepeats command, summing reads mapped across all gene exons of RefSeq genes.
RNA-Seq differential expression was carried out using edgeR v3.16.1 on the raw counts of duplicated replicates. FDR < 0.05 was used as cutoff to identify the DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet (count) for RNA-Seq data and annotated peaks in bed format for ChIP-Seq data.

molecule: polyA RNA

source_name: Embryonic Stem Cell H1

growth_protocol: H1 hESCs grow in TeSR media

extract_protocol:
PCR purification Kit (Qiaquick) from Qiagen  was used to extract the DNA for ChIP-seq experiments. Quick RNA miniprep Plus from Zymo was used to extract the RNA for RNA-seq
The ChIP DNA was end repaired and 5′ phosphorylated using T4 DNA Polymerase, Klenow, and T4 Polynucleotide Kinase (Enzymatics). Adaptor-ligated ChIP DNA fragments were subjected to 15 cycles of PCR amplification using Q5 polymerase (NEB). AMPure beads were used to purify DNA after each step (Beckman Coulter). ChIP fragments were sequenced in an Illumina HiSeq 2500 sequencer. RNA-seq libraries were performed using stranded  LT mRNA  kit from Illumina and sequenced in an Illumina HiSeq 4000 device.

treatment_protocol: H1 hESCs were grown in TeSR media. WT, YAP-KO and beta-catenin/YAP-KO hESC lines were engineered using CRISPR/Cas9 technology. For RNA-seq the different cell lines were left untreated or treated with the cytokines or molecules indicated (Activin, XV or ChIR) for 24h or 30h in TeSR media. For the 72h RNA-seq, cells were treated for 24h with the specific treatment, and then the media was changed, and cells were collected 48h later (72h total). For ChIP-seq experiments, the YAP1 and TEAD4 ChIP-seq were performed in hESCs growing in TeSR media. In addition, the YAP1 ChIP-seq was also performed in the YAP-KO cells. The beta-catenin, Smad2,3 and CTD-Ser7P RNAPII ChIP-seq experiments were performed in the WT and the YAP-KO hESCs after Activin exposure for 15h. The PiggyYAP cell line was generated by stably transfecting the YAP-KO cells with the transposon-based vector Piggyback containing a Flag-YAP cDNA construct under the control of a doxycycline-inducible promoter. This system allowed us to control YAP levels in the same hESC line from zero (-Dox) to over-expression levels (aprox. Dox 50ng/ml). The ChIP-seq of CTD-Ser7P RNAPII was performed in the PiggyYAP cells treated with Activin for 15h in absence (no dox) or in presence of doxycycline (+dox).

tag: genotype

value: YAP-

tag: treatment


title: RNASeq_YAP-_XV50_rep1

description:
RNASeq1_count.xlsx
YAP-_XV50_rep1


title: H2-Glom-HT1

source_name: Kidney Biopsy from Human H2-Glom-HT1


title: H1-Glom-TMD5

source_name: Kidney Biopsy from Human H1-Glom-TMD5

value: Thin Membrande Disease


title: RNASeq_YAP-_untreated_rep2

description:
RNASeq1_count.xlsx
YAP-_untreated_rep2


title: RNASeq_YAP-_untreated_rep1

description:
RNASeq1_count.xlsx
YAP-_untreated_rep1


title: RNASeq_YAP-_A50_rep1

description:
RNASeq1_count.xlsx
YAP-_A50_rep1

value: Activin A


title: RNASeq_WT_XV50_rep2

description:
RNASeq1_count.xlsx
WT_XV50_rep2

value: WT


title: RNASeq_WT_XV50_rep1

description:
RNASeq1_count.xlsx
WT_XV50_rep1


title: RNASeq_WT_untreated_rep2

description:
RNASeq1_count.xlsx
WT_untreated_rep2


title: RNASeq_WT_untreated_rep1

description:
RNASeq1_count.xlsx
WT_untreated_rep1


title: RNASeq_WT_A50_rep1

description:
RNASeq1_count.xlsx
WT_A50_rep1


title: RNASeq_WT_A50_rep2

description:
RNASeq1_count.xlsx
WT_A50_rep2


title: ChIPSeq_YAP_WT_H1

library_source: genomic

molecule: genomic DNA

tag: antibody

value: YAP


title: ChIPSeq_Smad2_3_YAP-_Act


title: ChIPSeq_YAP_YAP-_H1


title: ChIPSeq_Smad2_3_WT_Act


title: H2-Glom-HT20

source_name: Kidney Biopsy from Human H2-Glom-HT20


title: ChIPSeq_Ser7P_YAP-_ActPiggyNoDoxy

value: YAP-, Piggy


title: H2-Glom-HT5

source_name: Kidney Biopsy from Human H2-Glom-HT5


title: ChIPSeq_Input_YAP-_H1

value: Input Control


title: ChIPSeq_Ser7P_WT_Act


title: ChIPSeq_Ser7P_YAP-_ActPiggyDoxy

value: Activin A, Doxycycline


title: H2-Glom-HT14

source_name: Kidney Biopsy from Human H2-Glom-HT14


title: ChIPSeq_Ser7P_YAP-_Act


title: H2-Glom-HT13

source_name: Kidney Biopsy from Human H2-Glom-HT13


title: ChIPSeq_Input_YAP-_ActPiggyNoDoxy


title: ChIPSeq_Input_YAP-_ActPiggyDoxy


title: ChIPSeq_Input_YAP-_Act


title: ChIPSeq_Input_WT_hESC


title: ChIPSeq_Input_WT_H1


title: ChIPSeq_Input_WT_Act


title: ChIPSeq_Beta_YAP-_Act

value: beta-Catenin


title: RNASeq_YAP-_A50_rep2

description:
RNASeq1_count.xlsx
YAP-_A50_rep2


title: RNASeq_YAP-_CM_D25_rep1

description:
RNASeq3_count.xlsx
YAP-_CM_D25_rep1

data_processing:
FastQC v0.11.5 with default parameter was used for quality test.
Reads were mapped to hg19 reference genome by STAR v2.5.1 with default parameters. Only uniquely mapped reads were considered for downstream analysis.
RNA-Seq gene expression was quantified by HOMER analyzeRepeats command, summing reads mapped across all gene exons of RefSeq genes.
RNA-Seq differential expression was carried out using edgeR v3.16.1 on the raw counts of replicates. FDR < 0.05 was used as cutoff to identify the DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet (count) for RNA-Seq data.

extract_protocol:
Quick RNA miniprep Plus from Zymo was used to extract the RNA for RNA-seq
RNA-seq libraries were performed using stranded  LT mRNA  kit from Illumina and sequenced in an Illumina HiSeq 4000 device.

treatment_protocol: H1 hESCs were grown in TeSR media. WT, YAP-KO hESC lines were engineered using CRISPR/Cas9 technology. For RNA-seq the different cell lines were treated with the cytokines or molecules indicated (Activin, GSK3i, or Wnt inhibitor) and samples were extracted at Day 25 after differentiation.

value: Activin


title: RNASeq_YAP-_CM_D25_rep3

description:
RNASeq3_count.xlsx
YAP-_CM_D25_rep3


title: RNASeq_YAP-_CM_D25_rep2

description:
RNASeq3_count.xlsx
YAP-_CM_D25_rep2


title: ChIPSeq_Beta_WT_Act


title: RNASeq_H1_CM_D25_rep2

description:
RNASeq3_count.xlsx
H1_CM_D25_rep2

value: GSK3i+Wnt/β-catenin inhibitor

value: GSK3i for 24h, Wnt inhibitor for 48h


title: RNASeq_H1_CM_D25_rep3

description:
RNASeq3_count.xlsx
H1_CM_D25_rep3


title: RNASeq_H1_CM_D25_rep1

description:
RNASeq3_count.xlsx
H1_CM_D25_rep1


title: RNASeq_YAP-_untreated0h_rep2

description:
RNASeq2_count.xlsx
YAP-_untreated0h_rep2_R1


title: RNASeq_YAP-_ChIR72h_rep1

description:
RNASeq2_count.xlsx
YAP-_ChIR72h_rep1_R1

value: ChIR


title: ChIPSeq_TEAD4_WT_hESC


title: RNASeq_YAP-_ChIR24h_rep2

description:
RNASeq2_count.xlsx
YAP-_ChIR24h_rep2_R1


title: RNASeq_YAP-_untreated0h_rep1

description:
RNASeq2_count.xlsx
YAP-_untreated0h_rep1_R1


title: RNASeq_YAP-_ChIR72h_rep2

description:
RNASeq2_count.xlsx
YAP-_ChIR72h_rep2_R1


title: RNASeq_YAP-bCatenin-_untreated0h_rep2

description:
RNASeq2_count.xlsx
YAP-bCatenin-_untreated0h_rep2_R1

value: YAP-, bCatenin-


title: RNASeq_YAP-bCatenin-_untreated0h_rep1

description:
RNASeq2_count.xlsx
YAP-bCatenin-_untreated0h_rep1_R1


title: RNASeq_YAP-_ChIR24h_rep1

description:
RNASeq2_count.xlsx
YAP-_ChIR24h_rep1_R1


title: RNASeq_YAP-bCatenin-_Act24h_rep2

description:
RNASeq2_count.xlsx
YAP-bCatenin-_Act24h_rep2_R1


title: RNASeq_YAP-bCatenin-_Act24h_rep1

description:
RNASeq2_count.xlsx
YAP-bCatenin-_Act24h_rep1_R1


title: RNASeq_YAP-bCatenin-_ChIR24h_rep1

description:
RNASeq2_count.xlsx
YAP-bCatenin-_ChIR24h_rep1_R1


title: RNASeq_YAP-_ActChIR72h_rep2

description:
RNASeq2_count.xlsx
YAP-_ActChIR72h_rep2_R1

value: Activin A, ChIR


title: RNASeq_YAP-_ActChIR72h_rep1

description:
RNASeq2_count.xlsx
YAP-_ActChIR72h_rep1_R1


title: RNASeq_YAP-_ActChIR24h_rep1

description:
RNASeq2_count.xlsx
YAP-_ActChIR24h_rep1_R1


title: RNASeq_YAP-_Act72h_rep2

description:
RNASeq2_count.xlsx
YAP-_Act72h_rep2_R1


title: RNASeq_YAP-_ActChIR24h_rep2

description:
RNASeq2_count.xlsx
YAP-_ActChIR24h_rep2_R1


title: RNASeq_YAP-_Act24h_rep2

description:
RNASeq2_count.xlsx
YAP-_Act24h_rep2_R1


title: RNASeq_YAP-_Act72h_rep1

description:
RNASeq2_count.xlsx
YAP-_Act72h_rep1_R1


title: RNASeq_YAP-_Act24h_rep1

description:
RNASeq2_count.xlsx
YAP-_Act24h_rep1_R1


title: RNASeq_WT_untreated0h_rep2

description:
RNASeq2_count.xlsx
WT_untreated0h_rep2_R1


title: RNASeq_WT_untreated0h_rep1

description:
RNASeq2_count.xlsx
WT_untreated0h_rep1_R1


title: RNASeq_WT_ChIR24h_rep1

description:
RNASeq2_count.xlsx
WT_ChIR24h_rep1_R1


title: RNASeq_WT_ChIR72h_rep2

description:
RNASeq2_count.xlsx
WT_ChIR72h_rep2_R1


title: RNASeq_WT_ChIR24h_rep2

description:
RNASeq2_count.xlsx
WT_ChIR24h_rep2_R1


title: RNASeq_WT_ActChIR72h_rep2

description:
RNASeq2_count.xlsx
WT_ActChIR72h_rep2_R1


title: RNASeq_WT_ChIR72h_rep1

description:
RNASeq2_count.xlsx
WT_ChIR72h_rep1_R1


title: RNASeq_WT_ActChIR24h_rep1

description:
RNASeq2_count.xlsx
WT_ActChIR24h_rep1_R1


title: RNASeq_WT_ActChIR72h_rep1

description:
RNASeq2_count.xlsx
WT_ActChIR72h_rep1_R1


title: RNASeq_WT_Act72h_rep2

description:
RNASeq2_count.xlsx
WT_Act72h_rep2_R1


title: RNASeq_WT_ActChIR24h_rep2

description:
RNASeq2_count.xlsx
WT_ActChIR24h_rep2_R1


title: RNASeq_WT_Act72h_rep1

description:
RNASeq2_count.xlsx
WT_Act72h_rep1_R1


title: RNASeq_WT_Act24h_rep2

description:
RNASeq2_count.xlsx
WT_Act24h_rep2_R1


title: RNASeq_WT_Act24h_rep1

description:
RNASeq2_count.xlsx
WT_Act24h_rep1_R1


title: RNASeq_YAP-bCatenin-_ChIR24h_rep2

description:
RNASeq2_count.xlsx
YAP-bCatenin-_ChIR24h_rep2_R1


title: HEK 293T Kapa Total RNA

status: Public on Dec 20 2017

description: Kappa RNA cleanup protocol was used (see methods)

data_processing:
Sequenced reads were quality-tested using FASTQC(http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads from each method were combined prior to alignment to improve transcript diversity.
The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection (http://support.illumina.com/sequencing/sequencing_software/igenome.html) and sjdbOverhang value of 100. Reads mapping to more than one location in the genome were removed prior to transcript
Reads were aligned to the hg19 (Lander et al. 2001)human genome using the STAR aligner (Dobin et al. 2013) version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
Uniquely aligning reads were used to assembly transcripts using Cufflinks (Trapnel et. al. 2010), and the MAPS assembler introduced in this study. Cufflinks assembly was carried out with the --multi-read-correct --frag-bias-correct and --library-type fr-firststrand options. Other parameters were set to default values. MAPS assembly was run using a stringency of 0.375, with the consensus flag set, and using the library rf option.
Genome_build: hg19
Supplementary_files_format_and_content: zipped collections of assembled transcript coordinates (GTF), 3frame translated peptides (FASTA), transcript nucleotide sequence (FASTA), and open reading frame transcript coordinates (GTF).

source_name: embryonic kidney cells

growth_protocol: HEK293T cells were cultured using DMEM supplemented with 10% fetal bovine serum (FBS).  Cells were grown under an atmosphere of 5% CO2 at 37 °C until confluent.

extract_protocol:
Total RNA was isolated using Pure-Link RNA Mini Kit (Life Technologies) according to the manufacturer’s protocol. On-column digestion of genomic DNA was performed using DNase I (NEB) The Agilent Boianalyzer or Tape Station was used to determine RNA integrity (RIN) numbers prior to library preparation.
1 ug of total RNA was prepared into Illumina-compatible sequencing libraries using three different methods, 1) Illumina Stranded mRNA-Seq, 2) Illumina Total RNA-Seq and 3) KAPA Total RNA-Seq. Illumina Stranded mRNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Briefly, RNA with poly-A tail was isolated using magnetic beads conjugated to poly-T oligos. mRNA was then fragmented and reverse-transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. dUTP-incorporated second strand was not amplified. cDNA was then end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each steps of the library prep. Illumina Total Stranded mRNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Sample Prep with Ribo-Zero Gold Kit following manufacturer’s instructions (Illumina). First, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was depleted using biotinylated oligo probes complementary to ribosomal transcripts. Depleted RNA was then prepared into stranded RNA-Seq libraries using same protocol as mentioned above starting at the RNA fragmentation steps. KAPA Total RNA-Seq libraries were prepared using the KAPA Stranded RNA-Seq Kit with Ribo-erase (KAPA Biosystems). Protocol is similar to aforementioned total RNA-Seq libraries, except prior to RNA fragmentation, rRNA was hybridized to DNA oligos, then treated with RNase H and DNase to remove RNA-DNA duplexes, as well as original DNA oligos. All sequencing libraries were then quantified, pooled and sequenced at paired-end 150 base-pair using the Illumina NextSeq 500 at the Salk NGS Core. Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2).  Libraries were sequenced at an average depth of 519 million paired reads per library.

tag: cell line

value: HEK 293T

tag: molecule type

value: total RNA


title: Occ20

status: Public on Dec 11 2017

city: La Jolla

first: Kun

last: Zhang

address: 9500 Gilman Drive

institute: UCSD

description:
snDrop-seq data
[processed data file:]
VisualCortex_snDrop-seq_UMI_Count_Matrix_04-07-2017.txt

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
First, paired-end reads were filtered out if read 1 had more than 4 non-T bases in the last 10 bases (to remove all non poly T-captured contaminated reads), or had one or more bases with poor quality score (less than 10). And cell barcode and UMI information were then inferred from the first 12 bases and the next 8 bases of read 1 respectively. The right mate of each read pair was trimmed to remove any portion of the SMART adaptor sequence or large stretches of polyA tails (6 consecutive bp or greater).
The trimmed reads were then aligned to the human genome (GENCODE GRCH38) using STAR v2.5 with the default parameter settings
Reads mapping to intronic or exonic regions of genes as per the GENCODE gene annotation were both recorded. One further correction step to fix barcode synthesis errors was performed by inserting N at last base of the cell barcode for reads which had identical first 11 bases of the cell barcode and same last T base of UMI.
Digital expression matrix was then generated with genes as rows and cells as columns. UMI counts were assigned for each gene of each cell by collapsing UMI reads which had only 1 edit distance
Genome_build: GENCODE GRCH38
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each sample passing QC filtering. The README file on the series record contains where the adaptor information can be found and the script needed to generate the count matrices by cell barcode.

source_name: Brain

extract_protocol:
Cryofrozen post-mortem brain tissue was treated with nuclear extraction buffer, isolated nuclei was stained with DAPI and FACS purified.
Nuclei were loaded at the concentration of 100 nuclei/ml, and co-encapsulated in droplets with barcoded beads purchased from ChemGenes Corporation, Wilmington MA (Cat. # Macosko201110). When encapsulation was complete, droplets were heated to lyze the nuclei membrane, and were then broken by perfluorooctanol, following which beads were harvested, and hybridized RNA was reverse transcribed. Beads hybridized with RNA from individual nuclei was harvested, pooled and reverse transcribed. cDNA was then PCR amplified for 16 cycles with primer, buffer and cycle conditions identical to original Dropseq protocol and libraries were prepared by Nextera XT tagmentation according to Illumina's instructions and indexed with different Nextera index 1 primers

tag: experiment

tag: patient

value: brain

tag: brain region

value: Occipital Lobe, Visual Cortex

tag: brodmann area

tag: histology

value: Not specified

tag: age

value: 48 years

tag: Sex

value: Male

tag: race

value: African American

tag: source

value: U Miami Brain Endowment Bank


title: Occ21


title: Fcx10

description:
snDrop-seq data
[processed data file:]
FrontalCortex_snDrop-seq_UMI_Count_Matrix_04-07-2017.txt

value: Frontal Cortex


title: Occ24

description:
processed data file:
VisualCortex_snDrop-seq_UMI_Count_Matrix_08-01-2017.txt

source_name: snDrop-seq_visual cortex

tag: patient id

value: 35 years

value: Female

value: Caucasian

value: postmortem adult human brain

tag: region


title: Occ22

tag: tissue


title: Fcx12

description:
processed data file:
FrontalCortex_snDrop-seq_UMI_Count_Matrix_08-01-2017.txt

source_name: snDrop-seq_frontal cortex


title: Fcx8

value: 49 years


title: Fcx13


title: Occ17

value: Coronal sample, Section 31

value: 20 years

value: Maryland Brain Bank


title: Fcx9


title: Occ15


title: Occ14


title: Occ3

value: 23 years


title: Occ16

value: brain


title: Occ2

value: Occipital Lobe, Visual Cortex


title: Occ19

value: Not specified


title: Occ10


title: Fcx2

value: Coronal sample, Section 11


title: HEK 293T rRNA Depleted RNA

description: rRNA depletion protocol was used (see methods)

value: HEK 293T

value: rRNA depleted RNA


title: Fcx1

value: Male

value: African American


title: Occ13


title: Occ12


title: Occ11


title: Occ6


title: Fcx7

value: Frontal Cortex


title: Fcx3


title: Fcx6


title: Fcx4


title: HEK 293T PolyA Selected RNA

description: PolyA selection protocol was used (see methods)

value: polyA selected RNA


title: HR2 AS DNM3BKO iPS H3K4me3

status: Public on Dec 01 2017

data_processing:
Sequenced reads were quality-tested using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and aligned to the hg19 (Genome Sequencing Consortium 2001) human genome using the STAR aligner (Dobin 2013) version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection (http://support.illumina.com/sequencing/sequencing_software/igenome.html) and sjdbOverhang value of 100.
Reads uniquely mapping to the genome (>80%) were then used for peak calling with Homer (Heinz 2010), assuming a peak size of 500, extending the peaks to cover the full enriched region, assuming a fold enrichment of at least 4 over input reads, a poisson p-value threshold relative to input count of 1e-4, and at least 25 normalized read counts per peak.
Peaks from WTiPS, ASiPS, and ASHR2neoex samples, or peaks from ASDM3BKO, HR4ASDM3BKO, and HR14ASDM3BKO were merged using the Homer mergePeaks.pl program, and normalized read counts in peaks were used to calculate log fold change between conditions.
Homer makeUCSCfile.pl was used to generate normalized read count density tracks for peak visualization.
genome build: hg19
processed data files format and content: Gzipped bedGraph tracks show a continuous normalized (total of 1e7 reads) read alignment of reads to the hg19 genome. These files can be loaded into a genome browser to visualize and compare ChIP peaks. Input controls are indicated with _Input.

source_name: HR2 AS DNM3BKO iPS H3K4me3

growth_protocol: ESCs and iPSCs were cultured with TeSR medium on a Matrigel coated plate.

extract_protocol:
Fixed cells were sonicated using Bioruptor to achieve 200–700 bp size chromatin fragments. Solubilized chromatin was immunoprecipiated with antibody against H3K4me3 (Abcam 8580). Antibody–chromatin complexes were pulled down using Dynabeads protein A (Invitrogen), washed and then eluted. After cross-linking reversal, RNase and proteinase K treatment, immunoprecipiated DNA was purified using AMPure beads (Beckman Coulter).
ChIP DNA were end-repaired and 5′ phosphorylated using T4 DNA Polymerase, Klenow and T4 Polynucleotide Kinase (Enzymatics). A single adenine was added to 3′ ends by Klenow (3→5′ exo-), and double-stranded Bioo Illumina Adapters (Bioo Scientific) were ligated to the ends of the ChIP fragments. Adaptor-ligated ChIP DNA fragments were subjected to 15 cycles of PCR amplification using Q5 polymerase (NEB). AMPure beads were used to purify DNA after each step (Beckman Coulter). Pooled libraries were sequenced on the HiSeq2500 (V4 Chemistry) for single-end 50 bp according to the manufacturer’s instructions.

treatment_protocol: Cells were fixed with 1% formaldehyde at 37 °C for 10 min and then quenched with glycine at 37 °C for 5 min.

tag: source cell type

value: B-lymphocyte

tag: cell type

value: iPSC derived from Angelman syndrome patient

tag: genotype/variation

value: DNM3B gene was knocked out

value: CpG free neo cassette is integrated in SNURF/SNRPN locus


title: HR1 AS DNM3BKO iPS H3K4me3

source_name: HR1 AS DNM3BKO iPS H3K4me3


title: Occ23

value: 35 years

value: Female

value: Caucasian

value: postmortem adult human brain


title: Occ8

value: brain

value: Occipital Lobe, Visual Cortex

value: Coronal sample, Section 31

value: 23 years

value: Maryland Brain Bank


title: Occ7

value: Male


title: Fcx11

value: Not specified

value: 48 years

value: African American

value: U Miami Brain Endowment Bank


title: HR2 AS DNM3BKO iPS Input

source_name: HR2 AS DNM3BKO iPS Input

value: B-lymphocyte

value: iPSC derived from Angelman syndrome patient


title: AS iPS H3K4me3

source_name: AS iPS H3K4me3


title: AS iPS Input

source_name: AS iPS Input


title: Occ5


title: Occ18

value: 49 years


title: AS HR site 3 iPSCs

data_processing:
library strategy: Target enrichment-genome bisulfite sequencing
Base calling was carried out using bcl2fastq v1.8.4 (Illumina Inc.) using the arguments "--fastq-cluster-count 0 --force --mismatches 1"
Read quality was confirmed using fastqc with default options
Reads were mapped to the hg19 genome with Bismark (v0.7.12). Bismark uses a C to T converted version of the genome and Bowtie (v1.0.1) alignment to identified base-specific methylation percentages.
A custom script was run to generate methylated and unmethylated bedGraph files describing the percentage of methylated to unmethylated cytosines across the genome.
Methylation at enriched loci was checked manually using the Integrated Genome Viewer (IGV) v2.3.38
To confirm phasing of reads aligning to the MLH1 and SNRPN loci, bisulfite reads were mapped to custom sequences representing insertion of exogenous CpG free neo sequence into the MLH1 and SNRPN loci (MLH1andSNRPN.fa) as compared to the annotated endogenous MLH1 and SNRPN loci.
genome build: GRCh37/hg19
processed data files format and content: bedGraph files containg continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state. Two files are provided for each processed sample representing the methylated and unmethylated tracks. Methylated tracks have a mCpG.bedGraph or _m.bedGraph suffix, while unmethylated tracks have a unmCpG.bedGraph or _u.bedGraph suffix.  The fasta file, MLH1andSNRPN.fa has sequences describing the exogenous CpG free and neo ex sequences that were used for read phasing.

source_name: AS HR site 3 iPSCs

extract_protocol:
Genomic DNA was purified from iPSCs using DNeasy Blood & Tissue Kit (Qiagen).
Target enrichment-genome methyl sequence was performed by using SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies) with customized capture library following manufacturer's protocol. The biotinylated RNA capture probe library to capture specific genomic loci was designed to include three loci, chr3: 36600000-37410000, chr6: 144000000-144800000, and chr15: 24900000-25700000.

value: iPSC line derived from Angelman syndrome patient

value: CpG free neo cassette is integrated in SNURF/SNRPN locus at site3

value: DNA methylation-corrected AS iPSCs


title: Occ4


title: AS HR site 2 iPSCs

source_name: AS HR site 2 iPSCs

value: CpG free neo cassette is integrated in SNURF/SNRPN locus at site2


title: AS DNM3BKO iPS Input

source_name: AS DNM3BKO iPS Input

value: DNM3B gene was knocked out


title: AS HR5 neo ex iPSCs

source_name: AS HR5 neo ex iPSCs

value: CpG free neo cassette was excised from AS HR5 iPSCs


title: HR1 AS DNM3BKO iPS Input

source_name: HR1 AS DNM3BKO iPS Input

value: CpG free neo cassette is integrated in SNURF/SNRPN locus


title: Occ1

value: brain

value: Occipital Lobe, Visual Cortex

value: Coronal sample, Section 31

value: 23 years


title: Fcx5

value: Frontal Cortex

value: Coronal sample, Section 11

value: Male

value: Maryland Brain Bank


title: AS DNM3BKO iPS H3K4me3

source_name: AS DNM3BKO iPS H3K4me3

value: B-lymphocyte

value: iPSC derived from Angelman syndrome patient


title: SW48

data_processing:
library strategy: Target enrichment-genome bisulfite sequencing
Base calling was carried out using bcl2fastq v1.8.4 (Illumina Inc.) using the arguments "--fastq-cluster-count 0 --force --mismatches 1"
Read quality was confirmed using fastqc with default options
Reads were mapped to the hg19 genome with Bismark (v0.7.12). Bismark uses a C to T converted version of the genome and Bowtie (v1.0.1) alignment to identified base-specific methylation percentages.
A custom script was run to generate methylated and unmethylated bedGraph files describing the percentage of methylated to unmethylated cytosines across the genome.
Methylation at enriched loci was checked manually using the Integrated Genome Viewer (IGV) v2.3.38\n!Sample_data_processing = To confirm phasing of reads aligning to the MLH1 and SNRPN loci, bisulfite reads were mapped to custom sequences representing insertion of exogenous CpG free neo sequence into the MLH1 and SNRPN loci (MLH1andSNRPN.fa) as compared to the annotated endogenous MLH1 and SNRPN loci.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph files containg continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state. Two files are provided for each processed sample representing the methylated and unmethylated tracks. Methylated tracks have a mCpG.bedGraph or _m.bedGraph suffix, while unmethylated tracks have a unmCpG.bedGraph or _u.bedGraph suffix.  The fasta file, MLH1andSNRPN.fa has sequences describing the exogenous CpG free and neo ex sequences that were used for read phasing.

growth_protocol: ESCs and iPSCs were cultured with TeSR medium on Matrigel coated plate.

extract_protocol:
Genome DNA was purified from iPSCs using DNeasy Blood & Tissue Kit (Qiagen).
Target enrichment-genome methyl sequence was performed by using SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies) with customized capture library following manufacturer's protocol. The biotinylated RNA capture probe library to capture specific genomic loci was designed to include three loci, chr3: 36600000-37410000, chr6: 144000000-144800000, and chr15: 24900000-25700000.

tag: cell line

value: colon cancer cell

value: Epimutation is observed in MLH1 locus.


title: H1 MLH HR2 neo ex

source_name: H1 MLH HR2 neo ex

value: human embryonic stem cell line

value: CpG free neo cassette was excised by Cre transient expression


title: Occ9

value: African American


title: HR AS iPS 15 neo ex

source_name: AS HR2 neo ex  iPSCs

value: iPSC


title: HR AS iPS 9 neo ex

source_name: AS HR1 neo ex  iPSCs


title: H1 ES

source_name: H1 ES


title: WT iPS H3K4me3

source_name: WT iPS H3K4me3

value: wild type iPSC


title: AS HR2 iPS Input

source_name: AS HR2 Input

value: CpG free neo cassette is integrated in SNURF/SNRPN locus

value: DNA methylation-corrected AS iPSCs


title: WT iPS Input

source_name: WT iPS Input


title: WT iPS

source_name: WT iPSCs


title: AS HR site 3 prodel2 iPSCs

source_name: AS HR site 3 prodel2 iPSCs

value: iPSC line derived from Angelman syndrome patient

value: CpG free neo cassette is integrated in SNURF/SNRPN locus at site3 and SNURF promoter was deleted


title: AS HR site 3 prodel1 iPSCs

source_name: AS HR site 3 prodel1 iPSCs


title: AS HR5 iPSCs

source_name: AS HR5 iPSCs

value: CpG free neo cassette is integrated in SNURF/SNRPN locus on both allele


title: H1 MLH HR2

source_name: H1 MLH HR2

value: CpG free neo cassette is integrated in MLH1 locus in H1 ESCs


title: AS HR2 neo ex iPS H3K4me3

source_name: AS HR2 neo ex iPS H3K4me3

value: CpG free neo cassette was excised from AS HR5 iPSCs


title: H1 MLH HR1

source_name: H1 MLH HR1


title: AS iPS

source_name: AS iPSCs

value: Angeman Syndrome (AS)  iPSCs


title: mRNA_ColorectalCancer_rep18

status: Public on Aug 31 2017

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

hyb_protocol: After fragmentation, cRNA was hybridized with Affymetrix Hybridization,Wash, and Stain Kit on Affymetrix Human Genome GeneChip U133 Plus 2.0 array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA using Affymetrix Expression Console software.

source_name: fresh frozen colorectal tumor tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit  according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.

value: colorectal tumor

tag: gender

value: male


title: mRNA_ColorectalCancer_rep20

value: female


title: HR AS iPS 15

source_name: AS HR2 iPSCs

value: B-lymphocyte

value: CpG free neo cassette is integrated in SNURF/SNRPN locus in AS iPSCs


title: mRNA_ColorectalCancer_rep26


title: mRNA_ColorectalCancer_rep22


title: mRNA_ColorectalCancer_rep17


title: mRNA_ColorectalCancer_rep28


title: mRNA_ColorectalCancer_rep31


title: mRNA_ColorectalCancer_rep21


title: mRNA_ColorectalCancer_rep19


title: mRNA_ColorectalCancer_rep15


title: mRNA_ColorectalCancer_rep30


title: mRNA_ColorectalCancer_rep14


title: mRNA_ColorectalCancer_rep27


title: mRNA_ColorectalCancer_rep29


title: HR AS iPS 9

source_name: AS HR1 iPSCs


title: mRNA_ColorectalCancer_rep12


title: mRNA_ColorectalCancer_rep23


title: mRNA_ColorectalCancer_rep25


title: mRNA_ColorectalCancer_rep24


title: mRNA_ColorectalCancer_rep7


title: mRNA_ColorectalCancer_rep9


title: mRNA_ColorectalCancer_rep10


title: mRNA_ColorectalCancer_rep13


title: mRNA_ColorectalCancer_rep5


title: mRNA_ColorectalCancer_rep11


title: mRNA_ColorectalCancer_rep16


title: TALL16

status: Public on Sep 30 2017

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from a T-ALL pediatric patient at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA. For T-ALL samples removal batch effect were applied using ComBat in the sva package

source_name: T-ALL pediatric patient_bone marrow

label_protocol: For Batch1: Biotinylated cRNA were prepared according to the standard 3'IVT Affymetrix protocol from 100ng of Total RNA. For Batch2: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug of Total RNA(Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: No growth protocol

extract_protocol: For T-ALL patients RNA was exctracted from mononuclear cells using Trizol. For xenograft experiments, RNA was exctracted from engrafted T-cells in the spleen of mice using Trizol.

treatment_protocol: No treatment protocol

tag: subject status

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient

value: Bone Marrow

tag: mrd +78

value: Positive

tag: batch

value: Batch 1


title: mRNA_ColorectalCancer_rep6


title: mRNA_ColorectalCancer_rep1


title: mRNA_ColorectalCancer_rep4


title: Study patient 300

status: Public on Jun 26 2017

city: Madison

first: Jennifer

middle: M

last: Reinhart

state: WI

address: 2015 Linden Dr.

department: Medical Sciences

institute: University of Wisconsin-Madison

description:
SP300
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.

hyb_protocol: Following fragmentation and labeling, 5.0 ug of ss cDNA was hybridized to the Affymetrix Human Transcriptome 2.0 ST array according to manufacturer protocols for each sample.

scan_protocol: The GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G with Autoloader. Scanner serial #50208130.

data_processing: The gene data was extracted using RMA-Sketch in Affymetrix Expression Console version 1.14.46. The exon data was extracted using Alt Splice Analysis in Affymetrix Expression Console version 1.14.46.

source_name: CD*+ T cell-enriched peripheral blood mononuclear cells, HS

label_protocol: Biotinylated ss cDNA was prepared from 5 ng of total RNA using the Affymetrix GeneChip® WT Pico kit.

growth_protocol: 40ml of heparinized whole blood was collected from each patient.

extract_protocol: RNA was extracted using the Trizol/chloroform method, digested for gDNA (TURBO DNA-free, ThermoFisher Scientific), and residual extraction reagents removed using RNeasy MinElute Cleanup (Qiagen).

treatment_protocol: Peripheral blood mononuclear cells were extracted with gradient separation and enriched for CD*+ T cells using an antibody-based, negative selection magnetic bead system (MACS CD8+ T cell Isolation Kit; Miltenyi Biotec Inc.).

tag: sulfonamide antibiotics sensitivity

value: Hypersensitive (HS)


title: Study patient 232

description:
SP232
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient H

description:
SPH
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.

source_name: CD*+ T cell-enriched peripheral blood mononuclear cells, TOL

value: Tolerant (TOL)


title: Study patient G

description:
SPG
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient C

description:
SPC
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: mRNA_ColorectalCancer_rep2


title: Study patient 216

description:
SP216
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient 221

description:
SP221
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: mRNA_ColorectalCancer_rep3


title: Study patient 130

description:
SP130
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient 246

description:
SP246
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient F

description:
SPF
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: Study patient 219

description:
SP219
Gene expression data from human CD8+ T cell-enriched peripheral blood mononuclear cells.


title: H1-EPS-1

status: Public on Apr 06 2017

city: Beijing

first: Hongkui

last: Deng

address: this is for reviewer only

country: China

institute: Peking University

data_processing:
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using RPKM for mouse samples and FPKM for human samples respectively.
Genome_build: hg19 for human and GRCm38/mm10 for mouse
Supplementary_files_format_and_content: Excel files include the expression values for each sample

source_name: Human extended pluripotent stem cells

growth_protocol: Human primed pluripotent stem cells were maintained in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells in conventional human embryonic stem cell medium.Human extended pluripotent stem cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells. Mouse extended pluripotent stem cells were maintained in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates. Mouse embryonic stem cells were maintained in serum-free 2i medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or or Matrigel-coated plates.

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Human extended pluripotent stem cells