title: patient 360, RCC tumor tissue

description:
sample_id: 2020_360TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 356, RCC tumor tissue

status: Public on Feb 20 2021

type: RNA

city: Lyon

first: Jean-Noel

last: Hubert

address: 150 cours Albert Thomas

department: Genetics

country: France

institute: International Agency For Research on Cancer

description:
sample_id: 2020_356TU
non-normalized data in non_norm_matrix3.txt.gz

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed using vst transformation and quantile normalisation with the lumi package in R (Bioconductor).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney

label_protocol: Biotin labeled single-stranded cRNAs (Illumina TotalPrep RNA Amplification Kit from Ambion®).

extract_protocol: RNA was extracted withTotal RNA Isolation NucleoSpin® RNA II kit (Macherey Nagel) in accordance with the prescribed protocol provided with the kit. Quality control was performed withAgilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: kidney

tag: type

value: tumor

tag: Sex

value: female

tag: age

tag: histo

value: conventional RCC

tag: Stage

tag: grade


title: patient 368, RCC tumor tissue

description:
sample_id: 2020_368TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 335, RCC tumor tissue

description:
sample_id: 2020_335TU
non-normalized data in non_norm_matrix2.txt.gz

value: male


title: patient 355, RCC tumor tissue

description:
sample_id: 2020_355TU
non-normalized data in non_norm_matrix3.txt.gz


title: patient 352, RCC tumor tissue

description:
sample_id: 2020_352TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 353, RCC tumor tissue

description:
sample_id: 2020_353TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 351, RCC tumor tissue

description:
sample_id: 2020_351TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 350, RCC tumor tissue

description:
sample_id: 2020_350TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 346, RCC tumor tissue

description:
sample_id: 2020_346TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 327, RCC tumor tissue

description:
sample_id: 2020_327TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 326, RCC tumor tissue

description:
sample_id: 2020_326TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 328, RCC tumor tissue

description:
sample_id: 2020_328TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 338, RCC tumor tissue

description:
sample_id: 2020_338TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 341, RCC tumor tissue

description:
sample_id: 2020_341TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 349, RCC tumor tissue

description:
sample_id: 2020_349TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 347, RCC tumor tissue

description:
sample_id: 2020_347TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 342, RCC tumor tissue

description:
sample_id: 2020_342TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 322, RCC tumor tissue

description:
sample_id: 2020_322TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 336, RCC tumor tissue

description:
sample_id: 2020_336TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 348, RCC tumor tissue

description:
sample_id: 2020_348TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 320, RCC tumor tissue

description:
sample_id: 2020_320TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 332, RCC tumor tissue

description:
sample_id: 2020_332TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 333, RCC tumor tissue

description:
sample_id: 2020_333TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 334, RCC tumor tissue

description:
sample_id: 2020_334TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 317, RCC tumor tissue

description:
sample_id: 2020_317TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 319, RCC tumor tissue

description:
sample_id: 2020_319TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 316, RCC tumor tissue

description:
sample_id: 2020_316TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 313, RCC tumor tissue

description:
sample_id: 2020_313TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 330, RCC tumor tissue

description:
sample_id: 2020_330TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 329, RCC tumor tissue

description:
sample_id: 2020_329TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 325, RCC tumor tissue

description:
sample_id: 2020_325TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 337, RCC tumor tissue

description:
sample_id: 2020_337TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 323, RCC tumor tissue

description:
sample_id: 2020_323TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 324, RCC tumor tissue

description:
sample_id: 2020_324TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 321, RCC tumor tissue

description:
sample_id: 2020_321TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 318, RCC tumor tissue

description:
sample_id: 2020_318TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 314, RCC tumor tissue

description:
sample_id: 2020_314TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 331, RCC tumor tissue

description:
sample_id: 2020_331TU
non-normalized data in non_norm_matrix2.txt.gz


title: patient 307, RCC tumor tissue

description:
sample_id: 2020_307TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 312, RCC tumor tissue

description:
sample_id: 2020_312TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 304, RCC tumor tissue

description:
sample_id: 2020_304TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 305, RCC tumor tissue

description:
sample_id: 2020_305TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 306, RCC tumor tissue

description:
sample_id: 2020_306TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 311, RCC tumor tissue

description:
sample_id: 2020_311TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 309, RCC tumor tissue

description:
sample_id: 2020_309TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 315, RCC tumor tissue

description:
sample_id: 2020_315TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 294, RCC tumor tissue

description:
sample_id: 2020_294TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 302, RCC tumor tissue

description:
sample_id: 2020_302TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 301, RCC tumor tissue

description:
sample_id: 2020_301TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 303, RCC tumor tissue

description:
sample_id: 2020_303TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 300, RCC tumor tissue

description:
sample_id: 2020_300TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 298, RCC tumor tissue

description:
sample_id: 2020_298TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 299, RCC tumor tissue

description:
sample_id: 2020_299TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 293, RCC tumor tissue

description:
sample_id: 2020_293TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 288, RCC tumor tissue

description:
sample_id: 2020_288TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 310, RCC tumor tissue

description:
sample_id: 2020_310TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 291, RCC tumor tissue

description:
sample_id: 2020_291TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 290, RCC tumor tissue

description:
sample_id: 2020_290TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 289, RCC tumor tissue

description:
sample_id: 2020_289TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 287, RCC tumor tissue

description:
sample_id: 2020_287TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 285, RCC tumor tissue

description:
sample_id: 2020_285TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 281, RCC tumor tissue

description:
sample_id: 2020_281TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 279, RCC tumor tissue

description:
sample_id: 2020_279TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 284, RCC tumor tissue

description:
sample_id: 2020_284TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 282, RCC tumor tissue

description:
sample_id: 2020_282TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 280, RCC tumor tissue

description:
sample_id: 2020_280TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 278, RCC tumor tissue

description:
sample_id: 2020_278TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 297, RCC tumor tissue

description:
sample_id: 2020_297TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 296, RCC tumor tissue

description:
sample_id: 2020_296TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 283, RCC tumor tissue

description:
sample_id: 2020_283TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 295, RCC tumor tissue

description:
sample_id: 2020_295TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 277, RCC tumor tissue

description:
sample_id: 2020_277TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 276, RCC tumor tissue

description:
sample_id: 2020_276TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 273, RCC tumor tissue

description:
sample_id: 2020_273TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 308, RCC tumor tissue

description:
sample_id: 2020_308TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 268, RCC tumor tissue

description:
sample_id: 2020_268TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 292, RCC tumor tissue

description:
sample_id: 2020_292TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 275, RCC tumor tissue

description:
sample_id: 2020_275TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 267, RCC tumor tissue

description:
sample_id: 2020_267TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 271, RCC tumor tissue

description:
sample_id: 2020_271TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 272, RCC tumor tissue

description:
sample_id: 2020_272TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 266, RCC tumor tissue

description:
sample_id: 2020_266TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 274, RCC tumor tissue

description:
sample_id: 2020_274TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 265, RCC tumor tissue

description:
sample_id: 2020_265TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 286, RCC tumor tissue

description:
sample_id: 2020_286TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 270, RCC tumor tissue

description:
sample_id: 2020_270TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 269, RCC tumor tissue

description:
sample_id: 2020_269TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 264, RCC tumor tissue

description:
sample_id: 2020_264TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 263, RCC tumor tissue

description:
sample_id: 2020_263TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 262, RCC tumor tissue

description:
sample_id: 2020_262TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 261, RCC tumor tissue

description:
sample_id: 2020_261TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 256, RCC tumor tissue

description:
sample_id: 2020_256TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 254, RCC tumor tissue

description:
sample_id: 2020_254TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 255, RCC tumor tissue

description:
sample_id: 2020_255TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 257, RCC tumor tissue

description:
sample_id: 2020_257TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 259, RCC tumor tissue

description:
sample_id: 2020_259TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 254, non-tumor tissue

description:
sample_id: 2020_254NL
non-normalized data in non_norm_matrix1.txt.gz

value: normal


title: patient 258, RCC tumor tissue

description:
sample_id: 2020_258TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 251, RCC tumor tissue

description:
sample_id: 2020_251TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 253, RCC tumor tissue

description:
sample_id: 2020_253TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 252, non-tumor tissue

description:
sample_id: 2020_252NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 251, non-tumor tissue

description:
sample_id: 2020_251NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 252, RCC tumor tissue

description:
sample_id: 2020_252TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 253, non-tumor tissue

description:
sample_id: 2020_253NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 250, non-tumor tissue

description:
sample_id: 2020_250NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 250, RCC tumor tissue

description:
sample_id: 2020_250TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 249, non-tumor tissue

description:
sample_id: 2020_249NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 249, RCC tumor tissue

description:
sample_id: 2020_249TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 247, non-tumor tissue

description:
sample_id: 2020_247NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 246, non-tumor tissue

description:
sample_id: 2020_246NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 248, non-tumor tissue

description:
sample_id: 2020_248NL
non-normalized data in non_norm_matrix11.txt.gz


title: patient 247, RCC tumor tissue

description:
sample_id: 2020_247TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 243, RCC tumor tissue

description:
sample_id: 2020_243TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 244, non-tumor tissue

description:
sample_id: 2020_244NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 246, RCC tumor tissue

description:
sample_id: 2020_246TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 245, RCC tumor tissue

description:
sample_id: 2020_245TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 244, RCC tumor tissue

description:
sample_id: 2020_244TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 248, RCC tumor tissue

description:
sample_id: 2020_248TU
non-normalized data in non_norm_matrix11.txt.gz


title: patient 260, RCC tumor tissue

description:
sample_id: 2020_260TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 241, non-tumor tissue

description:
sample_id: 2020_241NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 240, non-tumor tissue

description:
sample_id: 2020_240NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 238, RCC tumor tissue

description:
sample_id: 2020_238TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 243, non-tumor tissue

description:
sample_id: 2020_243NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 237, non-tumor tissue

description:
sample_id: 2020_237NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 236, RCC tumor tissue

description:
sample_id: 2020_236TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 242, RCC tumor tissue

description:
sample_id: 2020_242TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 236, non-tumor tissue

description:
sample_id: 2020_236NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 240, RCC tumor tissue

description:
sample_id: 2020_240TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 242, non-tumor tissue

description:
sample_id: 2020_242NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 239, RCC tumor tissue

description:
sample_id: 2020_239TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 234, RCC tumor tissue

description:
sample_id: 2020_234TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 239, non-tumor tissue

description:
sample_id: 2020_239NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 233, non-tumor tissue

description:
sample_id: 2020_233NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 238, non-tumor tissue

description:
sample_id: 2020_238NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 237, RCC tumor tissue

description:
sample_id: 2020_237TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 230, RCC tumor tissue

description:
sample_id: 2020_230TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 230, non-tumor tissue

description:
sample_id: 2020_230NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 245, non-tumor tissue

description:
sample_id: 2020_245NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 229, RCC tumor tissue

description:
sample_id: 2020_229TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 235, RCC tumor tissue

description:
sample_id: 2020_235TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 234, non-tumor tissue

description:
sample_id: 2020_234NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 235, non-tumor tissue

description:
sample_id: 2020_235NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 233, RCC tumor tissue

description:
sample_id: 2020_233TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 232, RCC tumor tissue

description:
sample_id: 2020_232TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 241, RCC tumor tissue

description:
sample_id: 2020_241TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 227, RCC tumor tissue

description:
sample_id: 2020_227TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 228, RCC tumor tissue

description:
sample_id: 2020_228TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 229, non-tumor tissue

description:
sample_id: 2020_229NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 225, non-tumor tissue

description:
sample_id: 2020_225NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 226, non-tumor tissue

description:
sample_id: 2020_226NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 223, RCC tumor tissue

description:
sample_id: 2020_223TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 228, non-tumor tissue

description:
sample_id: 2020_228NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 222, RCC tumor tissue

description:
sample_id: 2020_222TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 231, non-tumor tissue

description:
sample_id: 2020_231NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 222, non-tumor tissue

description:
sample_id: 2020_222NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 224, RCC tumor tissue

description:
sample_id: 2020_224TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 226, RCC tumor tissue

description:
sample_id: 2020_226TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 225, RCC tumor tissue

description:
sample_id: 2020_225TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 231, RCC tumor tissue

description:
sample_id: 2020_231TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 221, RCC tumor tissue

description:
sample_id: 2020_221TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 227, non-tumor tissue

description:
sample_id: 2020_227NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 224, non-tumor tissue

description:
sample_id: 2020_224NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 220, non-tumor tissue

description:
sample_id: 2020_220NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 221, non-tumor tissue

description:
sample_id: 2020_221NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 232, non-tumor tissue

description:
sample_id: 2020_232NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 219, RCC tumor tissue

description:
sample_id: 2020_219TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 219, non-tumor tissue

description:
sample_id: 2020_219NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 218, RCC tumor tissue

description:
sample_id: 2020_218TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 218, non-tumor tissue

description:
sample_id: 2020_218NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 217, non-tumor tissue

description:
sample_id: 2020_217NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 216, RCC tumor tissue

description:
sample_id: 2020_216TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 223, non-tumor tissue

description:
sample_id: 2020_223NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 216, non-tumor tissue

description:
sample_id: 2020_216NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 215, RCC tumor tissue

description:
sample_id: 2020_215TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 214, non-tumor tissue

description:
sample_id: 2020_214NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 215, non-tumor tissue

description:
sample_id: 2020_215NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 213, RCC tumor tissue

description:
sample_id: 2020_213TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 212, RCC tumor tissue

description:
sample_id: 2020_212TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 213, non-tumor tissue

description:
sample_id: 2020_213NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 212, non-tumor tissue

description:
sample_id: 2020_212NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 211, RCC tumor tissue

description:
sample_id: 2020_211TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 214, RCC tumor tissue

description:
sample_id: 2020_214TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 210, RCC tumor tissue

description:
sample_id: 2020_210TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 209, RCC tumor tissue

description:
sample_id: 2020_209TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 210, non-tumor tissue

description:
sample_id: 2020_210NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 220, RCC tumor tissue

description:
sample_id: 2020_220TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 208, non-tumor tissue

description:
sample_id: 2020_208NL
non-normalized data in non_norm_matrix12.txt.gz


title: patient 209, non-tumor tissue

description:
sample_id: 2020_209NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 208, RCC tumor tissue

description:
sample_id: 2020_208TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 206, non-tumor tissue

description:
sample_id: 2020_206NL
non-normalized data in non_norm_matrix12.txt.gz


title: patient 207, non-tumor tissue

description:
sample_id: 2020_207NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 207, RCC tumor tissue

description:
sample_id: 2020_207TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 206, RCC tumor tissue

description:
sample_id: 2020_206TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 217, RCC tumor tissue

description:
sample_id: 2020_217TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 204, RCC tumor tissue

description:
sample_id: 2020_204TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 204, non-tumor tissue

description:
sample_id: 2020_204NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 205, non-tumor tissue

description:
sample_id: 2020_205NL
non-normalized data in non_norm_matrix12.txt.gz


title: patient 205, RCC tumor tissue

description:
sample_id: 2020_205TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 203, RCC tumor tissue

description:
sample_id: 2020_203TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 203, non-tumor tissue

description:
sample_id: 2020_203NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 202, non-tumor tissue

description:
sample_id: 2020_202NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 202, RCC tumor tissue

description:
sample_id: 2020_202TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 201, RCC tumor tissue

description:
sample_id: 2020_201TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 201, non-tumor tissue

description:
sample_id: 2020_201NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 200, non-tumor tissue

description:
sample_id: 2020_200NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 199, non-tumor tissue

description:
sample_id: 2020_199NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 200, RCC tumor tissue

description:
sample_id: 2020_200TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 199, RCC tumor tissue

description:
sample_id: 2020_199TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 198, RCC tumor tissue

description:
sample_id: 2020_198TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 211, non-tumor tissue

description:
sample_id: 2020_211NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 198, non-tumor tissue

description:
sample_id: 2020_198NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 197, RCC tumor tissue

description:
sample_id: 2020_197TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 192, non-tumor tissue

description:
sample_id: 2020_192NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 195, RCC tumor tissue

description:
sample_id: 2020_195TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 192, RCC tumor tissue

description:
sample_id: 2020_192TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 197, non-tumor tissue

description:
sample_id: 2020_197NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 196, RCC tumor tissue

description:
sample_id: 2020_196TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 191, RCC tumor tissue

description:
sample_id: 2020_191TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 195, non-tumor tissue

description:
sample_id: 2020_195NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 193, non-tumor tissue

description:
sample_id: 2020_193NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 194, non-tumor tissue

description:
sample_id: 2020_194NL
non-normalized data in non_norm_matrix12.txt.gz


title: patient 190, RCC tumor tissue

description:
sample_id: 2020_190TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 190, non-tumor tissue

description:
sample_id: 2020_190NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 193, RCC tumor tissue

description:
sample_id: 2020_193TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 189, RCC tumor tissue

description:
sample_id: 2020_189TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 194, RCC tumor tissue

description:
sample_id: 2020_194TU
non-normalized data in non_norm_matrix12.txt.gz


title: patient 191, non-tumor tissue

description:
sample_id: 2020_191NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 189, non-tumor tissue

description:
sample_id: 2020_189NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 188, RCC tumor tissue

description:
sample_id: 2020_188TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 188, non-tumor tissue

description:
sample_id: 2020_188NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 187, RCC tumor tissue

description:
sample_id: 2020_187TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 187, non-tumor tissue

description:
sample_id: 2020_187NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 185, non-tumor tissue

description:
sample_id: 2020_185NL
non-normalized data in non_norm_matrix7.txt.gz


title: patient 186, non-tumor tissue

description:
sample_id: 2020_186NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 186, RCC tumor tissue

description:
sample_id: 2020_186TU
non-normalized data in non_norm_matrix9.txt.gz


title: patient 184, RCC tumor tissue

description:
sample_id: 2020_184TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 185, RCC tumor tissue

description:
sample_id: 2020_185TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 184, non-tumor tissue

description:
sample_id: 2020_184NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 183, RCC tumor tissue

description:
sample_id: 2020_183TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 183, non-tumor tissue

description:
sample_id: 2020_183NL
non-normalized data in non_norm_matrix7.txt.gz


title: patient 196, non-tumor tissue

description:
sample_id: 2020_196NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 182, RCC tumor tissue

description:
sample_id: 2020_182TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 180, RCC tumor tissue

description:
sample_id: 2020_180TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 178, RCC tumor tissue

description:
sample_id: 2020_178TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 180, non-tumor tissue

description:
sample_id: 2020_180NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 179, RCC tumor tissue

description:
sample_id: 2020_179TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 178, non-tumor tissue

description:
sample_id: 2020_178NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 177, non-tumor tissue

description:
sample_id: 2020_177NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 177, RCC tumor tissue

description:
sample_id: 2020_177TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 179, non-tumor tissue

description:
sample_id: 2020_179NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 182, non-tumor tissue

description:
sample_id: 2020_182NL
non-normalized data in non_norm_matrix7.txt.gz


title: patient 181, RCC tumor tissue

description:
sample_id: 2020_181TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 181, non-tumor tissue

description:
sample_id: 2020_181NL
non-normalized data in non_norm_matrix13.txt.gz


title: MmGtsf1-Strep in Sf9 - input2

type: SRA

city: Cold Spring Harbor

first: Jonathan

middle: James

last: Ipsaro

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
Basecalling was performed with bcl2fastq2 v2.19 (Illumina).
Reads were trimmed to remove the first 3 nucleotides (contributed by the kit chemistry) and to remove low quality ends with trimmomatic. -threads 1 -phred33 fastq_in.fastqsanger fastq_out.fastqsanger HEADCROP:3 SLIDINGWINDOW:4:20
polyA tails (also contributed from the kit chemistry) were removed using a custom script.
Size selection was performed to retain reads between 30 and 85 nucleotides in length using Galaxy.
Reads with poor quality were filtered out using Galaxy. 95% of bases were required to have a Q-value over 24 to be retained.
To assess the most abundant reads, identical reads were counted and collapsed using Galaxy.
Genome_build: no mapping performed due to low quality genome assembly
Supplementary_files_format_and_content: *_final_collapsed.fasta; fasta-formatted reads, collapsed based on counts of sequencing reads that are identical after processing. The reads are sorted from most common to least common (from top to bottom) with identifier rows indicating the read number (1, 2, 3, etc.) and number of instances of that read (e.g. >6-36055 indicates the sixth most abundant sequence, being represented 36055 times in the library).

organism: Spodoptera frugiperda

growth_protocol: Sf9 cells were maintained in HyClone CCM3 medium and grown in suspension at 27°C with shaking. Cultures were monitored for Mycoplasma contamination using the MycoAlert Mycoplasma Detection Kit (Lonza). Mycoplasma contamination was not detected.

extract_protocol:
Cells were lysed by sonication in 50 mM Tris, pH 8.0, 100 mM KCl, 1 mM DTT, then purified by affinity chromatography using Strep-Tactin resin (IBA). The purified Gtsf1 protein and co-purifying nucleic acids were eluted in lysis buffer supplemented with 5 mM d-desthiobiotin. The eluted material was further purified by ion exchange chromatography (MonoQ column) and nucleic acid containing fractions were taken for library construction.
Small RNA libraries were prepared using the SMARTer smRNA-Seq Kit for Illumina sequencing (Takara). In addition to the co-purifying RNAs, total Sf9 RNAs were similarly processed as input controls. Size-selection was performed using Blue Pippin 2% agarose gel cassettes (Sage Science). All libraries were assessed by fluorometric quantification (Qubit 3.0) and by Bioanalyzer chip-based capillary electrophoresis.
Libraries were pooled in equimolar ratios according to their quantification by Bioanalyzer. Single-end reads with two 8-basepair barcodes were generated on an Illumina NextSeq resulting in approximately 10 million reads per library.

treatment_protocol: Asterix/Gtsf1 protein from mouse with a C-terminal TEV-Strep tag was expressed recombinantly using the MultiBac expression system. Briefly, the cDNA corresponding to the mouse Gtsf1 protein was cloned into a vector (pFL) that allows for bacmid incorporation and subsequent baculovirus generation upon transfection. The baculovirus was amplified after transfection through additional rounds of infection and medium harvesting. For large-scale expression, cells were harvested 72 hours post-infection.

tag: cell line

tag: pull-down

value: input


title: patient 176, non-tumor tissue

description:
sample_id: 2020_176NL
non-normalized data in non_norm_matrix1.txt.gz


title: MmGtsf1-Strep in Sf9 - rip2_1

value: Strep-Tactin beads pull-down


title: MmGtsf1-Strep in Sf9 - rip2_2


title: patient 176, RCC tumor tissue

description:
sample_id: 2020_176TU
non-normalized data in non_norm_matrix1.txt.gz


title: MmGtsf1-Strep in Sf9 - rip1_2


title: patient 175, RCC tumor tissue

description:
sample_id: 2020_175TU
non-normalized data in non_norm_matrix1.txt.gz


title: MmGtsf1-Strep in Sf9 - rip1_1


title: patient 175, non-tumor tissue

description:
sample_id: 2020_175NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 173, non-tumor tissue

description:
sample_id: 2020_173NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 173, RCC tumor tissue

description:
sample_id: 2020_173TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 174, RCC tumor tissue

description:
sample_id: 2020_174TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 174, non-tumor tissue

description:
sample_id: 2020_174NL
non-normalized data in non_norm_matrix1.txt.gz


title: RNAtagTest6_pool1

city: New York

first: Ian

middle: A

last: Mellis

institute: Columbia University

data_processing:
Base-calling performed by Illumina Basespace
Read filtering performed by Trimmomatic v0.32 with parameters MINLEN:11
Demultiplexing of samples from 32-sample pooled libraried performed by PyRNAtagSeq changeset 6ffd465 (Wallace, 2017, github)
Alignment to hg19 performed by STAR v2.5.2a using only the 55-nt R2 reads in single-end mode (excluding the RNAtag read on R1)
Gene counts quantified by HTSeq v0.6.1 with settings --mode=union \   --stranded=no \   --type=exon \   --order=name Genome_build: hg19
Supplementary_files_format_and_content: mapped counts is a csv containing the matrix of mapped counts for each ENSEMBL gene ID called by HTSeq in each of 576 samples. Top row = header. First column = ENSEMBL gene ID
Supplementary_files_format_and_content: colData for mapped counts is a tab-delimited text file containing a mapping between the sample IDs in the header of mapped counts and descriptions of the treatment conditions and quality controls for each sample

source_name: fibroblast

growth_protocol: Cardiac myocytes were obtained by differentiating human induced pluripotent stem cells to iPS-GM942-SeV3-CMs ("iPSC-CMs"), as previously described (Laflamme et al., 2007; Palpant et al., 2015; Shanmughapriya et al., 2018; Zhu et al., 2010, 2011). GM00942 (Coriell) human dermal fibroblasts were expanded per manufacturer's instructions.

extract_protocol:
RNaqueous-96 kits (Ambion) on day 4 after first drug treatment
RNAtag-seq (Shishkin et al., 2015) as previously described (includes rRNA depletion by Illumina RiboZero). Libraries sequenced 20:8:0:55 on a NextSeq550, with the RNAtag in R1 reads

treatment_protocol: In 96-well plates on Day 0 in 250µL media we added 0.7µL of drug stock in DMSO (See Table S1 of citation) or of DMSO (for control cultures), keeping total DMSO concentration of perturbation culture medium below 0.3% for all conditions.

tag: cell type

value: fibroblast


title: RNAtagTest5_pool2


title: RNAtagTest6_pool2


title: RNAtagTest6_pool3


title: patient 172, RCC tumor tissue

description:
sample_id: 2020_172TU
non-normalized data in non_norm_matrix1.txt.gz


title: MmGtsf1-Strep in Sf9 - input1


title: patient 171, non-tumor tissue

description:
sample_id: 2020_171NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 171, RCC tumor tissue

description:
sample_id: 2020_171TU
non-normalized data in non_norm_matrix1.txt.gz


title: RNAtagTest4_pool3

source_name: fibroblast and HeLa

value: fibroblast and HeLa

value: GM00942 and HeLa


title: RNAtagTest5_pool1


title: RNAtagTest4_pool2


title: RNAtagTest4_pool1


title: patient 170, RCC tumor tissue

description:
sample_id: 2020_170TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 172, non-tumor tissue

description:
sample_id: 2020_172NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 170, non-tumor tissue

description:
sample_id: 2020_170NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 169, RCC tumor tissue

description:
sample_id: 2020_169TU
non-normalized data in non_norm_matrix1.txt.gz


title: iCardTest6set100x_pool3

source_name: iPSC-derived cardiac myocyte

value: iPSC-derived cardiac myocyte


title: patient 169, non-tumor tissue

description:
sample_id: 2020_169NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 168, non-tumor tissue

description:
sample_id: 2020_168NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 168, RCC tumor tissue

description:
sample_id: 2020_168TU
non-normalized data in non_norm_matrix1.txt.gz


title: iCardTest6set100x_pool2


title: iCardTest6set100x_pool1


title: RNAtagTest5_pool3


title: iCardTest5set100x_pool2


title: iCardTest4set100x_pool3


title: patient 166, non-tumor tissue

description:
sample_id: 2020_166NL
non-normalized data in non_norm_matrix1.txt.gz


title: iCardTest4set100x_pool2


title: iCardTest4set100x_pool1


title: patient 167, RCC tumor tissue

description:
sample_id: 2020_167TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 167, non-tumor tissue

description:
sample_id: 2020_167NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 165, RCC tumor tissue

description:
sample_id: 2020_165TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 165, non-tumor tissue

description:
sample_id: 2020_165NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 164, RCC tumor tissue

description:
sample_id: 2020_164TU
non-normalized data in non_norm_matrix1.txt.gz


title: iCardTest5set100x_pool3


title: patient 164, non-tumor tissue

description:
sample_id: 2020_164NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 161, RCC tumor tissue

description:
sample_id: 2020_161TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 163, non-tumor tissue

description:
sample_id: 2020_163NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 163, RCC tumor tissue

description:
sample_id: 2020_163TU
non-normalized data in non_norm_matrix1.txt.gz


title: iCardTest5set100x_pool1


title: patient 162, non-tumor tissue

description:
sample_id: 2020_162NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 162, RCC tumor tissue

description:
sample_id: 2020_162TU
non-normalized data in non_norm_matrix1.txt.gz


title: 35Spro:RIF-RNAi #11 red receptacles rep3

city: Málaga

first: David

last: Posé

address: Avenida Louis Pasteur, 49

country: Spain

institute: Instituto de Hortofruticultura Subtropical y Mediterránea

description:
35SRIF-RNAi_#11_R_3
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt

data_processing:
CLC Genomics Workbench 9 software for trimming, mapping and expression analyses
Raw sequences were trimmed and mapped against using the assembly and annotation version v4.0.a1 of the F. vesca reference genome (https://www.rosacea.org/species/fragaria_vesca/genome_v4.0.a1; Edger et al., 2018; doi: 10.1093/gigascience/gix124)
Supplementary_files_format_and_content: txt files including the RPKM values, statistical analysis, and gene annotations

organism: Fragaria x ananassa

source_name: red strawberry receptacles

growth_protocol: 35Spro:RIF-RNAi transgenic lines and their respective control line were grown in a shading house, and EXP2pro:RIF-RNAi and 35S:RIF transgenic lines and their respective control line in a greenhouse. In both cases, they were grown under natural sunlight and ambient temperature. Each biological replicate comprise a minimum of 20 receptacles at either white or red stages of ripening.

extract_protocol:
Total RNA was isolated as previously described (Gambino et al., 2008; doi: 10.1002/pca.1078) from three biological replicates of receptacles after the removal of achenes for the control and transgenic lines.
Illumina mRNA libraries were generated using the strand specific mRNA library as described (Zhong et al., 2011; doi:10.1101/pdb-prot5652) for 35Spro:RIF-RNAi and control experiment. For EXP2pro:RIF-RNAi, 35S:RIF and control experiment, the libraries were generated using TruSeq stranded mRNA according to the manufacturer’s instructions (Illumina Inc., San Diego, CA, USA)

tag: cultivar

value: Camarosa

value: Strawberry receptacles

tag: ripening stage

value: red


title: patient 166, RCC tumor tissue

description:
sample_id: 2020_166TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 160, non-tumor tissue

description:
sample_id: 2020_160NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 160, RCC tumor tissue

description:
sample_id: 2020_160TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 161, non-tumor tissue

description:
sample_id: 2020_161NL
non-normalized data in non_norm_matrix1.txt.gz


title: 35Spro:RIF-RNAi #11 red receptacles rep1

description:
35SRIF-RNAi_#11_R_1
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: 35Spro:RIF-RNAi #11 red receptacles rep2

description:
35SRIF-RNAi_#11_R_2
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: 35Spro:RIF-RNAi #11 white receptacles rep3

description:
35SRIF-RNAi_#11_W_3
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt

source_name: white strawberry receptacles

value: white


title: patient 158, RCC tumor tissue

description:
sample_id: 2020_158TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 159, non-tumor tissue

description:
sample_id: 2020_159NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 159, RCC tumor tissue

description:
sample_id: 2020_159TU
non-normalized data in non_norm_matrix1.txt.gz


title: KCS3

city: Kyoto

first: Satoshi

last: Ogawa

state: Kyoto

address: 54 Syogoinkawahara-cho, Sakyo-ku, Kyoto

country: Japan

institute: Kyoto University Graduate School of Medicine

description:
AR3140_04
Gene expression of isolated acinar cells of Ptf1aCre; KrasLSL-G12D; Setdb1flox/flox pancreata.

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-074809 SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized on GeneSpring GX 14.9 (Agilent). Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ug Total RNA using the Pico WTA System (Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain/background

tag: genotype/variation

value: Ptf1aCre; KrasLSL-G12D; Setdb1flox/flox

value: Acinar cells


title: 35Spro:RIF-RNAi #11 white receptacles rep1

description:
35SRIF-RNAi_#11_W_1
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: 35Spro:RIF-RNAi #11 white receptacles rep2

description:
35SRIF-RNAi_#11_W_2
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: KCS2

description:
AR3140_03
Gene expression of isolated acinar cells of Ptf1aCre; KrasLSL-G12D; Setdb1flox/flox pancreata.


title: KC3

description:
AR3140_02
Gene expression of isolated acinar cells of Ptf1aCre; KrasLSL-G12D pancreata.

source_name: Ptf1aCre; KrasLSL-G12D pancreata

value: Ptf1aCre; KrasLSL-G12D


title: KC2

description:
AR3140_01
Gene expression of isolated acinar cells of Ptf1aCre; KrasLSL-G12D pancreata.


title: patient 157, RCC tumor tissue

description:
sample_id: 2020_157TU
non-normalized data in non_norm_matrix1.txt.gz

value: kidney

value: tumor

value: female


title: patient 158, non-tumor tissue

description:
sample_id: 2020_158NL
non-normalized data in non_norm_matrix1.txt.gz

value: normal

value: male

value: conventional RCC


title: 35Spro:RIF-RNAi #3 red receptacles rep2

description:
35SRIF-RNAi_#3_R_2
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: 35Spro:RIF-RNAi #3 red receptacles rep1

description:
35SRIF-RNAi_#3_R_1
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: 35Spro:RIF-RNAi #3 white receptacles rep1

description:
35SRIF-RNAi_#3_W_1
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: 35Spro:RIF-RNAi #3 white receptacles rep2

description:
35SRIF-RNAi_#3_W_2
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: 35Spro:RIF-RNAi #3 white receptacles rep3

description:
35SRIF-RNAi_#3_W_3
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: KC1

description:
AR3089_02
Gene expression of isolated acinar cells of Ptf1aCre; KrasLSL-G12D pancreata.


title: patient 154, RCC tumor tissue

description:
sample_id: 2020_154TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 155, RCC tumor tissue

description:
sample_id: 2020_155TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 156, non-tumor tissue

description:
sample_id: 2020_156NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 155, non-tumor tissue

description:
sample_id: 2020_155NL
non-normalized data in non_norm_matrix13.txt.gz


title: Control red receptacles rep1 (control for 35Spro:RIF-RNAi samples)

description:
Control_for_35SRIF-RNAi_R_1
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: patient 154, non-tumor tissue

description:
sample_id: 2020_154NL
non-normalized data in non_norm_matrix13.txt.gz


title: Control red receptacles rep3 (control for 35Spro:RIF-RNAi samples)

description:
Control_for_35SRIF-RNAi_R_3
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: Control white receptacles rep3 (control for 35Spro:RIF-RNAi samples)

description:
Control_for_35SRIF-RNAi_W_3
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: patient 153, RCC tumor tissue

description:
sample_id: 2020_153TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 153, non-tumor tissue

description:
sample_id: 2020_153NL
non-normalized data in non_norm_matrix1.txt.gz


title: Control white receptacles rep2 (control for 35Spro:RIF-RNAi samples)

description:
Control_for_35SRIF-RNAi_W_2
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: Control white receptacles rep1 (control for 35Spro:RIF-RNAi samples)

description:
Control_for_35SRIF-RNAi_W_1
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: patient 152, RCC tumor tissue

description:
sample_id: 2020_152TU
non-normalized data in non_norm_matrix7.txt.gz


title: 35Spro:RIF-RNAi #3 red receptacles rep3

description:
35SRIF-RNAi_#3_R_3
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt


title: patient 157, non-tumor tissue

description:
sample_id: 2020_157NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 156, RCC tumor tissue

description:
sample_id: 2020_156TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 150, RCC tumor tissue

description:
sample_id: 2020_150TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 151, non-tumor tissue

description:
sample_id: 2020_151NL
non-normalized data in non_norm_matrix7.txt.gz


title: patient 150, non-tumor tissue

description:
sample_id: 2020_150NL
non-normalized data in non_norm_matrix4.txt.gz


title: patient 149, RCC tumor tissue

description:
sample_id: 2020_149TU
non-normalized data in non_norm_matrix4.txt.gz


title: patient 149, non-tumor tissue

description:
sample_id: 2020_149NL
non-normalized data in non_norm_matrix4.txt.gz


title: MEKK1-/- treated rep 2

city: Vermillion

first: Bruce

last: Cuevas

state: SD

address: 414 E. Clark Street

department: Basic Biomedical Sciences

institute: University of South Dakota

description: replicate 2

hyb_protocol: not available

scan_protocol: not available

data_processing: not available

source_name: mouse mammary gland

label_protocol: All of the array protocols and data processing protocols, including labeling, hybridization, scanning, data processing and value definition were performed at Northwestern University, Feinberg School of Medicine, 750 North Lakes Shore Drive, Rubloff 11-144, Chicago, IL 60611. When these experiments were performed in 2010, the name of the facility was the Center for Genomic Medicine, Genomics Core Facility. All procedures were performed on a per-fee basis, and only normalized data was provided to our group at the end of the process. Any raw or non-normalized data were discarded one year after the service was provided.

growth_protocol: Primary mouse fibroblasts were isolated from inguinal mammary glands of 8-10 week-old female mice (MEKK1+/+ or MEKK1-/-) and grown in DMEM with 10% FBS.

extract_protocol: Total cell RNA was extracted with the Rneasy kit (Qiagen, Valencia CA, USA) per manufacturer recommendations.

treatment_protocol: Primary mouse fibroblasts were exposed to DMEM growth media (DMEM + 10% FBS, control) or Breast tumor-conditioned media (DMEM growth media harvested from MDA-MB231 breast tumor cell cultures, treated) for 8 hours, after which total RNA was extracted from both control and treated cells.

tag: genotype

value: mammary gland

value: mammary fibroblasts

tag: gender

tag: strain

value: 8-10 weeks

tag: treatment

value: breast tumor-conditioned cell culture media


title: patient 148, non-tumor tissue

description:
sample_id: 2020_148NL
non-normalized data in non_norm_matrix5.txt.gz

tag: tissue

tag: type


title: patient 148, RCC tumor tissue

description:
sample_id: 2020_148TU
non-normalized data in non_norm_matrix5.txt.gz

tag: Sex

tag: age


title: MEKK1-/- treated rep 1

description: replicate 1


title: MEKK1-/- treated rep 3

description: replicate 3


title: Obese_day_10_rep4

city: Chapel Hill

first: Abrar

middle: E

last: Al-Shaer

state: NC

address: 135 Dauer Dr

department: Nutrition

institute: University of North Carolina Chapel Hill

description: DESeq2_results_JLB_flu_HF_D0_HF_D10_GEO.csv

data_processing:
Illumina HiSeq 4000 software was used for base-calling
Quality of sequencing files ran through FASTQC
FASTQ files aligned to the Mus musculus UCSC MM10 reference genome using Bowtie2
Gene counts were generated via the subread featureCounts package
DESeq2 was used for normalization and statistical analysis of the gene counts file output from the featureCounts program
Genome_build: UCSC MM10
Supplementary_files_format_and_content: CSV data table with DESeq2 output (statistics + normalized gene counts)

source_name: Lung sorted CD3+CD8+CD44+ T cells

extract_protocol:
Live+CD3+CD8+CD44+ lung T cells were sorted on the FACSAria II into Trizol LS (Invitrogen) on ice
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumnia using manufacturer’s instructions
Ultra-low RNA-Seq

treatment_protocol: Mice were lightly anesthetized with isoflurane and infected intranasally with 50μL of sterile PBS containing 0.05 hemagglutination units (HAU) of A/PR/8/34 (ATCC® VR-95™, Manassas, VA, USA), a H1N1 influenza virus.

value: Lung

value: Live+CD3+CD8+CD44+ T cells

value: H1N1 influenza A/PR/8/34 virus

tag: infection timepoint

value: Day 10

tag: dietary group

value: Obese (60% kcal from fat)


title: MEKK1-/- control rep 3

description: replicate 3

value: control


title: patient 152, non-tumor tissue

description:
sample_id: 2020_152NL
non-normalized data in non_norm_matrix7.txt.gz

tag: histo

tag: Stage

tag: grade


title: Obese_day_10_rep5

tag: cell type


title: patient 147, RCC tumor tissue

description:
sample_id: 2020_147TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 146, RCC tumor tissue

description:
sample_id: 2020_146TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 151, RCC tumor tissue

description:
sample_id: 2020_151TU
non-normalized data in non_norm_matrix7.txt.gz


title: MEKK1-/- control rep 2

description: replicate 2


title: Obese_day_10_rep3


title: patient 145, RCC tumor tissue

description:
sample_id: 2020_145TU
non-normalized data in non_norm_matrix5.txt.gz


title: MEKK1-/- control rep 1

description: replicate 1


title: Lean_day_10_rep6

description: DESeq2_results_JLB_flu_Con_D0_Con_D10.csv

value: Lean (10% kcal from fat)


title: MEKK1-/- treated rep 4

description: replicate 4


title: patient 145, non-tumor tissue

description:
sample_id: 2020_145NL
non-normalized data in non_norm_matrix5.txt.gz

value: kidney


title: MEKK1+/+ treated rep 3

description: replicate 3

value: WT


title: patient 146, non-tumor tissue

description:
sample_id: 2020_146NL
non-normalized data in non_norm_matrix5.txt.gz


title: Control red receptacles rep2 (control for 35Spro:RIF-RNAi samples)

description:
Control_for_35SRIF-RNAi_R_2
TPC2020-RA-00833R1_SuppDS1_35SRIF-RNAi.txt

tag: cultivar

value: Camarosa

value: Strawberry receptacles

tag: ripening stage

value: red


title: Lean_day_10_rep5


title: patient 147, non-tumor tissue

description:
sample_id: 2020_147NL
non-normalized data in non_norm_matrix5.txt.gz

value: normal

value: male

value: conventional RCC


title: Lean_day_10_rep4


title: MEKK1-/- control rep 4

description: replicate 4

value: mammary gland

value: mammary fibroblasts

value: female

value: 8-10 weeks


title: patient 144, non-tumor tissue

description:
sample_id: 2020_144NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 143, RCC tumor tissue

description:
sample_id: 2020_143TU
non-normalized data in non_norm_matrix13.txt.gz

value: tumor


title: MEKK1+/+ treated rep 2

description: replicate 2

value: breast tumor-conditioned cell culture media


title: patient 144, RCC tumor tissue

description:
sample_id: 2020_144TU
non-normalized data in non_norm_matrix13.txt.gz


title: Obese_day_0_rep2

value: Lung

value: Live+CD3+CD8+CD44+ T cells

value: Day 0

value: Obese (60% kcal from fat)


title: patient 142, non-tumor tissue

description:
sample_id: 2020_142NL
non-normalized data in non_norm_matrix1.txt.gz

value: kidney


title: Obese_day_0_rep1


title: patient 140, RCC tumor tissue

description:
sample_id: 2020_140TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 140, non-tumor tissue

description:
sample_id: 2020_140NL
non-normalized data in non_norm_matrix1.txt.gz


title: Lean_day_0_rep3

value: Lean (10% kcal from fat)


title: Lean_day_0_rep2


title: MEKK1+/+ treated rep 4

description: replicate 4

value: WT


title: MEKK1+/+ control rep 4

description: replicate 4

value: control


title: MEKK1+/+ control rep 3

description: replicate 3


title: MEKK1+/+ treated rep 1

description: replicate 1


title: patient 139, non-tumor tissue

description:
sample_id: 2020_139NL
non-normalized data in non_norm_matrix13.txt.gz

value: normal


title: MEKK1+/+ control rep 2

description: replicate 2


title: patient 138, RCC tumor tissue

description:
sample_id: 2020_138TU
non-normalized data in non_norm_matrix5.txt.gz

value: male


title: KCS1

description:
AR3089_01
Gene expression of isolated acinar cells of Ptf1aCre; KrasLSL-G12D; Setdb1flox/flox pancreata.

tag: strain/background

tag: genotype/variation

value: Ptf1aCre; KrasLSL-G12D; Setdb1flox/flox

value: Acinar cells


title: MEKK1+/+ control rep 1

description: replicate 1

tag: genotype

value: mammary gland

value: mammary fibroblasts

tag: gender


title: Lean_day_0_rep1

tag: strain

tag: treatment


title: WT RAGKO RNA-seq rep2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
RAGKO_RNA-seq_2
processed data file:
RNA-seq_counts.txt

data_processing:
Libraries were sequenced on an Illumina HiSeq2500
Genome_build: NCBIM37
ATAC-seq: Libraries were purified using QIAquick PCR clean-up columns (Qiagen) and sequenced on an Illumina HiSeq (6 libraries/lane). Reads were mapped to the mouse genome build NCBI37/mm9 using Bowtie2 (v2.2.5) and quantified using the MACS peak caller within Seqmonk.
RNA-seq: Libraries were sequenced on an Illumina HiSeq2500 (4 libraries per lane). Reads were mapped to the mouse genome build NCBI37/mm9 using Tophat (v2.0.12), and quantified using Seqmonk (Babraham Bioinformatics; http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
VDJ-seq: VDJ-seq libraries were de-duplicated based on the sequence of read 2 (containing both VH-DJH and DH-JH junctions) and the sequence and position of the VH gene (Babraham LinkON pipeline described in Bolland et al., 2016). This method relies on the variability of gene usage, junction diversity and the sonication step; therefore, reduced variability in the junctions and in VH usage would lead to sequences being more likely to be identical, particularly in partially (DH-JH) recombined alleles. To overcome this issue, modified PE1 adaptors containing random barcodes were used to generate the IL-7Ra-/- and FL libraries, allowing PCR duplicates, biological duplicates and Illumina sequencing errors to be distinguished (Chovanec et al., 2018). Libraries were sequenced on an Illumina HiSeq (8-12 libraries/lane; 250 BP paired-end). Reads were mapped to the mouse genome build NCBI37/mm9 using Bowtie2 (2.2.5). To quantify individual V and D genes, probes were created over each gene segment and correctly orientated reads were quantified over each probe using Seqmonk.
Supplementary_files_format_and_content: raw counts

source_name: WT RAGKO RNA-seq

extract_protocol:
BM was depleted of macrophages, granulocytes, erythroid lineage and T cells using biotinylated antibodies against CD11b (MAC-1; ebioscience), Ly6G (Gr-1; ebioscience), Ly6C (Abd Serotec), Ter119 (ebioscience) and CD3e (ebioscience) followed by streptavidin MACs beads (Miltenyi). MACS depletion was carried out as for BM, using TER119-biotin at a higher concentration (1:200). Thereafter, pro-B cells from IL-7Ra-/- BM and WT FL were flow-sorted as B220+ CD19+, while IL-7Ra-/- x RAG2-/- and RAG2-/- BM B pro-B cells were sorted as a B220+ CD19+ CD43+ population on a BD FACSAria in the Babraham Institute Flow Cytometry facility. WT BM pro-B cells were sorted as B220+ CD19+ CD25- sIgM- CD43+ (Bolland et al., 2016). Sorting antibodies were from BD Bioscience
ATAC-seq was performed as previously described (Buenrostro et al., 2013; 2015) on 70,000-100,000 cells.
For VDJ-seq genomic DNA was isolated from mouse B cells using the DNeasy kit (Qiagen)
Total RNA was extracted from ~200,000 cells for each replicate using the RNeasy Plus kit (Qiagen).
VDJ-seq was performed as described (Bolland et al., 2016) for WT BM pro-B cells. VDJ-seq libraries for IL-7Ra-/- pro-B cells were constructed similarly with two exceptions: firstly, due to reduced cell numbers, IL-7Ra-/- VDJ-seq libraries were generated from 1.5-2 µg of DNA, compared to 10 µg of starting material used to generate the WT BM and FL libraries; secondly, due to the expectation for less variable VDJ events in IL-7Ra-/- cells, measures were taken to distinguish and discount technical duplicates in VDJ-seq libraries.
cDNA preparation was performed using the Ovation V2 kit (NuGen) protocol, and 200 ng of cDNA carried through to generate 50bp paired-end RNA-seq libraries for Illumina sequencing as described in Parkhomchuk et al., (2009) except polyA+ RNA selection and strand-specificity steps were omitted, and first strand cDNA synthesis was performed with random hexamer primers.

tag: strain background

value: 10-12 week old

value: RAGKO pro-B cells


title: WT RAGKO RNA-seq rep1

description:
RAGKO_RNA-seq_1
processed data file:
RNA-seq_counts.txt


title: patient 143, non-tumor tissue

description:
sample_id: 2020_143NL
non-normalized data in non_norm_matrix13.txt.gz

tag: tissue

tag: type

tag: Sex

value: conventional RCC


title: patient 137, RCC tumor tissue

description:
sample_id: 2020_137TU
non-normalized data in non_norm_matrix13.txt.gz

value: tumor

tag: age


title: patient 142, RCC tumor tissue

description:
sample_id: 2020_142TU
non-normalized data in non_norm_matrix1.txt.gz

value: female

tag: histo


title: patient 141, RCC tumor tissue

description:
sample_id: 2020_141TU
non-normalized data in non_norm_matrix1.txt.gz

tag: Stage


title: patient 138, non-tumor tissue

description:
sample_id: 2020_138NL
non-normalized data in non_norm_matrix5.txt.gz

tag: grade


title: patient 137, non-tumor tissue

description:
sample_id: 2020_137NL
non-normalized data in non_norm_matrix13.txt.gz


title: WT RAGKO ATAC-seq rep2

description:
RAGKO_ATAC-seq_2
processed data file:
ATAC-seq_RSS_counts.txt

library_source: genomic

molecule: genomic DNA

source_name: WT RAGKO ATAC-seq

tag: cell type


title: patient 136, non-tumor tissue

description:
sample_id: 2020_136NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 141, non-tumor tissue

description:
sample_id: 2020_141NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 136, RCC tumor tissue

description:
sample_id: 2020_136TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 139, RCC tumor tissue

description:
sample_id: 2020_139TU
non-normalized data in non_norm_matrix13.txt.gz


title: WT RAGKO ATAC-seq rep1

description:
RAGKO_ATAC-seq_1
processed data file:
ATAC-seq_RSS_counts.txt


title: patient 135, RCC tumor tissue

description:
sample_id: 2020_135TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 135, non-tumor tissue

description:
sample_id: 2020_135NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 134, RCC tumor tissue

description:
sample_id: 2020_134TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 134, non-tumor tissue

description:
sample_id: 2020_134NL
non-normalized data in non_norm_matrix13.txt.gz


title: IL7Ra-/- RAGKO RNA-seq rep1

description:
IL7RxRAGKO_RNA-seq_1
processed data file:
RNA-seq_counts.txt

source_name: IL7Ra-/- RAGKO RNA-seq

value: 6-8 week old

value: IL7Ra-/- RAGKO pro-B cells


title: patient 133, RCC tumor tissue

description:
sample_id: 2020_133TU
non-normalized data in non_norm_matrix13.txt.gz

value: kidney


title: patient 133, non-tumor tissue

description:
sample_id: 2020_133NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 132, RCC tumor tissue

description:
sample_id: 2020_132TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 132, non-tumor tissue

description:
sample_id: 2020_132NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 131, RCC tumor tissue

description:
sample_id: 2020_131TU
non-normalized data in non_norm_matrix13.txt.gz


title: IL7Ra-/- RAGKO ATAC-seq rep2

description:
IL7RKOxRAGKO_ATAC-seq_2
processed data file:
ATAC-seq_RSS_counts.txt

source_name: IL7Ra-/- RAGKO ATAC-seq


title: IL7Ra-/- RAGKO ATAC-seq rep1

description:
IL7RKOxRAGKO_ATAC-seq_1
processed data file:
ATAC-seq_RSS_counts.txt


title: IL7Ra-/- VDJ-seq rep2

description:
IL7RKO_VDJ-seq_2
processed data file:
VDJ-seq_D_counts.txt
VDJ-seq_V_counts.txt

data_processing:
Library strategy: VDJ-seq
Libraries were sequenced on an Illumina HiSeq2500
Genome_build: NCBIM37
ATAC-seq: Libraries were purified using QIAquick PCR clean-up columns (Qiagen) and sequenced on an Illumina HiSeq (6 libraries/lane). Reads were mapped to the mouse genome build NCBI37/mm9 using Bowtie2 (v2.2.5) and quantified using the MACS peak caller within Seqmonk.
RNA-seq: Libraries were sequenced on an Illumina HiSeq2500 (4 libraries per lane). Reads were mapped to the mouse genome build NCBI37/mm9 using Tophat (v2.0.12), and quantified using Seqmonk (Babraham Bioinformatics; http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
VDJ-seq: VDJ-seq libraries were de-duplicated based on the sequence of read 2 (containing both VH-DJH and DH-JH junctions) and the sequence and position of the VH gene (Babraham LinkON pipeline described in Bolland et al., 2016). This method relies on the variability of gene usage, junction diversity and the sonication step; therefore, reduced variability in the junctions and in VH usage would lead to sequences being more likely to be identical, particularly in partially (DH-JH) recombined alleles. To overcome this issue, modified PE1 adaptors containing random barcodes were used to generate the IL-7Ra-/- and FL libraries, allowing PCR duplicates, biological duplicates and Illumina sequencing errors to be distinguished (Chovanec et al., 2018). Libraries were sequenced on an Illumina HiSeq (8-12 libraries/lane; 250 BP paired-end). Reads were mapped to the mouse genome build NCBI37/mm9 using Bowtie2 (2.2.5). To quantify individual V and D genes, probes were created over each gene segment and correctly orientated reads were quantified over each probe using Seqmonk.
Supplementary_files_format_and_content: raw counts

source_name: IL7Ra-/- VDJ-seq

value: IL7Ra-/- pro-B cells


title: patient 131, non-tumor tissue

description:
sample_id: 2020_131NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 130, non-tumor tissue

description:
sample_id: 2020_130NL
non-normalized data in non_norm_matrix13.txt.gz


title: IL7Ra-/- VDJ-seq rep1

description:
IL7RKO_VDJ-seq_1
processed data file:
VDJ-seq_D_counts.txt
VDJ-seq_V_counts.txt


title: IL7Ra-/- RAGKO RNA-seq rep2

description:
IL7RxRAGKO_RNA-seq_2
processed data file:
RNA-seq_counts.txt


title: patient 128, RCC tumor tissue

description:
sample_id: 2020_128TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 129, non-tumor tissue

description:
sample_id: 2020_129NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 129, RCC tumor tissue

description:
sample_id: 2020_129TU
non-normalized data in non_norm_matrix13.txt.gz


title: FL VDJ-seq rep2

description:
FL_VDJ-seq_2
processed data file:
VDJ-seq_D_counts.txt
VDJ-seq_V_counts.txt

source_name: FL VDJ-seq

value: embryonic day 15.5

value: WT FL pro-B cells


title: FL VDJ-seq rep1

description:
FL_VDJ-seq_1
processed data file:
VDJ-seq_D_counts.txt
VDJ-seq_V_counts.txt


title: patient 127, RCC tumor tissue

description:
sample_id: 2020_127TU
non-normalized data in non_norm_matrix13.txt.gz


title: GFPRNAi

city: Beijing

first: Yongchao

last: Han

address: No. 7, Park Road, Zhongguancun Life Science Park, Changping District

country: China

institute: National Institute of Biological Sciences, Beijing

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Dmel (v6.30) whole genome using STAR v2.6.1a with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts (V1.6.3). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Dmel (v6.30)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Drosophila melanogaster

extract_protocol:
RNA Sequencing (RNA-seq) assays were performed to analyze the transcriptome of fly muscle cells (Kwon et al., 2015). Briefly, ~20 thoraces were dissected from 3-day-old male flies. Total RNA was prepared using Trizol reagent (Invitrogen, Carlsbad, USA), followed by TURBO DNA-free DNase treatment (Ambion, Austin, USA).
Libraries for mRNA abundance examination was prepared by using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: 3-day old

value: Muscle


title: pink1RNAi


title: jejunum_Sham_2W_rep4

city: Shanghai

first: Yongjun

last: Liang

address: 2800 Gongwei Road

institute: Shanghai Pudong Hospital

description: Gene expression after 2weeks in Sham-treated mouse jejunum

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R

source_name: jejunum, Sham, 2W, replicate4

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted from the duodenum with TRIzol reagent (Invitrogen™, Grand Island, NY, U.S.A.) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany) and RNase-Free DNase Set (Qiagen, Hilden, Germany) according to the manufacturer protocols. RNA quantity and quality were measured by NanoDrop ND-2000 and Agilent Bioanalyzer 2100 (Agilent Technology, Santa Clara, CA, U.S.A.), respectively. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Sixty C57BL/6 mice were fed with high fat diet (HFD) (Cat. #D12492, Research Diets Inc., New Brunswick, NJ, USA) starting from 6 weeks of age. After 12 weeks, 32 mice achieved typical diabetic phenotypes and were randomized into two groups undergoing either DJB (n = 18) or sham procedure (n = 14).

value: jejunum

value: male


title: jejunum_DJB_2W_rep4

description: Gene expression after 2weeks in DJB-treated mouse jejunum

source_name: jejunum, DJB, 2W, replicate4


title: jejunum_DJB_2W_rep3

source_name: jejunum, DJB, 2W, replicate3


title: jejunum_Sham_2W_rep1

source_name: jejunum, Sham, 2W, replicate1


title: E17plexo_2

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: CROWN.GRCm38_76.rsem_counts.txt file contains ENSEMBL gene Ids and RSEM-estimated raw counts for each gene and sample.

molecule: polyA RNA

source_name: Coronary vascular endothelial cells from murine embryonic hearts

extract_protocol:
RNA from freshly FACS sorted cell populations, from dissociated fetal hearts,  was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). Library preparation (New England Biolabs Nest Ultra RNA library prep Kit) and single read Next-generation sequencing (Illumina HiSeq 2500) were performed at the Genomics Unit at Centro Nacional de Investigaciones Cardiovasculares (CNIC).
200 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated, followed by uracile excision from the adaptor and PCR amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer and their concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific)

tag: batch

tag: developmental stage


title: jejunum_DJB_2W_rep2

source_name: jejunum, DJB, 2W, replicate2


title: patient 127, non-tumor tissue

description:
sample_id: 2020_127NL
non-normalized data in non_norm_matrix13.txt.gz

source_name: kidney

value: normal


title: jejunum_DJB_2W_rep1

source_name: jejunum, DJB, 2W, replicate1


title: patient 130, RCC tumor tissue

description:
sample_id: 2020_130TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 126, non-tumor tissue

description:
sample_id: 2020_126NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 126, RCC tumor tissue

description:
sample_id: 2020_126TU
non-normalized data in non_norm_matrix13.txt.gz


title: jejunum_Sham_2W_rep2

source_name: jejunum, Sham, 2W, replicate2


title: E17plexo_1


title: patient 125, RCC tumor tissue

description:
sample_id: 2020_125TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 124, non-tumor tissue

description:
sample_id: 2020_124NL
non-normalized data in non_norm_matrix5.txt.gz


title: patient 124, RCC tumor tissue

description:
sample_id: 2020_124TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 128, non-tumor tissue

description:
sample_id: 2020_128NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 123, RCC tumor tissue

description:
sample_id: 2020_123TU
non-normalized data in non_norm_matrix1.txt.gz


title: E13Plexo_4


title: E17endo_1

source_name: Endocardial cells from murine embryonic hearts


title: patient 123, non-tumor tissue

description:
sample_id: 2020_123NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 125, non-tumor tissue

description:
sample_id: 2020_125NL
non-normalized data in non_norm_matrix13.txt.gz


title: patient 122, RCC tumor tissue

description:
sample_id: 2020_122TU
non-normalized data in non_norm_matrix1.txt.gz


title: E13Plexo_3


title: E13Plexo_2


title: patient 121, non-tumor tissue

description:
sample_id: 2020_121NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 120, RCC tumor tissue

description:
sample_id: 2020_120TU
non-normalized data in non_norm_matrix1.txt.gz


title: MycER-BclXL-Fzd9 ko mouse 2

city: Barcelona

first: Mariano

middle: F

last: Zacarias-Fluck

address: Natzaret, 115-117

department: Preclinical and Translational Research Program

institute: Vall d'Hebron Institute of Oncology (VHIO)

hyb_protocol: Total RNA was linearly amplified using WT Plus (Affymetrix). The resulting ssDNA was used to hybridize Affimetrix microarrays. Hybridization data was acquired using the Affimetrix GeneChip/GeneTitan platforms. Transcriptomes were determined on a genome wide Mouse Gene 2.1 Array (Affimetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology and analyzed using Partek Genomic Suite followed by GSEA 3.0 software from Broad Institute.

label: Biotin

source_name: Insulinoma from MycER-BclXL-Fzd9 ko mouse

label_protocol: Labeling of samples was carried out according to the manufacturer’s standard protocol

growth_protocol: MycER;BclXl Fzd9 wt and Fzd9-/- C57Bl/6 mice

extract_protocol: 50-100 mg of tumor tissue was homogenized with a pestle in TRIzol. Total RNA were extracted using TRIzol following manufacturer's procedures. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were treated with Tamoxifen i.p. for three days

value: Fzd9 ko

tag: tumor type

value: Insulinoma


title: MycER-BclXL-Fzd9 ko mouse 4


title: MycER-BclXL-Fzd9 ko mouse 1


title: patient 120, non-tumor tissue

description:
sample_id: 2020_120NL
non-normalized data in non_norm_matrix1.txt.gz


title: E13Plexo_1


title: patient 121, RCC tumor tissue

description:
sample_id: 2020_121TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 122, non-tumor tissue

description:
sample_id: 2020_122NL
non-normalized data in non_norm_matrix1.txt.gz


title: T2

city: jinan

first: Duan

last: Li

address: Wenhua Xi Road

institute: Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University

description: mRNA expression profiling of human granulosa-like tumor cell line KGN

data_processing:
Clustering and sequencing  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Genome_build: hg38
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen)  according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.
Library preparation for lncRNA sequencing   A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, 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. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. 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 150~200 bp 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, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: condition

value: lncRNA DDGC knockdown

tag: cell line

value: Female


title: MycER-BclXL-Fzd9 wt mouse 4

source_name: Insulinoma from MycER-BclXL-Fzd9 wt mouse

tag: genotype

value: Fzd9 wt


title: patient 119, RCC tumor tissue

description:
sample_id: 2020_119TU
non-normalized data in non_norm_matrix5.txt.gz

value: tumor

value: female

value: conventional RCC


title: MycER-BclXL-Fzd9 ko mouse 3


title: patient 119, non-tumor tissue

description:
sample_id: 2020_119NL
non-normalized data in non_norm_matrix5.txt.gz

value: kidney


title: jejunum_Sham_2W_rep3

description: Gene expression after 2weeks in Sham-treated mouse jejunum

source_name: jejunum, Sham, 2W, replicate3

tag: strain

tag: gender


title: T1

source_name: human granulosa-like tumor cell line KGN


title: E13endo_4


title: MycER-BclXL-Fzd9 wt mouse 3


title: patient 118, RCC tumor tissue

description:
sample_id: 2020_118TU
non-normalized data in non_norm_matrix7.txt.gz


title: patient 118, non-tumor tissue

description:
sample_id: 2020_118NL
non-normalized data in non_norm_matrix7.txt.gz


title: patient 117, RCC tumor tissue

description:
sample_id: 2020_117TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 117, non-tumor tissue

description:
sample_id: 2020_117NL
non-normalized data in non_norm_matrix5.txt.gz


title: E13endo_2


title: Control 1

value: Negative control

value: human granulosa-like tumor cell line KGN


title: patient 116, RCC tumor tissue

description:
sample_id: 2020_116TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 116, non-tumor tissue

description:
sample_id: 2020_116NL
non-normalized data in non_norm_matrix1.txt.gz


title: POI8

description: LncRNA expression profiling of human granulosa cells from patients with bPOI

source_name: ovarian granulosa cells

value: bPOI

value: ovarian granulosa cells


title: POI7


title: Venous_tri_E17 3

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Sequencing adaptor contaminations were removed from reads using Cutadapt v1.3, and the first 8 nucleotides of each read, containing Ovation specific adapters, were eliminated with fastx_trimmer.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: AVCROWN.GRCm38_76.rsem_counts.txt file contains ENSEMBL gene Ids and RSEM-estimated raw counts for each gene and sample.

source_name: Venous-enriched coronary vascular endothelial cells.

extract_protocol:
RNA from freshly FACS sorted endothelial cell (EC) populations, from dissociated fetal hearts,  was isolated using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). Library preparation (New England Biolabs Nest Ultra RNA library prep Kit) and single read Next-generation sequencing (Illumina HiSeq 2500) were performed at the Genomics Unit at Centro Nacional de Investigaciones Cardiovasculares (CNIC).
Total RNA (1 ng) were used to generate barcoded RNA-seq libraries using the Ovation® Single Cell RNA-Seq System (NuGEN/Tecan).  The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific)


title: Venous_tri_E17 2


title: patient 115, RCC tumor tissue

description:
sample_id: 2020_115TU
non-normalized data in non_norm_matrix1.txt.gz


title: POI6


title: patient 115, non-tumor tissue

description:
sample_id: 2020_115NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 114, RCC tumor tissue

description:
sample_id: 2020_114TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 114, non-tumor tissue

description:
sample_id: 2020_114NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 113, RCC tumor tissue

description:
sample_id: 2020_113TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 112, non-tumor tissue

description:
sample_id: 2020_112NL
non-normalized data in non_norm_matrix1.txt.gz


title: Endoc_tri_E17 3

source_name: Endocardial cells.


title: POI4


title: patient 113, non-tumor tissue

description:
sample_id: 2020_113NL
non-normalized data in non_norm_matrix1.txt.gz


title: POI5


title: Venous_tri_E17 1


title: E13endo_3


title: patient 112, RCC tumor tissue

description:
sample_id: 2020_112TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 111, RCC tumor tissue

description:
sample_id: 2020_111TU
non-normalized data in non_norm_matrix1.txt.gz


title: Endoc_tri_E17 2


title: Control 2

description: mRNA expression profiling of human granulosa-like tumor cell line KGN


title: MycER-BclXL-Fzd9 wt mouse 1


title: patient 111, non-tumor tissue

description:
sample_id: 2020_111NL
non-normalized data in non_norm_matrix1.txt.gz


title: POI3


title: patient 110, RCC tumor tissue

description:
sample_id: 2020_110TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 110, non-tumor tissue

description:
sample_id: 2020_110NL
non-normalized data in non_norm_matrix1.txt.gz


title: E13endo_1


title: Endoc_tri_E17 1


title: POI2


title: patient 109, non-tumor tissue

description:
sample_id: 2020_109NL
non-normalized data in non_norm_matrix1.txt.gz


title: Arterial_tri_E17 3

source_name: Arterial-enriched coronary vascular endothelial cells.


title: POI1


title: patient 108, non-tumor tissue

description:
sample_id: 2020_108NL
non-normalized data in non_norm_matrix1.txt.gz


title: Arterial_tri_E17 2


title: C9

description: LncRNA expression profiling of human granulosa cells from normal control women

value: Control


title: Arterial_tri_E17 1


title: patient 107, non-tumor tissue

description:
sample_id: 2020_107NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 107, RCC tumor tissue

description:
sample_id: 2020_107TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 106, non-tumor tissue

description:
sample_id: 2020_106NL
non-normalized data in non_norm_matrix9.txt.gz


title: patient 106, RCC tumor tissue

description:
sample_id: 2020_106TU
non-normalized data in non_norm_matrix5.txt.gz


title: patient 105, non-tumor tissue

description:
sample_id: 2020_105NL
non-normalized data in non_norm_matrix13.txt.gz


title: C8


title: C7


title: patient 105, RCC tumor tissue

description:
sample_id: 2020_105TU
non-normalized data in non_norm_matrix13.txt.gz


title: patient 104, non-tumor tissue

description:
sample_id: 2020_104NL
non-normalized data in non_norm_matrix1.txt.gz


title: patient 103, RCC tumor tissue

description:
sample_id: 2020_103TU
non-normalized data in non_norm_matrix1.txt.gz


title: patient 104, RCC tumor tissue

description:
sample_id: 2020_104TU
non-normalized data in non_norm_matrix1.txt.gz


title: T5

city: Buffalo

first: Jiho

last: Sohn

state: New York

address: 3435 Main Street, 644 Biomedical Research Building

department: Oral Biology

institute: SUNY Buffalo

data_processing:
FASTQC quality control
Hisat2 alignment to a standard reference genome
Cufflinks Gene and Isoform level FPKM expression measurements
DEseq2 to determine differentially expressed genes
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: csv

source_name: Distal ileal tissue

extract_protocol:
Distal ileal tissue were removed, treated with RNAlater solution, and RNA was harvested using RNeasy Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ileum

value: BALB/c

tag: treatment

value: P. gingivalis treated


title: T3

tag: tissue


title: patient 103, non-tumor tissue

description:
sample_id: 2020_103NL
non-normalized data in non_norm_matrix1.txt.gz

tag: type

value: normal

value: male


title: T4


title: patient 109, RCC tumor tissue

description:
sample_id: 2020_109TU
non-normalized data in non_norm_matrix1.txt.gz

tag: Sex


title: patient 102, RCC tumor tissue

description:
sample_id: 2020_102TU
non-normalized data in non_norm_matrix1.txt.gz

tag: age


title: C6


title: C4


title: T6


title: C5


title: T2


title: patient 102, non-tumor tissue

description:
sample_id: 2020_102NL
non-normalized data in non_norm_matrix1.txt.gz

tag: histo


title: patient 108, RCC tumor tissue

description:
sample_id: 2020_108TU
non-normalized data in non_norm_matrix1.txt.gz

tag: Stage


title: C3


title: T1


title: C2


title: S6

value: PBS control


title: C1

value: Female


title: S5


title: S4


title: S3


title: cLTP_120 min_B

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

description: 120 min after cLTP treatment,biological repeat 2

data_processing:
Bases were called with Illumina's bcl2fastq software program.
Reads were trimmed for low quality (<30) 3' sequence to a minimum read length of 20 bp.
Reads were aligned to rat genome assembly rn6 using Tophat v2.1.0 and the Ensembl84 reference transcriptome.
Gene counts were quantified from BAM files using htseq-counts and the Ensembl84 reference transcriptome.
Differentially expressed genes were identified pairwise between each time point and mock control, using the R package edgeR.
Genome_build: RN6
Supplementary_files_format_and_content: Excel file with results compiled from all four pairwise comparisons (treatment vs control).

organism: Rattus norvegicus

source_name: cLTP_120 min_neurons

growth_protocol: Neurons were cultured with Neurobasal medium supplemented with SM1 and maintained at 37 °C in a humidified 5% CO2 atmosphere incubator. Cultures were fed three time a week.Glial growth was suppressed by the addition of 5-fluoro-2-deoxyuridine (20 mg/ml; Sigma-Aldrich) and uridine (20 mg/ml; Sigma-Aldrich) at day 4 after plating (DIV4).

extract_protocol:
Total RNA was extracted from neurons using RNeasy mini Kit (Qiagen). Ribosomal RNA was depleted with RiboZero kit (Epicenter). (Thermo).
Poly(A)-enriched RNA were separated by 3 rounds of Oligo(dT) magnetic beads

treatment_protocol: Ctrl samples were treated with mock-cLTP solution. Others were treated with cLTP solution.

value: Wistar

value: DIV 15

value: Hippocampus

value: Cultured rat hippocampal neurons

tag: treated with

value: chemical long-term potentiation (cLTP) solution

tag: time point

value: 120 min after cLTP treatment


title: cLTP_5 min_B

description: 5 min after cLTP treatment, biological repeat 2

source_name: cLTP_5 min_neurons

tag: cell type

value: 5 min after cLTP treatment


title: cLTP_60 min_B

description: 60 min after cLTP treatment, biological repeat 2

source_name: cLTP_60 min_neurons

value: 60 min after cLTP treatment


title: cLTP_10 min_B

description: 10 min after cLTP treatment, biological repeat 2

source_name: cLTP_10 min_neurons

value: 10 min after cLTP treatment


title: S2


title: cLTP_120 min_A

description: 120 min after cLTP treatment, biological repeat 1


title: Ctrl_B

description: mock-cLTP treatment,  biological repeat 2

value: mock-cLTP solution


title: ins-StrV_r3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

data_processing:
The raw FASTQ files were inspected using FastQC, the adapter sequences were trimmed using Cutadapt and additional quality control steps taken by fastq_quality_filter program as part of FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The mapping process was performed using align function in Rsubread package by aligning the clean fastq files against the cow reference genome retrieved from Ensembl release 96 (Bos taurus) and only uniquely-mapped alignments were recorded. The resulting BAM files were sorted and indexed by SAMtools. The reads were summarized at the gene level by means of featureCounts. DESeq2 in a paired sample design was used to identify differentially expressed protein-coding genes based on the cut-offs of a p value < 0.05 and a log2 Fold Change > 0.1 or < -0.1.
Genome_build: Bos taurus - Ensembl release 96

organism: Bos taurus

source_name: endometrium stroma

extract_protocol:
Total RNA was extracted from epithelial and stromal cells using the Mini RNeasy kit (Qiagen, Crawley, UK) following the manufacturer's recommendations. Cell samples were homogenized in 700 µL of Qiazol via vortexing for 1 min at RT. On-column DNase digestion was performed (15 min at room temperature (RT)) and RNA was eluted in 14 µL of RNase/DNase free water from the spin column membrane following centrifugation for 2 min at full speed and this step was performed twice.
Stranded RNA sequencing libraries were constructed using the Encore Complete RNA-Seq library system of NuGEN
All libraries were sequenced on Illumina NextSeq generating 75 bp single-end reads

value: insulin Vehicle


title: ins-StrV_r2


title: ins-Str1_r3

value: insulin 1 ng/mL treatment


title: cLTP_60 min_A

description: 60 min after cLTP treatment,  biological repeat 1


title: ins-StrV_r1


title: S1

value: Ileum

value: BALB/c


title: cLTP_10 min_A

description: 10 min after cLTP treatment,  biological repeat 1


title: ins-Str1_r2


title: Ctrl_A

description: mock-cLTP treatment, biological repeat 1


title: Keap1_KO_C

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: Keap1_KO_CD4+ CD25+ Treg

label_protocol: Fragmented, biotinylated cDNAs were prepared from 40 ng total RNA using  the NuGen Ovation Pico WTA System 2 Kit according to the manufacturers instructions.

growth_protocol: Experiments were performed with sex- and age-matched 6-10 week-old  VAVcre/Keapfl/fl  and respective WT mice;  VAVcreKeapfl/fl mice were generated by crossing Keap1-flox mice (Okawa et al. 2006) with VAVcre mice.

extract_protocol: Total RNA from isolated CD4+CD25+ (isolated by magnetic cell separation (MACS)) was isolated using RNeasy Micro Kit

treatment_protocol: CD4+CD25+  cells were isolated by MACS-separation from spleens, mice were untreated

tag: strain background

tag: genotype/variation

value: Keap1 -/-

value: 10-12 months

value: male

value: spleen

value: CD4+ CD25+ Treg


title: Keap1_KO_B


title: Keap1_KO_D


title: Keap1_WT_A

source_name: Keap1_WT_CD4+ CD25+ Treg

value: Keap1 +/+


title: Keap1_WT_F


title: Keap1_WT_D


title: cLTP_5 min_A

description: 5 min after cLTP treatment,  biological repeat 1

value: Wistar

value: DIV 15

value: Hippocampus

value: Cultured rat hippocampal neurons