title: MWCNT Exposed Worker-8 (Scientist)

city: morgantown

first: Anna

middle: A

last: Shvedova

state: WV

address: 1095 willowdale Rd

department: HELD

institute: CDC/NIOSH

description: whole blood lncRNA and mRNA expression in MWCNT-exposed workers

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 x 60K, Arraystar). Breifly, 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 15 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering between two groups.

source_name: Blood

label_protocol: total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre) was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was extracted from whole blood using the PAXgene™ Blood RNA System Kit following manufacturer's guidelines. Briefly, the samples were removed from -80°C and incubated at room temperature for 2 hours to ensure complete lysis. Following lysis the tubes were centrifuged for 10 min at 5,000 × g, the supernatant decanted and 500 μL of RNase-free water added to the pellet. After washing with 500 μl RNase-free water, the pellet was dissolved in 350 μl resuspension buffer and incubated with 300 μl binding buffer and 40 μl proteinase K for 10 min at 55°C in a shaker-incubator. The lysate was transferred into a PAXgene shredder spin column and centrifuged (at 18,000 g for 3 min). The flow-through fraction was mixed with 350 μl ethanol and transferred to a PAXgene RNA spin column. After washing the column with washing buffer 1, samples were incubated with 10 μl of DNase I for 15 min. PAXgene RNA spin columns were washed with washing buffer and RNA eluted with 40 μl elution buffer. The RNA yield was estimated by measuring absorbance at 260 nm in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). RNA purity was calculated from the ratio of absorbance at 260 nm and 280 nm, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: gender

value: Male

value: Whole Blood

tag: age


title: prostate_BX_b9close_I

status: Public on Mar 09 2016

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: CA

address: 10355 Science Center Dr

country: USA

institute: GenomeDx Biosciences

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE, prostate, normal, BX

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: At CSMC and UCSF, tumor tissues were sampled from FFPE biopsy cores by dissecting a portion of the tumor tissue directly from the blocks in the areas corresponding to marked areas on each H&E slide using a sterile biopsy punch tool, and then extracting RNA as described below. The histologically benign peripheral zone glandular tissue was sampled in an analogous manner. Benign tissues were defined as adjacent to tumor (benign adjacent) when they were within 1mm to 5 mm of the tumor.  Benign contralateral tissues were obtained from a biopsy core from the opposite side of the prostate relative to the primary tumor site, and from as far away from any other tumor or high grade PIN areas as possible. For each case, RP tissue was punched in the same manner at locations matching those where the biopsy punches were taken for each tissue type (tumor, benign adjacent to tumor, and benign contralateral to tumor). Benign contralateral to tumor in RPs was taken at least 1 cm away from any other tumor or high grade PIN areas. At UHN, both biopsy and RP specimens were sliced  as 4 μm thick unstained sections and the areas of interest were macrodissected (scraped) from the slides for nucleic acid extraction. Six unstained sections were used to collect biopsy tissue and four to collect RP tissue. RP tissue was sampled in locations matching the location of tumor in the biopsy cores. Total RNA was extracted and purified using the RNeasy FFPE kit (Qiagen, Valencia, CA). RNA was amplified and labeled using the Ovation WTA FFPE system (NuGen, San Carlos, CA).

treatment_protocol: Not Applicable

tag: tissue

value: normal

value: BX

tag: location

value: adjacent

tag: patient

value: I


title: MWCNT Exposed Worker-6 (Technical Operator)


title: prostate_RP_b9away_F

source_name: FFPE, prostate, normal, RP

value: RP

value: contralateral

value: F


title: prostate_RP_b9close_W

value: W


title: prostate_BX_b9away_Q

value: Q


title: prostate_RP_b9close_S

value: S


title: MWCNT Exposed Worker-4 (Engineer)


title: prostate_BX_b9close_R

value: R


title: MWCNT Exposed Worker-5 (Scientist)


title: MWCNT Exposed Worker-7 (PhD Student)


title: MWCNT Exposed Worker-2 (Foreman)


title: MWCNT Exposed Worker-3 (Engineer)


title: MWCNT Exposed Worker-1 (Technical Operator)


title: prostate_RP_tumor_G

source_name: FFPE, prostate, tumor, RP

value: tumor

value: G


title: prostate_BX_b9away_A

value: A


title: prostate_RP_b9away_V

value: V


title: Unexposed Worker-6 (Scientist)

description: whole blood lncRNA and mRNA expression in unexposed workers

value: Male


title: prostate_RP_b9away_E

value: E


title: prostate_BX_tumor_GG

source_name: FFPE, prostate, tumor, BX

value: GG


title: Unexposed Worker-7 (Scientist)

value: Whole Blood


title: prostate_RP_tumor_Z

value: Z


title: prostate_RP_b9close_N

value: normal

value: adjacent

value: N


title: Unexposed Worker-2 (Scientist)


title: prostate_RP_b9close_D

value: RP

value: D


title: Unexposed Worker-4 (Engineer)


title: prostate_RP_tumor_CC

value: CC


title: prostate_BX_b9away_S

value: BX

value: contralateral

value: S


title: prostate_BX_b9close_K

value: K


title: prostate_BX_b9away_V


title: Unexposed Worker-1 (Engineer)


title: Unexposed Worker-5 (PhD Student)


title: prostate_BX_b9close_E


title: prostate_RP_b9away_T

value: T


title: prostate_RP_tumor_W

value: tumor

value: W


title: Resistant CAF, biologic rep 1

city: Los Angeles

first: Paul

last: Toste

institute: UCLA

hyb_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

data_processing:
Data was analyzed using the Partek Genomics Suite. RMA normalization was performed using the default settings.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.2.0.20

source_name: Gemcitabine treated human pancreatic CAF

growth_protocol: Immortalized pancreatic CAFs were grown in DMEM with 10% FBS with or without 100nM GEM for 30 days.

extract_protocol: Total RNA was isolated using the miRNeasy mini kit according to instructions (Qiagen)

tag: cell type

value: Immortalized human pancreatic cancer associated fibroblast (CAFs)

tag: treated with

value: 100nM Gemcitabine for 30 days


title: prostate_RP_tumor_EE

value: EE


title: prostate_BX_tumor_X

value: X


title: Naive CAF, biologic rep 2

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

source_name: Treatement naive human pancreatic CAF

value: none (Naïve)


title: primary breast tumor_438

status: Public on Mar 08 2016

city: Windber

first: Rachel

last: Ellsworth

state: PA

address: 620 Seventh Street

department: Clinical Breast Care Project

institute: Windber Research Institute

hyb_protocol: Hybridization to U133A 2.0 arrays following manufacturer's instructions

scan_protocol: Scanning as instructed using Affymetrix protocols

data_processing: Data were processed using Partek Genomics Suite 6.6

source_name: Primary breast tumor_BMI 30+

label_protocol: Biotinylated cRNA were prepared after two rounds of amplification (Field et al. 2011)

extract_protocol: isolated using RNAqueous-Micro after laser microdissection

tag: patient ethnicity

value: European American

tag: bmi

tag: tumor grade

value: Moderately differentiated (grade 2)

tag: tumor subtype (via breastprs)

value: Luminal A

tag: tumor stage

value: Stage IIB


title: SY5YtetCASZ1b_control_replicate 2

city: Bethesda

first: Zhihui

last: Liu

state: Maryland

address: 9000 rockville pike

institute: National Cancer Institute

description: Gene expression after 24 hr culture in the medium without tetracycline

hyb_protocol: cRNA was fragmented to uniform size and verified on the Bioanalyzer. Agilent Whole Genome 4x44K arrays were hybridiezed with the cRNA target.

scan_protocol: Slides were washed and scanned on an Agilent G2565 Microarray Scanner.

data_processing: Data was analyzed with Agilent Feature Extraction software package, and furthur processed using Partek Genomics Suite 6.6 software. Intensity values are normalized to the 75th percentile of each array.

source_name: SY5YtetCASZ1b cells without tetracyline treatment, replicate 2

label_protocol: First and second strand cDNA was prepared from the total RNA samples. Cy3 cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

extract_protocol: RNA was prepared using the RNeasy kit (Qiagen, Valencia, CA) following the manufacturer's recommendations.

treatment_protocol: SY5YtetCASZ1b cells were cultured in 6-well plate overnight, then treated with or without 1 µg/ml tetracyline for 24 hr.

tag: cell line

value: neuroblastoma

tag: agent


title: primary breast tumor_437

source_name: Primary breast tumor_BMI 25-29.99

value: Well-differentiated (grade 1)

value: Stage IIA


title: Naive CAF, biologic rep 1

label_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)


title: SY5YtetCASZ1b_control_replicate 3

source_name: SY5YtetCASZ1b cells without tetracyline treatment, replicate 3


title: primary breast tumor_439

value: Poorly differentiated (grade 3)

value: Luminal B


title: SY5YtetCASZ1b_tet_treated_replicate 1

description: Gene expression after 24 hr culture in the medium containing 1 µg/ml tetracycline

source_name: SY5YtetCASZ1b cells treated with tetracycline, replicate 1

value: tetracycline


title: SY5YtetCASZ1b_tet_treated_replicate 2

source_name: SY5YtetCASZ1b cells treated with tetracycline, replicate 2


title: primary breast tumor_431

value: Stage I


title: primary breast tumor_429

source_name: Primary breast tumor_BMI <25


title: Resistant CAF, biologic rep 2


title: primary breast tumor_432

value: Stage IIIA


title: primary breast tumor_434

value: HER2 enriched


title: primary breast tumor_430


title: primary breast tumor_442

value: Asian


title: SY5YtetCASZ1b_control_replicate 1

source_name: SY5YtetCASZ1b cells without tetracyline treatment, replicate 1


title: primary breast tumor_428


title: primary breast tumor_433


title: primary breast tumor_436


title: primary breast tumor_443


title: primary breast tumor_435


title: Unexposed Worker-3 (Engineer)

value: Male

value: Whole Blood


title: SY5YtetCASZ1b_tet_treated_replicate 3

source_name: SY5YtetCASZ1b cells treated with tetracycline, replicate 3


title: primary breast tumor_425


title: primary breast tumor_422

value: Hispanic


title: primary breast tumor_402

value: European American


title: primary breast tumor_426

value: Moderately differentiated (grade 2)


title: primary breast tumor_421

value: Luminal A


title: primary breast tumor_414

value: Stage IIIC


title: primary breast tumor_416

value: Stage IIB


title: primary breast tumor_395


title: primary breast tumor_427

value: Well-differentiated (grade 1)


title: primary breast tumor_406

source_name: Primary breast tumor_BMI Unk

value: Unk


title: primary breast tumor_396


title: primary breast tumor_420

value: Poorly differentiated (grade 3)

value: Basal Like


title: primary breast tumor_404


title: primary breast tumor_399

value: Stage IIA


title: primary breast tumor_423


title: primary breast tumor_403

value: Stage I


title: primary breast tumor_409


title: primary breast tumor_394


title: primary breast tumor_401

value: Luminal B


title: primary breast tumor_424


title: primary breast tumor_398


title: primary breast tumor_407


title: primary breast tumor_397


title: primary breast tumor_405


title: primary breast tumor_392

value: HER2 enriched


title: primary breast tumor_393


title: primary breast tumor_390


title: primary breast tumor_389


title: primary breast tumor_385


title: primary breast tumor_400


title: primary breast tumor_386


title: primary breast tumor_382

value: Stage IIIA


title: primary breast tumor_391


title: primary breast tumor_388


title: primary breast tumor_375


title: primary breast tumor_378


title: primary breast tumor_377


title: primary breast tumor_379

value: Stage IV


title: primary breast tumor_381

value: Asian


title: primary breast tumor_383


title: primary breast tumor_370


title: primary breast tumor_376


title: primary breast tumor_374


title: primary breast tumor_387


title: primary breast tumor_371


title: primary breast tumor_367


title: primary breast tumor_364

value: Otherher


title: primary breast tumor_384

value: Hispanic


title: primary breast tumor_373

value: European American


title: primary breast tumor_380

value: Moderately differentiated (grade 2)

value: Luminal A


title: primary breast tumor_368


title: primary breast tumor_369


title: primary breast tumor_363

value: African American

value: Stage IIB


title: primary breast tumor_366

value: Data not available


title: primary breast tumor_372


title: primary breast tumor_365

value: Poorly differentiated (grade 3)


title: primary breast tumor_362

value: Stage IIIC


title: primary breast tumor_361


title: primary breast tumor_358

value: Stage IIA


title: primary breast tumor_356


title: primary breast tumor_355


title: primary breast tumor_353

value: Basal Like


title: primary breast tumor_354

value: Stage I


title: primary breast tumor_347


title: primary breast tumor_360


title: primary breast tumor_349


title: primary breast tumor_346


title: primary breast tumor_345


title: primary breast tumor_341


title: primary breast tumor_357

value: Well-differentiated (grade 1)


title: primary breast tumor_350


title: primary breast tumor_334

value: Unk


title: primary breast tumor_352


title: primary breast tumor_359


title: primary breast tumor_351


title: primary breast tumor_343


title: primary breast tumor_342


title: primary breast tumor_344


title: primary breast tumor_335

value: Luminal B


title: primary breast tumor_337

value: HER2 enriched


title: primary breast tumor_336


title: primary breast tumor_339


title: primary breast tumor_333


title: primary breast tumor_340


title: primary breast tumor_338

value: Stage IIIA


title: primary breast tumor_331


title: primary breast tumor_332


title: primary breast tumor_324


title: primary breast tumor_325


title: primary breast tumor_330


title: primary breast tumor_329


title: primary breast tumor_323


title: primary breast tumor_317


title: primary breast tumor_327


title: primary breast tumor_318


title: primary breast tumor_322


title: primary breast tumor_319


title: primary breast tumor_326


title: primary breast tumor_311


title: primary breast tumor_320


title: primary breast tumor_316


title: primary breast tumor_321


title: primary breast tumor_312

value: Unknown


title: primary breast tumor_313


title: primary breast tumor_314


title: primary breast tumor_315


title: primary breast tumor_306

value: European American


title: primary breast tumor_310


title: primary breast tumor_309


title: primary breast tumor_307


title: primary breast tumor_303

value: Moderately differentiated (grade 2)


title: primary breast tumor_308


title: primary breast tumor_292


title: primary breast tumor_296

value: Luminal A


title: primary breast tumor_298

value: Hispanic


title: primary breast tumor_328


title: primary breast tumor_302


title: primary breast tumor_300


title: primary breast tumor_295

value: African American


title: primary breast tumor_304


title: primary breast tumor_293


title: primary breast tumor_297


title: primary breast tumor_289


title: primary breast tumor_294


title: primary breast tumor_287


title: primary breast tumor_305


title: primary breast tumor_282

value: Asian


title: primary breast tumor_288


title: primary breast tumor_301


title: primary breast tumor_299

value: Poorly differentiated (grade 3)


title: primary breast tumor_277


title: primary breast tumor_284


title: primary breast tumor_283

value: Stage IIB


title: primary breast tumor_281


title: primary breast tumor_276


title: primary breast tumor_278


title: primary breast tumor_285

value: Stage IIA


title: primary breast tumor_280


title: primary breast tumor_275


title: primary breast tumor_291

value: Basal Like

value: Stage IV


title: primary breast tumor_286


title: primary breast tumor_274


title: primary breast tumor_270

value: Stage I


title: primary breast tumor_271


title: primary breast tumor_269


title: primary breast tumor_268


title: primary breast tumor_262

value: Otherher


title: primary breast tumor_267


title: primary breast tumor_264

value: Luminal B


title: primary breast tumor_263


title: primary breast tumor_259


title: primary breast tumor_255

value: Well-differentiated (grade 1)


title: primary breast tumor_261


title: primary breast tumor_266


title: primary breast tumor_256


title: primary breast tumor_248


title: primary breast tumor_249


title: primary breast tumor_272


title: primary breast tumor_247

value: Unk


title: primary breast tumor_265


title: primary breast tumor_260


title: primary breast tumor_257

value: HER2 enriched


title: primary breast tumor_258

value: European American


title: primary breast tumor_253


title: primary breast tumor_252

value: Moderately differentiated (grade 2)


title: primary breast tumor_250

value: Luminal A


title: primary breast tumor_251


title: primary breast tumor_240


title: primary breast tumor_238

value: Stage IIIA


title: primary breast tumor_239


title: primary breast tumor_254

value: African American


title: primary breast tumor_241


title: primary breast tumor_273


title: primary breast tumor_236

value: Stage IIA R


title: primary breast tumor_237


title: primary breast tumor_232


title: primary breast tumor_233


title: primary breast tumor_234

value: Stage IIIC


title: primary breast tumor_227


title: primary breast tumor_225


title: primary breast tumor_230


title: primary breast tumor_231


title: primary breast tumor_226

value: Poorly differentiated (grade 3)


title: primary breast tumor_219

value: Stage IIA


title: primary breast tumor_223


title: primary breast tumor_235


title: Roots of YH_low P_rep3

city: Nanjing

first: Qing

last: Wang

address: No.1 Weigang

country: China

institute: Nanjing Agricultural University

hyb_protocol: Following fragmentation and Terminal Labeling, 5 ug of cDNA were hybridized for 16 hr at 45℃ on Affymetrix Soybean Gene 1.1 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Glycine max

source_name: Roots_YH_low P condition

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 0.1 ug total RNA (Expression Analysis Technical Manual, 2013, Affymetrix).

growth_protocol: Soybean seedlings were grown in hydroponic boxes with a 16h/8h (day/night) photoperiod and a temperature of 26-28°C/22°C (day/night) temperature cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Soybean seedlings were treated with normal phosphorus condition (half Hoagland with 0.5 mmol/L P ) and low phosphorus condition(half Hoagland with 0.005mmol/L P ).

tag: accession

value: YH

tag: phentoype

value: low-P sensitive

tag: phosphorus condition

value: low (half Hoagland with 0.005mmol/L P)

value: Roots


title: Roots of YH_low P_rep2


title: Leaves of YH_low P_rep1

source_name: Leaves_YH_low P condition

value: Leaves


title: primary breast tumor_228

value: Luminal B

value: Stage IIB


title: primary breast tumor_218


title: primary breast tumor_221


title: primary breast tumor_220

value: Well-differentiated (grade 1)


title: Roots of YH_low P_rep1


title: primary breast tumor_229

value: European American

value: Stage I


title: primary breast tumor_217

value: Hispanic

value: Moderately differentiated (grade 2)

value: Luminal A


title: primary breast tumor_224


title: primary breast tumor_215

value: Basal Like


title: primary breast tumor_214


title: Leaves of YH_normal P_rep3

source_name: Leaves_YH_normal P condition

value: normal (half Hoagland with 0.5 mmol/L P)


title: Leaves of YH_low P_rep2


title: primary breast tumor_216

value: Poorly differentiated (grade 3)


title: Leaves of YH_low P_rep3


title: primary breast tumor_222

value: Stage IIA


title: Leaves of YH_normal P_rep2

value: YH


title: primary breast tumor_211


title: Roots of YH_normal P_rep2

source_name: Roots_YH_normal P condition

value: low-P sensitive


title: primary breast tumor_212


title: primary breast tumor_210

value: African American


title: Leaves of CD_low P_rep3

source_name: Leaves_CD_low P condition

value: CD

value: low-P tolerant

value: low (half Hoagland with 0.005mmol/L P)


title: Roots of YH_normal P_rep1

value: Roots


title: Leaves of CD_low P_rep1

value: Leaves


title: primary breast tumor_208

value: European American


title: primary breast tumor_204

value: Otherher

value: HER2 enriched

value: Stage IIIC


title: Leaves of YH_normal P_rep1


title: primary breast tumor_203

value: Stage IIB


title: primary breast tumor_205

value: Basal Like

value: Stage IIIA


title: Roots of CD_low P_rep3

source_name: Roots_CD_low P condition


title: primary breast tumor_209

value: Poorly differentiated (grade 3)

value: Stage I


title: primary breast tumor_201

value: Moderately differentiated (grade 2)

value: Luminal A


title: primary breast tumor_202

value: Luminal B

value: Stage IIIB


title: Roots of CD_low P_rep1

value: CD

value: low-P tolerant


title: Roots of CD_normal P_rep3

source_name: Roots_CD_normal P condition

value: normal (half Hoagland with 0.5 mmol/L P)

value: Roots


title: primary breast tumor_206

value: European American

value: Stage IIA


title: Roots of CD_low P_rep2

value: low (half Hoagland with 0.005mmol/L P)


title: Leaves of CD_normal P_rep2

source_name: Leaves_CD_normal P condition

value: Leaves


title: Leaves of CD_normal P_rep1


title: primary breast tumor_207

source_name: Primary breast tumor_BMI 30+


title: Leaves of CD_normal P_rep3


title: Roots of CD_normal P_rep2


title: Leaves of CD_low P_rep2


title: primary breast tumor_199


title: Roots of CD_normal P_rep1


title: Roots of YH_normal P_rep3

value: YH

value: low-P sensitive


title: primary breast tumor_198

source_name: Primary breast tumor_BMI 25-29.99


title: primary breast tumor_195


title: primary breast tumor_196


title: primary breast tumor_194


title: primary breast tumor_193

value: Well-differentiated (grade 1)


title: primary breast tumor_189

value: African American

value: Poorly differentiated (grade 3)

value: Basal Like


title: wild type_gdna_rep4

type: genomic

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

description: S. aureus stationary phase culture_replicate 4

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing:
The chromosome background was estimated locally using a running median of size 12943 probes (116487 bp since the tiling step is 9 bp when strand is ignored) to account for chromosome dosage variations due to replication timing.
The log2 ratio between the probe-level intensity and the local background was then computed as previously described to account for probe affinity variations in transcriptomics (Nicolas et al., 2009, Bioinformatics 25, 2341-2347).

molecule: genomic DNA

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_wild type

label_protocol: 5 µg of genomic DNA were sonicated and labeled using Cy3-9mer primers by Roche NimbleGen (Madison, WI, USA).

growth_protocol: An overnight culture of S. aureus HG001 in TSB medium was diluted 100 times in fresh TSB medium where cells were grown to stationary phase.

extract_protocol: Genomic DNA was isolated by using the Qiagen DNeasy Blood & Tissue Kit with the pre-treatment for Gram-Positive Bacteria. The size of the DNA was controlled on an 0.8 % agarose-TBE-gel.

tag: strain

tag: genotype

value: wild type


title: primary breast tumor_192

value: Moderately differentiated (grade 2)

value: Luminal A

value: Stage I


title: primary breast tumor_197


title: wild type_gdna_rep2

description: S. aureus stationary phase culture_replicate 2


title: primary breast tumor_188

value: HER2 enriched

value: Stage IIIA


title: primary breast tumor_187

value: Stage IIB


title: wild type_gdna_rep3

description: S. aureus stationary phase culture_replicate 3


title: primary breast tumor_185

value: European American

value: Luminal B


title: primary breast tumor_190

value: Stage IIA


title: primary breast tumor_191


title: primary breast tumor_186


title: wild type_gdna_rep1

description: S. aureus stationary phase culture_replicate 1


title: primary breast tumor_184


title: intTHP1-6h_3

description: internalization of S. aureus by THP-1 cells_6h post infection_replicate 3

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in Nicolas et al., 2009, Bioinformatics 25, 2341-2347.
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008, Nucl Acids Res 36, 2926-2938).

source_name: Staphylococcus aureus cells

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009, Mol Microbiol 73, 1043-1057).

growth_protocol:
S. aureus HG001 was grown under different conditions including different growth media, presence of sub-inhibitory concentrations of antibiotics, anaerobic growth conditions, and internalization in eukaryotic host cells.
The complete description of the growth protocols can be found in the Supplementary Online Material (Mäder, Nicolas et al., to be submitted).

extract_protocol: Total RNA was isolated as described previously (Nicolas et al., 2012, Science 335, 1103-1106). The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.

treatment_protocol: Detailed treatment protocols can be found in the Supplementary Online Material (Mäder, Nicolas et al., to be submitted)

tag: treatment

value: internalization of S. aureus by THP-1 cells 6h post infection


title: primary breast tumor_179


title: primary breast tumor_181


title: primary breast tumor_183


title: primary breast tumor_178


title: primary breast tumor_180


title: primary breast tumor_177


title: primary breast tumor_182


title: intTHP1-6h_2

description: internalization of S. aureus by THP-1 cells_6h post infection_replicate 2


title: primary breast tumor_213


title: primary breast tumor_176


title: intTHP1-2h_3

description: internalization of S. aureus by THP-1 cells_2h post infection_replicate 3

value: internalization of S. aureus by THP-1 cells 2h post infection


title: primary breast tumor_200


title: delta rho_RPMI-t4_rep2

description: S. aureus rho mutant grown in RPMI medium_4h stationary phase

data_processing:
The log2 expression signal was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in Nicolas et al., 2009, Bioinformatics 25, 2341-2347.
Normalization involved three steps : (i) an aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region (Mäder, Nicolas et al., to be submitted) as the median log2 expression signal intensity of probes lying entirely within the corresponding region; (ii) aggregated expression values across the 16 hybridizations were normalized using the quantile method; (iii) probe-level expression profiles were subjected to the quantile-normalization transformations estimated in step (ii). This procedure is consistent with the observation that rho-deletion has a very limited impact on growth-rate (and hence probably a limited impact on the expression of regular genes) but it makes it possible to detect massive up- or down-regulation of expression elsewhere on the genome.

source_name: Staphylococcus aureus_rho mutant

growth_protocol: S. aureus wild-type and rho-mutant cells were grown aerobically at 37 °C in TSB and RPMI medium, respectively. Samples for tiling array analysis were taken during exponential phase and 4 hours after entry into stationary phase.

value: delta rho


title: delta rho_RPMI-t4_rep1

value: grown in RPMI medium_4h stationary phase


title: primary breast tumor_175


title: RPMI/FCS-exp_2

description: growth in RPMI medium with FCS_exponential phase_replicate 2

value: growth in RPMI medium with FCS exponential phase


title: intTHP1-2h_2

description: internalization of S. aureus by THP-1 cells_2h post infection_replicate 2


title: wild type_RPMI-exp_rep1

description: S. aureus wild type grown in RPMI medium_exponential phase

value: grown in RPMI medium_exponential phase


title: primary breast tumor_172

value: Poorly differentiated (grade 3)

value: Basal Like


title: wild type_RPMI-exp_rep2

value: wild type


title: delta rho_RPMI-exp_rep1

description: S. aureus rho mutant grown in RPMI medium_exponential phase


title: intTHP1-2h_1

description: internalization of S. aureus by THP-1 cells_2h post infection_replicate 1


title: primary breast tumor_171

value: African American


title: T/SmxTSB-t4_3

description: growth in TSB medium with trimethoprim-sulfamethoxazole_4h stationary phase_replicate 3

value: growth in TSB medium with trimethoprim-sulfamethoxazole 4h stationary phase


title: wild type_RPMI-t4_rep1

description: S. aureus wild type grown in RPMI medium_4h stationary phase


title: lineTSB-t4_2

description: growth in TSB medium with linezolid_4h stationary phase_replicate 2

value: growth in TSB medium with linezolid 4h stationary phase


title: wild type_TSB-t4_rep2

description: S. aureus wild type grown in TSB medium_4h stationary phase

value: grown in TSB medium_4h stationary phase


title: primary breast tumor_168

value: Stage I


title: T/SmxTSB-t4_1

description: growth in TSB medium with trimethoprim-sulfamethoxazole_4h stationary phase_replicate 1


title: wild type_RPMI-t4_rep2


title: primary breast tumor_166

source_name: Primary breast tumor_BMI <25

value: European American

value: Moderately differentiated (grade 2)

value: Luminal A


title: T/SmxTSB-t4_2

description: growth in TSB medium with trimethoprim-sulfamethoxazole_4h stationary phase_replicate 2


title: RPMI/FCS-exp_3

description: growth in RPMI medium with FCS_exponential phase_replicate 3


title: primary breast tumor_170

value: Stage IIIA


title: primary breast tumor_173

value: Well-differentiated (grade 1)


title: primary breast tumor_167


title: primary breast tumor_165


title: lineTSB-t4_1

description: growth in TSB medium with linezolid_4h stationary phase_replicate 1


title: primary breast tumor_169

value: Stage IIIC


title: RPMI/FCS-exp_1

description: growth in RPMI medium with FCS_exponential phase_replicate 1


title: wild type_TSB-t4_rep1


title: delta rho_RPMI-exp_rep2

value: delta rho


title: primary breast tumor_174


title: delta rho_TSB-exp_rep2

description: S. aureus rho mutant grown in TSB medium_exponential phase

value: grown in TSB medium_exponential phase


title: delta rho_TSB-t4_rep1

description: S. aureus rho mutant grown in TSB medium_4h stationary phase


title: wild type_TSB-exp_rep1

description: S. aureus wild type grown in TSB medium_exponential phase


title: delta rho_TSB-t4_rep2


title: primary breast tumor_163

value: Stage IV


title: delta rho_TSB-exp_rep1


title: wild type_TSB-exp_rep2


title: clindTSB-t4_3

description: growth in TSB medium with clindamycin_4h stationary phase_replicate 3

value: growth in TSB medium with clindamycin 4h stationary phase


title: clindTSB-t4_2

description: growth in TSB medium with clindamycin_4h stationary phase_replicate 2


title: eryTSB-t4_3

description: growth in TSB medium with erythromycin_4h stationary phase_replicate 3

value: growth in TSB medium with erythromycin 4h stationary phase


title: eryTSB-t4_1

description: growth in TSB medium with erythromycin_4h stationary phase_replicate 1

value: wild type


title: eryTSB-t4_2

description: growth in TSB medium with erythromycin_4h stationary phase_replicate 2


title: ciproTSB-t4_1

description: growth in TSB medium with ciprofloxacin_4h stationary phase_replicate 1

value: growth in TSB medium with ciprofloxacin 4h stationary phase


title: TSB-t4-B3_2

description: growth in TSB medium_4h stationary phase_replicate B3.2

value: growth in TSB medium 4h stationary phase


title: primary breast tumor_160

value: Poorly differentiated (grade 3)

value: HER2 enriched


title: ciproTSB-t4_3

description: growth in TSB medium with ciprofloxacin_4h stationary phase_replicate 3


title: TSB-t4-B3_1

description: growth in TSB medium_4h stationary phase_replicate B3.1


title: primary breast tumor_162

value: Stage IIB


title: primary breast tumor_161

value: European American

value: Stage IIA


title: clindTSB-t4_1

description: growth in TSB medium with clindamycin_4h stationary phase_replicate 1


title: primary breast tumor_158

value: Moderately differentiated (grade 2)

value: Luminal A


title: TSB-t4-B3_3

description: growth in TSB medium_4h stationary phase_replicate B3.3


title: primary breast tumor_155

value: African American

value: Luminal B


title: primary breast tumor_157


title: ciproTSB-t4_2

description: growth in TSB medium with ciprofloxacin_4h stationary phase_replicate 2


title: T/SmxTSB-exp_3

description: growth in TSB medium with trimethoprim-sulfamethoxazole_exponential phase_replicate 3

value: growth in TSB medium with trimethoprim-sulfamethoxazole exponential phase


title: primary breast tumor_152


title: primary breast tumor_159


title: primary breast tumor_154

value: Basal Like


title: primary breast tumor_156

value: Stage I


title: primary breast tumor_153


title: primary breast tumor_151

value: Stage IV


title: T/SmxTSB-exp_2

description: growth in TSB medium with trimethoprim-sulfamethoxazole_exponential phase_replicate 2


title: T/SmxTSB-exp_1

description: growth in TSB medium with trimethoprim-sulfamethoxazole_exponential phase_replicate 1


title: lineTSB-exp_3

description: growth in TSB medium with linezolid_exponential phase_replicate 3

value: growth in TSB medium with linezolid exponential phase


title: primary breast tumor_148


title: lineTSB-exp_2

description: growth in TSB medium with linezolid_exponential phase_replicate 2

value: wild type


title: primary breast tumor_149

value: Stage IIIA


title: lineTSB-exp_1

description: growth in TSB medium with linezolid_exponential phase_replicate 1


title: eryTSB-exp_2

description: growth in TSB medium with erythromycin_exponential phase_replicate 2

value: growth in TSB medium with erythromycin exponential phase


title: primary breast tumor_147

value: Poorly differentiated (grade 3)


title: clindTSB-exp_3

description: growth in TSB medium with clindamycin_exponential phase_replicate 3

value: growth in TSB medium with clindamycin exponential phase


title: clindTSB-exp_1

description: growth in TSB medium with clindamycin_exponential phase_replicate 1


title: eryTSB-exp_1

description: growth in TSB medium with erythromycin_exponential phase_replicate 1


title: clindTSB-exp_2

description: growth in TSB medium with clindamycin_exponential phase_replicate 2


title: primary breast tumor_145


title: primary breast tumor_146

value: Well-differentiated (grade 1)


title: primary breast tumor_144

value: European American


title: eryTSB-exp_3

description: growth in TSB medium with erythromycin_exponential phase_replicate 3


title: primary breast tumor_142

value: Stage IIA


title: primary breast tumor_150


title: primary breast tumor_143

value: HER2 enriched


title: primary breast tumor_138


title: TSB-exp-B3_3

description: growth in TSB medium_exponential phase_replicate B3.3

value: growth in TSB medium exponential phase


title: TSB-exp-B3_2

description: growth in TSB medium_exponential phase_replicate B3.2


title: ciproTSB-exp_1

description: growth in TSB medium with ciprofloxacin_exponential phase_replicate 1

value: growth in TSB medium with ciprofloxacin exponential phase


title: primary breast tumor_139

value: African American

value: Luminal B


title: ciproTSB-exp_2

description: growth in TSB medium with ciprofloxacin_exponential phase_replicate 2


title: primary breast tumor_141

value: Moderately differentiated (grade 2)

value: Luminal A


title: primary breast tumor_136

value: Stage I


title: primary breast tumor_140


title: ciproTSB-exp_3

description: growth in TSB medium with ciprofloxacin_exponential phase_replicate 3


title: primary breast tumor_135

value: Stage IIB


title: TSB-exp-B3_1

description: growth in TSB medium_exponential phase_replicate B3.1

value: wild type


title: nonad50-1h_1

description: non-adherent bacteria at MOI 50 after 1h of co-incubation with S9 cells_replicate 1


title: nonad50-1h_2

description: non-adherent bacteria at MOI 50 after 1h of co-incubation with S9 cells_replicate 2


title: primary breast tumor_137


title: intS9-6h_3

description: internalization of S. aureus by S9 cells_6.5h post infection_replicate 3

value: internalization of S. aureus by S9 cells 6.5h post infection


title: nonad25-1h_3

description: non-adherent bacteria at MOI 25 after 1h of co-incubation with S9 cells_replicate 3


title: nonad25-1h_2

description: non-adherent bacteria at MOI 25 after 1h of co-incubation with S9 cells_replicate 2


title: nonad25-1h_1

description: non-adherent bacteria at MOI 25 after 1h of co-incubation with S9 cells_replicate 1


title: intS9-6h_2

description: internalization of S. aureus by S9 cells_6.5h post infection_replicate 2


title: primary breast tumor_132


title: primary breast tumor_133


title: primary breast tumor_130


title: primary breast tumor_131


title: primary breast tumor_129


title: lineTSB-t4_3

description: growth in TSB medium with linezolid_4h stationary phase_replicate 3

value: growth in TSB medium with linezolid 4h stationary phase


title: intS9-6h_1

description: internalization of S. aureus by S9 cells_6.5h post infection_replicate 1


title: primary breast tumor_164

value: Poorly differentiated (grade 3)

value: Basal Like


title: primary breast tumor_128

value: Well-differentiated (grade 1)


title: primary breast tumor_126

value: Stage IIIA


title: intS9-2h_3

description: internalization of S. aureus by S9 cells_2.5h post infection_replicate 3

value: internalization of S. aureus by S9 cells 2.5h post infection


title: intS9-2h_2

description: internalization of S. aureus by S9 cells_2.5h post infection_replicate 2


title: intS9-2h_1

description: internalization of S. aureus by S9 cells_2.5h post infection_replicate 1


title: anaer-2h_3

description: 2.5h of anaerobic incubation of exponential phase cells in pMEM medium_replicate 3


title: anaer-2h_2

description: 2.5h of anaerobic incubation of exponential phase cells in pMEM medium_replicate 2


title: anaer-2h_1

description: 2.5h of anaerobic incubation of exponential phase cells in pMEM medium_replicate 1


title: primary breast tumor_124

value: European American


title: primary breast tumor_125

value: Stage IIA


title: primary breast tumor_123

value: HER2 enriched


title: CO2-6h_2

description: 6.5h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 2


title: CO2-2h_3

description: 2.5h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 3


title: CO2-6h_1

description: 6.5h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 1


title: primary breast tumor_127

value: African American

value: Normal-like


title: primary breast tumor_120


title: primary breast tumor_122


title: primary breast tumor_121

value: Stage IV


title: CO2-1h_3

description: 1h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 3


title: primary breast tumor_116

value: Otherher

value: Moderately differentiated (grade 2)


title: primary breast tumor_117

value: Stage I


title: CO2-2h_1

description: 2.5h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 1

value: wild type


title: primary breast tumor_118

value: Luminal A

value: Stage IIB


title: primary breast tumor_119


title: CO2-1h_1

description: 1h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 1


title: primary breast tumor_114


title: CO2-2h_2

description: 2.5h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 2


title: primary breast tumor_134

value: Poorly differentiated (grade 3)


title: pMEM-exp-C2_3

description: growth in pMEM medium_exponential phase_replicate C2.3

value: growth in pMEM medium exponential phase


title: pMEM-exp-C2_2

description: growth in pMEM medium_exponential phase_replicate C2.2


title: CO2-1h_2

description: 1h of incubation in infection medium (4% FCS) at 5% CO2 without agitation_replicate 2


title: primary breast tumor_113


title: primary breast tumor_111

value: Basal Like


title: primary breast tumor_115


title: primary breast tumor_110


title: colist-exp_1

description: growth in TSB medium with 50 µg/ml colistin_exponential phase_replicate 1

value: growth in TSB medium with 50 µg/ml colistin exponential phase


title: vancRPMI-t4_3

description: growth in RPMI medium with vancomycin_4h stationary phase_replicate 3

value: growth in RPMI medium with vancomycin 4h stationary phase


title: vancRPMI-t4_1

description: growth in RPMI medium with vancomycin_4h stationary phase_replicate 1


title: vancRPMI-t4_2

description: growth in RPMI medium with vancomycin_4h stationary phase_replicate 2


title: colist-exp_2

description: growth in TSB medium with 50 µg/ml colistin_exponential phase_replicate 2


title: primary breast tumor_109

value: European American

value: Stage IIIA


title: flucRPMI-t4_3

description: growth in RPMI medium with flucloxacillin_4h stationary phase_replicate 3

value: growth in RPMI medium with flucloxacillin 4h stationary phase


title: vancRPMI-exp_3

description: growth in RPMI medium with vancomycin_exponential phase_replicate 3

value: growth in RPMI medium with vancomycin exponential phase


title: vancRPMI-exp_1

description: growth in RPMI medium with vancomycin_exponential phase_replicate 1


title: vancRPMI-exp_2

description: growth in RPMI medium with vancomycin_exponential phase_replicate 2


title: flucRPMI-t4_2

description: growth in RPMI medium with flucloxacillin_4h stationary phase_replicate 2


title: primary breast tumor_106

value: Well-differentiated (grade 1)

value: Stage IIA


title: primary breast tumor_104

value: African American


title: pMEM-exp-C2_1

description: growth in pMEM medium_exponential phase_replicate C2.1


title: primary breast tumor_107

value: Moderately differentiated (grade 2)

value: HER2 enriched


title: primary breast tumor_99


title: primary breast tumor_105


title: flucRPMI-t4_1

description: growth in RPMI medium with flucloxacillin_4h stationary phase_replicate 1

value: wild type


title: primary breast tumor_108

value: Luminal A

value: Stage I


title: flucRPMI-exp_2

description: growth in RPMI medium with flucloxacillin_exponential phase_replicate 2

value: growth in RPMI medium with flucloxacillin exponential phase


title: primary breast tumor_102


title: primary breast tumor_103

value: Poorly differentiated (grade 3)


title: primary breast tumor_100

value: Normal-like


title: primary breast tumor_101

value: Basal Like

value: Stage IIIC


title: primary breast tumor_98


title: primary breast tumor_97


title: primary breast tumor_96

value: European American


title: primary breast tumor_112


title: primary breast tumor_95

value: Stage IIIA


title: flucRPMI-exp_3

description: growth in RPMI medium with flucloxacillin_exponential phase_replicate 3


title: primary breast tumor_93


title: primary breast tumor_91


title: colist-exp_3

description: growth in TSB medium with 50 µg/ml colistin_exponential phase_replicate 3

value: growth in TSB medium with 50 µg/ml colistin exponential phase


title: RPMI-exp-A2_2

description: growth in RPMI medium_exponential phase_replicate A2.2

value: growth in RPMI medium exponential phase


title: RPMI-exp-A2_3

description: growth in RPMI medium_exponential phase_replicate A2.3


title: primary breast tumor_92

value: Asian


title: RPMI-exp-A2_1

description: growth in RPMI medium_exponential phase_replicate A2.1


title: RPMI-t4-A2_1

description: growth in RPMI medium_4h stationary phase_replicate A2.1

value: growth in RPMI medium 4h stationary phase


title: vancTSB-t4_2

description: growth in TSB medium with vancomycin_4h stationary phase_replicate 2

value: growth in TSB medium with vancomycin 4h stationary phase


title: vancTSB-t4_1

description: growth in TSB medium with vancomycin_4h stationary phase_replicate 1


title: vancTSB-exp_2

description: growth in TSB medium with vancomycin_exponential phase_replicate 2

value: growth in TSB medium with vancomycin exponential phase


title: primary breast tumor_94

value: Moderately differentiated (grade 2)

value: Stage IIA


title: vancTSB-t4_3

description: growth in TSB medium with vancomycin_4h stationary phase_replicate 3

value: wild type


title: vancTSB-exp_1

description: growth in TSB medium with vancomycin_exponential phase_replicate 1


title: flucTSB-t4_3

description: growth in TSB medium with flucloxacillin_4h stationary phase_replicate 3

value: growth in TSB medium with flucloxacillin 4h stationary phase


title: primary breast tumor_89


title: primary breast tumor_87

value: African American

value: Luminal B


title: primary breast tumor_88

value: Poorly differentiated (grade 3)

value: Stage IIB


title: primary breast tumor_82

value: Luminal A

value: Stage I


title: primary breast tumor_81

value: European American

value: Well-differentiated (grade 1)


title: vancTSB-exp_3

description: growth in TSB medium with vancomycin_exponential phase_replicate 3


title: primary breast tumor_90

value: Basal Like


title: primary breast tumor_84


title: flucTSB-t4_1

description: growth in TSB medium with flucloxacillin_4h stationary phase_replicate 1


title: primary breast tumor_86


title: primary breast tumor_85


title: flucTSB-t4_2

description: growth in TSB medium with flucloxacillin_4h stationary phase_replicate 2


title: primary breast tumor_83

value: Asian


title: flucTSB-exp_3

description: growth in TSB medium with flucloxacillin_exponential phase_replicate 3

value: growth in TSB medium with flucloxacillin exponential phase


title: primary breast tumor_77


title: flucTSB-exp_1

description: growth in TSB medium with flucloxacillin_exponential phase_replicate 1


title: flucTSB-exp_2

description: growth in TSB medium with flucloxacillin_exponential phase_replicate 2


title: primary breast tumor_80

value: Normal-like


title: flucRPMI-exp_1

description: growth in RPMI medium with flucloxacillin_exponential phase_replicate 1

value: growth in RPMI medium with flucloxacillin exponential phase


title: primary breast tumor_76


title: TSB-t4-B2_1

description: growth in TSB medium_4h stationary phase_replicate B2.1

value: growth in TSB medium 4h stationary phase


title: TSB-exp-B2_3

description: growth in TSB medium_exponential phase_replicate B2.3

value: growth in TSB medium exponential phase


title: TSB-t4-B2_2

description: growth in TSB medium_4h stationary phase_replicate B2.2

value: wild type


title: TSB-exp-B2_2

description: growth in TSB medium_exponential phase_replicate B2.2


title: plasma-t4_2

description: growth in human plasma_4h stationary phase_replicate 2

value: growth in human plasma 4h stationary phase


title: plasma-t4_3

description: growth in human plasma_4h stationary phase_replicate 3


title: primary breast tumor_78

value: HER2 enriched

value: Stage IIA


title: TSB-exp-B2_1

description: growth in TSB medium_exponential phase_replicate B2.1


title: plasma-t4_1

description: growth in human plasma_4h stationary phase_replicate 1


title: primary breast tumor_70

value: Unk

value: Moderately differentiated (grade 2)

value: Stage IIIC


title: primary breast tumor_71

value: Hispanic

value: Luminal A


title: primary breast tumor_74

value: African American

value: Poorly differentiated (grade 3)

value: Stage IV


title: primary breast tumor_66

value: European American

value: Basal Like


title: plasma-exp_2

description: growth in human plasma_exponential phase_replicate 2

value: growth in human plasma exponential phase


title: primary breast tumor_69

value: Stage I


title: primary breast tumor_67


title: primary breast tumor_72

value: Well-differentiated (grade 1)


title: plasma-exp_1

description: growth in human plasma_exponential phase_replicate 1

value: wild type


title: primary breast tumor_75


title: primary breast tumor_68


title: CDM-t4_4

description: growth in CDM medium_4h stationary phase_replicate 4

value: growth in CDM medium 4h stationary phase


title: primary breast tumor_64


title: primary breast tumor_65

value: HER2 enriched


title: plasma-exp_3

description: growth in human plasma_exponential phase_replicate 3


title: RPMI-t4-A2_2

description: growth in RPMI medium_4h stationary phase_replicate A2.2

value: growth in RPMI medium 4h stationary phase


title: primary breast tumor_63


title: CDM-t4_3

description: growth in CDM medium_4h stationary phase_replicate 3


title: RPMI-t4-A2_3

description: growth in RPMI medium_4h stationary phase_replicate A2.3


title: CDM-t4_2

description: growth in CDM medium_4h stationary phase_replicate 2


title: CDM-t2_4

description: growth in CDM medium_2h stationary phase_replicate 4

value: growth in CDM medium 2h stationary phase


title: CDM-t2_3

description: growth in CDM medium_2h stationary phase_replicate 3


title: CDM-t2_2

description: growth in CDM medium_2h stationary phase_replicate 2


title: CDM-t2_1

description: growth in CDM medium_2h stationary phase_replicate 1


title: primary breast tumor_61

value: Stage IIA


title: primary breast tumor_79


title: CDM-exp_4

description: growth in CDM medium_exponential phase_replicate 3

value: growth in CDM medium exponential phase


title: primary breast tumor_59


title: primary breast tumor_56


title: CDM-exp_1

description: growth in CDM medium_exponential phase_replicate 1


title: primary breast tumor_60

value: Luminal B

value: Stage IIIA


title: pMEM-t4-C1_3

description: growth in pMEM medium_4h stationary phase_replicate C1.3

value: growth in pMEM medium 4h stationary phase


title: pMEM-t4-C1_2

description: growth in pMEM medium_4h stationary phase_replicate C1.2


title: pMEM-t4-C1_1

description: growth in pMEM medium_4h stationary phase_replicate C1.1


title: primary breast tumor_57

value: African American

value: Moderately differentiated (grade 2)

value: Luminal A

value: Stage IIB


title: pMEM-t2-C1_3

description: growth in pMEM medium_2h stationary phase_replicate C1.3

value: growth in pMEM medium 2h stationary phase


title: primary breast tumor_58

value: European American


title: primary breast tumor_54

value: Stage I


title: primary breast tumor_62

value: Hispanic

value: Poorly differentiated (grade 3)


title: primary breast tumor_55

value: Well-differentiated (grade 1)


title: pMEM-t2-C1_2

description: growth in pMEM medium_2h stationary phase_replicate C1.2

value: wild type


title: CDM-exp_2

description: growth in CDM medium_exponential phase_replicate 2


title: primary breast tumor_52


title: pMEM-t2-C1_1

description: growth in pMEM medium_2h stationary phase_replicate C1.1


title: primary breast tumor_49

value: HER2 enriched


title: primary breast tumor_53

value: Stage IIA


title: pMEM-exp-C1_3

description: growth in pMEM medium_exponential phase_replicate C1.3

value: growth in pMEM medium exponential phase


title: primary breast tumor_50


title: pMEM-exp-C1_2

description: growth in pMEM medium_exponential phase_replicate C1.2


title: primary breast tumor_46


title: pMEM-exp-C1_1

description: growth in pMEM medium_exponential phase_replicate C1.1


title: TSB-t4-C_1

description: growth in TSB medium_4h stationary phase_replicate C1

value: growth in TSB medium 4h stationary phase


title: primary breast tumor_47


title: TSB-t2-C_3

description: growth in TSB medium_2h stationary phase_replicate C3

value: growth in TSB medium 2h stationary phase


title: primary breast tumor_45

value: Stage IIIA


title: primary breast tumor_43

value: Asian

value: Basal Like


title: primary breast tumor_48

value: Luminal B

value: Stage IV


title: TSB-exp-C_3

description: growth in TSB medium_exponential phase_replicate C3

value: growth in TSB medium exponential phase


title: TSB-t2-C_1

description: growth in TSB medium_2h stationary phase_replicate C1


title: TSB-t2-C_2

description: growth in TSB medium_2h stationary phase_replicate C2


title: TSB-exp-C_2

description: growth in TSB medium_exponential phase_replicate C2


title: primary breast tumor_44

value: European American

value: Moderately differentiated (grade 2)


title: primary breast tumor_39


title: primary breast tumor_42

value: Stage IIB


title: TSB-exp-C_1

description: growth in TSB medium_exponential phase_replicate C1


title: TSB-t4-C_3

description: growth in TSB medium_4h stationary phase_replicate C3


title: primary breast tumor_37

value: Poorly differentiated (grade 3)


title: TSB-t4-B1_2

description: growth in TSB medium_4h stationary phase_replicate B1.2


title: TSB-t4-C_2

description: growth in TSB medium_4h stationary phase_replicate C2


title: primary breast tumor_40

value: Well-differentiated (grade 1)

value: Luminal A


title: primary breast tumor_41


title: TSB-t4-B1_1

description: growth in TSB medium_4h stationary phase_replicate B1.1

value: wild type


title: primary breast tumor_36

value: Stage IIIC


title: primary breast tumor_35

value: African American

value: Stage I


title: TSB-t2-B1_3

description: growth in TSB medium_2h stationary phase_replicate B1.3

value: growth in TSB medium 2h stationary phase


title: primary breast tumor_38

value: Stage IIA


title: primary breast tumor_73


title: TSB-t2-B1_1

description: growth in TSB medium_2h stationary phase_replicate B1.1


title: TSB-t2-B1_2

description: growth in TSB medium_2h stationary phase_replicate B1.2


title: primary breast tumor_34


title: primary breast tumor_33

value: Asian


title: primary breast tumor_32

value: Basal Like

value: Stage IIIB


title: TSB-exp-B1_3

description: growth in TSB medium_exponential phase_replicate B1.3


title: TSB-exp-A_3

description: growth in TSB medium_exponential phase_replicate A3


title: TSB-exp-A_2

description: growth in TSB medium_exponential phase_replicate A2


title: TSB-exp-B1_2

description: growth in TSB medium_exponential phase_replicate B1.2


title: TSB-exp-B1_1

description: growth in TSB medium_exponential phase_replicate B1.1


title: primary breast tumor_30


title: primary breast tumor_27

value: Unk


title: primary breast tumor_28


title: TSB-exp-A_1

description: growth in TSB medium_exponential phase_replicate A1

value: growth in TSB medium exponential phase


title: primary breast tumor_31


title: RPMI-exp-A1_1

description: growth in RPMI medium_exponential phase_replicate A1.1

value: growth in RPMI medium exponential phase


title: RPMI-t2-A1_2

description: growth in RPMI medium_2h stationary phase_replicate A1.2

value: growth in RPMI medium 2h stationary phase


title: primary breast tumor_24

value: European American

value: Moderately differentiated (grade 2)

value: Stage IV


title: primary breast tumor_25

value: Poorly differentiated (grade 3)


title: primary breast tumor_26

value: Luminal A

value: Stage IIIA


title: primary breast tumor_21

value: HER2 enriched

value: Stage IIIC


title: primary breast tumor_23

value: Well-differentiated (grade 1)


title: primary breast tumor_22

value: African American


title: primary breast tumor_20

value: Stage IIA


title: primary breast tumor_19


title: primary breast tumor_16

value: Stage IIB


title: primary breast tumor_18


title: primary breast tumor_17

value: Stage I


title: primary breast tumor_11

value: Basal Like


title: primary breast tumor_13


title: primary breast tumor_14


title: primary breast tumor_10


title: SAMPLE_96_74_310629

city: Porto Alegre

first: Andressa

last: Bortoluzzi

state: RS

address: Ramiro Barcelos, 2350

department: Psychiatric

country: Brazil

institute: Universidade Federal do Rio Grande do Sul -UFRGS

hyb_protocol: EZ DNA Methylation-Gold Kit (Zymo Research) was used to DNA bisulphite convertion and the DNA sample was amplified, fragmented and hybridised to Infinium HumanMethylation450 BeadChip Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data processing workflow described in the lumi R package have been used for color bias and background adjustments, qc plots and quantile normalization based on color balance adjusted data.

label: Cy3, Cy5

source_name: Saliva

label_protocol: Standard Infinium HumanMethylation450 BeadChip Illumina Protocol

extract_protocol: genomic DNA of saliva was extracted using DNA collection Oragene Kit (DNA Genotek, Ottawa, Canada) according to standard instructions

tag: gender

value: female

tag: collection year

tag: disorder state

value: control

tag: psychiatric disorder status

value: Typically Developing Adolescent

tag: sample type

value: saliva


title: primary breast tumor_15

tag: patient ethnicity

value: Otherher

tag: bmi

value: Normal-like


title: primary breast tumor_12

value: European American

tag: tumor grade

value: Moderately differentiated (grade 2)

tag: tumor subtype (via breastprs)


title: TSB-t4-B2_3

description: growth in TSB medium_4h stationary phase_replicate B2.3

value: wild type

value: growth in TSB medium 4h stationary phase


title: SAMPLE_92_67_replicated_641115

value: male

value: Remittent Anxiety Disorder


title: primary breast tumor_8

value: Luminal A

tag: tumor stage


title: primary breast tumor_6

value: Unk

value: Poorly differentiated (grade 3)


title: primary breast tumor_7

value: Well-differentiated (grade 1)

value: Stage I


title: SAMPLE_89_64_620224

value: female

value: anxiety disorder

value: Persistent Anxiety Disorder


title: SAMPLE_93_68_541311

value: control

value: Typically Developing Adolescent

value: saliva


title: SAMPLE_94_69_570116


title: SAMPLE_91_67_641115


title: SAMPLE_90_66_630205


title: primary breast tumor_29

value: European American

value: Stage IIIB


title: primary breast tumor_4

value: Moderately differentiated (grade 2)


title: primary breast tumor_5


title: primary breast tumor_3


title: primary breast tumor_2

value: African American

value: Luminal B


title: SAMPLE_86_61_331101


title: SAMPLE_84_59_560213

value: male


title: SAMPLE_85_60_170125

value: Remittent Anxiety Disorder


title: SAMPLE_87_62_351128

value: Incident Anxiety Disorder


title: SAMPLE_88_63_641309


title: SAMPLE_83_58_361328


title: primary breast tumor_1

value: Basal Like

value: Stage IV


title: primary breast tumor_9

value: Poorly differentiated (grade 3)

value: Stage IIB


title: SAMPLE_82_55_331103

value: anxiety disorder


title: RPMI-exp-A1_3

description: growth in RPMI medium_exponential phase_replicate A1.3

value: wild type

value: growth in RPMI medium exponential phase


title: primary breast tumor_51

value: Luminal A


title: SAMPLE_80_51_320210

value: female

value: control

value: Typically Developing Adolescent

value: saliva


title: SAMPLE_79_50_670134


title: SAMPLE_81_52_571308

value: Persistent Anxiety Disorder


title: SAMPLE_72_43_341123


title: SAMPLE_78_49_541204


title: SAMPLE_75_46_550202


title: SAMPLE_95_70_331104


title: SAMPLE_77_48_560101


title: SAMPLE_73_44_570202


title: SAMPLE_74_45_641227


title: SAMPLE_70_40_341132


title: SAMPLE_71_41_440116


title: SAMPLE_76_47_650301


title: SAMPLE_69_37_351307


title: SAMPLE_68_36_341228


title: SAMPLE_65_29_430110


title: SAMPLE_59_18_580214


title: SAMPLE_66_30_310127


title: SAMPLE_61_24_320222


title: SAMPLE_55_11_381113


title: SAMPLE_51_4_351109


title: SAMPLE_62_25_330127


title: SAMPLE_67_35_680232


title: SAMPLE_64_28_371232


title: SAMPLE_50_2_341219


title: SAMPLE_63_26_371222


title: SAMPLE_58_15_641124


title: SUM149-SCRAMBLE_shRNA-rep3

first: Nicholas

middle: Alexander

last: Graham

address: 570 Westwood Blvd, CNSI 4338

department: Molecular and Medical Pharmacology

institute: University of California, Los Angeles

description: SUM149 cells expressing a scrambled shRNA (ie, control)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affy H133 PLUS 2.0 Genome Array.  The Genechip was wasted and stained in the Affymetrix Fluidics Station 400.

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: HS578T cells were grown in DMEM media with 1% Penstrep, and 10% FBS. SUM149PT and SUM159PT cells were grown in F12 media with 1% Penstrep, 10% FBS, 10 ug/ml insulin, 10 ug/ml hydrocortisone, 10 ng/ml EGF, and 0.5 mg/ml of gentamicin.

extract_protocol: Total RNA was extracted using Qiagen RNeasy

treatment_protocol: For shRNA experiments, breast cancer cell lines were infected with lentivirus containing scrambled or MCT1 shRNA, and cells were selected in 2 µg/ml puromycin for 5 days before RNA extraction.  For drug treatment experiments, breast cancer cell lines were treated for 24 hours with either DMSO or AZD3965 (MCT1 inhibitor).

tag: cell line

tag: drug treatment

tag: shRNA vector

value: SCRAMBLE shRNA


title: SAMPLE_52_5_361314

value: male


title: SAMPLE_54_9_361223


title: SAMPLE_47_539_571308


title: SAMPLE_60_23_540125


title: SAMPLE_53_6_450107


title: SAMPLE_46_531_550202


title: SAMPLE_56_12_561302


title: SAMPLE_57_13_620230


title: SAMPLE_39_455_450107


title: SAMPLE_48_560_541311


title: SAMPLE_40_461_570116

value: Remittent Anxiety Disorder


title: SAMPLE_45_512_570202


title: SUM149-MCT1_shRNA-rep2

description: SUM149 cells expressing an shRNA against MCT1

value: MCT1 shRNA


title: SAMPLE_44_506_430110


title: SUM149-MCT1_shRNA-rep1


title: SAMPLE_41_469_541204

value: Incident Anxiety Disorder


title: SAMPLE_43_498_561302


title: SUM149-SCRAMBLE_shRNA-rep2


title: SAMPLE_42_496_560101


title: SAMPLE_38_443_540125


title: SAMPLE_37_441_560213


title: SAMPLE_49_1_550122


title: SUM149-MCT1i-rep3

description: SUM149 cells treated for 24 h with AZD3965

value: MCT1 inhibitor AZD3965


title: SUM159-MCT1i-rep3

description: SUM159 cells treated for 24 h with AZD3965


title: SUM159-DMSO-rep3

description: SUM159 cells treated for 24 h with DMSO

value: DMSO


title: SAMPLE_35_410_580214


title: SUM159-MCT1i-rep2


title: SUM159-DMSO-rep1

description: SUM159 cells treated for 24 h with DMSO


title: SUM159-MCT1i-rep1


title: SUM149-MCT1i-rep2


title: HS578T-MCT1i-rep3

description: HS578T cells treated for 24 h with AZD3965


title: SUM149-DMSO-rep3

description: SUM149 cells treated for 24 h with DMSO


title: SUM159-DMSO-rep2

description: SUM159 cells treated for 24 h with DMSO


title: SUM149-MCT1i-rep1


title: HS578T-DMSO-rep3

description: HS578T cells treated for 24 h with DMSO


title: HS578T-MCT1i-rep1


title: SUM149-DMSO-rep1

description: SUM149 cells treated for 24 h with DMSO


title: SUM149-DMSO-rep2

description: SUM149 cells treated for 24 h with DMSO


title: SUM149-SCRAMBLE_shRNA-rep1


title: SUM149-MCT1_shRNA-rep3


title: HS578T-DMSO-rep2

description: HS578T cells treated for 24 h with DMSO


title: HS578T-MCT1i-rep2


title: SAMPLE_28_304_330127


title: SAMPLE_34_405_680232


title: SAMPLE_31_369_641309


title: SAMPLE_32_379_440116


title: SAMPLE_29_312_641115


title: SAMPLE_27_292_650301


title: SAMPLE_30_316_641227


title: SAMPLE_33_401_550122


title: SAMPLE_26_282_641124


title: SAMPLE_36_411_170125


title: SAMPLE_18_196_320210


title: SAMPLE_17_192_320222


title: HS578T-DMSO-rep1

description: HS578T cells treated for 24 h with DMSO


title: A431_24hr_0.1%DMSO

city: Beijing

first: Yanbo

last: Zheng

address: 1# Tiantan Xili

institute: Institute of Medicinal Biotechnology

description: Gene expression after 24hr in 0.1% DMSO treated A431 cells

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: A-431 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 μg/mL streptomycin and 100 U/mL penicillin and maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was prepared using TRIzol reagent (Invitrogen) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: A431 cells were seeded in T75 flask. After culturing at 37°C for 24 h,100 nM IMB5046 and vehicle(0.1% DMSO) were added.  The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: human epidermoid carcinoma cell line A431

tag: age


title: ADin #36

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: The labelled samples were hybridized to the Affymetrix Human Gene 2.1 ST Array for 16h at 45 C

scan_protocol: The arrays were scanned in an Affymetrix 3000 7G scanner

data_processing: Data were normalized using Robust Multichip Average (RMA) normalization in Expression Console, build 1.3.1.187 (Affymetrix). Please note, that this is a GENE level analysis.

label: Biotin

source_name: Intrinsic AD lesional skin

label_protocol: WT_PLUS labeling kit (Affymetrix) according to the manufacturers´ instructions

extract_protocol: RNA was extracted with the mirVana kit (Life Technologies) following the manufacturer’s procedures.

treatment_protocol: Skin biopsies for RNA extraction were sampled in RNAlater and stored at -80°C. For purification, the biopsies were placed in Precellys tubes containing beads and lysis/binding buffer and homogenized using a Precellys.

tag: tissue

value: Skin

tag: diagnosis

value: Intrinsic atopic dermatitis


title: ADin #35


title: A431_24hr_100nMIMB5046

description: Gene expression after 24hr in 100 nM IMB5046 treated A431 cells


title: SAMPLE_9_124_371232


title: SAMPLE_22_218_361328

value: anxiety disorder


title: SAMPLE_16_190_341228


title: SAMPLE_13_162_341123


title: SAMPLE_8_93_670134


title: ADin #33


title: ADin #31


title: SAMPLE_19_208_351307


title: SAMPLE_7_87_620230


title: SAMPLE_12_156_310127


title: SAMPLE_25_262_341219


title: SAMPLE_11_136_310629


title: ADin #32


title: SAMPLE_10_128_341132


title: ADex #29

source_name: Extrinsic AD lesional skin

value: Extrinsic atopic dermatitis


title: SAMPLE_15_186_331101

value: female


title: SAMPLE_6_75_361223

value: control


title: SAMPLE_20_214_331104


title: SAMPLE_14_180_331103


title: SAMPLE_24_240_630205


title: SAMPLE_2_8_replicated_361314


title: ADin #34


title: SAMPLE_4_54_381113


title: ADex #28


title: SAMPLE_1_8_361314


title: SAMPLE_5_69_371222


title: SAMPLE_23_238_620224


title: BEA23: 8691803132_B5_non-obese

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: Human male liver

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

data_processing: Data was normalized and analyzed using Genom Studio software, R packages and Qlucore software.

source_name: Human liver, non-obese

label_protocol: Standard Illumina protocol for Human Methylation 450K DNA Analysis bead chip

extract_protocol: Genomic DNA was extracted with the DNeasy kit (Qiagen) and assays were performed according to the illumina protocol

tag: status

value: non-obese metabolically healthy

value: liver


title: non-obese4

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data was pre-processed using Plier (in Expression Console).  The Robust Multi-array Average (RMA) normalization method was used to normalize all data sets. A p-value cutoff <=0.05 was used to extract genes for Principle Component Analysis (PCA) and hierarchical clustering analyses using Qlucore Omics Explorer (Qlucore AB, Lund, Sweden).

label_protocol: Affymetrix standard protocol

extract_protocol: The method for RNA extraction was the miRNeasy Kit from Qiagen (Cat. No 217004). This involved a Trizol/chloroform extraction followed by column purification. The RNA was treated with DNase (on-column treatment).

tag: gender

tag: subject status


title: NN #25

source_name: Healthy skin

value: Healthy


title: BEA24: 8691803132_B6_non-obese

description: Human male liver


title: non-obese1


title: SAMPLE_3_45_351109

tag: collection year

tag: disorder state

value: saliva


title: non-obese5

value: male


title: Pso #23

source_name: Psoriasis plaque

value: Psoriasis


title: BEA22: 8691803132_B4_non-obese

description: Human male liver


title: non-obese2


title: non-obese3


title: BEA21: 8691803132_B3_non-obese

description: Human male liver


title: NN #26


title: Pso #21


title: T2D-obese7

value: obese type 2 diabetic patient


title: non-obese6


title: T2D-obese6


title: T2D-obese5


title: NN #24


title: Pso #19


title: T2D-obese2


title: Pso #18


title: BEA18: 8691803111_B6_non-obese

description: Human male liver


title: BEA19: 8691803132_B1_non-obese

description: Human male liver


title: Pso #20


title: ADin #30


title: T2D-obese3


title: BEA17: 8691803111_B5_T2D-obese

description: Human male liver

source_name: Human liver, T2D-obese


title: Pso #22


title: T2D-obese1


title: BEA13: 8691803111_B1_T2D-obese

description: Human male liver


title: ND-obese8

value: obese non-diabetic


title: ADin #15


title: ADex #11


title: ND-obese7


title: ADex #12


title: ADin #17


title: T2D-obese4


title: BEA12: 8691803132_A6_ND-obese

description: Human male liver

source_name: Human liver, ND-obese


title: BEA15: 8691803111_B3_T2D-obese

description: Human male liver


title: BEA10: 8691803132_A4_T2D-obese

description: Human male liver


title: BEA14: 8691803111_B2_T2D-obese

description: Human male liver


title: ND-obese6


title: NN #27


title: NN #8


title: NN #9


title: SAMPLE_21_216_351128

tag: psychiatric disorder status

value: Incident Anxiety Disorder

tag: sample type


title: BEA11: 8691803132_A5_ND-obese

description: Human male liver


title: BEA9: 8691803132_A3_ND-obese

description: Human male liver


title: ND-obese4


title: NN #6


title: NN #7


title: ND-obese2


title: Pso #2


title: BEA20: 8691803132_B2_non-obese

description: Human male liver


title: BEA8: 8691803132_A2_T2D-obese

description: Human male liver


title: Pso #4


title: ND-obese5


title: NHEK_5-cytokine(lacking IL-17C)-stimulated_24h_rep1

city: Sapporo

first: Ryuta

last: Muromoto

state: Hokkaido

address: Kita 12 Nishi 6, Kita-ku

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Hokkaido University

description: Gene expression after 24hr in human keratinocyte treated with  5 cytokine lacking IL-17C (IL-17A, TNF-a, IFN-g, IL-22, IL-36g)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to microarrays for 17 hours at 65°C in a rotating 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers and Population outliers were excluded.

source_name: NHEK, 5-cytokine(lacking IL-17C)-stimulated, 24h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Primary normal human epidermal keratinocytes (NHEKs) were purchased from KURABO (Tokyo, Japan) and cultured in DermaLife K Comp kit (KURABO).

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

treatment_protocol: NHEKs were seeded and precultured for 24 h and subsequently exposed to the combination of the six cytokines (IL-17A: 100 ng/ml, TNF-a: 10 ng/ml, IFN-g: 10 ng/ml, IL-17C: 100 ng/ml, IL-22: 100 ng/ml, IL-36g: 500 ng/ml) , or to the different combinations of five of the six cytokines (in total, 7 different treatments and one untreated control) , for 24 h.

tag: cell type

value: Epidermal keratinocyte

tag: race

value: Caucasian


title: NHEK_5-cytokine(lacking IL-36g)-stimulated_24h_rep1

description: Gene expression after 24hr in human keratinocyte treated with  5 cytokine lacking IL-36g (IL-17A, TNF-a, IFN-g, IL-17C, IL-22)

source_name: NHEK, 5-cytokine(lacking IL-36g)-stimulated, 24h, replicate 1


title: NHEK_5-cytokine(lacking IL-22)-stimulated_24h_rep1

description: Gene expression after 24hr in human keratinocyte treated with  5 cytokine lacking IL-22 (IL-17A, TNF-a, IFN-g, IL-17C, IL-36g)

source_name: NHEK, 5-cytokine(lacking IL-22)-stimulated, 24h, replicate 1


title: ND-obese3


title: BEA4: 8691803111_A4_ND-obese

description: Human male liver


title: BEA6: 8691803111_A6_ND-obese

description: Human male liver


title: ND-obese1


title: BEA7: 8691803132_A1_ND-obese

description: Human male liver


title: BEA5: 8691803111_A5_ND-obese

description: Human male liver


title: NHEK_5-cytokine(lacking IL-17A)-stimulated_24h_rep1

description: Gene expression after 24hr in human keratinocyte treated with  5 cytokine lacking IL-17A (TNF-a, IFN-g, IL-17C, IL-22, IL-36g)

source_name: NHEK, 5-cytokine(lacking IL-17A)-stimulated, 24h, replicate 1


title: NHEK_5-cytokine(lacking TNF-a)-stimulated_24h_rep1

description: Gene expression after 24hr in human keratinocyte treated with  5 cytokine lacking TNF-a (IL-17A, IFN-g, IL-17C, IL-22, IL-36g)

source_name: NHEK, 5-cytokine(lacking TNF-a)-stimulated, 24h, replicate 1


title: NHEK_5-cytokine(lacking IFN-g)-stimulated_24h_rep1

description: Gene expression after 24hr in human keratinocyte treated with  5 cytokine lacking IFN-g (IL-17A, TNF-a, IL-17C, IL-22, IL-36g)

source_name: NHEK, 5-cytokine(lacking IFN-g)-stimulated, 24h, replicate 1


title: Pso #1

value: Skin


title: Patient#424-IgM

status: Public on Mar 07 2016

type: protein

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

hyb_protocol: Probe: DyLight 488-conjugated F(ab’)2 fragment goat anti-human IgM (mu chain specific) (Jackson ImmunoResearch)

scan_protocol: Arrays were scanned by FLAIR Fluorescent Array Imaging Reader (Sensovation).

data_processing: Local background of spot ('Bkg.Median') was substracted from the value of signal ('Spot.Median'). Values were multiplied by 65535 and rounded to be integers. Negative signals values were clamped to arbitrary value 1.

label: fluorescent antibodies

molecule: protein

source_name: serum

label_protocol: Dried arrays were rinsed in PBS for 15 minutes before use, then incubated with diluted serum at 37°C for 1 hour. Two separated measurements were applied on each sample for detection of bound components. Five-fold serum dilution in 2.5mM Ca2+, 0.7mM Mg2+ and  5% BSA complemented PBS buffer was used for detection of deposited C3 and C4 complement fragments. 125-fold serum dilution in 25mM EDTA, 0.05% Tween 20 and 5% BSA complemented PBS buffer was applied for measurement of bound antigen specific IgG and IgM antibodies. Serum treated slides were washed with PBS containing 0.05% Tween 20, then incubated in the mixture of 1:5,000 diluted FITC-conjugated F(ab’)2 fragment of goat anti-human C3 antibody (Cappel) and 1:1000 diluted Alexa 647 conjugated goat anti-human C4 (Cappel, in-house conjugation) or 1:2500 diluted DyLight 488-conjugated F(ab’)2 fragment goat anti-human IgM (mu chain specific) (Jackson ImmunoResearch) and 1:2,500 diluted DyLight 649-conjugated F(ab’)2 fragment goat anti-human IgG (gamma chain specific) (Jackson ImmunoResearch). Labeling with fluorescent antibodies was carried out at room temperature for 30 minutes in PBS containing 5% BSA and 0.05% Tween 20. After washing in PBS containing 0.05% Tween 20, arrays were dried and scanned

extract_protocol: Serum sample was centrifuged for 6min at 15000g for removing particles

treatment_protocol: Serum samples were stored at -70C

value: Female

tag: disease group (nhs-normal human serum; sle-systemic lupus erythematosus ;uctd-undifferentiated connective tissue disease; sjs-sjörgen's syndrome;ssc-systemic sclerosis; psa-psoriatic arthritis)

value: NHS

tag: age in years

tag: printing batches (1,2)

tag: slide no.


title: Patient#425-IgM

value: Male


title: Patient#422-IgM

value: UCTD


title: Patient#423-IgM


title: Cudraflavone C, rep2

city: Bukit Jalil

first: Chee-Onn

last: Leong

country: Malaysia

institute: International Medical University

description: Gene expression of Caco2 cells treated with 10uM of Cudraflavone C for 48h

hyb_protocol: The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to GeneChip® Human Transcriptome Array 2.0 arrays for 16 hours at 45C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing: The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC. RMA normalization was performed on the samples to generate the quality control (QC) metrics that we routinely use to determine data quality. These include, perfect match mean (PM_Mean), Background mean (Bgd_Mean), positive and negative probes (POS vs NEG AUC), bacterials spike controls, and polyA controls.

source_name: Caco2 cells treated with 10uM Cidraflavone C for 48h

growth_protocol: Caco2 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin at 37°C, 5% CO2.

extract_protocol: Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm.

treatment_protocol: Cells were treated with vehicle control (DMSO) or 10uM of Cudraflavone C for 48h

value: Colorectal cancer cell line

tag: cell line


title: Patient#419-IgM


title: Patient#420-IgM

value: SSc


title: Control, rep 1

description: Gene expression of Caco2 cells treated with vehicle control (DMSO) for 48h

label_protocol: The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to GeneChip® Human Transcriptome Array 2.0 arrays for 16 hours at 45C with rotation at 60 rpm.


title: Patient#421-IgM


title: Cudraflavone C, rep1


title: Patient#418-IgM


title: Control, rep 2

source_name: Caco2 cells treated with vehicle control (DMSO) for 48h


title: NHEK_unstimulated_24h_rep1

description: Gene expression after 24hr in unstimulated human keratinocyte

source_name: NHEK, unstimulated, 24h, replicate 1

value: female

tag: age


title: BEA2: 8691803111_A2_T2D-obese

description: Human male liver

tag: tissue

value: liver


title: Patient#415-IgM


title: Patient#416-IgM


title: Patient#414-IgM

value: SLE


title: NHEK_6-cytokine-stimulated_24h_rep1

description: Gene expression after 24hr in human keratinocyte treated with  6 cytokine mixture (IL-17A, TNF-a, IFN-g, IL-17C, IL-22, IL-36g)

source_name: NHEK, 6-cytokine-stimulated, 24h, replicate 1


title: Patient#417-IgM


title: Patient#408-IgM


title: Patient#412-IgM


title: Patient#407-IgM


title: Patient#413-IgM


title: BEA3: 8691803111_A3_T2D-obese

description: Human male liver

value: male


title: Patient#405-IgM


title: Patient#410-IgM


title: Patient#409-IgM


title: Patient#401-IgM


title: Patient#404-IgM


title: Patient#402-IgM


title: Patient#400-IgM


title: Patient#398-IgM

value: SjS


title: Patient#399-IgM


title: Patient#396-IgM


title: Patient#394-IgM


title: Patient#395-IgM


title: Patient#411-IgM


title: Patient#392-IgM


title: Patient#406-IgM


title: Patient#391-IgM


title: BEA1: 8691803111_A1_ND-obese

description: Human male liver


title: Patient#390-IgM


title: Patient#389-IgM


title: Patient#387-IgM


title: Patient#385-IgM


title: Patient#384-IgM


title: Patient#388-IgM


title: Patient#386-IgM


title: Patient#383-IgM


title: Patient#379-IgM


title: Patient#378-IgM


title: Patient#397-IgM


title: BEA16: 8691803111_B4_T2D-obese

description: Human male liver

value: obese type 2 diabetic patient


title: Patient#382-IgM


title: Patient#380-IgM


title: Patient#377-IgM


title: Patient#393-IgM


title: Patient#373-IgM


title: Patient#376-IgM


title: Patient#374-IgM


title: Patient#375-IgM


title: Patient#372-IgM


title: Patient#371-IgM


title: Patient#370-IgM


title: Patient#367-IgM


title: Patient#365-IgM


title: Patient#369-IgM


title: Patient#364-IgM


title: Patient#366-IgM


title: Patient#368-IgM


title: Patient#363-IgM


title: Patient#362-IgM


title: Patient#360-IgM


title: Patient#359-IgM


title: Patient#358-IgM


title: Patient#356-IgM


title: Patient#351-IgM


title: Patient#357-IgM


title: Patient#381-IgM


title: Patient#355-IgM


title: Patient#354-IgM


title: Patient#353-IgM


title: Patient#349-IgM


title: Patient#347-IgM


title: Patient#348-IgM


title: Patient#346-IgM


title: Patient#345-IgM


title: Patient#344-IgM


title: Patient#361-IgM


title: Patient#340-IgM


title: Patient#341-IgM


title: Patient#342-IgM


title: Patient#339-IgM


title: Patient#337-IgM


title: Patient#336-IgM


title: Patient#333-IgM


title: Patient#352-IgM


title: Patient#331-IgM


title: Patient#332-IgM


title: Patient#328-IgM


title: Patient#329-IgM


title: Patient#334-IgM


title: Patient#350-IgM


title: Patient#327-IgM


title: Patient#326-IgM


title: Patient#330-IgM


title: Patient#343-IgM


title: Patient#325-IgM


title: Patient#323-IgM


title: Patient#324-IgM


title: Patient#338-IgM


title: Patient#320-IgM


title: Patient#319-IgM


title: Patient#318-IgM


title: Patient#335-IgM


title: Patient#321-IgM


title: Patient#317-IgM


title: Patient#316-IgM


title: Patient#315-IgM


title: Patient#314-IgM


title: Patient#313-IgM


title: Patient#311-IgM


title: Patient#310-IgM


title: Patient#309-IgM


title: Patient#308-IgM


title: Patient#322-IgM


title: Patient#305-IgM


title: Patient#304-IgM


title: Patient#307-IgM


title: Patient#306-IgM


title: Patient#303-IgM


title: Patient#297-IgM


title: Patient#302-IgM


title: Patient#299-IgM


title: Patient#301-IgM


title: Patient#300-IgM


title: Patient#298-IgM


title: Patient#312-IgM


title: Patient#291-IgM


title: Patient#292-IgM


title: Patient#295-IgM


title: Patient#294-IgM


title: Patient#289-IgM


title: Patient#287-IgM


title: Patient#286-IgM


title: Patient#288-IgM


title: Patient#285-IgM


title: Patient#284-IgM


title: Patient#282-IgM


title: Patient#281-IgM


title: Patient#280-IgM


title: Patient#283-IgM


title: Patient#277-IgM


title: Patient#278-IgM


title: Patient#279-IgM


title: Patient#275-IgM


title: Patient#296-IgM


title: Patient#293-IgM


title: Patient#276-IgM


title: Patient#274-IgM


title: Patient#269-IgM


title: Patient#273-IgM


title: Patient#290-IgM


title: Patient#268-IgM


title: Patient#272-IgM


title: Patient#271-IgM


title: Patient#265-IgM


title: Patient#263-IgM


title: Patient#267-IgM


title: Patient#264-IgM


title: Patient#259-IgM


title: Patient#262-IgM


title: Patient#266-IgM


title: Patient#403-IgM


title: Patient#260-IgM


title: Patient#257-IgM


title: Patient#256-IgM


title: Patient#270-IgM


title: Patient#255-IgM


title: Patient#254-IgM


title: Patient#253-IgM


title: Patient#252-IgM


title: Patient#250-IgM


title: Patient#251-IgM


title: Patient#249-IgM


title: Patient#248-IgM


title: Patient#247-IgM


title: Patient#246-IgM


title: Patient#244-IgM


title: Patient#245-IgM


title: Patient#261-IgM


title: Patient#243-IgM


title: Patient#258-IgM


title: Patient#239-IgM


title: Patient#242-IgM


title: Patient#237-IgM


title: Patient#234-IgM


title: Patient#241-IgM


title: Patient#238-IgM


title: Patient#235-IgM


title: Patient#236-IgM


title: Patient#227-IgM


title: Patient#225-IgM


title: Patient#228-IgM


title: Patient#223-IgM


title: Patient#240-IgM


title: Patient#220-IgM


title: Patient#222-IgM


title: Patient#221-IgM


title: Patient#219-IgM


title: Patient#218-IgM


title: Patient#226-IgM


title: Patient#229-IgM


title: Patient#224-IgM


title: Patient#217-IgM


title: Patient#231-IgM


title: Patient#230-IgM


title: Patient#232-IgM


title: Patient#233-IgM


title: Patient#212-IgM


title: Patient#207-IgM


title: Patient#213-IgM


title: Patient#195-IgM


title: Patient#208-IgM


title: Patient#214-IgM


title: Patient#215-IgM


title: Patient#197-IgM


title: Patient#198-IgM


title: Patient#206-IgM


title: Patient#204-IgM


title: Patient#209-IgM


title: Patient#216-IgM


title: Patient#211-IgM


title: Patient#210-IgM


title: Patient#205-IgM


title: Patient#203-IgM


title: Patient#200-IgM


title: Patient#194-IgM


title: Patient#199-IgM


title: Patient#202-IgM


title: Patient#201-IgM


title: Patient#193-IgM


title: Patient#192-IgM


title: Patient#196-IgM


title: Patient#190-IgM


title: Patient#187-IgM


title: Patient#191-IgM


title: Patient#189-IgM


title: Patient#176-IgM


title: Patient#186-IgM


title: Patient#183-IgM


title: Patient#179-IgM


title: Patient#182-IgM


title: Patient#171-IgM


title: Patient#184-IgM


title: Patient#175-IgM


title: Patient#174-IgM


title: Patient#181-IgM


title: Patient#165-IgM


title: Patient#172-IgM


title: Patient#166-IgM


title: Patient#167-IgM


title: Patient#170-IgM


title: Patient#163-IgM


title: Patient#177-IgM


title: Patient#188-IgM


title: Patient#168-IgM


title: Patient#169-IgM


title: Patient#180-IgM


title: Patient#162-IgM


title: Patient#185-IgM


title: Patient#173-IgM


title: Patient#160-IgM


title: Patient#164-IgM


title: Patient#161-IgM


title: Patient#158-IgM


title: Patient#159-IgM


title: Patient#178-IgM


title: Patient#157-IgM


title: Patient#156-IgM


title: Patient#154-IgM


title: Patient#144-IgM


title: Patient#148-IgM


title: Patient#155-IgM


title: Patient#150-IgM


title: Patient#135-IgM


title: Patient#138-IgM


title: Patient#149-IgM


title: Patient#151-IgM


title: Patient#141-IgM


title: Patient#146-IgM


title: Patient#145-IgM


title: Patient#153-IgM


title: Patient#134-IgM


title: Patient#128-IgM


title: Patient#139-IgM


title: Patient#143-IgM


title: Patient#132-IgM


title: Patient#147-IgM


title: Patient#140-IgM


title: Patient#130-IgM


title: Patient#136-IgM


title: Patient#133-IgM


title: Patient#137-IgM


title: Patient#129-IgM


title: Patient#142-IgM


title: Patient#152-IgM

value: PsA


title: Patient#127-IgM


title: Patient#125-IgM


title: Patient#123-IgM


title: Patient#122-IgM


title: Patient#121-IgM


title: Patient#124-IgM


title: Patient#131-IgM


title: Patient#126-IgM


title: Patient#116-IgM


title: Patient#118-IgM


title: Patient#115-IgM


title: Patient#110-IgM


title: Patient#120-IgM


title: Patient#119-IgM


title: Patient#114-IgM


title: Patient#113-IgM


title: Patient#117-IgM


title: Patient#104-IgM


title: Patient#101-IgM


title: Patient#106-IgM


title: Patient#107-IgM


title: Patient#112-IgM


title: Patient#102-IgM


title: Patient#100-IgM


title: Patient#108-IgM


title: Patient#105-IgM


title: Patient#111-IgM


title: Patient#99-IgM


title: Patient#98-IgM


title: Patient#97-IgM


title: Patient#109-IgM


title: Patient#93-IgM


title: Patient#91-IgM


title: Patient#96-IgM


title: Patient#103-IgM


title: Patient#92-IgM


title: Patient#89-IgM


title: Patient#88-IgM


title: Patient#87-IgM


title: Patient#83-IgM


title: Patient#79-IgM


title: Patient#86-IgM


title: Patient#85-IgM


title: Patient#84-IgM


title: Patient#95-IgM


title: Patient#74-IgM


title: Patient#81-IgM


title: Patient#77-IgM


title: Patient#82-IgM


title: Patient#80-IgM


title: Patient#78-IgM


title: Patient#75-IgM


title: Patient#76-IgM


title: Patient#94-IgM


title: Patient#72-IgM


title: Patient#71-IgM


title: Patient#73-IgM


title: Patient#70-IgM


title: Patient#69-IgM


title: Patient#64-IgM


title: Patient#68-IgM


title: Patient#67-IgM


title: Patient#65-IgM


title: Patient#90-IgM


title: Patient#61-IgM


title: Patient#63-IgM


title: Patient#66-IgM


title: Patient#60-IgM


title: Patient#59-IgM


title: Patient#51-IgM


title: Patient#52-IgM


title: Patient#58-IgM


title: Patient#53-IgM


title: Patient#57-IgM


title: Patient#50-IgM


title: Patient#49-IgM


title: Patient#56-IgM


title: Patient#47-IgM


title: Patient#54-IgM


title: Patient#46-IgM


title: Patient#55-IgM


title: Patient#40-IgM


title: Patient#42-IgM


title: Patient#48-IgM


title: Patient#39-IgM


title: Patient#36-IgM


title: Patient#35-IgM


title: Patient#45-IgM


title: Patient#44-IgM


title: Patient#43-IgM


title: Patient#41-IgM


title: Patient#62-IgM


title: Patient#37-IgM


title: Patient#33-IgM


title: Patient#32-IgM


title: Patient#38-IgM


title: Patient#34-IgM


title: Patient#29-IgM


title: Patient#28-IgM


title: Patient#31-IgM


title: Patient#27-IgM


title: Patient#20-IgM


title: Patient#23-IgM


title: Patient#24-IgM


title: Patient#22-IgM


title: Patient#19-IgM


title: Patient#30-IgM


title: Patient#26-IgM


title: Patient#18-IgM


title: Patient#21-IgM


title: Patient#12-IgM


title: Patient#14-IgM


title: Patient#11-IgM


title: Patient#13-IgM


title: Patient#17-IgM


title: Patient#10-IgM


title: Patient#5-IgM


title: Patient#9-IgM


title: Patient#6-IgM


title: Patient#25-IgM


title: Patient#3-IgM


title: Patient#7-IgM


title: Patient#1-IgM


title: Patient#15-IgM


title: Patient#424-IgG

hyb_protocol: Probe: DyLight 649-conjugated F(ab’)2 fragment goat anti-human IgG (gamma chain specific) (Jackson ImmunoResearch)


title: Patient#425-IgG


title: Patient#16-IgM


title: Patient#8-IgM


title: Patient#423-IgG


title: Patient#421-IgG


title: Patient#418-IgG


title: Patient#422-IgG


title: Patient#416-IgG


title: Patient#415-IgG


title: Patient#2-IgM


title: Patient#414-IgG


title: Patient#413-IgG


title: Patient#420-IgG


title: Patient#4-IgM


title: Patient#411-IgG


title: Patient#419-IgG


title: Patient#404-IgG


title: Patient#408-IgG


title: Patient#412-IgG


title: Patient#407-IgG


title: Patient#406-IgG


title: Patient#410-IgG


title: Patient#402-IgG


title: Patient#403-IgG


title: Patient#417-IgG


title: Patient#398-IgG


title: Patient#400-IgG


title: Patient#399-IgG


title: Patient#409-IgG


title: Patient#395-IgG


title: Patient#396-IgG


title: Patient#397-IgG


title: Patient#392-IgG


title: Patient#393-IgG


title: Patient#390-IgG


title: Patient#405-IgG


title: Patient#394-IgG


title: Patient#385-IgG


title: Patient#388-IgG


title: Patient#387-IgG


title: Patient#391-IgG


title: Patient#389-IgG


title: Patient#386-IgG


title: Patient#383-IgG


title: Patient#382-IgG


title: Patient#380-IgG


title: Patient#401-IgG


title: Patient#384-IgG


title: Patient#378-IgG


title: Patient#381-IgG


title: Patient#379-IgG


title: Patient#376-IgG


title: Patient#375-IgG


title: Patient#372-IgG


title: Patient#373-IgG


title: Patient#374-IgG


title: Patient#371-IgG


title: Patient#368-IgG


title: Patient#370-IgG


title: Patient#369-IgG


title: Patient#366-IgG


title: Patient#367-IgG


title: Patient#363-IgG


title: Patient#365-IgG


title: Patient#377-IgG


title: Patient#362-IgG


title: Patient#356-IgG


title: Patient#361-IgG


title: Patient#357-IgG


title: Patient#359-IgG


title: Patient#358-IgG


title: Patient#354-IgG


title: Patient#360-IgG


title: Patient#353-IgG


title: Patient#355-IgG


title: Patient#352-IgG


title: Patient#348-IgG


title: Patient#349-IgG


title: Patient#347-IgG


title: Patient#350-IgG


title: Patient#346-IgG


title: Patient#345-IgG


title: Patient#364-IgG


title: Patient#344-IgG


title: Patient#341-IgG


title: Patient#340-IgG


title: Patient#343-IgG


title: Patient#336-IgG


title: Patient#330-IgG


title: Patient#339-IgG


title: Patient#338-IgG


title: Patient#329-IgG


title: Patient#331-IgG


title: Patient#334-IgG


title: Patient#351-IgG


title: Patient#327-IgG


title: Patient#337-IgG


title: Patient#320-IgG