title: Sample_190


title: Sample_185

status: Public on Sep 05 2017

type: SRA

city: Boston

first: Margaret

last: Parker

state: MA

address: 181 Longwood Ave

department: Medicine

country: USA

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
reads trimmed of adapters using Skewer with default parameters
alignment to grch28 reference genome with STAR v2.4.0h
gene/exon level counts generated using Rsubreads, ensembl v81 annotation
counts were normalized for library size using the TMM method implemented in the calcNormFactors function in the edgeR package
Genome_build: grch38
Supplementary_files_format_and_content: tab-delimited text files including normalized counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
PAXgene using Qiagen PreAnalytiX PAXgene
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded Total RNAprotocols

treatment_protocol: Globin reduction with Ribo-Zero Globin kit

tag: age

tag: race

value: NHW

tag: Sex

value: male

tag: packyrs

tag: smoke


title: Sample_212

value: AA


title: Sample_187


title: Sample_182

value: female


title: Sample_181


title: Sample_180


title: Sample_179


title: Sample_178


title: Sample_177


title: Sample_176


title: Sample_173


title: Sample_172


title: Sample_171


title: Sample_170


title: Sample_167


title: Sample_168


title: Sample_169


title: Sample_196


title: Sample_165


title: Sample_164


title: Sample_159


title: Sample_166


title: Sample_160


title: Sample_162


title: Sample_161


title: Sample_157


title: Sample_158


title: Sample_154


title: Sample_153


title: Sample_155


title: Sample_152


title: Sample_151


title: Sample_149


title: Sample_156


title: Sample_150


title: Sample_147


title: Sample_146


title: Sample_148


title: Sample_142


title: Sample_145


title: Sample_143


title: Sample_144


title: Sample_141


title: Sample_140


title: Sample_163


title: Sample_139


title: Sample_138


title: Sample_137


title: Sample_136


title: Sample_135


title: Sample_134


title: Sample_132


title: Sample_130


title: Sample_129


title: Sample_128


title: Sample_133


title: Sample_127


title: Sample_125


title: Sample_126


title: Sample_123


title: Sample_122


title: Sample_121


title: Sample_120


title: Sample_124


title: Sample_118


title: Sample_119


title: Sample_117


title: Sample_115


title: Sample_114


title: Sample_113


title: Sample_112


title: Sample_111


title: Sample_110


title: Sample_109


title: Sample_107


title: Sample_106


title: Sample_108


title: Sample_131


title: Sample_105


title: Sample_103


title: Sample_104


title: Sample_101


title: Sample_96


title: Sample_98


title: Sample_99


title: Sample_95


title: Sample_102


title: Sample_93


title: Sample_92


title: Sample_100


title: Sample_94


title: Sample_89


title: Sample_88


title: Sample_91


title: Sample_116


title: Sample_84


title: Sample_81


title: Sample_86


title: Sample_80


title: Sample_79


title: Sample_78


title: Sample_75


title: Sample_76


title: Sample_77


title: Sample_74


title: Sample_73


title: Sample_97


title: Sample_72


title: Sample_70


title: Sample_71


title: Sample_68


title: Sample_69


title: Sample_67


title: Sample_87


title: Sample_66


title: Sample_65


title: Sample_64


title: Sample_60


title: Sample_61


title: Sample_58


title: Sample_63


title: Sample_59


title: Sample_62


title: Sample_57


title: Sample_82


title: Sample_56


title: Sample_55


title: Sample_53


title: Sample_52


title: Sample_54


title: Sample_51


title: Sample_50


title: Sample_46


title: Sample_44


title: Sample_48


title: Sample_49


title: Sample_42


title: Sample_47


title: Sample_41


title: Sample_38


title: Sample_37


title: Sample_40


title: Sample_35


title: Sample_31


title: Sample_29


title: Sample_34


title: Sample_39


title: Sample_33


title: Sample_30


title: Sample_27


title: Sample_26


title: Sample_23


title: Sample_22


title: Sample_24


title: Sample_21


title: Sample_20


title: Sample_43


title: Sample_19


title: Sample_15


title: Sample_18


title: Sample_14


title: Sample_16


title: Sample_13


title: Sample_36


title: Sample_17


title: Sample_12


title: Sample_32


title: Sample_9


title: Sample_7


title: Sample_6


title: Sample_8


title: Sample_4


title: Sample_10


title: Sample_3


title: Sample_28


title: Sample_2


title: Sample_1


title: Sample_5


title: Sample_11


title: Ct-PHT58-VitD-0

type: RNA

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

description: total RNA

hyb_protocol: GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing:
Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing (Partek Software, v.6.5: RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); Biostatistical data analysis:

label: biotin

source_name: Isolated and in vitro cultured placental cells

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Primary human villous cytotrophoblasts were isolated as described {Chen et al., 2010, Am J Physiol Cell Physiol, 299, C968-76; Chen et al., 2015, Placenta, 36, 847-53} and washed thoroughly 4 h after plating, to eliminate villous fragments and nonviable cells. Cytotrophoblasts were cultured for a total time of 24 h.

extract_protocol: RNA isolation with TRI REAGENT according to manufacturer

treatment_protocol: Primary cultures (n = 6) of human trophoblast from term placentas, with phenotypes previously characterized in our lab (Wang Reproduction 1521: 97). Ethanol control or 100 nM 1,25(OH)2D were added for the final 6 h

tag: cell type

value: cytotrophoblasts

tag: treatment

value: Ethanom control


title: LNCAP treated with 10 nM DHT for 2h, biological rep3

city: Darlinghurst

first: Fatima

last: Valdes Mora

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description: DHT time-series gene expression

hyb_protocol: As per standard Affymetrix protocol for the Human21.1ST arrays

data_processing: Data were processed in R using the rma function in the Oligo package

source_name: Androgen-sensitive human prostate adenocarcinoma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Human 2.1ST arrays

growth_protocol: Human LNCaP prostate cancer cells were maintained in RPMI Medium 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS),  for at least 72 hrs to 70-80% confluence before seeding for starvation and DHT treatment.

extract_protocol: Total RNA extraction was performed using Trizol Reagent  (invitrogen) following manufacturer's instructions

treatment_protocol: LNCaP cell were seeded to 8x105 cell per 10cm dish and starved for 3 days in RPMI Medium 1640-no-phenol red (Gibco) and 5% chracoal stripped FVBS (CSFBS). Then LNCaP cells were treated with or without (vehicle, ETOH) 10nM of DHT for 30mins, 2h, 4h and 16h. Cells were then harvested for RNA extraction

value: 10 nM DHT (2h)


title: LNCAP treated with 10 nM DHT for 16h, biological rep1

description: DHT time-series gene expression

scan_protocol: As per standard Affymetrix protocol for the Human21.1ST arrays

value: 10 nM DHT (16h)


title: Ct-PHT62-VitD-0

description: total RNA


title: Ct-PHT58-VitD-100

description: total RNA


title: Ct-PHT54-VitD-100

description: total RNA


title: Ct-PHT56-VitD-0

description: total RNA


title: LNCAP treated with 10 nM DHT for 16h, biological rep2

description: DHT time-series gene expression


title: LNCAP treated with 10 nM DHT for 4h, biological rep1

description: DHT time-series gene expression

value: 10 nM DHT (4h)


title: LNCAP treated with 10 nM DHT for 4h, biological rep3

description: DHT time-series gene expression


title: LNCAP treated with 10 nM DHT for 2h, biological rep1

description: DHT time-series gene expression


title: LNCAP treated with 10 nM DHT for 2h, biological rep2

description: DHT time-series gene expression


title: Ct-PHT62-VitD-100

description: total RNA


title: Ct-PHT60-VitD-100

description: total RNA


title: LNCAP treated with 10 nM DHT for 4h, biological rep2

description: DHT time-series gene expression


title: LNCAP treated with 10 nM DHT for 16h, biological rep3

description: DHT time-series gene expression


title: Ct-PHT54-VitD-0

description: total RNA


title: LNCAP treated with ETOH (vehicle), biological rep3

description: DHT control gene expression

value: vehicle (ETOH)


title: Ct-PHT60-VitD-0

description: total RNA


title: LNCAP treated with ETOH (vehicle), biological rep2

description: DHT control gene expression


title: Ct-PHT57-VitD-100

description: total RNA


title: Ct-PHT57-VitD-0

description: total RNA


title: LNCAP treated with ETOH (vehicle), biological rep1

description: DHT control gene expression


title: Ct-PHT56-VitD-100

description: total RNA


title: park.mcgill.new.lcm 97_Tumor Stroma

city: Montreal

first: Morag

last: Park

state: Quebec

address: 1160 Ave. des Pins O.

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

description: Amplified RNA

hyb_protocol: Agilent Technologies SurePrint G3 Hmn GE 8x60K Microarrays (Cat#G4851A) were used for all experiments. RNA samples (300 ng) were subjected to fragmentation followed by 17 h hybridization, washing, and scanning (Agilent Technologies, model G2505C) according to the manufacturer’s protocol (manual ID #G4140-90050). Cy3-labeled samples were hybridized against Cy5-labeled Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA).

scan_protocol: Scanned on an Agilent G2505C scanner. Microarray data were feature extracted using Feature Extraction Software (v. 10.7.3.1) from Agilent with the default parameters.

data_processing: The R statistical framework with Bioconductor (R version 3.20; Bioconductor version 3.1) was used to load raw sample files and analyze the data. The limma package was used to normalize the data. Specifically, Loess normalization was applied to correct for dye bias and quantile normalization was used to normalize between arrays.

source_name: laser capture microdissected tissue, tumor stroma

label_protocol: For samples (ch1), 100 pg to 5 ng of total RNA was subjected to two rounds of T7 linear amplification using the Arcturus® RiboAmp® HS PLUS Kit (Catalog number: KIT0525) and labeled with Cy3 dye (Arcturus® Cy3 Turbo Labeling™ Kit Catalog number: KIT0609) according to the manufacturer’s protocol. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (NanoDrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

extract_protocol: Normal and tumor epithelium and stroma were separately microdissected from tissue samples using a PixCell IIe LCM system (Arcturus). All microdissections were performed within three hours of tissue staining. Total RNA was extracted from each population of microdissected cells using an Arcturus PicoPure RNA Isolation Kit (Cat# 12204-01).

treatment_protocol: Tissue compartments isolated from OCT-embedded frozen human tissue samples by laser capture microscopy following HistoGene staining and pathologist's evaluation.

tag: disease state

value: HER2+ breast cancer

tag: breast tissue compartment

value: Tumor stroma

source_name: Amplified Universal Human Reference RNA (Stratagene)

label_protocol: For reference (ch2), RNA was subjected to two rounds of T7 linear amplification using the Arcturus® RiboAmp® HS PLUS Kit (Catalog number: KIT0525) and labeled with Cy5 dye (Arcturus® Cy3 Turbo Labeling™ Kit Catalog number: KIT0610) according to the manufacturer’s protocol. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (NanoDrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

tag: sample type

value: Reference


title: park.mcgill.new.lcm 99_Tumor Stroma

description: Amplified RNA

extract_protocol: Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA).


title: park.mcgill.new.lcm 94_Tumor Epithelium

description: Amplified RNA

source_name: laser capture microdissected tissue, tumor epithelium

value: Tumor epithelium


title: park.mcgill.new.lcm 95_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 96_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 98_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 92_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 93_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 89_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 86_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 90_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 81_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 88_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 84_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 78_Normal Stroma

description: Amplified RNA

source_name: laser capture microdissected tissue, normal stroma

value: Breast cancer

value: Normal stroma


title: park.mcgill.new.lcm 87_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 85_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 91_Tumor Stroma

description: Amplified RNA


description:
Amplified RNA
Samples 'park.mcgill.new.lcm 76_Normal Epithelium_replicate1' and 'park.mcgill.new.lcm 76_Normal Epithelium_replicate2' were obtained from the same individual.

source_name: laser capture microdissected tissue, normal epithelium

value: Normal epithelium


title: park.mcgill.new.lcm 76_Normal Epithelium_replicate2


title: park.mcgill.new.lcm 80_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 83_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 77_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 73_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 71_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 74_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 72_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 79_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 70_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 68_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 65_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 69_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 82_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 67_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 75_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 64_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 66_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 62_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 54_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 53_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 52_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 51_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 61_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 55_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 59_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 58_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 56_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 60_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 63_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 57_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 49_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 40_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 44_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 45_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 47_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 41_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 43_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 48_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 39_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 46_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 36_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 38_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 50_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 35_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 42_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 34_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 37_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 32_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 26_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 245_Normal Stroma

description: Amplified RNA


description:
Amplified RNA
Samples 'park.mcgill.new.lcm 244_Normal Epithelium_replicate1' and 'park.mcgill.new.lcm 244_Normal Epithelium_replicate2' were obtained from the same individual.


title: park.mcgill.new.lcm 214_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 225_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 33_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 210_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 211_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 244_Normal Epithelium_replicate2


title: park.mcgill.new.lcm 215_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 17_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 161_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 140_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 27_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 224_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 226_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 16_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 125_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 119_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 164_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 137_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 138_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 113_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 112_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 132_Normal Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 136_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 124_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 120_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 111_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 110_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 108_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 109_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 107_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 106_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 227_Normal Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 105_Tumor Stroma

description: Amplified RNA


title: park.mcgill.new.lcm 102_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 101_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 103_Tumor Epithelium

description: Amplified RNA


title: park.mcgill.new.lcm 100_Tumor Epithelium

description: Amplified RNA


title: S20_H005

city: Tainan

first: Seonghoe

last: Jang

state: Tainan

address: No.59, Siraya Blvd. Xinshi Dist.

country: Taiwan

institute: Academia Sinica

description: Lamina joint region (collar) samples at 84 days old stage were harvested.

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4200AL scanner (635nm power 100 PMT 310 ) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

organism: Oryza sativa

source_name: pOsBUL1:OsBDG3 (#20)

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trisol solution (provided by Thermo Fisher Scientific). RNA purity was checked by optical density of NanoDrop ND-2000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

tag: cultivar

tag: genotype/variation

value: pOsBUL1:OsBDG3 (#20)

tag: tissue

value: lamina joint


title: S1_H002

description: Lamina joint region (collar) samples at 81 days old stage were harvested.

source_name: WT (TNG67)

value: WT


title: S20_H006

description: Lamina joint region (collar) samples at 85 days old stage were harvested.

source_name: pOsBUL1:OsBDG4 (#20)

value: pOsBUL1:OsBDG4 (#20)


title: S1_H001

description: Lamina joint region (collar) samples at 80 days old stage were harvested.


title: OsBUL1KO L11 [S4_H007]

description: Lamina joint region (collar) samples at heading stage were harvested.

value: Dongjin

value: Lamina joint


title: KO P11 [S2_H004]

description: Young panicle samples (less than 10 cm in length) were harvested.

value: panicle


title: OsBUL1KO L11 [S4_H008]


title: S13_H003

description: Lamina joint region (collar) samples at 82 days old stage were harvested.

source_name: pOsBUL1:OsBDG1 (#13)

value: pOsBUL1:OsBDG1 (#13)


title: park.mcgill.new.lcm 104_Tumor Stroma

description: Amplified RNA


title: WT L6 [S3_H006]

source_name: WT (Dongjin)


title: WT L6 [S3_H005]


title: WT P6 [S1_H002]


title: WT P6 [S1_H001]


title: KO P11 [S2_H003]


title: hCT1 - replicate 2

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

hyb_protocol: 300 ng of total RNA was amplified, labeled and hybridized to the array (Affymetrix Rat GeneChip 2.0ST)

scan_protocol: According to standard Affymetrix protocol using an Affymetrix GeneChip scanner 3000 7G.

data_processing: RMA xpression values were generated using Affymetrix Expression Console using default analysis settings

organism: Rattus norvegicus

source_name: hCT1 treated cells

label_protocol: Biotin labeling according to standard Affymetrix protocol.

growth_protocol: Serum-free medium supplemented with hypertrophic agonist.

extract_protocol: Total RNA was isolated (in triplicates) for hCT1 and Ctrl samples using TRIzol extraction and cleaned using the Rneasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Primary neonatal cardiomyocytes treated for 24 hours with hCT1 or control serum-free medium (Ctrl).

tag: strain

value: Sprague-Dawley

tag: tissue origin

value: cardiac muscle

value: primary cardiomyocytes


title: S13_H004

description: Lamina joint region (collar) samples at 83 days old stage were harvested.

source_name: pOsBUL1:OsBDG2 (#13)

value: pOsBUL1:OsBDG2 (#13)


title: hCT1 - replicate 3


title: gWAT_HFD_CD_HFD_rep5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from gWAT of mice treated with high fat diet treatment for 20 weeks, control diet for 7 weeks, high fat diet for 48h

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.4.1.46) including median polish and Sketch-Quantile normalisation

organism: Mus musculus

source_name: gWAT, high fat diet treatment for 20 weeks, control diet for 7 weeks, high fat diet for 48h

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)

growth_protocol: Animals were housed in a conventional animal facility at constant ambient temperature and humidity with a 12h light-dark cycle

extract_protocol: With Qiazol in combination with the RNeasy Kit (Qiagen), according to the manufacturer’s instruction

treatment_protocol: As described in the paper. Male C57BL6/J mice were purchased from Charles River (Germany) at the age of 7-8 weeks. All mice were maintained in a conventional animal facility at constant ambient temperature and humidity with a 12h light-dark cycle. After two weeks of acclimatization, mice were weighed and randomly assigned the high-fat diet (obese, n=24) or the control diet (lean=12) group or to the other groups. Mice of the obese group received a high-fat high-sucrose diet (Research Diets D 12331, 58% kcal from fat) for 20 weeks, while mice of the lean group were given the low-fat control diet (Research Diets D 12329, 10.5% kcal from fat) ad libitum. After 20 weeks of feeding, a group of HFD- fed mice was switched to the low-fat containing control diet ad libitum (formerly obese, n=12). All animal experiments were approved by the German Animal Welfare Act.

value: gonadal white adipose tissue

value: 35 weeks

tag: gender

value: male

tag: genotype

value: wild type


title: Control - replicate 3

source_name: Control treated cells


title: gWAT_HFD_CD_HFD_rep6

tag: age


title: hCT1 - replicate 1


title: Control - replicate 2


title: gWAT_HFD_CD_HFD_rep2


title: gWAT_CD_HFD_rep5

description: Gene expression data from gWAT of mice fed with control diet for 27 weeks followed by high fat diet treatment for 48h

source_name: gWAT, control diet for 27 weeks, high fat diet treatment for 48h


title: gWAT_CD_HFD_rep6


title: gWAT_HFD_CD_HFD_rep4


title: gWAT_obese_rep6

description: Gene expression data from gWAT of mice treated with high fat diet treatment for 27 weeks

source_name: gWAT, high fat diet treatment for 27 weeks


title: Control - replicate 1


title: gWAT_CD_HFD_rep2


title: gWAT_CD_HFD_rep3


title: gWAT_CD_HFD_rep4


title: gWAT_HFD_CD_HFD_rep1


title: gWAT_CD_HFD_rep1


title: gWAT_HFD_CD_HFD_rep3


title: gWAT_obese_rep1


title: gWAT_obese_rep3


title: C57Smoke [Sample108]

first: Jeong

middle: H

last: Yun

institute: BRIGHAM AND WOMEN'S HOSPITAL

description: C57Smoke [Sample108]

hyb_protocol: 750ng of total RNA for each sample was hybridized onto a Sentrix MouseRef-8 v2.0 Expression BeadChip Array (Illumina, San Diego, CA), based on the manufacturer's protocol.

scan_protocol: The BeadChip Array was scanned using an Illumina BeadArray Reader and quality control analysis was performed using Illumina GenomeStudio v3.1.3 software, Gene Expression Module version 1.1.1, and the statistical package R v3.3.1.

data_processing: Each of the samples and all probes passed quality control, and the data were background corrected, log2 transformed and quantile normalized.

source_name: mouse lung

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted from murine lung tissues using Allprep kit (Qiagen, Valencia, CA).

treatment_protocol: Mice were exposed to mixed main-stream and side-stream CS from 3R4F Kentucky Research cigarettes for 5 days/week for 6 months in Teague TE 10z chambers (TSP ~ 100-200 mg/m 3 and CO levels ~6 ppm).

value: Smoke


title: gWAT_obese_rep5


title: C57Smoke [Sample109]

description: C57Smoke [Sample109]


title: gWAT_obese_rep4


title: gWAT_lean_rep6

description: Gene expression data from gWAT of mice fed with control diet for 27 weeks

source_name: gWAT, control diet for 27 weeks


title: C57Air [Sample107]

description: C57Air [Sample107]

value: Air

value: NZWLacJ


title: gWAT_obese_rep2


title: gWAT_lean_rep1


title: gWAT_lean_rep5


title: HHIPHetSmoke [Sample106]

description: HHIPHetSmoke [Sample106]

value: HHIPHet


title: HHIPHetSmoke [Sample102]

description: HHIPHetSmoke [Sample102]


title: gWAT_formerly_obese_rep6

description: Gene expression data from gWAT of mice treated with high fat diet treatment for 20 weeks, followed by control diet for 7 weeks

source_name: gWAT, high fat diet treatment for 20 weeks, followed by control diet for 7 weeks


title: gWAT_lean_rep4


title: gWAT_lean_rep3


title: gWAT_formerly_obese_rep5


title: Liver_HFD_CD_HFD_rep6

description: Gene expression data from liver of mice treated with high fat diet treatment for 20 weeks, control diet for 7 weeks, high fat diet for 48h

source_name: Liver, high fat diet treatment for 20 weeks, control diet for 7 weeks, high fat diet for 48h

value: liver


title: HHIPHetSmoke [Sample103]

description: HHIPHetSmoke [Sample103]


title: gWAT_formerly_obese_rep3


title: gWAT_formerly_obese_rep2


title: C57Air [Sample104]

description: C57Air [Sample104]

value: WT


title: gWAT_formerly_obese_rep4


title: FAM13AKOSmoke [Sample101]

description: FAM13AKOSmoke [Sample101]


title: HHIPHetSmoke [Sample105]

description: HHIPHetSmoke [Sample105]


title: gWAT_lean_rep2


title: C57Smoke [Sample099]

description: C57Smoke [Sample099]


title: C57Smoke [Sample100]

description: C57Smoke [Sample100]


title: gWAT_formerly_obese_rep1


title: Liver_HFD_CD_HFD_rep5


title: C57Air [Sample098]

description: C57Air [Sample098]


title: Liver_HFD_CD_HFD_rep1


title: Liver_HFD_CD_HFD_rep4


title: Liver_HFD_CD_HFD_rep3


title: Liver_HFD_CD_HFD_rep2


title: HHIPHetSmoke [Sample097]

description: HHIPHetSmoke [Sample097]


title: Liver_CD_HFD_rep6

description: Gene expression data from liver of mice fed with control diet for 27 weeks followed by high fat diet treatment for 48h

source_name: Liver, control diet for 27 weeks, high fat diet treatment for 48h


title: Liver_CD_HFD_rep5


title: Liver_CD_HFD_rep4


title: C57Air [Sample094]

description: C57Air [Sample094]


title: Liver_obese_rep5

description: Gene expression data from liver of mice treated with high fat diet treatment for 27 weeks

source_name: Liver, high fat diet treatment for 27 weeks


title: Liver_CD_HFD_rep1


title: C57Air [Sample096]

description: C57Air [Sample096]


title: Liver_CD_HFD_rep3


title: C57Smoke [Sample095]

description: C57Smoke [Sample095]


title: Liver_CD_HFD_rep2


title: C57Smoke [Sample093]

description: C57Smoke [Sample093]


title: Liver_lean_rep4

description: Gene expression data from liver of mice fed with control diet for 27 weeks

source_name: Liver, control diet for 27 weeks


title: Liver_obese_rep3


title: FAM13AKOSmoke [Sample091]

description: FAM13AKOSmoke [Sample091]


title: Liver_obese_rep1


title: C57Smoke [Sample089]

description: C57Smoke [Sample089]


title: C57Air [Sample090]

description: C57Air [Sample090]


title: Liver_lean_rep2


title: Liver_lean_rep6


title: Liver_lean_rep1


title: C57Air [Sample092]

description: C57Air [Sample092]


title: Liver_formerly_obese_rep6

description: Gene expression data from liver of mice treated with high fat diet treatment for 20 weeks, followed by control diet for 7 weeks

source_name: Liver, high fat diet treatment for 20 weeks, followed by control diet for 7 weeks


title: C57Air [Sample088]

description: C57Air [Sample088]


title: Liver_formerly_obese_rep5


title: Liver_lean_rep5


title: Liver_lean_rep3


title: Liver_obese_rep2


title: Liver_obese_rep4


title: C57Air [Sample087]

description: C57Air [Sample087]


title: Liver_formerly_obese_rep4


title: Liver_formerly_obese_rep3


title: FAM13AKOSmoke [Sample086]

description: FAM13AKOSmoke [Sample086]


title: Liver_formerly_obese_rep2


title: C57Air [Sample082]

description: C57Air [Sample082]


title: C57Air [Sample085]

description: C57Air [Sample085]


title: C57Air [Sample081]

description: C57Air [Sample081]


title: C57Smoke [Sample084]

description: C57Smoke [Sample084]


title: FAM13AKOSmoke [Sample080]

description: FAM13AKOSmoke [Sample080]


title: Liver_formerly_obese_rep1


title: Liver_obese_rep6


title: HHIPHetSmoke [Sample083]

description: HHIPHetSmoke [Sample083]


title: C57Air [Sample076]

description: C57Air [Sample076]


title: FAM13AKOSmoke [Sample075]

description: FAM13AKOSmoke [Sample075]


title: C57Smoke [Sample079]

description: C57Smoke [Sample079]


title: C57Air [Sample074]

description: C57Air [Sample074]


title: C57Air [Sample078]

description: C57Air [Sample078]


title: C57Smoke [Sample077]

description: C57Smoke [Sample077]


title: C57Air [Sample073]

description: C57Air [Sample073]


title: C57Air [Sample070]

description: C57Air [Sample070]


title: C57Smoke [Sample072]

description: C57Smoke [Sample072]


title: C57Air [Sample071]

description: C57Air [Sample071]


title: C57Smoke [Sample069]

description: C57Smoke [Sample069]


title: HHIPHetAir [Sample064]

description: HHIPHetAir [Sample064]


title: C57Air [Sample067]

description: C57Air [Sample067]


title: C57Smoke [Sample063]

description: C57Smoke [Sample063]


title: HHIPHetSmoke [Sample065]

description: HHIPHetSmoke [Sample065]


title: C57Smoke [Sample066]

description: C57Smoke [Sample066]


title: C57Smoke [Sample061]

description: C57Smoke [Sample061]


title: C57Air [Sample058]

description: C57Air [Sample058]


title: HHIPHetAir [Sample059]

description: HHIPHetAir [Sample059]


title: HHIPHetSmoke [Sample057]

description: HHIPHetSmoke [Sample057]


title: FAM13AKOSmoke [Sample062]

description: FAM13AKOSmoke [Sample062]


title: C57Air [Sample050]

description: C57Air [Sample050]


title: HHIPHetSmoke [Sample053]

description: HHIPHetSmoke [Sample053]


title: FAM13AKOAir [Sample055]

description: FAM13AKOAir [Sample055]


title: HHIPHetAir [Sample054]

description: HHIPHetAir [Sample054]


title: C57Smoke [Sample068]

description: C57Smoke [Sample068]


title: HHIPHetAir [Sample049]

description: HHIPHetAir [Sample049]


title: HHIPHetSmoke [Sample047]

description: HHIPHetSmoke [Sample047]


title: C57Smoke [Sample048]

description: C57Smoke [Sample048]


title: FAM13AKOSmoke [Sample045]

description: FAM13AKOSmoke [Sample045]


title: C57Smoke [Sample046]

description: C57Smoke [Sample046]


title: C57Air [Sample052]

description: C57Air [Sample052]


title: C57Smoke [Sample060]

description: C57Smoke [Sample060]


title: HHIPHetAir [Sample042]

description: HHIPHetAir [Sample042]


title: C57Smoke [Sample043]

description: C57Smoke [Sample043]


title: FAM13AKOSmoke [Sample051]

description: FAM13AKOSmoke [Sample051]


title: FAM13AKOSmoke [Sample044]

description: FAM13AKOSmoke [Sample044]


title: C57Smoke [Sample039]

description: C57Smoke [Sample039]


title: C57Smoke [Sample040]

description: C57Smoke [Sample040]


title: C57Air [Sample036]

description: C57Air [Sample036]


title: C57Smoke [Sample037]

description: C57Smoke [Sample037]


title: C57Air [Sample041]

description: C57Air [Sample041]


title: HHIPHetAir [Sample034]

description: HHIPHetAir [Sample034]


title: C57Smoke [Sample038]

description: C57Smoke [Sample038]


title: FAM13AKOAir [Sample033]

description: FAM13AKOAir [Sample033]


title: HHIPHetAir [Sample032]

description: HHIPHetAir [Sample032]


title: FAM13AKOSmoke [Sample029]

description: FAM13AKOSmoke [Sample029]


title: C57Smoke [Sample028]

description: C57Smoke [Sample028]


title: C57Air [Sample031]

description: C57Air [Sample031]


title: FAM13AKOSmoke [Sample025]

description: FAM13AKOSmoke [Sample025]


title: C57Smoke [Sample035]

description: C57Smoke [Sample035]


title: C57Air [Sample024]

description: C57Air [Sample024]


title: HHIPHetSmoke [Sample030]

description: HHIPHetSmoke [Sample030]


title: C57Air [Sample022]

description: C57Air [Sample022]


title: HHIPHetAir [Sample027]

description: HHIPHetAir [Sample027]


title: HHIPHetAir [Sample023]

description: HHIPHetAir [Sample023]


title: HHIPHetAir [Sample020]

description: HHIPHetAir [Sample020]


title: HHIPHetAir [Sample026]

description: HHIPHetAir [Sample026]


title: FAM13AKOAir [Sample019]

description: FAM13AKOAir [Sample019]


title: FAM13AKOSmoke [Sample011]

description: FAM13AKOSmoke [Sample011]


title: C57Smoke [Sample008]

description: C57Smoke [Sample008]


title: HHIPHetSmoke [Sample018]

description: HHIPHetSmoke [Sample018]


title: FAM13AKOAir [Sample010]

description: FAM13AKOAir [Sample010]


title: C57Smoke [Sample009]

description: C57Smoke [Sample009]


title: FAM13AKOSmoke [Sample014]

description: FAM13AKOSmoke [Sample014]


title: HHIPHetSmoke [Sample013]

description: HHIPHetSmoke [Sample013]


title: C57Smoke [Sample016]

description: C57Smoke [Sample016]


title: C57Air [Sample017]

description: C57Air [Sample017]


title: C57Smoke [Sample015]

description: C57Smoke [Sample015]


title: C57Smoke [Sample021]

description: C57Smoke [Sample021]


title: FAM13AKOAir [Sample006]

description: FAM13AKOAir [Sample006]


title: C57Smoke [Sample012]

description: C57Smoke [Sample012]


title: C57Smoke [Sample005]

description: C57Smoke [Sample005]


title: MI Day14

city: Miami

first: Eliana

middle: C

last: Martinez

state: FL

address: 1501 N.W. 10th Avenue. BRB 803

institute: University of Miami Miller School of Medicine

description: Total RNA (500ng) was 3′-end–labeled with Hy3 dye and hybridized on miRCURY LNA™ Arrays

hyb_protocol: Samples were then hybridized on miRCURY LNATM Arrays using MAUI® hybridization system

scan_protocol: The microarray chips were then washed and scanned using InnoScan700, microarray scanner (Innopsys, Carbonne, France) and analysed on Mapix® Ver4.5 software (Innopsys, Carbonne, France).

data_processing: Background-subtracted median signal intensities were normalized using software GeneSpring gx v.13 with quantile normalization. Fold change analysis was performed using the same software. Unpaired ttest was performed using the raw signals to eliminate those miRNAs that were not significant between 2 groups. miRNAs with raw signal intensity >300 at least in 1 group were further selected. The final differentially expressed miRNAs were selected based an absolute fold change ≥ 1.2 and ≤ -1.2.

label: Hy 3

source_name: rat heart tissue

label_protocol: Total RNA (1 µg for Day 2 and 500ng for D14) was 3′-end–labeled with Hy3 dye using the miRCURY LNATM Power Labeling Kit (Exiqon, Denmark)

extract_protocol: Frozen heart tissues were grounded into powder under liquid nitrogen and lysed by TRIZOL reagent (Invitrogen, Life Technologies Inc., Frederick, MA, USA). Total RNA + miRNAs was extracted according to manufacturer’s protocol, followed by treatment with Dnase I (Rnase-free 2U/µL, Life Technologies Inc., Carlsbad, CA, US).

treatment_protocol: Rats in Sham Day 2 group underwent lateral thoracotomy and percardiotomy. Hearts were harvested 2 days post surgery

value: Wistar

tag: treament

value: Rat undergone lateral thoracotomy and pericardiactomy and LAD ligation


title: FAM13AKOAir [Sample004]

description: FAM13AKOAir [Sample004]


title: C57Air [Sample001]

description: C57Air [Sample001]


title: HHIPHetAir [Sample007]

description: HHIPHetAir [Sample007]


title: MI Day2

description: Total RNA (1 µg) was 3′-end–labeled with Hy3 dye and hybridized on miRCURY LNA™ Arrays

tag: Sex


title: Sham Day14

value: Rat undergone lateral thoracotomy and pericardiactomy


title: IMR90Ras10h

city: Philadelphia

first: Lin

last: Zhang

state: Pennsylvania

address: 421 Curie Blvd

institute: University of Pennsylvania

hyb_protocol: Hhybridization was performed by the Molecular Profiling Facility according to manufacturer’s instruction.

scan_protocol: Scan was performed by the Molecular Profiling Facility using Agilent Technologies Scanner G2505C US23502332

data_processing: The normalized microarray data were managed and analyzed by GeneSpring (Agilent), microarray software  suite 4.

source_name: IMR90 Cell Line

label_protocol: Labeling was performed by the Molecular Profiling   Facility according to manufacturer’s instruction.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) and reverse-transcribed to cDNA using random primers.

treatment_protocol: KRASG12D- expressing or control lentiviruses were used to infect IMR90 cells, and total  RNAs were harvested from cells at different time points (0, 4, 7, and 10 days for KRas cells and 0, 7, and  10 days for control cells).

tag: cell line

tag: infection

value: KRASG12D- expressing lentiviruses for 10h


title: IMR90Ras4h

value: KRASG12D- expressing lentiviruses for 4h


title: IMR90Ras7h

value: KRASG12D- expressing lentiviruses for 7h


title: DOHH2_BAY1238097_4H

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalised using quantile method

source_name: DOHH2 cell lines treated 4hrs with BAY 1238097

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: in vitro

extract_protocol: RNA extraction was performed using a commercially available kit (RNeasy, Qiagen, Frederick,MD) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyzer).

treatment_protocol: treatment with BAY 1238097, a novel BET Bromodomain inhibitor

tag: cell line type

tag: time point


title: C57Smoke [Sample003]

description: C57Smoke [Sample003]

tag: treatment


title: DOHH2_BAY1238097_24H

source_name: DOHH2 cell lines treated 24hrs with BAY 1238097


title: DOHH2_DMSO _24H

source_name: DOHH2 cell lines treated 24hrs with DMSO

value: DMSO


title: IMR90Ctrl10h

value: control lentiviruses for 10h


title: DOHH2_BAY1238097_12H

source_name: DOHH2 cell lines treated 12hrs with BAY 1238097


title: DOHH2_BAY1238097_8H

source_name: DOHH2 cell lines treated 8hrs with BAY 1238097


title: IMR90Ctrl7h

value: control lentiviruses for 7h


title: DOHH2_DMSO_12H

source_name: DOHH2 cell lines treated 12hrs with DMSO


title: IMR90Ctrl0h

value: control lentiviruses for 0h


title: Sham Day2

value: male


title: C57Air [Sample002]

description: C57Air [Sample002]


title: Gr. 6 = ZR75 WT Tamoxifen 2

status: Public on Sep 04 2017

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Gr. 6 = ZR75 WT Tamoxifen

hyb_protocol: Standard Affymetix protocol for 3' IVT design

scan_protocol: Scanner GCS3000 7G

data_processing: The data were analyzed with  Partek and BRB Array Tools software, RMA method for expression estimation

source_name: Breast cancer cell line

label_protocol: 3' IVT express

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

treatment_protocol: breast cancer cell lines

tag: wt or y537s

value: Tamoxifen


title: Gr. 7 = ZR75 Y537S Control 1

description: Gr. 7 = ZR75 Y537S Control

value: Control


title: Gr. 8 = ZR75 Y537S Tamoxifen 1

description: Gr. 8 = ZR75 Y537S Tamoxifen


title: Gr. 7 = ZR75 Y537S Control 2

description: Gr. 7 = ZR75 Y537S Control


title: Gr. 8 = ZR75 Y537S Tamoxifen 2

description: Gr. 8 = ZR75 Y537S Tamoxifen


title: Gr. 5 = ZR75 WT Control 1

description: Gr. 5 = ZR75 WT Control


title: DOHH2_DMSO_4H

source_name: DOHH2 cell lines treated 4hrs with DMSO


title: Gr. 4 = MCF7C Y537S Tamoxifen 3

description: Gr. 4 = MCF7C Y537S Tamoxifen


title: DOHH2_DMSO_8H

source_name: DOHH2 cell lines treated 8hrs with DMSO


title: Gr. 6 = ZR75 WT Tamoxifen 1

description: Gr. 6 = ZR75 WT Tamoxifen


title: Gr. 4 = MCF7C Y537S Tamoxifen 2

description: Gr. 4 = MCF7C Y537S Tamoxifen


title: Gr. 5 = ZR75 WT Control 2

description: Gr. 5 = ZR75 WT Control


title: Gr. 8 = ZR75 Y537S Tamoxifen 3

description: Gr. 8 = ZR75 Y537S Tamoxifen


title: Gr. 6 = ZR75 WT Tamoxifen 3

description: Gr. 6 = ZR75 WT Tamoxifen


title: siP300_HPM_T48 diff

city: Toulouse

first: Laurence

last: Vandel

address: 118 ROute de Narbonne

department: CBD

country: France

institute: CNRS

hyb_protocol: Following fragmentation and end-labeling, 3 μg of cDNAs were hybridized for 16 h at 45oC on GeneChip® Human Gene 2.0 ST arrays (Affymetrix)

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm

data_processing:
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.
CEL files were further processed with Affymetrix Expression Console software version 1.3.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default setings

source_name: HPM transfected with sip300 at time 48h

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit and the Affymetrix GeneChip® WT Terminal Labeling Kit according to Affymetrix recommendations

growth_protocol: myoblasts were plated in Petri dishes and cultured in growth medium containing Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 20% fetal bovine serum (GE Healthcare, PAA) 1% Ultroser G serum substitute (PALL life sciences) and 50μg/ml Gentamicin (Thermo Scientific) at 37°C in humidified atmosphere with 5% CO2. All experiments were carried out between P4 and P8 to avoid cell senescence. Myogenic differentiation of confluent cells was induced by changing growth medium to DMEM containing 2% FBS and 50μg/ml Gentamicin (differentiation medium).

extract_protocol: Total RNAs were extracted from cells using Aurum Total RNA Mini Kit (Bio-rad) according to manufacturer’s instructions

treatment_protocol: Human Primary Myoblasts (HPM) were grown to confluence, transfectedor not  with siRNA (either control, or CBP or CBP or CBP+p300) and induced 24h later for differentiation by decreasing serum concentration.

tag: time

value: 48h of differentiation

tag: cell type

value: Primary myoblasts

tag: patient id


title: siP300_HPM_T24 diff

source_name: HPM transfected with sip300 at time 24h

value: 24h of differentiation


title: Gr. 3 = MCF7C Y537S Control 2

description: Gr. 3 = MCF7C Y537S Control


title: Gr. 3 = MCF7C Y537S Control 3

description: Gr. 3 = MCF7C Y537S Control


title: siCTR_HPM_96 diff

source_name: HPM transfected with siCTR at time 96h

value: 96h of differentiation


title: Gr. 7 = ZR75 Y537S Control 3

description: Gr. 7 = ZR75 Y537S Control


title: Gr. 3 = MCF7C Y537S Control 1

description: Gr. 3 = MCF7C Y537S Control


title: siP300_HPM_T72 diff

source_name: HPM transfected with sip300 at time 72h

value: 72h of differentiation


title: Gr. 4 = MCF7C Y537S Tamoxifen 1

description: Gr. 4 = MCF7C Y537S Tamoxifen


title: Gr. 2 = MCF7C WT Tamoxifen 2

description: Gr. 2 = MCF7C WT Tamoxifen

value: WT


title: siP300_HPM_T96 diff

source_name: HPM transfected with sip300 at time 96h


title: HHIPHetSmoke [Sample056]

description: HHIPHetSmoke [Sample056]

source_name: mouse lung

value: HHIPHet

value: Smoke


title: siCTR_HPM_48 diff

source_name: HPM transfected with siCBP at time 48h


title: siCTR_HPM_72 diff

source_name: HPM transfected with siCTR at time 72h


title: Gr. 1 = MCF7C WT Control 3

description: Gr. 1 = MCF7C WT Control


title: Gr. 2 = MCF7C WT Tamoxifen 1

description: Gr. 2 = MCF7C WT Tamoxifen


title: Gr. 2 = MCF7C WT Tamoxifen 3

description: Gr. 2 = MCF7C WT Tamoxifen


title: Gr. 1 = MCF7C WT Control 2

description: Gr. 1 = MCF7C WT Control


title: Gr. 1 = MCF7C WT Control 1

description: Gr. 1 = MCF7C WT Control


title: siCBPsip300_HPM_T48 diff

source_name: HPM transfected with siCBP+sip300 at time 48h


title: siCTR_HPM_T24 diff

source_name: HPM transfected with siCTR at time 24h


title: S DI Sheep TTSS (rep 4)

city: Dublin 4

first: Marion

middle: Teresa

last: Ryan

address: Belfield

department: Veterinary Sciences

country: Ireland

institute: University College Dublin

hyb_protocol: The fragmented and labeled cDNA was added to the hybridisation cocktail in accordance with the NuGEN guidelines.  Following hybridisation for 18 hr at 45°C, the array was washed and stained on the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA), inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: The microarrays were processed using a custom pipeline written in R using bioconductor libraries. The arrays were read in using functions from simpleaffy, pre-processed and normalised using the RMA algorithm.

source_name: Caco 2 cells

label_protocol: Five μg of the amplified single-stranded cDNA was fragmented and labeled using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos, CA) in accordance with manufacturers guidelines.  The enzymatically and chemically fragmented products (50–100nt) were labeled via the attachment of biotinylated nucleotides onto the 3' end of the fragmented cDNA.

growth_protocol: Caco-2 Cell Lines: Human Caco-2 cell lines (HPACC 86010202) were used as a model for the distal ileum epithelium. Monolayers were cultured (passage 50-55) according to Health Protection Agency Culture Collection recommendations in Greiner 6-well plates and Corning HTS transwell 24-well plates (6.5mm diameter, 0.04µm pore).

extract_protocol: Total RNA was extracted using Trizol® reagent (Sigma-Aldrich Corp., St. Louis, MO, USA) and Tissue Lyzer ™ (Qiagen, Hilden, Germany) according to the manufacturer's protocols. The extracted RNA was treated with DNase I (Qiagen, Hilden, Germany) at room temperature for 10 min to remove genomic DNA. Total RNA was quantified and assessed for purity on a NanoDrop™ 1000  Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and samples with a 260/280 ratio ≥ 2.0 were considered suitable for cDNA synthesis. Total RNA integrity number (RIN) was assessed on the Agilent 2100 Bioanalyser version A.02.12 (Agilent Technologies Inc., CA, USA) using an RNA 6000 Nano LabChip kit (Caliper Technologies Corp. MA, USA).

treatment_protocol: Caco-2 cells were challenged for 8 different time points (10mins, 20mins, 30mins, 1hr, 2hrs, 4hrs, 8hrs). Sterile serum-free-media (SFM) acted as a control. For time points above 20 minutes, wells were washed with phosphate-buffered saline (PBS) and SFM was added for the remaining incubation period.

tag: group

value: TTSS-Human


title: siCBP_HPM_T24 diff

source_name: HPM transfected with siCBP at time 24h


title: siCBPsip300_HPM_T96 diff

source_name: HPM transfected with siCBP+sip300 at time 96h


title: S DI Sheep TTSS (rep 1)

scan_protocol: Following hybridisation for 18 hr at 45°C, the array was washed and stained on the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA), inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).


title: CO28 TTSS -ve human (rep 4)


title: siCBP_HPM_T72 diff

source_name: HPM transfected with siCBP at time 72h


title: siCBPsip300_HPM_T72 diff

source_name: HPM transfected with siCBP+sip300 at time 72h


title: siCBP_HPM_T48 diff


title: siCBPsip300_HPM_T24 diff

source_name: HPM transfected with siCBP+sip300 at time 24h


title: Mock_HPM_T96h diff

source_name: non transfected HPM at time 96h


title: S DI Sheep TTSS (rep 2)


title: Mock_HPM_T72h diff

source_name: non transfected HPM at time 72h


title: CO28 TTSS -ve human (rep 2)


title: siCBP_HPM_T96 diff

source_name: HPM transfected with siCBP at time 96h


title: S DI Sheep TTSS (rep 3)


title: CO28 TTSS -ve human (rep 1)


title: FFA Case [B455]

city: London

first: John

middle: Alexander

last: McGrath

address: Great Maze Pond

department: St John's Institute of Dermatology

country: United Kingdom

institute: King's College London

description:
plasma
B455

data_processing: The miRNA PCR Array Data Analysis Web Portal( http://www.qiagen.com/de/shop/genes-and-pathways/data-analysis-center-overview-page/ ) used for the analysis. miScript PCR Controls are primers designed to quantify a panel of 5 snoRNAs (SNORD61, SNORD68, SNORD72, SNORD95, and SNORD96A) and the snRNA RNU6B (RNU6-2). Normalization was done using global Ct mean. miScript PCR Controls serve as normalization controls for relative quantification using the miScript PCR System.

source_name: peripheral blood

extract_protocol: Plasma was isolated by centrifuging blood at 2,000g for 20 minutes at 4oC and stored at -80oC until analysis. MicroRNAs were isolated using Qiagen miRNeasy Serum/Plasma Kit, according to the manufacturer’s protocol.

tag: tissue

value: peripheral blood

tag: tissue compartment

value: plasma

tag: diagnosis

value: FFA


title: FFA Case [B454]

description:
plasma
B454


title: CO28 TTSS -ve human (rep 3)


title: Mock_HPM_T24h diff

source_name: non transfected HPM at time 24h


title: P DI Porcine (rep 2)

value: Porcine


title: FFA Case [B451]

description:
plasma
B451


title: FFA Case [B450]

description:
plasma
B450


title: P DI Porcine (rep 4)


title: Mock_HPM T0

source_name: non transfected HPMat time 0

value: time 0 of differentiation


title: FFA Case [B417]

description:
plasma
B417


title: Mock_HPM_T48h diff

source_name: non transfected HPM at time 48h


title: FFA Case [B409]

description:
plasma
B409


title: P DI Porcine (rep 3)


title: FFA Case [B416]

description:
plasma
B416


title: FFA Case [B430]

description:
plasma
B430


title: Control [B804]

description:
plasma
B804

value: healthy


title: FFA Case [B401]

description:
plasma
B401


title: S DI Sheep (rep 4)

value: Ovine


title: FFA Case [B429]

description:
plasma
B429


title: P DI Porcine (rep 1)


title: Control [B700]

description:
plasma
B700


title: S DI Sheep (rep 3)


title: S DI Sheep (rep 2)


title: Control [B698]

description:
plasma
B698


title: S DI Sheep (rep 1)


title: JIB Inter Ref (rep 3)

value: International Reference


title: Control [B677]

description:
plasma
B677


title: C0 DI Human (rep 4)

value: Human


title: C0 DI Human (rep 3)


title: JIB Inter Ref (rep 1)


title: JIB Inter Ref (rep 2)


title: JIB Inter Ref (rep 4)


title: C0 DI Human (rep 1)


title: Control [B701]

description:
plasma
B701


title: Control [B605]

description:
plasma
B605


title: Neg Control (rep 4)

value: Control


title: Control [B606]

description:
plasma
B606


title: Control [B582]

description:
plasma
B582


title: C0 DI Human (rep 2)


title: Control [B563]

description:
plasma
B563


title: Day 0 16_1

city: Bergisch Gladbach

first: Jutta

last: Kollet

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyibiotec GmbH

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: purified human natural killer cells

label_protocol: 10 ng total RNA  was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was isolated using the NucleoSpin® RNA kit (Macherey-Nagel)

treatment_protocol: Freshly isolated NK cells on day 0 were directly resuspended in RA1 buffer from the NucleoSpin® RNA kit (Macherey-Nagel) and stored at -20°C until use. Proliferating (dim) and Non-proliferating (bright) NK cells from 5-day cultures with autologous feeder cells were re-isolated from co-cultures, and sorted using a FACSAria III cytometer (BD Bioscience) according to their CD3negative/CD56+ phenotype and the brightness of a cell trace dye (dim or bright). Sorted samples were immediatley resuspended in RA1 and stored at -20°C until use.

value: peripheral blood buffy coats

tag: Stage

tag: donor


title: Neg Control (rep 3)


title: B DI Bovine (rep 4)

value: Bovine


title: Neg Control (rep 2)


title: Neg Control (rep 1)


title: DIM 67

source_name: 5-days cultured NK cells with high number of cell divisions completed

value: non proliferating after 5 days

value: NP


title: Control [B554]

description:
plasma
B554


title: DIM 16

source_name: 5-days cultured NK cells with low number of cell divisions completed

value: proliferating after 5 days

value: P


title: Day 0 10_1


title: BRIGHT 67


title: Day 0 67_1


title: BRIGHT 16


title: BRIGHT 10


title: DIM 10


title: BRIGHT 71


title: DIM 71


title: B DI Bovine (rep 1)


title: BRIGHT 72


title: Day 0 71_1


title: DIM 72


title: B DI Bovine (rep 3)


title: Day 0 72_2


title: Control Group, CC3

status: Public on Sep 03 2017

city: Ribeirão Preto

first: Marcela

middle: Augusta de Souza

last: Pinhel

state: Sao Paulo

address: Avenida dos Bandeirantes, 3900

department: Internal Medicine

country: Brazil

institute: University of Sao Paulo

description:
SAMPLE 35
3999874062_K
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using average normalisation with GenomeStudio.

label: Biotin

source_name: peripheral blood mononuclear cells, control

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-g Biotin a-RNA Labeling kit from Epicentre na Illumina company.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser and only samples with RNA integrity number (RIN) greater than 7.0 were included in this protocol.

treatment_protocol: All patients underwent Roux-en-Y gastric bypass for the same team of surgeons and collection of biological material (peripheral blood) was held the day before the surgery. Exactly six months after surgery, the patients returned to the hospital and underwent new collection of peripheral blood. The control group of patients had normal weight and they were subjected only a period of collection of peripheral blood.

value: peripheral blood mononuclear cells

tag: disease state

value: normal weight

tag: gender

value: female

tag: age

tag: body mass index (bmi)

tag: identification


title: Control Group, C17

description:
SAMPLE 33
3999874062_I
Replicate 1


title: Control Group, CC2

description:
SAMPLE 34
3999874062_J
Replicate 1


title: Control Group, C3

description:
SAMPLE 27
3999874062_C
Replicate 1


title: Postoperative Period, PP41

description:
SAMPLE 25
3999874062_A
Replicate 1

source_name: peripheral blood mononuclear cells, postoperative period

value: Roux-en-Y gastric bypass

tag: time point

value: 6 months post-surgery


title: Control Group, C12

description:
SAMPLE 31
3999874062_G
Replicate 1

tag: treatment


title: Postoperative Period, PP42

description:
SAMPLE 26
3999874062_B
Replicate 1


title: Postoperative Period, PP40

description:
SAMPLE 24
3999305025_L
Replicate 1


title: Control Group, C13

description:
SAMPLE 32
3999874062_H
Replicate 1


title: Control Group, C7

description:
SAMPLE 29
3999874062_E
Replicate 1


title: Control Group, C9B

description:
SAMPLE 30
3999874062_F
Replicate 1


title: Control Group, C5

description:
SAMPLE 28
3999874062_D
Replicate 1


title: B DI Bovine (rep 2)

source_name: Caco 2 cells


title: Postoperative Period, PP28

description:
SAMPLE 19
3999305025_G
Replicate 1


title: Postoperative Period, PP29

description:
SAMPLE 20
3999305025_H
Replicate 1


title: Postoperative Period, PP31

description:
SAMPLE 22
3999305025_J
Replicate 1


title: Preoperative Period, P30

description:
SAMPLE 8
3999874075_H
Replicate 1

source_name: peripheral blood mononuclear cells, preoperative period

value: obese


title: Postoperative Period, PP9

description:
SAMPLE 14
3999305025_B
Replicate 1


title: Postoperative Period, PP30

description:
SAMPLE 21
3999305025_I
Replicate 1


title: Postoperative Period, PP25

description:
SAMPLE 18
3999305025_F
Replicate 1


title: Preoperative Period, P42

description:
SAMPLE 13
3999305025_A
Replicate 1


title: Postoperative Period, PP11

description:
SAMPLE 15
3999305025_C
Replicate 1


title: Postoperative Period, PP16

description:
SAMPLE 17
3999305025_E
Replicate 1


title: Postoperative Period, PP12

description:
SAMPLE 16
3999305025_D
Replicate 1


title: r5-6_RA_Hoxa5_2

status: Public on Sep 02 2017

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

description:
HoxA5_N/C_Fw_AGT
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGTAAGGATCGAAATAGCTCATG
Raw data files for this sample are available on GSM1868848.

library_source: genomic

data_processing:
Library strategy: 4C-seq
HCS 2.2.58 was used with default parameters for base calling.
bcl2fastq 1.8.4 (Illumina) was used to generate fastq files
Raw sequence reads were pre-processed by removing the 4C-primer sequence from the 5'-end, and truncated reads were split by sample using the barcode contained in the 4C-primer sequence. Reads whose barcode sequence did not match exactly to a single expected barcode were discarded.
Truncated reads were aligned to the genome using QuasR (Gaidatzis et al., Bioinformatics 2015) with bowtie (Langmead et al., Genome Biology 2009) and default settings (only report uniquely mapped reads)
4C-Fragment coordinates were obtained by "in silico" digestion of the reference genome and the number of alignments per sample and fragment was counted using QuasR. The normalized number of alignments per fragment was obtained by dividing through the total number of alignments on the cis-chromosome (the chromosome containing the viewpoint) and multiplying with one million.
Genome_build: All analyses are based on the mm10 Mus musculus genome assembly obtained from UCSC, corresponding to the Dec. 2011 Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)
Supplementary_files_format_and_content: Fragment coordinates and normalized alignment counts were exported in BedGraph format (http://genome.ucsc.edu/goldenpath/help/bedgraph.html).

molecule: genomic DNA

source_name: rhombomers 5 & 6

extract_protocol: 4C template was prepared as described in (van de Werken et al., 2012) with modifications. Briefly, cells were dissociated (30’ @ 37°C in 0.25% trypsin; 1mg/ml collagenase type II; 5mM EDTA). Cells were fixed using 2% formaldehyde/10%FCS/PBS for 10’ at RT. Cells were lysed for 10’ on ice (50mM Tris-HCl pH 7.5, 150mM NaCl, 5mM EDTA, 0.5% NP40 substitute, 1% Triton-X100, 1X proteinase inhibitors). Chromatin was digested in the context of the nucleus using the restriction enzymes NlaIII, followed by ligation. Ligated chromatin was de-crosslinked in the presence of proteinase K at 65°C O/N and subsequently treated with RNase A. Genomic DNA was extracted by beads purification and subsequently digested O/N using the restriction enzymes Csp6I and ligated under diluted conditions (16°C, O/N) favoring intra-molecular ligations. Genomic DNA was cleaned up using bead purification. The 4C PCR was performed as described in (van de Werken et al., 2012) using the primers indicated for each sample in 'description' field and on the series record.

tag: strain

value: rhombomers 5 & 6

tag: developmental stage


title: r8_WT_Hoxa5_2

description:
HoxA5_N/C_Fw_TCA
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTTCAAAGGATCGAAATAGCTCATG
Raw data files for this sample are available on GSM1868848.

source_name: rhombomer 8

value: rhombomer 8


title: Preoperative Period, P29

description:
SAMPLE 7
3999874075_G
Replicate 1

tag: cell type


title: Postoperative Period, PP32

description:
SAMPLE 23
3999305025_K
Replicate 1


title: Preoperative Period, P31

description:
SAMPLE 9
3999874075_I
Replicate 1


title: Preoperative Period, P41

description:
SAMPLE 12
3999874075_L
Replicate 1


title: Preoperative Period, P32

description:
SAMPLE 10
3999874075_J
Replicate 1


title: Preoperative Period, P28

description:
SAMPLE 6
3999874075_F
Replicate 1


title: Preoperative Period, P11

description:
SAMPLE 2
3999874075_B
Replicate 1


title: Preoperative Period, P12

description:
SAMPLE 3
3999874075_C
Replicate 1


title: PBZ_T0-2

city: shanghai

first: Benke

last: Kuai

state: shanghai

department: Insititute of plant biology

country: China

institute: fudan university

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C,60 rpm on GeneChip Drosophila Genome Array.

scan_protocol: GeneChips were scanned using the GeneArrayTM scanner 3000.

data_processing: The data were analyzed witha GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf before PBZ treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Plants were grown under a short-day photoperiod (8h light/16h dark) at 23±2 °C, with 70 % relative humidity and 100 μmol m-2 s-1 light intensity.

extract_protocol: RNA was extracted from 100 mg of respective leaf samples using Trizol (Invitrogen) and dissolved in 10 μl of DEPC-treated water.

treatment_protocol: We applied 0.5 mM PBZ by root drenching to induce endogenous SA biosynthesis.

value: 5 week

value: 5-8 rosette leaves

tag: treated with

value: none (before treatment)


title: PBZ_T72-2

source_name: Arabidopsis leaf after PBZ treatment

value: 0.5 mM probenazole (PBZ)


title: Preoperative Period, P40

description:
SAMPLE 11
3999874075_K
Replicate 1


title: PBZ_T0-1


title: r8_RA_Hoxa5_2

description:
HoxA5_N/C_Fw_GAC
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGACAAGGATCGAAATAGCTCATG
Raw data files for this sample are available on GSM1868848.


title: PBZ_T72-1


title: Cortex_RA_Hoxa5_2

description:
HoxA5_N/C_Fw_TTG
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTTTGAAGGATCGAAATAGCTCATG
Raw data files for this sample are available on GSM1868848.

source_name: Cortex

value: Cortex


title: Cortex_WT_Hoxa5_2

description:
HoxA5_N/C_Fw
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAAGGATCGAAATAGCTCATG
Raw data files for this sample are available on GSM1868848.


title: r8_RA_Hoxb5_1

description:
HoxB5_N/C_Fw_CTT
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTCTTAAAGACATTGAAGGAACATG
Raw data files for this sample are available on GSM1868848.


title: Preoperative Period, P25

description:
SAMPLE 5
3999874075_E
Replicate 1


title: Preoperative Period, P16

description:
SAMPLE 4
3999874075_D
Replicate 1


title: Preoperative Period, P9

description:
SAMPLE 1
3999874075_A
Replicate 1


title: r8_WT_Hoxb5_1

description:
HoxB5_N/C_Fw_GAC
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGACAAAGACATTGAAGGAACATG
Raw data files for this sample are available on GSM1868848.

source_name: rhombomer 8 (r8)


title: r5-6_RA_Hoxb5_1

description:
HoxB5_N/C_Fw_AAG
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAAGAAAGACATTGAAGGAACATG
Raw data files for this sample are available on GSM1868848.


title: Cortex_RA_Hoxb5_1

description:
HoxB5_N/C_Fw_GTA
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGTAAAAGACATTGAAGGAACATG
Raw data files for this sample are available on GSM1868848.


title: r5-6_WT_Hoxb5_1

description:
HoxB5_N/C_Fw_AGT
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGTAAAGACATTGAAGGAACATG
Raw data files for this sample are available on GSM1868848.

source_name: rhombomers 5 & 6 (r5-6)


title: Atrial Fibrillation_left ventricle_112

status: Public on Sep 01 2017

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

institute: Ming Chuan Univ

description: ejection fraction > 60%

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with SST-RMA by Affymetrix Expression Console Ver 1.4

source_name: Human heart tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated from LV appendages with the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and was further purified and concentrated by using the WelPrep tissue RNA array (Welgene, Taipei, Taiwan). The quality and quantity of total RNA were analyzed by using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA)

value: Heart

value: Female

tag: condition

value: Hight ejection fraction


title: Saccharomyces cerevisiae

city: Walnut Creek

first: Denis

last: Tolkunov

state: CA

address: 2800 Mitchell Dr

institute: DOE Joint Genome Institute

description: [Third-party re-analysis] Raw SMRT sequencing  data was retrieved from: https://gist.github.com/pb-jchin/6359919. Ref: Kim, K. E. et al. Scientific Data 1, 140045 (2014), doi:10.1038/sdata.2014.45

data_processing:
SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: SGD sacCer3
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference.  The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae_Whole organism

tag: tissue

value: Whole organism


title: Atrial Fibrillation_left ventricle_102

description: ejection fraction > 60%


title: Atrial Fibrillation_left ventricle_101

description: ejection fraction < 60%

value: Low ejection fraction


title: Atrial Fibrillation_left ventricle_110

description: ejection fraction > 60%

value: male


title: Atrial Fibrillation_left ventricle_107

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_99

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_95

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_97

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_89

description: ejection fraction > 60%


title: Atrial Fibrillation_left ventricle_98

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_92

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_88

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_90

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_111

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_103

description: ejection fraction > 60%


title: Atrial Fibrillation_left ventricle_93

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_113

description: ejection fraction > 60%


title: Atrial Fibrillation_left ventricle_109

description: ejection fraction > 60%


title: Atrial Fibrillation_left ventricle_86

description: ejection fraction > 60%


title: Atrial Fibrillation_left ventricle_94

description: ejection fraction > 60%


title: WESTERN DIET 1

city: San Francisco

first: Caroline

last: Duwaerts

address: 1001 Potrero Ave - Building 40 - Room 4102

department: Medicine-GI

institute: UCSF

data_processing: nSolver 2.5 software was used to analyse raw data files

source_name: C3H/HeOuJ eWAT

extract_protocol: mRNA was extracted from epididymal white adipose tissue using the commercial kit: RNeasy Lipid Tissue Mini Kit from Qiagen

treatment_protocol: Animals were fed for 6 months with free access to custom or commercially available diets as described above

value: epididymal white adipose tissue

tag: experimental group

value: WESTERN DIET


title: WESTERN DIET 4


title: shNon-target, 1

city: Birmingham

first: Ichiro

last: Nakano

state: AL

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

hyb_protocol: Labeled targets were hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA 2.0) for 16 h at 45°C and washed according to Affymetrix standard protocols.

scan_protocol: The Genechips were scanned with an Affymetrix G7 scanner.

data_processing: The raw data (.CEL) files were preprocessed, normalized with with RMASketch method using Expression Console software (V1.3.1).

source_name: GBM patient derived GSCs

label_protocol: A 100 ng aliquot of total RNA from four independent incubations was amplified using the GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) following the manufacturer’s instructions and then 5.5 ug of cDNA was fragmented and terminally labeled.

growth_protocol: All cells were cultured using DMEM/F12/Glutamax(Invitrogen) supplemented with B27(Invitrogen), epidermal growth factor (EGF, 20 ng/ml; R&D Systems), basic fibroblast growth factor (bFGF, 20 ng/ml; R&D Systems), Heparin(2.5 ug/ml; Sigma) in suspension.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), including DNase I treatment before the final elution to eliminate any DNA contamination, following the manufacturer’s directions.

treatment_protocol: Infection of shNon-target or shMLK4_1 lentivirus

value: glioma sphere cells

tag: cell line

value: GBM

tag: transfection

value: pLKO 1.0- shNon-targeting vector


title: Atrial Fibrillation_left ventricle_91

description: ejection fraction < 60%


title: Atrial Fibrillation_left ventricle_116

description: ejection fraction > 60%


title: shNon-target, 2


title: STARCH/OLEATE 8

value: STARCH/OLEATE


title: WESTERN DIET 5


title: WESTERN DIET 2


title: WESTERN DIET 7


title: WESTERN DIET 3


title: STARCH/OLEATE 9


title: STARCH/OLEATE 7


title: shMLK4, 3

value: pLKO1.0 shMLK4_1


title: shMLK4, 1


title: shNon-target, 3


title: r5-6_WT_Hoxa5_2

description:
HoxA5_N/C_Fw_CTT
AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTCTTAAGGATCGAAATAGCTCATG
Raw data files for this sample are available on GSM1868848.

value: rhombomers 5 & 6


title: shMLK4, 2


title: Rb KO mouse retina at P8, biological rep3

city: Toronto

first: Sean

middle: R

last: McCurdy

address: 27 King's College Circle

department: Laboratory Medicine and Pathobiology

institute: University of Toronto

description: RB KO

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: GeneChips were scanned using the GeneChip Scanner

data_processing: Data were processed using R. RMA background correction was applied to probe intensities, gene level expression were summarized from the corrected intensities and then log2 transformed.

source_name: Mouse Retina

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse retina dissected from postnatal day 8

extract_protocol: Samples were snap frozen in liquid N2 and genotyped. Tail samples were collected for genotyping. RNA was extracted using RNAeasy (Qiagen). Wild-type and mutants samples of sufficient RNA integrity scores (>8, assessed by Bioanalyzer) were included. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: retina

tag: genotype

value: Rb KO


title: STARCH/OLEATE 1


title: STARCH/OLEATE 2


title: STARCH/OLEATE 3


title: SUCROSE/OLEATE 8

value: SUCROSE/OLEATE


title: SUCROSE/OLEATE 6


title: SUCROSE/OLEATE 5


title: SUCROSE/OLEATE 7


title: SUCROSE/OLEATE 3


title: SUCROSE/OLEATE 2


title: SUCROSE/OLEATE 4


title: STARCH/OLEATE 4


title: WESTERN DIET 6


title: STARCH/OLEATE 6


title: STARCH/OLEATE 5


title: SUCROSE/OLEATE 1


title: STARCH/PALMITATE 4

value: STARCH/PALMITATE


title: SUCROSE/OLEATE 9


title: WT mouse retina at P8, biological rep1

description: WT

value: wildtype


title: STARCH/PALMITATE 3


title: STARCH/PALMITATE 7


title: STARCH/PALMITATE 5


title: STARCH/PALMITATE 6


title: WT mouse retina at P8, biological rep2

description: WT


title: Rb KO mouse retina at P8, biological rep1

description: RB KO


title: Rb/p107 DKO mouse retina at P8, biological rep2

description: RB/P107 DKO

value: Rb/p107 DKO


title: WT mouse retina at P8, biological rep3

description: WT


title: Rb/p107 DKO mouse retina at P8, biological rep3

description: RB/P107 DKO


title: Rb/p107 DKO mouse retina at P8, biological rep1

description: RB/P107 DKO


title: Rb KO mouse retina at P8, biological rep2

description: RB KO


title: STARCH/PALMITATE 2


title: SUCROSE/PALMITATE 8

value: SUCROSE/PALMITATE


title: SUCROSE/PALMITATE 7


title: SUCROSE/PALMITATE 6


title: SUCROSE/PALMITATE 5


title: STARCH/PALMITATE 1


title: SUCROSE/PALMITATE 4


title: SUCROSE/PALMITATE 2


title: SUCROSE/PALMITATE 1


title: CHOW 8

value: CHOW


title: CHOW 3


title: CHOW 5


title: CHOW 2


title: SUCROSE/PALMITATE 3


title: CHOW 1


title: healthy subjects as control 1

city: Hangzhou

first: Xi

last: Jin

address: No.79 Qingchun Road

department: Department of

institute: The First Affilated Hospital, School of Medicine, Zhejiang University

description: lncRNAs and mRNAs expression in the colon cancer tissue of CRC patients without metastasis

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: control sample, 30min

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: M

value: blood


title: CHOW 4

value: epididymal white adipose tissue


title: CHOW 7


title: CHOW 6


title: patients with crohn's disease 2

description: lncRNAs and mRNAs expression in the colon cancer tissue of CRC patients with liver metastasis

source_name: human CD, 30 min


title: healthy subjects as control 3


title: patients with crohn's disease 3

description: lncRNAs and mRNAs expression in the rectal cancer tissue of CRC patients with liver metastasis


title: healthy subjects as control 2

value: F


title: patients with crohn's disease 1


title: T84, bacteria mix rep1 (CTR glut bmix, bmix and gluten)

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

description:
SAMPLE 7
7677153004_F.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background was first subtracted from the data and then normalized using Beadstudios cubic spline algorithm.

source_name: T84, bacteria mix

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted from T84 polarized tight monolayers by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

value: colon carcinoma cell line T84

value: bacteria mix


title: T84, bacteria mix + Gluten rep2 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 11
7677153004_B.

source_name: T84, bacteria mix + Gluten

value: bacteria mix + Gluten


title: T84, bacteria mix rep3 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 9
7677153004_D.


title: T84, Gluten rep1 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 4
7677153004_I.

source_name: T84, Gluten

value: Gluten


title: T84, Gluten rep3 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 6
7677153004_G.


title: T84, Gluten rep2 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 5
7677153004_H.


title: T84, CTR rep2 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 2
7677153004_K.

source_name: T84, CTR

value: CTR


title: T84, CTR rep3 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 3
7677153004_J.


title: T84, CTR rep1 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 1
7677153004_L.


title: T84, bacteria mix + Gluten rep1 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 10
7677153004_C.


title: T84, bacteria mix + Gluten rep3 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 12
7677153004_A.


title: T84, bacteria mix rep2 (CTR glut bmix, bmix and gluten)

description:
SAMPLE 8
7677153004_E.


title: IgE + GC donor D

first: David

middle: Jonathan

last: Fear

address: 5th Floor, Tower Wing, Great Maze Pond

department: Respiratory Medicine and Allergy

institute: Kings College London

description: IgE + GC donor D

data_processing: The data were normalised using RMA normalization using Illumina’s Genome Studio Suite v1.0

source_name: In vitro cultured tonsillar B cells

label_protocol: cDNA was synthesized and amplified from 40ng RNA using the Ovation Pico WTA system V2 (NuGEN). 4 ug of amplified cDNA was biotin labeled with Encore Biotin Module (NuGen)

growth_protocol: RPMI culture in hum

extract_protocol: total RNA from fixed and permeabilised cultured human tonsil B cells was isolated using the PureLink FFPE total RNA isolation kit (Invitrogen)

value: Germinal Centre B cell

tag: isotype

value: IgE+

tag: donor id

value: D


title: IgE + GC donor A

description: IgE + GC donor A

value: A


title: IgG + PB donor A

description: IgG + PB donor A

value: Plasma blast

value: IgG+


title: IgG + PC donor A

description: IgG + PC donor A

value: Plasma Cell


title: IgG + PC donor C

description: IgG + PC donor C

value: C


title: IgG + PB donor D

description: IgG + PB donor D


title: IgE + PB donor D

description: IgE + PB donor D


title: IgE + PB donor C

description: IgE + PB donor C


title: IgE + PC donor D

description: IgE + PC donor D


title: IgG + GC donor C

description: IgG + GC donor C


title: IgG + GC donor A

description: IgG + GC donor A


title: IgE + PB donor A

description: IgE + PB donor A


title: IgE + PC donor A

description: IgE + PC donor A


title: IgG + GC donor D

description: IgG + GC donor D


title: IgG + GC donor B

description: IgG + GC donor B

value: B


title: IgE + GC donor B

description: IgE + GC donor B


title: IgE + GC donor C

description: IgE + GC donor C


title: IgE + PC donor C

description: IgE + PC donor C


title: IgE + PC donor B

description: IgE + PC donor B


title: IgG + PB donor C

description: IgG + PB donor C


title: IgE + PB donor B

description: IgE + PB donor B


title: IgG + PC donor D

description: IgG + PC donor D


title: IgG + PC donor B

description: IgG + PC donor B


title: IgG + PB donor B

description: IgG + PB donor B


title: PBSHMS-live cells

first: Goodwin

middle: G

last: Jinesh

state: TX

address: 1515 Holecombe Blvd.,

department: Urology

institute: UT MD Anderson Cancer Center

description: SAMPLE 6

hyb_protocol: The hybridization protocol used was Illumina's Whole Genome Gene Expression Direct Hybridization assay where the samples are hybridized to the beadchip, where bound target is detected using CY3 fluorescence

scan_protocol: Samples were scanned using Illumina's iScan scanner as per manufacturer's protocol.

data_processing: Raw data processing was achieved using Illumina's Genome Studio software and the data were quantile normalized.

source_name: Fusion cell line derived by RT4 bladder cancer blebbishield and human PBMC fusion

label_protocol: Biotinylated cRNAs were prepared using Illumina TotalPrep RNA amplification kit from Ambion.

growth_protocol: Cells were grown in MEM (with L-Glutamine) with 10% FBS, pyruvate, nonessential amino acids, vitamins, penicillin, and streptomycin supplements.

extract_protocol: Total RNA was extracted with Ambion miRVANA reagent, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatments for samples 1, 4, 5, and 6; Samples 2 and 3 were treated with 1uM cisplatin + 20 mM Lithium chloride for 24hrs to induce blebbishield formation and sample 3 was subjected to further 4hr transformation and isolation of pure spheres

value: Live cells


title: RT4P-live cells

description: SAMPLE 1

source_name: Human bladder cancer cell line-ATCC


title: RT4v6-live cells

description: SAMPLE 5

source_name: RT4 bladder cancer cells serially passaged in mice six times to enrich cancer stem cells


title: RT4P-transformed spheres

description: SAMPLE 3

source_name: Transformed sphere from apoptotic RT4 human bladder cancer cell line

value: Post-apoptotic but forms spheres


title: RT4P-Blebbishields

description: SAMPLE 2

source_name: Apoptotic RT4 human bladder cancer cell line

value: Post-apoptotic (includes sphere forming and non-sphere forming lebbishields)


title: Patient_901_Baseline

city: Lund

first: Ingrid

last: Hedenfalk

address: Medicon Village

department: Div of Omcology & Pathology, Dept of Clinical Sciences

institute: Lund University

description: Direct Hyb

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE

source_name: Primary breast cancer

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: Qiagen Allprep DNA/RNA mini kit, with a QIAcube

value: Baseline (no treatment)

value: Breast


title: Patient_703_Baseline

description: Direct Hyb


title: Patient_702_Cycle 2

description: Direct Hyb

value: Cycle 2 (chemo only)


title: Patient_703_Cycle 2

description: Direct Hyb


title: Patient_701_Baseline

description: Direct Hyb


title: Patient_615_Surgery

description: Direct Hyb

value: Surgery (chemo+bevacizumab)


title: Patient_619_Cycle 2

description: Direct Hyb


title: Patient_619_Surgery

description: Direct Hyb


title: Patient_617_Baseline

description: Direct Hyb


title: Patient_901_Cycle 2

description: Direct Hyb


title: Patient_704_Baseline

description: Direct Hyb


title: Patient_617_Surgery

description: Direct Hyb


title: Patient_616_Cycle 2

description: Direct Hyb


title: Patient_614_Cycle 2

description: Direct Hyb


title: Patient_616_Surgery

description: Direct Hyb


title: Patient_615_Cycle 2

description: Direct Hyb


title: Patient_616_Baseline

description: Direct Hyb


title: Patient_902_Baseline

description: Direct Hyb


title: Patient_614_Baseline

description: Direct Hyb


title: Patient_614_Surgery

description: Direct Hyb


title: Patient_613_Cycle 2

description: Direct Hyb


title: Patient_615_Baseline

description: Direct Hyb


title: Patient_619_Baseline

description: Direct Hyb


title: Patient_611_Surgery

description: Direct Hyb


title: Patient_613_Baseline

description: Direct Hyb


title: Patient_902_Cycle 2

description: Direct Hyb


title: Patient_611_Cycle 2

description: Direct Hyb


title: Patient_612_Baseline

description: Direct Hyb


title: Patient_610_Cycle 2

description: Direct Hyb


title: Patient_607_Cycle 2

description: Direct Hyb


title: RT4P-BSE2-live cells

description: SAMPLE 4

source_name: RT4 bladder cancer cells that undergone blebbishield emergency program twice serially


title: Patient_608_Baseline

description: Direct Hyb


title: Patient_603_Surgery

description: Direct Hyb


title: Patient_611_Baseline

description: Direct Hyb


title: Patient_610_Baseline

description: Direct Hyb


title: Patient_605_Baseline

description: Direct Hyb


title: Patient_602_Baseline

description: Direct Hyb


title: Patient_609_Surgery

description: Direct Hyb


title: Patient_604_Baseline

description: Direct Hyb


title: Patient_606_Surgery

description: Direct Hyb


title: Patient_509_Surgery

description: Direct Hyb


title: Patient_608_Cycle 2

description: Direct Hyb


title: Patient_507_Surgery

description: Direct Hyb


title: Patient_509_Baseline

description: Direct Hyb


title: Patient_507_Cycle 2

description: Direct Hyb


title: Patient_505_Surgery

description: Direct Hyb


title: Patient_507_Baseline

description: Direct Hyb


title: Patient_506_Surgery

description: Direct Hyb


title: Patient_505_Cycle 2

description: Direct Hyb


title: Patient_510_Baseline

description: Direct Hyb


title: Patient_603_Cycle 2

description: Direct Hyb


title: Patient_502_Baseline

description: Direct Hyb


title: Patient_504_Baseline

description: Direct Hyb


title: Patient_510_Surgery

description: Direct Hyb


title: Patient_501_Surgery

description: Direct Hyb


title: Patient_606_Cycle 2

description: Direct Hyb


title: Patient_602_Surgery

description: Direct Hyb


title: Patient_502_Cycle 2

description: Direct Hyb


title: Patient_501_Cycle 2

description: Direct Hyb


title: Patient_403_Baseline

description: Direct Hyb


title: Patient_401_Baseline

description: Direct Hyb


title: Patient_327_Surgery

description: Direct Hyb


title: Patient_326_Baseline

description: Direct Hyb


title: Patient_327_Baseline

description: Direct Hyb


title: Patient_320_Baseline

description: Direct Hyb


title: Patient_318_Surgery

description: Direct Hyb


title: Patient_324_Cycle 2

description: Direct Hyb


title: Patient_324_Surgery

description: Direct Hyb


title: Patient_319_Baseline

description: Direct Hyb


title: Patient_326_Cycle 2

description: Direct Hyb


title: Patient_320_Surgery

description: Direct Hyb


title: Patient_323_Surgery

description: Direct Hyb


title: Patient_501_Baseline

description: Direct Hyb


title: Patient_316_Baseline

description: Direct Hyb


title: Patient_401_Cycle 2

description: Direct Hyb


title: Patient_322_Baseline

description: Direct Hyb


title: Patient_315_Surgery

description: Direct Hyb


title: Patient_317_Cycle 2

description: Direct Hyb


title: Patient_313_Baseline

description: Direct Hyb


title: Patient_323_Baseline

description: Direct Hyb


title: Patient_321_Baseline

description: Direct Hyb


title: Patient_318_Baseline

description: Direct Hyb


title: Patient_315_Baseline

description: Direct Hyb


title: Patient_317_Baseline

description: Direct Hyb


title: Patient_314_Baseline

description: Direct Hyb


title: Patient_323_Cycle 2

description: Direct Hyb


title: Patient_320_Cycle 2

description: Direct Hyb


title: Patient_314_Cycle 2

description: Direct Hyb


title: Patient_314_Surgery

description: Direct Hyb


title: Patient_324_Baseline

description: Direct Hyb


title: Patient_313_Cycle 2

description: Direct Hyb


title: Patient_312_Surgery

description: Direct Hyb


title: Patient_311_Surgery

description: Direct Hyb


title: Patient_309_Cycle 2

description: Direct Hyb


title: Patient_307_Surgery

description: Direct Hyb


title: Patient_310_Baseline

description: Direct Hyb


title: Patient_309_Surgery

description: Direct Hyb


title: Patient_303_Cycle 2

description: Direct Hyb


title: Patient_311_Baseline

description: Direct Hyb


title: Patient_308_Baseline

description: Direct Hyb


title: Patient_311_Cycle 2

description: Direct Hyb


title: Patient_301_Baseline

description: Direct Hyb


title: Patient_306_Baseline

description: Direct Hyb


title: Patient_303_Baseline

description: Direct Hyb


title: Patient_224_Cycle 2

description: Direct Hyb


title: Patient_303_Surgery

description: Direct Hyb


title: Patient_302_Baseline

description: Direct Hyb


title: Patient_302_Cycle 2

description: Direct Hyb


title: Patient_227_Baseline

description: Direct Hyb


title: Patient_225_Surgery

description: Direct Hyb


title: Patient_310_Cycle 2

description: Direct Hyb


title: Patient_225_Baseline

description: Direct Hyb


title: Patient_226_Cycle 2

description: Direct Hyb


title: Patient_304_Baseline

description: Direct Hyb


title: Patient_305_Baseline

description: Direct Hyb


title: Patient_227_Cycle 2

description: Direct Hyb


title: Patient_223_Surgery

description: Direct Hyb


title: Patient_306_Surgery

description: Direct Hyb


title: Patient_224_Surgery

description: Direct Hyb


title: Patient_224_Baseline

description: Direct Hyb


title: Patient_226_Baseline

description: Direct Hyb


title: Patient_225_Cycle 2

description: Direct Hyb


title: Patient_223_Cycle 2

description: Direct Hyb


title: Patient_222_Surgery

description: Direct Hyb


title: Patient_218_Baseline

description: Direct Hyb