title: SAMPLE 29 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 24 CD326+ uterus epithelial cell

status: Public on Jun 30 2017

type: RNA

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

country: China

institute: Zhejiang University

description: single cell

data_processing:
raw data was collected from the Fluidigm Real-Time PCR Analysis software
single cell data could be furthor analized in R software with the Package SINGuLAR™ 3.0

label: Eva Green

molecule: total RNA

organism: Mus musculus

source_name: uterus

label_protocol: QPCR was performed on the 96.96 IFC using the pre-amplified product on the Fluidigm Biomark platform according to the manufacture's instructions

extract_protocol: single cells were lysed and preamplified with the kit (CellsDirect™ One-Step qRT-PCR Kit, Thermo, 11753100)

treatment_protocol: Post-natal day7 mice uterus were digested into single cell syspension by type I collagenase, then cells were labeled with anti-CD326 antibody, and sorted the CD326+ single cell into each well of 96-well plate

tag: cell type

value: CD326+ cells sorted by FACS


title: SAMPLE 23 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S2

type: genomic

city: Parkville

first: Andrew

middle: David

last: Fox

state: VIC

address: 30 Royal Parade

department: MS Division

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

description: Bisulphite converted genomic DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Illumina iScan standard protocol

data_processing: Standard background and Illumina preprocessing (R 'minfi' package), followed by SWAN normalization, then convertion to beta values (proportion methylated 0.001-0.999).

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Case-WholeBlood

label_protocol: Standard Illumina Protocol

extract_protocol: QIAamp DNA Micro kit (QIAGEN) according to standard instructions

tag: sentrix id

tag: sentrix row & column

value: WholeBlood

tag: disease state

value: Case

tag: person id


title: Neutrophil-Control-L3

description: Bisulphite converted genomic DNA

source_name: Control-Neutrophil

value: Neutrophil

value: Control


title: WholeBlood-Control-L2

description: Bisulphite converted genomic DNA

source_name: Control-WholeBlood


title: SAMPLE 22 CD326+ uterus epithelial cell

description: single cell


title: CD4T-Control-L3

description: Bisulphite converted genomic DNA


title: SAMPLE 21 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 20 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 18 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 16 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 19 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 17 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 14 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 13 CD326+ uterus epithelial cell

description: single cell


title: WBC-Control-L2

description: Bisulphite converted genomic DNA

source_name: Control-WBC

value: WBC


title: SAMPLE 15 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 12 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 11 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 9 CD326+ uterus epithelial cell

description: single cell


title: CD8T-Control-L2

description: Bisulphite converted genomic DNA


title: Monocyte-Control-L3

description: Bisulphite converted genomic DNA

source_name: Control-Monocyte

value: Monocyte


title: NKcell-Control-L2

description: Bisulphite converted genomic DNA

source_name: Control-NKcell

value: NKcell


title: SAMPLE 7 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 10 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 6 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 5 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Control-L1

description: Bisulphite converted genomic DNA


title: NKcell-Control-L1

description: Bisulphite converted genomic DNA


title: Neutrophil-Control-L2

description: Bisulphite converted genomic DNA


title: SAMPLE 4 CD326+ uterus epithelial cell

description: single cell


title: CD4T-Control-L2

description: Bisulphite converted genomic DNA


title: SAMPLE 3 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 2 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S1

description: Bisulphite converted genomic DNA


title: CD19B-Control-L1

description: Bisulphite converted genomic DNA


title: SAMPLE 1 CD326+ uterus epithelial cell

description: single cell


title: CD19B-Control-L2

description: Bisulphite converted genomic DNA


title: WBC-Control-L1

description: Bisulphite converted genomic DNA


title: SAMPLE 8 CD326+ uterus epithelial cell

description: single cell


title: Monocyte-Control-L2

description: Bisulphite converted genomic DNA


title: CD8T-Control-L1

description: Bisulphite converted genomic DNA


title: Monocyte-Control-L1

description: Bisulphite converted genomic DNA


title: Neutrophil-Control-L1

description: Bisulphite converted genomic DNA


title: T23 biological rep3  vs. C23 biological rep3

status: Public on Jun 29 2017

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

hyb_protocol: Equal amounts of labeled RNA were then hybridized on the chip, per the Agilent protocol, at 60 degrees overnight. The hybridization mixes were prepared using the Gene Expression Hybridization Kit from Agilent following the manufacturer’s protocol. After hybridization, the slide was washed first with Gene Expression Wash Buffer 1(Agilent) and then Gene Expression Wash Buffer 2(Agilent). This was followed by a acetonitrile wash and finally the slides were placed in Stabilization& Drying Solution (Agilent). The washed slides were scanned on on an Agilent G2565BA scanner. Feature extraction was performed using the Feature extraction software from Agilent

scan_protocol: Scanned on an Agilent G2565BA microarray scanner

data_processing: The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (version 9.5.1.1 Agilent Technologies, Santa Clara, CA). The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed.

organism: Stylophora pistillata

label_protocol: 200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer’s protocol.

extract_protocol: Total RNA extracted using Trizol

treatment_protocol: Coral fragments of Stylophora pistillata were incubated for 1.5 hours in two different calcium concentrations natural calcium concentration (SW) and natural calcium concentration add with 100 mg/L (SW+100). Three coral fragments, for each treatment and time point, were sampled after the incubation, snap froze in liquid nitrogen and stored in -80 C until further handled.

tag: treated with

value: additional 100mg/L calcium (SW+100)

tag: time point

tag: tissue

value: coral fragments

value: natural concentration of calcium (SW)


title: Q3_mono_1_C11_S227

type: SRA

city: Cambridge

first: Sanjay

last: Prakadan

state: MA

address: 77 Massachusetts Ave, E25-356

country: USA

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
TopHat was used to align data
RSEM was used to generate estimates of transcripts per million reads for each single cell
Genome_build: hg19
processed data file content: Human Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y

source_name: Human patient-derived dendritic cell transcriptome

extract_protocol:
cDNA from single-cell transcriptomes was generated as described in Nirschl, et al. Cell 2017. Briefly, single cells were lysed, the mRNA was extracted, followed by RT-PCR which was then prepared for next-generation sequencing
cDNA was prepared to sequencing libraries using an Illumina Nextera XT protocol. RNA-Seq was performed on a NextSeq 500 with a paired-end 2x30 bp read structure.

value: Monocyte-derived sorted cell


title: Q3_mono_4_F09_S549


title: Q1_BDCA_DC_1_D08_S44

value: BDCA1+ sorted dendritic cell


title: Q3_mono_4_G11_S563


title: T23 biological rep1  vs. C23 biological rep1


title: C11 biological rep5  vs. plan biological rep1

source_name: plan

value: free swimming larvae (plan)


title: Q3_mono_1_A05_S197


title: Q3_mono_4_B10_S502


title: Q3_mono_4_F04_S544


title: Q4_BDCA_DC_2_H10_S382


title: Q3_mono_4_F11_S551


title: Q4_BDCA_DC_2_D11_S335


title: Q1_mono_3_E05_S437


title: Q3_mono_4_C09_S513


title: Q3_mono_1_H03_S279


title: Q3_mono_1_D10_S238


title: C11 biological rep1  vs. T11 biological rep1


title: T23 biological rep2  vs. C23 biological rep2


title: C11 biological rep2  vs. T11 biological rep2


title: C11 biological rep3  vs. T11 biological rep3


title: Q1_mono_3_E06_S438


title: CD4T-Control-L1

description: Bisulphite converted genomic DNA


title: Q1_mono_3_E02_S434


title: Q1_BDCA_DC_1_A12_S12


title: Q4_BDCA_DC_2_H02_S374


title: C11 biological rep4  vs. C23 biological rep4


title: Q1_mono_3_A01_S385


title: Q2_mono_2_F01_S157


title: Q3_mono_1_A06_S198


title: Q3_mono_4_G04_S556


title: Q3_mono_4_G07_S559


title: Q4_BDCA_DC_2_B04_S304


title: Q3_mono_1_G11_S275


title: Q3_mono_1_D01_S229


title: Q4_BDCA_DC_2_G02_S362


title: Q1_mono_3_C10_S418


title: Q1_BDCA_DC_1_E08_S56


title: Q4_BDCA_DC_2_B07_S307


title: Q1_mono_3_H11_S479


title: Q4_BDCA_DC_2_G12_S372


title: Q3_mono_4_G02_S554


title: Q4_BDCA_DC_2_C09_S321


title: Q4_BDCA_DC_2_F10_S358


title: Q3_mono_1_B10_S214


title: Q3_mono_1_A11_S203


title: Q4_BDCA_DC_2_H09_S381


title: Q1_BDCA_DC_1_E04_S52


title: Q4_BDCA_DC_2_F09_S357


title: Q3_mono_1_B03_S207


title: Q1_BDCA_DC_1_H01_S85


title: Q3_mono_4_C08_S512


title: Q2_mono_2_F12_S168


title: Q1_BDCA_DC_1_E09_S57


title: Q3_mono_1_H11_S287


title: Q3_mono_1_G07_S271


title: Q1_mono_3_D03_S423


title: Q4_BDCA_DC_2_C04_S316


title: Q4_BDCA_DC_2_D08_S332


title: Q1_mono_3_B11_S407


title: Q1_mono_3_G03_S459


title: Q3_mono_1_A09_S201


title: Q1_mono_3_A05_S389


title: Q3_mono_4_B11_S503


title: Q2_mono_2_H02_S182


title: Q1_mono_3_H12_S480


title: Q3_mono_1_H05_S281


title: Q1_mono_3_G01_S457


title: Q3_mono_1_E01_S241


title: Q4_BDCA_DC_2_A08_S296


title: Q3_mono_4_A10_S490


title: Q3_mono_4_B07_S499


title: Q4_BDCA_DC_2_F02_S350


title: Q4_BDCA_DC_2_E10_S346


title: Q4_BDCA_DC_2_D12_S336


title: Q3_mono_1_A10_S202


title: Q3_mono_4_G12_S564


title: Q3_mono_1_A02_S194


title: Q3_mono_1_C01_S217


title: Q1_mono_3_E12_S444


title: Q3_mono_1_B06_S210


title: Q1_mono_3_A10_S394


title: OIR [ID45_514_C07]

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed and stained slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Arrays were scanned using standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: The arrays were subsequently pre-processed using Affymetrix Expression Console with the following settings: summarization: PLIER, and normalization: global-median. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probeset scaling-to-target signal of 250.

label: biotin

source_name: WAT, OIR

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted from WAT specimens (300 mg) using RNeasy Lipid tissue (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: Patients had been fasting overnight.

tag: disease status

value: obese

tag: insulin sensitivity

value: resistant

value: abdominal subcutaneous white adipose tissue (WAT)

tag: gender

value: female

tag: age (yr)


title: OIS [ID46_4603_G05]

source_name: WAT, OIS

value: sensitive


title: OIR [ID43_1794_B05]


title: OIS [ID47_328_G05]


title: OIR [ID44_4642_E07]


title: OIS [ID48_2656_E07]


title: Q4_BDCA_DC_2_H08_S380


title: Q1_mono_3_C03_S411


title: Q3_mono_1_B01_S205


title: Q4_BDCA_DC_2_D10_S334


title: Q1_mono_3_D12_S432


title: Q3_mono_4_B12_S504


title: Q1_mono_3_C12_S420


title: Q3_mono_4_A04_S484


title: Q3_mono_1_D04_S232


title: Q2_mono_2_G06_S174


title: Q1_mono_3_E03_S435


title: Q3_mono_1_C04_S220


title: OIR [ID40_4810_G07]


title: OIR [ID36_5171_C09]


title: OIR [ID35_4991_C09]


title: OIR [ID42_4275_H07]


title: OIR [ID41_4639_F07]


title: OIR [ID37_4649_C07]


title: OIR [ID39_4910_D07]


title: OIR [ID38_4640_D05]


title: Q3_mono_4_E04_S532


title: OIR [ID34_4965_A07]


title: OIR [ID33_2658_F07]


title: Q2_mono_2_A02_S98


title: Q3_mono_1_D11_S239


title: Q2_mono_2_G09_S177


title: Q1_mono_3_E04_S436


title: OIR [ID32_4921_F09]


title: Q4_BDCA_DC_2_H04_S376


title: OIS [ID26_2663_A09]


title: OIR [ID30_4982_H05]


title: Q3_mono_4_E02_S530


title: OIR [ID31_4957_B07]


title: OIS [ID25_2645_E09]


title: Q3_mono_4_G09_S561


title: Q4_BDCA_DC_2_B09_S309


title: Q3_mono_1_G10_S274


title: Q4_BDCA_DC_2_G09_S369


title: Q1_mono_3_D06_S426


title: Q1_mono_3_B12_S408


title: Q1_BDCA_DC_1_A10_S10


title: Q1_mono_3_A06_S390


title: Q3_mono_1_H02_S278


title: OIR [ID29_4967_G09]


title: OIS [ID23_4594_F05]


title: OIS [ID22_3699_B05]


title: OIS [ID24_4270_F09]


title: OIR [ID28_4973_H09]


title: OIS [ID27_2629_A05_3]


title: OIS [ID21_2652_H05]


title: Q1_BDCA_DC_1_A05_S5


title: Q3_mono_1_C10_S226


title: Q3_mono_4_A08_S488


title: Q2_mono_2_E07_S151


title: Q1_mono_3_H02_S470


title: OIS [ID18_3713_D05]


title: Q2_mono_2_D12_S144


title: OIS [ID20_4281_F05]


title: Q3_mono_1_G06_S270


title: Q3_mono_1_G12_S276


title: OIS [ID19_4662_G07]


title: OIS [ID16_4264_B07]


title: OIS [ID17_3718_B09]


title: OIS [ID14_3689_C05]


title: OIS [ID15_325_A07]


title: OIS [ID12_2183_E05]


title: Q4_BDCA_DC_2_C12_S324


title: OIS [ID13_1529_D07]


title: Q1_mono_3_F12_S456


title: OIS [ID11_4589_E05]


title: Q2_mono_2_A11_S107


title: Q3_mono_4_A09_S489


title: Q1_mono_3_A11_S395


title: Q1_BDCA_DC_1_G10_S82


title: CONTROL [ID09_1796_E09]

source_name: WAT, control

value: lean


title: CONTROL [ID08_1034_G09]


title: Q3_mono_4_F12_S552


title: Q1_BDCA_DC_1_B12_S24


title: Q3_mono_1_F03_S255


title: Q4_BDCA_DC_2_D04_S328


title: Q3_mono_1_G04_S268


title: Q3_mono_4_C11_S515


title: CONTROL [ID03_1141_B09]


title: Q1_mono_3_H10_S478


title: Q3_mono_4_B02_S494


title: CONTROL [ID07_4618_A05]


title: Q3_mono_4_C02_S506


title: CONTROL [ID05_4638_D09]


title: Q3_mono_1_G02_S266


title: CONTROL [ID06_1732_H07]


title: Q2_mono_2_F02_S158


title: OIS [ID10_2636_A09]


title: CONTROL [ID04_791_C05]


title: CONTROL [ID01_751_D09]


title: Q2_mono_2_E09_S153


title: Q1_mono_3_E10_S442


title: Q2_mono_2_B11_S119


title: Q4_BDCA_DC_2_G04_S364


title: Q1_mono_3_D05_S425


title: CONTROL [ID02_884_H09]


title: Q1_mono_3_G06_S462


title: Q3_mono_4_D08_S524


title: Q3_mono_1_F04_S256


title: Q1_mono_3_C06_S414


title: Q1_mono_3_F01_S445


title: Q1_mono_3_B06_S402


title: Q2_mono_2_B03_S111


title: Q3_mono_1_E10_S250


title: Q3_mono_4_D10_S526


title: Q3_mono_4_A07_S487


title: Q1_mono_3_D10_S430


title: Q1_mono_3_H05_S473


title: Q1_BDCA_DC_1_E03_S51


title: Q3_mono_4_F02_S542


title: Q4_BDCA_DC_2_F12_S360


title: Q4_BDCA_DC_2_A11_S299


title: Q3_mono_4_G08_S560


title: Q1_mono_3_C02_S410


title: Q2_mono_2_C12_S132


title: Q3_mono_1_C05_S221


title: Q1_mono_3_F05_S449


title: Q1_mono_3_A04_S388


title: Q4_BDCA_DC_2_E08_S344


title: Q1_mono_3_H03_S471


title: Q1_mono_3_G02_S458


title: Q3_mono_4_E09_S537


title: Q4_BDCA_DC_2_E12_S348


title: Q3_mono_4_A12_S492


title: Q3_mono_4_H10_S574


title: Q4_BDCA_DC_2_E11_S347


title: Q3_mono_1_C02_S218


title: Q3_mono_1_B04_S208


title: Q4_BDCA_DC_2_B08_S308


title: Q4_BDCA_DC_2_C08_S320


title: Q1_BDCA_DC_1_G06_S78


title: Q4_BDCA_DC_2_G08_S368


title: Q3_mono_1_F01_S253


title: Q4_BDCA_DC_2_C02_S314


title: Q1_mono_3_D02_S422


title: Q4_BDCA_DC_2_H07_S379


title: Q4_BDCA_DC_2_C07_S319


title: Q2_mono_2_E01_S145


title: Q1_BDCA_DC_1_G01_S73


title: Q3_mono_4_D02_S518


title: Q3_mono_1_G08_S272


title: Q4_BDCA_DC_2_F04_S352


title: Q3_mono_1_H06_S282


title: Q4_BDCA_DC_2_F08_S356


title: Q1_mono_3_F11_S455


title: Q3_mono_1_C12_S228


title: Q2_mono_2_A09_S105


title: Q3_mono_4_E11_S539


title: Q4_BDCA_DC_2_H11_S383


title: Q4_BDCA_DC_2_F07_S355


title: Q3_mono_1_B05_S209


title: Q4_BDCA_DC_2_E07_S343


title: Q4_BDCA_DC_2_B12_S312


title: Q4_BDCA_DC_2_E04_S340


title: Q1_mono_3_D11_S431


title: Q3_mono_1_H08_S284


title: Q4_BDCA_DC_2_B11_S311


title: Q3_mono_4_C04_S508


title: Q4_BDCA_DC_2_F11_S359


title: Q2_mono_2_H06_S186


title: Niro_dcell_1_A07_S7

value: BDCA3+ sorted dendritic cell


title: Niro_dcell_2_G02_S170


title: Niro_dcell_1_E07_S55


title: Niro_dcell_2_D03_S135


title: Niro_dcell_2_A07_S103


title: Niro_dcell_2_F06_S162


title: Q3_mono_1_D08_S236


title: Q4_BDCA_DC_2_A07_S295


title: Q4_BDCA_DC_2_F05_S353


title: Q4_BDCA_DC_2_B10_S310


title: Q3_mono_1_F10_S262


title: Niro_dcell_1_E01_S49


title: Niro_dcell_2_G03_S171


title: Niro_dcell_1_G11_S83


title: Q1_mono_3_E01_S433


title: Niro_dcell_2_E10_S154


title: Niro_dcell_1_G04_S76


title: Niro_dcell_2_B02_S110


title: Niro_dcell_2_H03_S183


title: Niro_dcell_2_D09_S141


title: Niro_dcell_2_A06_S102


title: Niro_dcell_2_H02_S182


title: Niro_dcell_1_A05_S5


title: Niro_dcell_1_C09_S33


title: Q4_BDCA_DC_2_G07_S367


title: Niro_dcell_1_A10_S10


title: Niro_dcell_1_F12_S72


title: Niro_dcell_1_E05_S53


title: Niro_dcell_2_H01_S181


title: Niro_dcell_2_G10_S178


title: Niro_dcell_1_H10_S94


title: Niro_dcell_2_E02_S146


title: Niro_dcell_2_C02_S122


title: Niro_dcell_2_C12_S132


title: Niro_dcell_1_E12_S60


title: Niro_dcell_1_F02_S62


title: Niro_dcell_1_H11_S95


title: Niro_dcell_1_E09_S57


title: Niro_dcell_1_E11_S59


title: Niro_dcell_2_E06_S150


title: Niro_dcell_2_B04_S112


title: Niro_dcell_2_D11_S143


title: Niro_dcell_1_C11_S35


title: Niro_dcell_2_E04_S148


title: Niro_dcell_1_E03_S51


title: Niro_dcell_2_B06_S114


title: Niro_dcell_2_C06_S126


title: Niro_dcell_2_C05_S125


title: Niro_dcell_1_G01_S73


title: Niro_dcell_1_H05_S89


title: Niro_dcell_2_E11_S155


title: Niro_dcell_1_B11_S23


title: Niro_dcell_2_E05_S149


title: Niro_dcell_2_G05_S173


title: Niro_dcell_1_D04_S40


title: Niro_dcell_2_H11_S191


title: Niro_dcell_1_G09_S81


title: Niro_dcell_1_A04_S4


title: Niro_dcell_1_G03_S75


title: Niro_dcell_1_D06_S42


title: Niro_dcell_2_H06_S186


title: Niro_dcell_2_H08_S188


title: Niro_dcell_2_C11_S131


title: Niro_dcell_2_D12_S144


title: Niro_dcell_1_D10_S46


title: Niro_dcell_1_D07_S43


title: Niro_dcell_2_B01_S109


title: Niro_dcell_1_G12_S84


title: Niro_dcell_1_C01_S25


title: Niro_dcell_1_F11_S71


title: Niro_dcell_1_C12_S36


title: Niro_dcell_2_H12_S192


title: Niro_dcell_2_F11_S167


title: Niro_dcell_2_A02_S98


title: Niro_dcell_1_F06_S66


title: Niro_dcell_2_C03_S123


title: Niro_dcell_2_E08_S152


title: Niro_dcell_1_G07_S79


title: Niro_dcell_2_F02_S158


title: Niro_dcell_1_B10_S22


title: Niro_dcell_2_A10_S106


title: Niro_dcell_2_G01_S169


title: Niro_dcell_2_D06_S138


title: Niro_dcell_2_B09_S117


title: Niro_dcell_1_B06_S18


title: Niro_dcell_2_E07_S151


title: Niro_dcell_1_A06_S6


title: Niro_dcell_1_C05_S29


title: Niro_dcell_2_F10_S166


title: Niro_dcell_2_G04_S172


title: Niro_dcell_2_H07_S187


title: Niro_dcell_1_E06_S54


title: Niro_dcell_1_F05_S65


title: Niro_dcell_2_E03_S147


title: Niro_dcell_1_F03_S63


title: Niro_dcell_2_D04_S136


title: Niro_dcell_1_E04_S52


title: Niro_dcell_2_C07_S127


title: Niro_dcell_1_C06_S30


title: Niro_dcell_2_G11_S179


title: Niro_dcell_2_A05_S101


title: Niro_dcell_1_D09_S45


title: Niro_dcell_2_C10_S130


title: Niro_dcell_1_G06_S78


title: Niro_dcell_1_D03_S39


title: Niro_dcell_1_D12_S48


title: Niro_dcell_1_H07_S91


title: Niro_dcell_1_B09_S21


title: Niro_dcell_1_G05_S77


title: Niro_dcell_2_F05_S161


title: Niro_dcell_2_B11_S119


title: Niro_dcell_2_E12_S156


title: Niro_dcell_2_H04_S184


title: Niro_dcell_1_D11_S47


title: Niro_dcell_1_G02_S74


title: Niro_dcell_1_A12_S12


title: Niro_dcell_2_C04_S124


title: Niro_dcell_2_C08_S128


title: Niro_dcell_1_H02_S86


title: Niro_dcell_2_A03_S99


title: Niro_dcell_1_D05_S41


title: Niro_dcell_2_B07_S115


title: Niro_dcell_1_D01_S37


title: Niro_dcell_2_D01_S133


title: Niro_dcell_2_H09_S189


title: Niro_dcell_2_F09_S165


title: Niro_dcell_2_G09_S177


title: Niro_dcell_2_F01_S157


title: Niro_dcell_1_C07_S31


title: Niro_dcell_1_G10_S82


title: Niro_dcell_1_F09_S69


title: Niro_dcell_1_C02_S26


title: Niro_dcell_2_F12_S168


title: Niro_dcell_2_A11_S107


title: Niro_dcell_1_D08_S44


title: Niro_dcell_1_F07_S67


title: Niro_dcell_2_B08_S116


title: Niro_dcell_2_D05_S137


title: siNEGC [243_siRNANegC_A07]

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 2.1 ST Arrays, and then washed and stained slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

data_processing:
These arrays were pre-processed with RMA, which includes normalization, summarization of probes to probesets, and background correction.
Analysis Method: rma-gene-full
Analysis Software: Expression Console
Data Transformation: log2
Annotations: hg19/GRCh37
NetAffx build: 33

source_name: primary adipocyte culture, siNEGC

growth_protocol: Primary adipocyte culture for in vitro studies was obtained from subcutaneous WAT from healthy non-obese men and women (BMI <30 kg/m2) undergoing cosmetic liposuction. The stroma vascular fraction (SVF) cells were isolated. The precursor cells obtained from separate individuals were not mixed. Part of plastic-adherent SVF cells were directly plated (30,000-50,000 cells/cm2) and differentiated to adipocytes as described. The degree of differentiation was controlled under the microscope as accumulation of lipids, and response to insulin in lipogenesis assay was evaluated.

extract_protocol: Total RNA was extracted using NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: In vitro differentiated adipocytes (day 10-12 post induction) were transfected with ON-TARGETplus SMARTpool small interfering RNAs (siRNAs) targeting KLF15, SLC25A10 or non-targeting siRNA pool at 40 nM final concentration (Dharmacon, Lafayette, CO) in 24- or 48-well plates and HiPerfect Transfection Reagent (Qiagen), respectively 4.5 or 2 µl according to the manufacturer's protocol. The cells were incubated for 48 or 72 hours at which time in vitro lipogenesis was assessed in cells plated on 48-well plates and RNA were collected.

value: healthy, non-obese

value: adipocytes

tag: sirna

value: siNEGC


title: siNEGC [234_siRNANegC_B05]


title: siKLF15 [219_siKLF15_D05]

source_name: primary adipocyte culture, siKLF15


title: siSLC25A10 [247_siSLC25A10_D07]

source_name: primary adipocyte culture, siSLC25A10


title: siKLF15 [220_siKLF15_A05]


title: siKLF15 [239_siKLF15_F05]


title: siKLF15 [237_siKLF15_C09]


title: siNEGC [228_siRNANegC_A09]


title: siSLC25A10 [246_siSLC25A10_D09]


title: siKLF15 [203_siKLF15_E09]


title: siSLC25A10 [226_siSLC25A10_H05]


title: siSLC25A10 [194_siSLC25A10_F09]


title: ExVivoHairFollicle_24hr_20uMSFN_donor208

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

description: Gene expression after 24hr in 20uM Sulforaphane treated human Hair Follicle

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented, hybridized to Agilent SurePrint G3 Human Gene Expression v2 8x60K Microarrays and washed  in accordance with the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C using one color scan setting for 8X60k array slides according to manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Filtering and analysis of data was carried out using GeneSpring GX13: data was per sample normalized by percentile shift to the 75th percentile, and baseline transformed to the time matched vehicle control sample from the same donor. Normalized data was filtered by detection flag and by signal intensity: 20597 gene entities flagged detected and has signal intensity >100 in all replicates of at least 1 experimental condition was used for further analysis by moderated T test.

source_name: Hair Follicle, 24hr, 20uM SFN, Donor 208

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Agilent Quick Amp Labeling Kit (one-color) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked using a UV Spectrophotometer.

growth_protocol: Human Anagen VI HFs were microdissected and maintained as previously described (Philpott, Green, 1990, Sanders et al. , 1994).

extract_protocol: Total RNA was extracted from 5 HFs per sample group using the Qiagen RNeasy Microkit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: For Nrf2 activation, media was prepared with the addition of either vehicle control (DMSO) or Sulforaphane (SFN)

value: Hair Follicle

value: male


title: siKLF15 [204_siKLF15_G05]


title: siNEGC [200_siRNANegC_E07_2]


title: siKLF15 [187_siKLF15_E05]


title: N_3_LAE16_SB_2

city: Seoul

first: Taek-Seung

last: Kim

address: Anam-ro 145

department: school of civil, Environmental & Architectural Engineering

country: South Korea

institute: Korea University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: Planktonic bacteria in AB medium

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: Growth of P. aeruginosa strain UCBPP-PA14 for 24h in AB medium

extract_protocol: Total RNA was extracted from planktonic P. aeruginosa cells treated without and with LAE using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions.

treatment_protocol: P. aeruginosa as a control sample was cultured in a shaking incubator at 250 rpm and 37℃ for 24 hr in AB medium. And P. aeruginosa cells treated with 50 μM LAE was further cultured at 37 ℃ for 4 hr.

tag: strain


title: siSLC25A10 [212_siSLC25A10_C07]


title: siSLC25A10 [213_siSLC25A10_G07]


title: siNEGC [184_siRNANegC_C05]


title: siNEGC [216_siRNANegC_F07]


title: siNEGC [210_siRNANegC_B09]


title: siKLF15 [186_siKLF15_B07]


title: N_3_LAE16_SB_1

description: P. aeruginosa cells treated with 50 μM LAE was further cultured at 37 ℃ for 4 hr.


title: siSLC25A10 [195_siSLC25A10_G09]


title: ExVivoHairFollicle_24hr_20uMSFN_donor202

source_name: Hair Follicle, 24hr, 20uM SFN, Donor 202


title: ExVivoHairFollicle_24hr_20uMSFN_donor225

source_name: Hair Follicle, 24hr, 20uM SFN, Donor 225


title: siNEGC [200_siRNANegC_E07]


title: ExVivoHairFollicle_24hr_0uMSFN_donor225

description: Gene expression after 24hr in Vehicle Control treated human Hair Follicle

source_name: Hair Follicle, 24hr, Vehicle Control, Donor 225


title: ExVivoHairFollicle_24hr_0uMSFN_donor202

source_name: Hair Follicle, 24hr, Vehicle Control, Donor 202


title: N_1_control_SB_2

description: P. aeruginosa was cultured in a shaking incubator at 250 rpm and 38℃ using an AB medium.


title: N_1_control_SB_1

description: P. aeruginosa was cultured in a shaking incubator at 250 rpm and 37℃ using an AB medium.


title: ExVivoHairFollicle_24hr_0uMSFN_donor208

source_name: Hair Follicle, 24hr, Vehicle Control, Donor 208


title: N244(2nd)_24hpi_rep3

city: Serdang

first: Mohammad Reza

last: Etemadi

state: Selangor

department: Medical Microbiology and Parasitology

country: Malaysia

institute: UPM

hyb_protocol: Hybridization cocktail composed of 10 µg of fragmented aRNA and hybridization controls was hybridized to the GeneChip at 45 ˚C for 16 hours and 60 rpm rotation in hybridization oven.

scan_protocol: The arrays were washed and stained in GeneChip® Fluidics Station 450 prior to scanning with GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, USA).

data_processing:
The array fluorescent  signals were obtained as DAT files and converted to probe intensity data (.CEL)  files using Gene Chip® Command Console® (AGCC) Software.Summarized expression values (CHP files) were created using Robust Multichip Analysis (RMA) summarization algorithm  (25) implemented in Affymetrix® Expression Console™ Software 1.3
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: mock-infected A549 cells at 24hpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of input RNA

growth_protocol: A human adenocarcinomic alveolar basal epithelial cell line, A549, (ATCC®CCL-185™) was cultured in F12K medium (ATCC).

extract_protocol: Viral RNA was extracted from cell culture supernatants at 6, 12, 24, and 48 hpi and also from third PBS wash of the cell monolayer before collecting the cells using GeneJET Viral DNA and RNA Purification Kit.

treatment_protocol: The A549 cells grown in 25 cm2 culture flasks were infected with HRV72 at multiplicity of infection (MOI) of 10 or mock-infected at three independent replicates with a week interval.

tag: cell line

tag: infected with

value: mock


title: V243_24hpi_rep3

description: Vi_24hpi_3rd batch_(PrimeView)

source_name: HRV-infected A549 cells at 24hpi

value: human adenocarcinomic alveolar basal epithelial cell line

value: HRV species B (HRV-B)


title: N244_24hpi_rep1


title: N483_48hpi_rep1

description: NTC_48h_3rd batch_(PrimeView)

source_name: mock-infected A549 cells at 48hpi


title: N485_48hpi_rep3


title: V483_48hpi_rep1

description: Vi_48hpi_3rd batch_(PrimeView)

source_name: HRV-infected A549 cells at 48hpi


title: V244(2nd)_24hpi_rep2


title: V244_24hpi_rep1


title: N484_48hpi_rep2


title: V485_48hpi_rep3


title: V484_48hpi_rep2


title: N245_24hpi_rep2


title: V123_12hpi_rep1

source_name: HRV-infected A549 cells at 12hpi


title: V125_12hpi_rep3


title: N124_12hpi_rep2

source_name: mock-infected A549 cells at 12hpi


title: N123_12hpi_rep1


title: V124_12hpi_rep2


title: N63_ 6hpi_rep2

source_name: mock-infected A549 cells at 6hpi


title: V63_6hpi_rep2

source_name: HRV-infected A549 cells at 6hpi


title: breast_tissue_16_BS

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth College

description: tissue16_BS derived from the same biological sample

hyb_protocol: 1.4ug was carried forward through oxBS conversion with the TrueMethyl protocol, and 1.05ug through the bisulfite conversion arm of the protocol with manufacturer recommended mass and volume.  DNA was then hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

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

data_processing:
minfi, Aryee et al Bioinformatics 2014
minfi, Aryee et al Bioinformatics 2014
We used maximum likelihood to fit the data generating model under the constraints of each C modification (5C, 5mC, 5hmC) > 0, 5C + 5mC + 5hmC = 1, thus estimating parameters 5C (unmethylated proportion), 5mC  (5mC proportion), and 5hmC (5hmC proportion)

extract_protocol: Tumor DNA was extracted with the QIAmp DNeasy tissue kit (Qiagen) according to the manufacturer’s instructions.

value: Breast tissue

tag: Sex

value: Female

tag: subject bmi

tag: subject age


title: V65_6hpi_rep3

tag: cell type


title: breast_tissue_10_BS

description: tissue10_BS derived from the same biological sample


title: V64_6hpi_rep1


title: N64_ 6hpi_rep1


title: N125_12hpi_rep3


title: breast_tissue_13_BS

description: tissue13_BS derived from the same biological sample


title: breast_tissue_1_BS

description: tissue1_BS derived from the same biological sample


title: breast_tissue_6_BS

description: tissue6_BS derived from the same biological sample


title: breast_tissue_17_BS

description: tissue17_BS derived from the same biological sample


title: GK islets (3)

city: Lausanne

first: Imene

last: Henaoui

state: Vaud

address: Rue du Bugnon 9

country: Switzerland

institute: Unil-DNF

description: GK islets_RNA-3

hyb_protocol: After stopping the labeling procedure, the Cy3-labeled samples were hybridized on the Arraystar Rat piRNA Array. Hybridization was performed at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers. After being washed in an ozone-free environment, the slides were fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, piRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Rattus norvegicus

source_name: Islet total RNA

label_protocol: Sample labeling was performed using a RNA ligase method. Briefly, One microgram of each sample was 3'-end-labeled with Cy3 fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Cy3), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA from rat islets was extracted with the miRNeasy kit (Qiagen), following the manufacturer's recommendations.  For microarray analysis, pancreatic islets total RNA were extracted individually. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Goto-Kakizaki (GK)

value: Pancreatic islets

tag: age

value: 3 months


title: breast_tissue_12_BS

description: tissue12_BS derived from the same biological sample


title: breast_tissue_4_BS

description: tissue4_BS derived from the same biological sample


title: breast_tissue_14_BS

description: tissue14_BS derived from the same biological sample


title: breast_tissue_11_BS

description: tissue11_BS derived from the same biological sample


title: breast_tissue_15_BS

description: tissue15_BS derived from the same biological sample


title: breast_tissue_8_BS

description: tissue8_BS derived from the same biological sample


title: breast_tissue_18_BS

description: tissue18_BS derived from the same biological sample


title: breast_tissue_9_BS

description: tissue9_BS derived from the same biological sample


title: breast_tissue_2_BS

description: tissue2_BS derived from the same biological sample


title: breast_tissue_3_BS

description: tissue3_BS derived from the same biological sample


title: breast_tissue_5_BS

description: tissue5_BS derived from the same biological sample


title: Adult_rat-islet_1

extract_protocol: Total RNA from rat islets was extracted with the miRNeasy kit (Qiagen), following the manufacturer's recommendations.  For microarray analysis, pancreatic islets from two P10 pups were pooled while islets from adult rats were extracted individually. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.


title: GK islets (2)

description: GK islets_RNA-2


title: Adult_rat-islet_2


title: P10_rat-islet_3

value: 10 days


title: Wistar islets (2)

description: Wistar islets _RNA-2

value: Wistar


title: Wistar islets (3)

description: Wistar islets _RNA-3


title: Wistar islets (1)

description: Wistar islets _RNA-1


title: A549_siMYEOV_2 rep1

status: Public on Jun 28 2017

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

description: Gene expression data from A549 cells transfected with siMYEOV #2

hyb_protocol: Biotin-labeled sense-strand cDNA were hybridized for 16 hours at 45C on GeneChip with GeneChip Hybridization Oven 640 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: CEL files were obtained by Affymetrix GeneChip Command Console.　Data were normalized by the RMA (Robust Multi-array Average) procedure in R package.

source_name: human lung cancer cell line A549

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: Cells were transfected with siRNA, using Lipofectamine RNAiMAX (Invitrogen), according to the manufacturer's instructions.Total RNA was extracted from A549 cells 48h after transfection.

tag: transfection

value: siMYEOV #2


title: breast_tissue_7_BS

description: tissue7_BS derived from the same biological sample


title: A549_siMYEOV_1 rep1

description: Gene expression data from A549 cells transfected with siMYEOV #1

value: siMYEOV #1


title: P10_rat islet_1

description: P10_rat islet_RNA-1


title: GK islets (1)

description: GK islets_RNA-1


title: VWAT_MeDIP_LG-SC06

city: Chicago

first: Riyue

last: Bao

state: IL

address: 900 E 57 Street

department: Center for Research Informatics

institute: University of Chicago

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2009

hyb_protocol: According to Affymetrix standard protocols

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction

data_processing: GCOS 1.3 software (Affymetrix) was used to produce .cel files. Data were analyzed using the Partek Genomic Suite Software (PGS) (St. Louis, MO).  Signals were adjusted according to probe sequence and background corrected using the Robust Multiarray method (RMA) . Model-based analysis of tiling-arrays (MAT) was used to identify regions of differential DNA methylation by combining adjacent probes showing significant differences between the groups. A sliding windows of 500 bp was set, according to the average size of the fragments produced in the amplicon preparation step

source_name: VWAT DNA from offspring of mother exposed to late gestational sleep control conditions

growth_protocol: Timed pregnant C57BL/6J female mice (6.5 dpc) were obtained from a commercial supplier (Jackson Laboratory, Bar Harbor, ME). All mice were allowed access to food and water ad libitum, and received standard chow containing 10 kcal% fat (Research Diet, New Brunswick) throughout the experiments

extract_protocol: Animals were sacrificed after 3 hours fasting and VWAT samples were collected at age 24 weeks, and immediately snap frozen until processing. DNA was isolated using DNeasy Tissue kit (Qiagen, Valencia, CA) and quantified on a Nanodrop 2000 (NanoDrop products, Wilmington, DE). Isolated DNA was stored at -20 °C until use. The methylated fraction of the genome was immunoprecipitated using the MeDIP protocol (Mohn el atl, 2009). The immunoprecipitated DNA was amplified using an adaptor mediated PCR strategy. MeDIP DNA was blunted using T4 DNA polymerase (NEB, Ipswich MA) and universal adaptors were ligated by overnight incubation at 4°C with T4 ligase (NEB, Ipswich MA). Blunt universal adaptors were prepared by annealing two oligonucleotides (oligo 1: GCGGTGACCCGGGAGATCTGAATTC and oligo 2: GAATTCAGATC).Adaptor-ligated DNA was amplified in 25 µL final volume under the following conditions: 1x PCR buffer (Sigma-Aldrich, St. Lous MO) 2.875 mM MgCl2 (Sigma-Aldrich, Sigma-Aldrich, St. Lous MO), 275 µM aminoallyl dNTP mix (Ambion, Austin, TX), 1.6 µM oligo 1 and 25 units Taq DNA polymerase (NEB, Ipswich MA). A "two-cycling" PCR strategy was used. The first PCR program started with an initial extension at 72°C for 5 min followed by 10 cycles of denaturation at 95°C for 1 minute, annealing at 94°C for 40 seconds and elongation at 72°C for 2.5 minutes, with a final extension step at 72°C for 5 minutes. Five mL of the first PCR product were used a template for the second PCR program. The second PCR program was identical to the first program, but used 15 cycles of denaturation/annealing/extension. Amplification was checked by electrophoresis in agarose gels. PCR products were purified using the MinElute kit (Qiagen, Valencia CA) and quantified using a Nanodrop 2000

treatment_protocol: Pregnant mice were maintained in custom made cages operated under a 12 hour light-dark cycle (7 AM to 7 PM) and exposed to IH, from 15 days post coitus (dpc) until delivery. IH exposures was performed as previously described (Almendros et al. 2014). In brief, mice were subjected to IH with alternating cycles of 90 seconds (6% FIO2 followed by 21% FIO2, 20 cycles/hour) for 12 hours/day during daylight followed by 21% FIO2 for the remaining 12 hours.

value: visceral white adipose tissue (VWAT)

tag: group


title: VWAT_MeDIP_LG-SC05

label_protocol: According to Affymetrix standard protocols

value: late gestational sleep control conditions


title: N65_6hpi_rep3

tag: time point


title: A549_siMYEOV_1 rep2


title: VWAT_MeDIP_LG-SC02

tag: tissue


title: VWAT_MeDIP_LG-SC01


title: VWAT_MeDIP_LG-SC03


title: VWAT_MeDIP_LG-SC04


title: VWAT_MeDIP_LG-SC07


title: VWAT_MeDIP_LG-SC08


title: P10_rat islet_2

description: P10_rat islet_RNA-2


title: A549_siNC_rep2

description: Gene expression data from A549 cells transfected with siNC

value: siNC


title: A549_siMYEOV_2 rep2


title: A549_siNC_rep1


title: VWAT_MeDIP_LG-IH06

source_name: VWAT DNA from offspring of mother exposed to late gestational intermittent hypoxia

value: late gestational intermittent hypoxia


title: MDL-860 treatment

city: Tokyo

first: Minetaro

last: Arita

state: Japan

address: 4-7-1 Gakuen, Musashimurayama-shi,

department: Department of Virology II

country: Japan

institute: National Institute of Infectious Diseases

description: Gene expression after 24 h MDL-86- (20 uM) treatment.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human 8x60K ver.3.0 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting (Scan resolution 3 um, TIFF file dynamic range 20 bit).

data_processing: The scanned images were analyzed and quantified with Feature Extraction Software 10.7.3.1 (Agilent). The raw data was normalized by using a GeneSpring software (Agilent) with 75 Percentile shift.

source_name: MDL-860-treated RD cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using a Low Input Quick Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy mini spin column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RD cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal calf serum at 37°C.

extract_protocol: RNA was prepared using an RNeasy plus mini kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer series II (Agilent Technologies).

treatment_protocol: Supernatant of the cells were removed, and then fresh medium with or without MDL-860 (final concentration of 20 uM) was added to the cells. The cultures were incubated for 24 hours at 37ºC in a humidified incubator with 5% CO2.

value: RD

value: rhabdomyosarcoma cell line

tag: treatment


title: VWAT_MeDIP_LG-IH05

value: male


title: Mock treatment

description: Gene expression after 24 h mock treatment.

source_name: Mock-treated RD cells

value: Mock


title: VWAT_MeDIP_LG-IH04


title: VWAT_MeDIP_LG-IH03


title: VWAT_MeDIP_LG-IH01


title: VWAT_MeDIP_LG-IH07


title: VWAT_MeDIP_LG-IH08


title: SAEC_5AZA+TSA

description: SAMPLE 2

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instruction, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Primary human small airway epithelial cells (SAEC, Lonza, and Walkersville, MD) were cultured in SAGM medium.

extract_protocol: miRNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: SAECs were treated with 3 μg/ml of DNA demethylating agent, 5-aza-2-deoxycytidine (5-aza-dC) on day1, 3, and 1 μg/ml of histone deacetylase (HDAC) inhibitor, trichostatin A (TSA) on day4. Total RNA was extracted on day5.

value: SAEC

value: human small airway epithelial cells

tag: treated with

value: 3 μg/ml of 5-aza-dC on day1, 3 and 1 μg/ml of TSA on day4

value: day 5


title: SAEC_control

description: SAMPLE 1

value: none (control)


title: lung adenocarcinoma cell line_osteoblastic metastasis [Yang2BM(YANG2-3-YSF)]

city: Shanghai

first: Shunfang

last: Yang

address: 241 Huaihai west Road

department: Nuclear Medicine

institute: Shanghai Chest Hospital

description: Gene expression data from osteoblastic metastasis lesion in knee joint

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Human lung adenocarcinoma cell lines

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Human lung adenocarcinoma cell lines (CPA-Yang1, CPA-Yang2, CPA-Yang3, SPC-A-1) and human larger cell lung cancer cell line NCI-H460 were injected into left cardiac ventricle of nude mice for bone metastases clone, respectively. Bone metastatic lesions were detected by bone scintigraphy with 99mTc-methylene diphophonate and X ray. Removed bone metastatic lesions for cell primary culture, chromosome analysis for determine the bone metastatic cells have a characterization of unchanged humanization, in the anesthesia death mice. Through in vivo ~ in vitro selections, the bone-seeking clones 2th, 3th, 4th, 13th, 8th generation cells of CPA-Yang1, CPA-Yang2, CPA-Yang3, SPC-A-1, NCI-H460

value: osteoblastic metastasis lesion

tag: cycles(in vivo-in vtrio)

value: 3 cycles

tag: x-ray treatment

value: NO

tag: organs of metastasis

value: osteoblastic BM


title: lung adenocarcinoma cell line_osteoblastic metastasis clone [SPC-A-1BM(Y15-YSF)]

description: Gene expression data from lung adenocarcinoma cell lines

value: 8 cycles

value: osteoblastic BM,submaxillary gland, adrenal gland,lymph nodes


title: spleen CD1c+.CD141- DC from donor S74

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description:
CD1c+.CD141- DC isolated from spleen tissue of donor S74
SP_CD1c+CD141-.DC_S74

hyb_protocol: Hybridization of cRNA was performed on Illumina Human-HT12 Version 4 chips for 16 hours at 58°C. The arrays were then washed and stained base on Illumina Wash Protocol

scan_protocol: The chips were scanned using BeadArray Scanner 500GX

data_processing: Probe level expression data were exported from Illlumina GenomeStudio software without background subtraction. These raw data were quantile normalized and log (base 2) transformed and in R (3.1.2) using Bioconductor lumi (version 2.18.0) package.

source_name: spleen

label_protocol: Biotinylated cRNA was prepared according to the protocol by Epicentre TargetAmpTM 2-Round Biotin-aRNA Amplification Kit 3.0 using 500pg of total RNA.

extract_protocol: Total RNA was isolated from FACS-sorted fetal skin and spleen (17 -22 wk EGA) DC subsets following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy Micro clean-up procedure according to the manufacturer's protocol. Total RNA integrity was assessed using Agilent Bioanalyzer.

tag: celltype

tag: donorid


title: human larger cell lung cancer cell line_parental [NCI-H460(H460)]

description: Gene expression data from human larger cell lung cancer cell line

source_name: human larger cell lung cancer cell line

tag: cell line

value: human larger cell lung cancer cell line

value: 0 cycle

value: osteoblastic BM, lung, renal, adrenal gland and lymph nodes


title: skin CD1c+.CD141- DC from donor S73

description:
CD1c+.CD141- DC isolated from skin tissue of donor S73
SK_CD1c+CD141-.DC_S73

source_name: skin


title: spleen CD14+ DC from donor S74

description:
CD14+ DC isolated from spleen tissue of donor S74
SP_CD14+.DC_S74


title: Chinese lung adenocarcinoma cell line_parental [CPA-Yang1(Y1-YSF)]

value: lung adenocarcinoma from pericardial effusion

value: YES

value: osteolytic/mixed BM,brain


title: skin CD14+ DC from donor S73

description:
CD14+ DC isolated from skin tissue of donor S73
SK_CD14+.DC_S73


title: Chinese lung adenocarcinoma cell line_parental [CPA-Yang3(Y3-8-YSF)]

value: lung adenocarcinoma from pleural effusion

value: YES/NO

value: bone, lung, liver, adrenal gland, submaxillary gland


title: human larger cell lung cancer cell line_bone metastatic clone_8 cycle [H460BM(S8)]

value: targeted osteoblastic metastases


title: spleen CD141+ DC from donor S74

description:
CD141+ DC isolated from spleen tissue of donor S74
SP_CD141+.DC_S74


title: spleen CD1c+.CD141- DC from donor S20

description:
CD1c+.CD141- DC isolated from spleen tissue of donor S20
SP_CD1c+CD141-.DC_S20


title: spleen CD1c+.CD141- DC from donor S83

description:
CD1c+.CD141- DC isolated from spleen tissue of donor S83
SP_CD1c+CD141-.DC_S83


title: Chinese lung adenocarcinoma cell line_parental [SPC-A-1(A1-YSF)]

value: lung adenocarcinoma  pleural metastasis nodules were surgically removed

value: bone,lung, brain, liver, adrenal gland, lymph nodes


title: skin CD14+ DC from donor S78

description:
CD14+ DC isolated from skin tissue of donor S78
SK_CD14+.DC_S78


title: skin CD1c+.CD141- DC from donor S11

description:
CD1c+.CD141- DC isolated from skin tissue of donor S11
SK_CD1c+CD141-.DC_S11


title: skin CD1c+.CD141- DC from donor S78

description:
CD1c+.CD141- DC isolated from skin tissue of donor S78
SK_CD1c+CD141-.DC_S78


title: Chinese lung adenocarcinoma cell line_parental [CPA-Yang2(Y2-6-YSF)]

value: lung adenocarcinoma from ascites

value: osteoblastic BM,brain, lung, adrenal gland, liver


title: lung adenocarcinoma cell line_targeted osteoblastic metastasis [Yang3BM(Y3-4-YSF)]

value: osteoblastic metastasis lesion

value: 4 cycles

value: osteoblastic BM


title: spleen CD141+ DC from donor S83

description:
CD141+ DC isolated from spleen tissue of donor S83
SP_CD141+.DC_S83


title: spleen CD141+ DC from donor S20

description:
CD141+ DC isolated from spleen tissue of donor S20
SP_CD141+.DC_S20


title: spleen CD14+ DC from donor S83

description:
CD14+ DC isolated from spleen tissue of donor S83
SP_CD14+.DC_S83


title: spleen CD14+ DC from donor S20

description:
CD14+ DC isolated from spleen tissue of donor S20
SP_CD14+.DC_S20


title: skin CD141+ DC from donor S78

description:
CD141+ DC isolated from skin tissue of donor S78
SK_CD141+.DC_S78


title: skin CD141+ DC from donor S73

description:
CD141+ DC isolated from skin tissue of donor S73
SK_CD141+.DC_S73


title: skin CD14+ DC from donor S11

description:
CD14+ DC isolated from skin tissue of donor S11
SK_CD14+.DC_S11


title: lung adenocarcinoma cell line_osteolytic / mixed bone metastasis [Yang1BM(776T-YSF)]

description: Gene expression data from lung adenocarcinoma cell lines

value: osteolytic metastasis lesion

value: 1 cycle

value: osteolytic/mixed BM


title: skin CD141+ DC from donor S11

description:
CD141+ DC isolated from skin tissue of donor S11
SK_CD141+.DC_S11


title: Adult_rat-islet_3

value: Pancreatic islets

value: 3 months


title: VWAT_MeDIP_LG-IH02

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2009

tag: strain

tag: gender

value: male

value: visceral white adipose tissue (VWAT)

value: late gestational intermittent hypoxia


title: control5

city: Jinan

first: Ya-Wen

last: Wang

address: Wen Hua Xi Road 107

institute: Shandong University

description: healthy controls

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: age-matched healthy controls

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Blood samples were collected from 12 females, including 6 breast cancer patients and 6 healthy age-matched female volunteers who served as controls for this study, at Qilu Hospital of Shandong University (Shandong, China). All patients had histologically confirmed breast cancer. The control blood samples were collected from healthy women with no current or previous malignancy, or inflammatory condition. All blood samples were collected before any therapeutic procedures, such as surgery, chemotherapy and radiotherapy, were performed.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The unprocessed whole blood sample was immediately stored at -80°C until further analysis.

value: female

tag: sample type

value: blood


title: control6

description: healthy controls


title: control3

description: healthy controls


title: control4

description: healthy controls


title: control2

description: healthy controls


title: control1

description: healthy controls


title: 2K003

description: breast cancer patients

source_name: breast cancer patients


title: 2K004

description: breast cancer patients


title: 2K002

description: breast cancer patients


title: 2K006

description: breast cancer patients


title: 2K005

description: breast cancer patients


title: 14 days after electroporation_e

city: Marseille

first: christophe

last: beclin

state: Bouches du Rhone

address: campus de Luminy, case 907

department: Aix-Marseille université

country: France

institute: CNRS

description: Biological replicate 4 of 4 of the 14 days time-point

hyb_protocol: Cy3 and Cy5 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (4x44K, AMADID) 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 and a final wash step with acetonitrile for 30 sec at RT.

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 10.5.1.1 ) was used to read out and process the microarray image files.

molecule: polyA RNA

source_name: GFP cells FACS sorted after in vivo electroporation

label_protocol: 200 ng of each of the amplified cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: RNA was extracted in the SuperAmp™ Lysis Buffer following manufacturer's instructions.  mRNAs were amplified according   to Miltenyi Biotec’s SuperAmp Service undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

tag: time after electroporation

value: 14 days

tag: targeted tissue

value: Progenitors of the SVZ dorsal wall

tag: developmental stage

value: Progenitors of the SVZ lateral wall


title: 14 days after electroporation_a

description: Biological replicate 1 of 4 of the 14 days time-point


title: 1 day after electroporation_d

description: Biological replicate 3 of 3 of the 1 day time-point

value: 1 day


title: 2K001

description: breast cancer patients


title: 7 days after electroporation_b

description: Biological replicate 2 of 3 of the 7 days time-point

value: 7 days


title: 7 days after electroporation_a

description: Biological replicate 1 of 3 of the 7 days time-point


title: 4 days after electroporation_a

description: Biological replicate 1 of 3 of the 4 days time-point

value: 4 days


title: 4 days after electroporation_b

description: Biological replicate 2 of 3 of the 4 days time-point


title: 14 days after electroporation_b

description: Biological replicate 2 of 4 of the 14 days time-point


title: 2 days after electroporation_a

description: Biological replicate 1 of 2 of the 2 days time-point

value: 2 days


title: 2 days after electroporation_b

description: Biological replicate 2 of 2 of the 2 days time-point


title: 1 day after electroporation_c

description: Biological replicate 2 of 3 of the 1 day time-point


title: 8 hours after electroporation_a

description: Biological replicate 1 of 2 of the 8 hours time-point

value: 8 hours


title: 14 days after electroporation_d

description: Biological replicate 3 of 4 of the 14 days time-point


title: AS_F6_1-25-0624-3

status: Public on Jun 27 2017

city: Boston

first: Joseph

last: Perez-Rogers

address: 72 East Concord St

department: Bioinformatics

institute: Boston University

description: Gene expression data from NEC specimen

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: All 505 microarray CEL files were normalized together using the RMA algorithm implemented in the affy Bioconductor R package and the corresponding default Gene 1.0 ST CDF. ComBat (sva Bioconductor package) was used to correct for microarray batch effects. No covariates other than batch were included in the ComBat model.

source_name: NEC specimen

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: not applicable

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

treatment_protocol: not applicable

tag: lung cancer status

value: No Lung Cancer

tag: smoking status

value: Current Smoker

tag: time since quit

tag: mass size

tag: age

value: Male

tag: rin

tag: batch

tag: pack years


title: 4 days after electroporation_c

description: Biological replicate 3 of 3 of the 4 days time-point


title: 7 days after electroporation_c

description: Biological replicate 3 of 3 of the 7 days time-point


title: AS_F7_1-16-0711-3

description: Gene expression data from NEC specimen

value: Lung Cancer


title: AS_F6_1-23-0521-3

description: Gene expression data from NEC specimen

value: Former Smoker

value: Female


title: AS_F6_1-15-0558-3

description: Gene expression data from NEC specimen


title: AS_F5_1-25-0567-3

description: Gene expression data from NEC specimen


title: AS_F5_1-16-0685-3

description: Gene expression data from NEC specimen


title: 8 hours after electroporation_b

description: Biological replicate 2 of 2 of the 8 hours time-point


title: 1 day after electroporation_b

description: Biological replicate 1 of 3 of the 1 day time-point


title: AS_F3_1-15-0575-3Re

description: Gene expression data from NEC specimen

value: Ill defined infiltrate


title: AS_F4_1-25-0554-3

description: Gene expression data from NEC specimen


title: AS_F5_1-18-0509-3

description: Gene expression data from NEC specimen


title: AS_F1_1-24-0507-3

description: Gene expression data from NEC specimen


title: AS_F2_1-7-0543-3

description: Gene expression data from NEC specimen


title: AS_F3_1-17-0541-3

description: Gene expression data from NEC specimen


title: AS_F1_1-17-0548-3

description: Gene expression data from NEC specimen


title: AS_F3_1-25-0718-3

description: Gene expression data from NEC specimen


title: AS_F3_1-15-0549-3

description: Gene expression data from NEC specimen


title: AS_F4_1-21-0569-3

description: Gene expression data from NEC specimen


title: AS_E8_1-22-0538-3

description: Gene expression data from NEC specimen


title: AS_E8_1-25-0716-3

description: Gene expression data from NEC specimen


title: AS_E8_1-16-0691-3

description: Gene expression data from NEC specimen


title: AS_E8_1-12-0566-3

description: Gene expression data from NEC specimen


title: AS_E7_1-16-0630-3

description: Gene expression data from NEC specimen


title: AS_F1_1-16-0628-3

description: Gene expression data from NEC specimen


title: AS_E6_1-23-0515-3

description: Gene expression data from NEC specimen


title: AS_E6_1-19-0525-3

description: Gene expression data from NEC specimen


title: AS_F2_1-26-0571-3

description: Gene expression data from NEC specimen


title: AS_F1_1-11-0541-3

description: Gene expression data from NEC specimen


title: AS_F2_1-21-0564-3

description: Gene expression data from NEC specimen


title: AS_E6_1-16-0745-3

description: Gene expression data from NEC specimen


title: AS_E7_1-5-0595-3

description: Gene expression data from NEC specimen


title: AS_E5_1-23-0529-3

description: Gene expression data from NEC specimen


title: AS_E6_1-26-0570-3

description: Gene expression data from NEC specimen


title: AS_E5_1-17-0527-3

description: Gene expression data from NEC specimen


title: AS_E5_1-16-0652-3

description: Gene expression data from NEC specimen


title: AS_E5_1-16-0624-3

description: Gene expression data from NEC specimen


title: AS_E3_1-15-0530-3

description: Gene expression data from NEC specimen


title: AS_E3_1-28-0521-3

description: Gene expression data from NEC specimen


title: AS_E4_1-21-0542-3

description: Gene expression data from NEC specimen


title: AS_E2_1-16-0632-3

description: Gene expression data from NEC specimen


title: AS_E4_1-5-0594-3

description: Gene expression data from NEC specimen


title: AS_E2_1-25-0747-3

description: Gene expression data from NEC specimen


title: AS_E2_1-5-0621-3

description: Gene expression data from NEC specimen


title: AS_E5_1-16-0679-3

description: Gene expression data from NEC specimen


title: AS_D8_1-23-0530-3

description: Gene expression data from NEC specimen


title: AS_E1_1-22-0563-3

description: Gene expression data from NEC specimen


title: AS_D5_1-29-0504-3

description: Gene expression data from NEC specimen


title: AS_E1_1-18-0508-3

description: Gene expression data from NEC specimen


title: AS_D3_1-26-0561-3Re

description: Gene expression data from NEC specimen


title: AS_E1_1-22-0544-3

description: Gene expression data from NEC specimen


title: AS_D5_1-16-0675-3

description: Gene expression data from NEC specimen


title: AS_D8_1-26-0564-3

description: Gene expression data from NEC specimen


title: AS_D3_1-16-0663-3

description: Gene expression data from NEC specimen


title: AS_D7_1-7-0547-3

description: Gene expression data from NEC specimen


title: AS_D6_1-15-0599-3

description: Gene expression data from NEC specimen


title: AS_E1_1-16-0659-3

description: Gene expression data from NEC specimen


title: AS_D3_1-7-0546-3

description: Gene expression data from NEC specimen


title: AS_E1_1-16-0670-3

description: Gene expression data from NEC specimen


title: AS_D2_1-25-0553-3

description: Gene expression data from NEC specimen


title: AS_D7_1-12-0572-3

description: Gene expression data from NEC specimen


title: AS_D2_1-25-0635-3

description: Gene expression data from NEC specimen


title: AS_D1_1-26-0548-3

description: Gene expression data from NEC specimen


title: AS_D1_1-5-0622-2

description: Gene expression data from NEC specimen


title: AS_D1_1-25-0650-3

description: Gene expression data from NEC specimen


title: AS_C6_1-15-0554-3

description: Gene expression data from NEC specimen


title: AS_C8_1-16-0733-3

description: Gene expression data from NEC specimen


title: AS_D2_1-22-0546-3

description: Gene expression data from NEC specimen


title: AS_C7_1-17-0549-3

description: Gene expression data from NEC specimen


title: AS_C5_1-17-0555-3

description: Gene expression data from NEC specimen


title: AS_C5_1-5-0578-3

description: Gene expression data from NEC specimen


title: AS_C4_1-26-0525-3

description: Gene expression data from NEC specimen


title: AS_C5_1-25-0609-3

description: Gene expression data from NEC specimen


title: AS_C3_1-5-0604-3

description: Gene expression data from NEC specimen


title: AS_C3_1-16-0688-3

description: Gene expression data from NEC specimen


title: AS_C4_1-16-0743-3

description: Gene expression data from NEC specimen


title: AS_B8_1-22-0547-3

description: Gene expression data from NEC specimen


title: AS_B7_1-16-0653-3

description: Gene expression data from NEC specimen


title: AS_C2_1-5-0580-3

description: Gene expression data from NEC specimen


title: AS_C1_1-22-0570-3

description: Gene expression data from NEC specimen


title: AS_C1_1-17-0550-3

description: Gene expression data from NEC specimen


title: AS_B7_1-12-0562-3

description: Gene expression data from NEC specimen


title: AS_C2_1-16-0722-3

description: Gene expression data from NEC specimen


title: AS_B8_1-17-0558-3

description: Gene expression data from NEC specimen


title: AS_C3_1-15-0585-3

description: Gene expression data from NEC specimen


title: AS_C1_1-26-0535-3

description: Gene expression data from NEC specimen


title: AS_C1_1-16-0744-3

description: Gene expression data from NEC specimen


title: AS_B7_1-25-0752-3

description: Gene expression data from NEC specimen


title: AS_B8_1-16-0703-3

description: Gene expression data from NEC specimen


title: AS_B6_1-25-0556-3

description: Gene expression data from NEC specimen


title: AS_B6_1-16-0741-3

description: Gene expression data from NEC specimen


title: AS_B6_1-23-0527-3

description: Gene expression data from NEC specimen


title: AS_B5_1-22-0539-3

description: Gene expression data from NEC specimen


title: AS_B6_1-24-0508-3

description: Gene expression data from NEC specimen


title: AS_B5_1-5-0588-3

description: Gene expression data from NEC specimen


title: AS_B4_1-5-0610-3

description: Gene expression data from NEC specimen


title: AS_B4_1-25-0644-3

description: Gene expression data from NEC specimen


title: AS_B4_1-15-0532-3

description: Gene expression data from NEC specimen


title: AS_B4_1-22-0567-3

description: Gene expression data from NEC specimen


title: AS_B4_1-21-0557-3

description: Gene expression data from NEC specimen


title: AS_B3_1-18-0512-3

description: Gene expression data from NEC specimen


title: AS_B3_1-16-0689-3

description: Gene expression data from NEC specimen


title: AS_B2_1-24-0502-3

description: Gene expression data from NEC specimen


title: AS_B2_1-5-0582-3

description: Gene expression data from NEC specimen


title: AS_B3_1-25-0613-3

description: Gene expression data from NEC specimen


title: AS_B2_1-12-0539-3

description: Gene expression data from NEC specimen


title: AS_B1_1-25-0547-3

description: Gene expression data from NEC specimen


title: AS_B2_1-21-0535-3

description: Gene expression data from NEC specimen


title: AS_B3_1-21-0540-3

description: Gene expression data from NEC specimen


title: AS_B1_1-16-0629-3

description: Gene expression data from NEC specimen


title: AS_B1_1-21-0562-3

description: Gene expression data from NEC specimen


title: AS_A8_1-25-0623-3

description: Gene expression data from NEC specimen


title: AS_A7_1-16-0735-3

description: Gene expression data from NEC specimen


title: AS_A8_1-19-0519-3

description: Gene expression data from NEC specimen


title: AS_A7_1-16-0664-2

description: Gene expression data from NEC specimen


title: AS_A7_1-22-0534-3

description: Gene expression data from NEC specimen


title: AS_A7_1-26-0572-3

description: Gene expression data from NEC specimen


title: AS_A8_1-15-0564-3

description: Gene expression data from NEC specimen


title: AS_A6_1-7-0551-3

description: Gene expression data from NEC specimen


title: AS_A7_1-25-0712-3

description: Gene expression data from NEC specimen


title: AS_A5_1-26-0565-3

description: Gene expression data from NEC specimen


title: AS_A5_1-16-0700-3

description: Gene expression data from NEC specimen


title: AS_A5_1-16-0720-3

description: Gene expression data from NEC specimen


title: AS_A4_1-17-0531-3

description: Gene expression data from NEC specimen


title: AS_A4_1-25-0733-3

description: Gene expression data from NEC specimen


title: AS_A3_1-16-0654-3

description: Gene expression data from NEC specimen


title: AS_A2_1-21-0573-3

description: Gene expression data from NEC specimen


title: AS_A3_1-16-0669-3

description: Gene expression data from NEC specimen


title: AS_A5_1-22-0561-3

description: Gene expression data from NEC specimen


title: AS_A5_1-25-0725-3

description: Gene expression data from NEC specimen


title: AS_A3_1-25-0545-3

description: Gene expression data from NEC specimen


title: AS_F6_1-26-0507-3

description: Gene expression data from NEC specimen


title: AS_A4_1-22-0555-3

description: Gene expression data from NEC specimen


title: AS_F4_1-25-0520-3

description: Gene expression data from NEC specimen


title: AS_F8_1-5-0574-3

description: Gene expression data from NEC specimen


title: AS_A1_1-22-0562-3

description: Gene expression data from NEC specimen


title: AS_F4_1-6-0030-3

description: Gene expression data from NEC specimen


title: AS_F4_1-10-0032-2

description: Gene expression data from NEC specimen


title: AS_F3_1-13-0165-3

description: Gene expression data from NEC specimen


title: AS_F5_1-16-0562-3

description: Gene expression data from NEC specimen


title: AS_E8_1-12-0540-3

description: Gene expression data from NEC specimen


title: AS_F2_1-3-0011-3

description: Gene expression data from NEC specimen


title: AS_E7_1-5-0510-3

description: Gene expression data from NEC specimen


title: AS_F5_1-14-0137-3

description: Gene expression data from NEC specimen


title: AS_E4_1-25-0523-3

description: Gene expression data from NEC specimen


title: AS_F2_1-23-0506-3

description: Gene expression data from NEC specimen


title: AS_E7_1-18-0503-3

description: Gene expression data from NEC specimen


title: AS_E6_1-25-0521-3

description: Gene expression data from NEC specimen


title: AS_E3_1-19-0515-3

description: Gene expression data from NEC specimen


title: AS_F1_1-17-0516-3

description: Gene expression data from NEC specimen


title: AS_E4_1-12-0021-3

description: Gene expression data from NEC specimen


title: AS_E2_1-16-0543-3

description: Gene expression data from NEC specimen


title: AS_D7_1-16-0549-3

description: Gene expression data from NEC specimen


title: AS_D7_1-5-0525-3

description: Gene expression data from NEC specimen


title: AS_D8_1-16-0522-3

description: Gene expression data from NEC specimen


title: AS_E2_1-14-0038-3

description: Gene expression data from NEC specimen


title: AS_E4_1-17-0506-3

description: Gene expression data from NEC specimen


title: AS_E3_1-10-0018-3

description: Gene expression data from NEC specimen


title: AS_D8_1-17-0513-3

description: Gene expression data from NEC specimen


title: AS_E3_1-16-0542-3

description: Gene expression data from NEC specimen


title: AS_D7_1-14-0105-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_668A

city: Bethesda

first: Xin

middle: Wei

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using GeneChip Scanner 3000 uisng AGCC software

data_processing:
PARTEK Genomic suite (6.6) was used to import allele intensity from the CEL files. Interrogating probes was imported without filtering probes. Adjusmentt for fragment length and probe sequence was performed using the Partek default option. Post import values were corrected for localized GC content using the inbuilt Partek feature based on methods described in Diskin et al. (Nucleic Acids Research. 2008. 36:19). Copy number data was estimated from signal intensity on Affmetrix SNP 6.0 arrays. Copy number ratio values were generated in Partek Genomics Suite (v 6.6) using a paired non-tumor sample as reference following the paired workflow.
Copy number ratio values of tumor sample using a paired non-tumor sample as reference (total 153 columns)

source_name: CCA Tumor Tissue

label_protocol: Standard Affymetrix procedures

extract_protocol: Total DNA was extracted from frozen tissue using Phenol/Chloroform extraction protocol. Samples with sufficient amount of double-stranded DNA as confirmed by Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) were included for array studies.

tag: tissue

value: Liver Tumor Tissue

tag: disease state

value: Cholangiocarcinoma (CCA)

tag: sample name matched with transcriptome data

tag: individual


title: CCA Tumor Tissue LCS_674A


title: CCA Tumor Tissue LCS_664A


title: AS_D5_1-14-0064-3

description: Gene expression data from NEC specimen

tag: gender


title: CCA Tumor Tissue LCS_581A


title: AS_D6_1-20-0505-3

description: Gene expression data from NEC specimen


title: AS_D6_1-22-0518-3

description: Gene expression data from NEC specimen


title: AS_D5_1-16-0590-3

description: Gene expression data from NEC specimen


title: AS_D6_1-5-0544-3

description: Gene expression data from NEC specimen


title: AS_D4_1-7-0537-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_642A


title: AS_D4_1-5-0515-3

description: Gene expression data from NEC specimen


title: AS_D8_1-22-0521-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_567A

source_name: HCC Tumor Tissue

value: Hepatocellular carcinoma (HCC)


title: HCC Tumor Tissue LCS_523A


title: HCC Tumor Tissue LCS_550A


title: AS_D4_1-22-0513-3

description: Gene expression data from NEC specimen


title: AS_D4_1-11-0530-3

description: Gene expression data from NEC specimen


title: AS_D6_1-25-0532-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_625A


title: AS_D4_1-25-0529-3

description: Gene expression data from NEC specimen


title: AS_D3_1-5-0537-RE

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_657A


title: AS_D3_1-21-0520-3

description: Gene expression data from NEC specimen


title: AS_D2_1-01-0070-3

description: Gene expression data from NEC specimen


title: AS_D2_1-12-0561-3

description: Gene expression data from NEC specimen


title: AS_D1_1-15-0507-1

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_679A


title: CCA Tumor Tissue LCS_678A


title: CCA Tumor Tissue LCS_620A


title: HCC Tumor Tissue LCS_535A


title: CCA Tumor Tissue LCS_604A


title: AS_D1_1-5-0569-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_609A


title: HCC Tumor Tissue LCS_553A


title: CCA Tumor Tissue LCS_670A


title: HCC Tumor Tissue LCS_558A


title: CCA Tumor Tissue LCS_608A


title: AS_C7_1-5-0572-3

description: Gene expression data from NEC specimen


title: AS_C7_1-26-0513-3

description: Gene expression data from NEC specimen


title: AS_C7_1-20-0507-3

description: Gene expression data from NEC specimen


title: AS_C8_1-7-0508-3

description: Gene expression data from NEC specimen


title: AS_C7_1-26-0506-3

description: Gene expression data from NEC specimen


title: AS_C6_1-17-0517-3

description: Gene expression data from NEC specimen


title: AS_C6_1-23-0505-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_615A


title: AS_C5_1-11-0540-3

description: Gene expression data from NEC specimen


title: AS_C6_1-14-0118-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_585A


title: CCA Tumor Tissue LCS_596A


title: HCC Tumor Tissue LCS_543A


title: HCC Tumor Tissue LCS_519A


title: AS_C4_1-22-0501-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_583A


title: AS_C4_1-6-0022-3

description: Gene expression data from NEC specimen


title: AS_C5_1-11-0012-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_592A


title: HCC Tumor Tissue LCS_518A


title: HCC Tumor Tissue LCS_507A


title: AS_C4_1-16-0613-3

description: Gene expression data from NEC specimen


title: AS_C3_1-26-0523-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_651A


title: CCA Tumor Tissue LCS_639A


title: CCA Tumor Tissue LCS_648A


title: HCC Tumor Tissue LCS_525A


title: HCC Tumor Tissue LCS_551A


title: CCA Tumor Tissue LCS_633A


title: HCC Tumor Tissue LCS_509A


title: HCC Tumor Tissue LCS_563A


title: HCC Tumor Tissue LCS_532A


title: AS_C2_1-8-0527-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_667A


title: AS_B8_1-3-0019-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_527A


title: AS_C1_1-22-0530-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_671A


title: AS_C2_1-5-0570-3

description: Gene expression data from NEC specimen


title: AS_B7_1-6-0023-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_520A


title: AS_C3_1-26-0505-3

description: Gene expression data from NEC specimen


title: AS_B8_1-18-0502-3

description: Gene expression data from NEC specimen


title: AS_B8_1-22-0510-2

description: Gene expression data from NEC specimen


title: AS_B7_1-16-0612-3

description: Gene expression data from NEC specimen


title: AS_C2_1-6-0026-3

description: Gene expression data from NEC specimen


title: AS_B6_1-7-0535-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_610A


title: AS_B6_1-15-0527-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_552A


title: AS_B5_1-16-0531-3

description: Gene expression data from NEC specimen


title: AS_B5_1-11-0526-3

description: Gene expression data from NEC specimen


title: AS_B5_1-12-0516-3

description: Gene expression data from NEC specimen


title: AS_B5_1-20-0506-3

description: Gene expression data from NEC specimen


title: AS_B3_1-15-0519-3-RE

description: Gene expression data from NEC specimen


title: AS_B3_1-7-0531-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_631A


title: CCA Tumor Tissue LCS_621A


title: CCA Tumor Tissue LCS_606A


title: AS_B1_1-16-0614-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_646A


title: AS_B4_1-7-0536-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_544A


title: HCC Tumor Tissue LCS_547A


title: CCA Tumor Tissue LCS_614A


title: HCC Tumor Tissue LCS_536A


title: CCA Tumor Tissue LCS_684A


title: HCC Tumor Tissue LCS_534A


title: AS_A8_1-16-0553-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_616A


title: AS_A8_1-12-0521-3

description: Gene expression data from NEC specimen


title: AS_A7_1-13-0170-3

description: Gene expression data from NEC specimen


title: AS_B2_1-5-0522-3

description: Gene expression data from NEC specimen


title: AS_B1_1-11-0515-3

description: Gene expression data from NEC specimen


title: AS_A8_1-14-0141-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_600A


title: AS_B2_1-16-0580-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_658A


title: AS_A6_1-16-0558-3

description: Gene expression data from NEC specimen


title: AS_A6_1-12-0533-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_688B

scan_protocol: Standard Affymetrix procedures using GeneChip Scanner 3000 and AGCC software

data_processing: Raw gene expression data were analyzed on gene level and normalized using the Robust Multi-array Average (RMA) method and sketch-quantile normalization method on Affymetrix Expression Console Software Build 1.3.1.187.

source_name: CCA Non-Tumor Tissue

extract_protocol: Total RNA was isolated from frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: Liver Non-Tumor Tissue


title: CCA Non-Tumor Tissue LCS_682B


title: CCA Non-Tumor Tissue LCS_683B


title: AS_A6_1-12-0534-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_685B


title: CCA Tumor Tissue LCS_688A


title: AS_A5_1-25-0526-3

description: Gene expression data from NEC specimen


title: AS_A6_1-11-0506-3

description: Gene expression data from NEC specimen


title: AS_A6_1-19-0506-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_683A


title: CCA Non-Tumor Tissue LCS_687B


title: CCA Tumor Tissue LCS_654A


title: CCA Tumor Tissue LCS_652A


title: CCA Tumor Tissue LCS_687A


title: CCA Tumor Tissue LCS_640A


title: CCA Non-Tumor Tissue LCS_681B


title: CCA Non-Tumor Tissue LCS_684B


title: CCA Tumor Tissue LCS_685A


title: CCA Tumor Tissue LCS_684A


title: CCA Tumor Tissue LCS_682A


title: CCA Tumor Tissue LCS_630A


title: CCA Tumor Tissue LCS_635A


title: CCA Tumor Tissue LCS_681A


title: CCA Tumor Tissue LCS_587A


title: CCA Non-Tumor Tissue LCS_680B


title: CCA Non-Tumor Tissue LCS_679B


title: AS_A3_1-16-0519-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_679A


title: AS_A4_1-12-0031-3

description: Gene expression data from NEC specimen


title: AS_A4_1-5-0571-3

description: Gene expression data from NEC specimen


title: AS_A4_1-5-0013-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_566A


title: CCA Tumor Tissue LCS_680A


title: CCA Tumor Tissue LCS_572A


title: CCA Tumor Tissue LCS_571A


title: CCA Non-Tumor Tissue LCS_678B


title: CCA Tumor Tissue LCS_678A


title: AS_A3_1-16-0619-3

description: Gene expression data from NEC specimen


title: AS_A3_1-11-0024-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_677B


title: AS_A2_1-20-0512-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_677A


title: CCA Non-Tumor Tissue LCS_675B


title: CCA Non-Tumor Tissue LCS_674B


title: AS_A2_1-14-0133-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_675A


title: CCA Non-Tumor Tissue LCS_671B


title: AS_A2_1-14-0128-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_674A


title: HCC Tumor Tissue LCS_559A


title: HCC Tumor Tissue LCS_516A


title: CCA Tumor Tissue LCS_687A


title: CCA Tumor Tissue LCS_688A


title: AS_A2_1-14-0094-3

description: Gene expression data from NEC specimen


title: HCC Tumor Tissue LCS_510A


title: CCA Tumor Tissue LCS_670A


title: CCA Tumor Tissue LCS_671A


title: CCA Tumor Tissue LCS_677A


title: CCA Tumor Tissue LCS_668A


title: AS_A1_1-19-0509-3

description: Gene expression data from NEC specimen


title: AS_A2_1-05-0078-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_667B


title: CCA Non-Tumor Tissue LCS_670B


title: CCA Non-Tumor Tissue LCS_668B


title: AS_A1_1-21-0524-3

description: Gene expression data from NEC specimen


title: AS_A1_1-01-0044-3

description: Gene expression data from NEC specimen


title: AS_A1_1-16-0563-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_602A


title: AS_A1_1-14-0076-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_669B


title: CCA Tumor Tissue LCS_667A


title: CCA Non-Tumor Tissue LCS_654B


title: AS_C1_1-23-0507-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_658A


title: CCA Non-Tumor Tissue LCS_653B


title: AS_E3_1-11-0514-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_657A


title: CCA Non-Tumor Tissue LCS_658B


title: CCA Tumor Tissue LCS_669A


title: CCA Tumor Tissue LCS_664A


title: HCC Tumor Tissue LCS_511A


title: CCA Non-Tumor Tissue LCS_657B


title: CCA Tumor Tissue LCS_653A


title: CCA Tumor Tissue LCS_654A


title: CCA Non-Tumor Tissue LCS_664B


title: CCA Tumor Tissue LCS_634A


title: CCA Tumor Tissue LCS_644A


title: AS_E8_1-26-0501-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_603A


title: CCA Tumor Tissue LCS_650A


title: CCA Tumor Tissue LCS_643A


title: CCA Non-Tumor Tissue LCS_652B


title: CCA Tumor Tissue LCS_645A


title: HCC Tumor Tissue LCS_530A


title: CCA Tumor Tissue LCS_597A


title: CCA Non-Tumor Tissue LCS_650B


title: CCA Non-Tumor Tissue LCS_651B


title: AS_D4_1-25-0512-3

description: Gene expression data from NEC specimen


title: AS_E5_1-6-0031-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_652A


title: AS_B8_10-0501_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_649B


title: CCA Tumor Tissue LCS_650A


title: CCA Tumor Tissue LCS_651A


title: AS_A7_7918_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_645B


title: AS_B8_1-1-0027-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_627A


title: CCA Tumor Tissue LCS_644A


title: CCA Non-Tumor Tissue LCS_646B


title: CCA Tumor Tissue LCS_646A


title: CCA Tumor Tissue LCS_649A


title: AS_E1_1-14-0096-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_648A


title: CCA Tumor Tissue LCS_669A


title: CCA Non-Tumor Tissue LCS_643B


title: CCA Non-Tumor Tissue LCS_648B


title: AS_B7_7860_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_C5_1-12-0507-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_644B


title: CCA Tumor Tissue LCS_685A


title: CCA Tumor Tissue LCS_645A


title: CCA Tumor Tissue LCS_579A


title: CCA Tumor Tissue LCS_641A


title: CCA Tumor Tissue LCS_613A


title: HCC Tumor Tissue LCS_545A


title: CCA Tumor Tissue LCS_642A


title: HCC Tumor Tissue LCS_531A


title: AS_E4_1-14-0052-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_641B


title: CCA Non-Tumor Tissue LCS_639B


title: HCC Tumor Tissue LCS_584A


title: AS_C5_1-15-0521-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_641A


title: CCA Tumor Tissue LCS_590A


title: AS_E3_1-12-0549-3

description: Gene expression data from NEC specimen


title: AS_C2_1-16-0564-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_640B


title: AS_C7_6-0008_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_642B


title: CCA Non-Tumor Tissue LCS_638B


title: AS_E7_7861_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_B6_1-5-0542-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_636B


title: CCA Tumor Tissue LCS_639A


title: CCA Tumor Tissue LCS_638A


title: HCC Tumor Tissue LCS_539A


title: AS_B8_1-6-0027-3

description: Gene expression data from NEC specimen


title: AS_A8_1-6-0035-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_640A


title: CCA Non-Tumor Tissue LCS_635B


title: CCA Non-Tumor Tissue LCS_634B


title: CCA Tumor Tissue LCS_637A


title: CCA Non-Tumor Tissue LCS_637B


title: CCA Tumor Tissue LCS_574A


title: CCA Tumor Tissue LCS_635A


title: CCA Tumor Tissue LCS_636A


title: CCA Tumor Tissue LCS_683A


title: HCC Tumor Tissue LCS_568A


title: CCA Tumor Tissue LCS_601A


title: CCA Tumor Tissue LCS_598A


title: HCC Tumor Tissue LCS_524A


title: HCC Tumor Tissue LCS_533A


title: CCA Tumor Tissue LCS_631A


title: CCA Non-Tumor Tissue LCS_633B


title: AS_F8_7916_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_633A


title: AS_B3_1-6-0017-3

description: Gene expression data from NEC specimen


title: AS_D2_1-1-0022-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_631B


title: AS_D7_1-21-0513-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_628B


title: AS_B3_1-25-0505-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_630A


title: CCA Non-Tumor Tissue LCS_630B


title: AS_B7_1-13-0156-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_634A


title: CCA Tumor Tissue LCS_627A


title: CCA Tumor Tissue LCS_626A


title: HCC Tumor Tissue LCS_546A


title: CCA Non-Tumor Tissue LCS_624B


title: CCA Non-Tumor Tissue LCS_625B


title: AS_C6_1-16-0552-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_625A


title: AS_E3_1-16-0585-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_628A


title: CCA Non-Tumor Tissue LCS_626B


title: CCA Tumor Tissue LCS_624A


title: CCA Non-Tumor Tissue LCS_627B


title: CCA Tumor Tissue LCS_570A


title: CCA Tumor Tissue LCS_580A


title: CCA Non-Tumor Tissue LCS_623B


title: HCC Tumor Tissue LCS_564A


title: CCA Tumor Tissue LCS_623A


title: CCA Tumor Tissue LCS_682A


title: AS_B4_1-21-0511-3

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_586A


title: CCA Tumor Tissue LCS_594A


title: AS_D3_1-16-0570-3

description: Gene expression data from NEC specimen


title: AS_C4_14-0059_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: AS_D3_7888_(HuGene-1_0-st-v1)

description: Gene expression data from NEC specimen


title: CCA Tumor Tissue LCS_643A


title: CCA Tumor Tissue LCS_649A


title: CCA Tumor Tissue LCS_623A


title: AS_D5_1-14-0126-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_619B


title: CCA Non-Tumor Tissue LCS_618B


title: CCA Tumor Tissue LCS_618A


title: AS_D5_1-10-0014-3

description: Gene expression data from NEC specimen


title: AS_B2_1-12-0526-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_616B


title: CCA Tumor Tissue LCS_615A


title: CCA Non-Tumor Tissue LCS_621B


title: AS_C8_1-16-0528-3

description: Gene expression data from NEC specimen


title: CCA Non-Tumor Tissue LCS_620B


title: CCA Tumor Tissue LCS_620A


title: CCA Non-Tumor Tissue LCS_615B


title: CCA Tumor Tissue LCS_621A


title: CCA Tumor Tissue LCS_613A


title: CCA Tumor Tissue LCS_680A