title: higA mutant of PA14

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: Gene expression data for IPTG induction of cells containing pCA24N_dosP.

hyb_protocol: Following affymetrix protocol.  Prepared hybridization cocktail for Single Probe Array (169 mini Format) with total 80 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labeled cDNA.  After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45°C, with 60 rpm for 16 hours.  After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol.  After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: Data was analyzed in the Affymetrix GenomeChipOperating Software (GCOS).

organism: Pseudomonas aeruginosa PA14

source_name: PA14 higA mutant

label_protocol: Following affymetrix protocol.  cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

growth_protocol: Strains were grown in LB for the wild-type and LBGm15 for the higA mutant at 37°C with shaking at 250 rpm.  16 h overnight cultures were diluted to OD600 = 0.05 into fresh LB, grown to OD600 ~ 2.0.

extract_protocol: Cells were lysed using a bead beater (Biospec) and mRNA was isolated using a Qiagen RNeasy mini kit (Cat# 74104).

treatment_protocol: Cells were pelleted in the presence of RNALater (Applied Biosystems) and flash frozen in ethanol-dry ice.

value: higA


title: MG1363_Butanol_60min_Rep1

status: Public on Nov 04 2016

type: RNA

city: Kgs. Lyngby

first: Mogens

last: Kilstrup

address: Building 301 room 158

department: DTU Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Hydridzation according to Aglient Protocol. Aglient 8x15k custom microarray G2509F

scan_protocol: Aglient technologies scanner G2505C. Aglient’s Feature Extraction Software

data_processing: Quantile normalization

molecule: total RNA

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: MG1363, Butanol (10 mg/ml), 60 min, Biological Replica 1

label_protocol: Labbeling according to aglient protocol using random hexamer and Cy3

growth_protocol: Exponentially growing strains in SA medium with 1% glucose and 2 ug/ml lipoic acid. Alcohol stress (Ethanol 55 mg/ml, butanol 10mg/ml, or hexanol 2 mg/ml) were added following harvesting the references and the stressed cultures were harvested after 5 min and 60 min

extract_protocol: Cells were pelleted by centrifugation and washed in ice cold salin water (0.9% NaCl). RNA was extracted by the hot phenol method

treatment_protocol: Growth was stopped immidiately by transfer of 10 ml culture sample into a glass flask precolled on ice followed rapid swirling

tag: treatment

value: Butanol (10 mg/ml), 60 min


title: E1

status: Public on Nov 05 2016

city: Galveston

first: Robin

last: Stephens

state: Texas

address: 301 University Blvd

department: Infectious Diseases

country: USA

institute: UTMB

hyb_protocol: Cyanine-3 (Cy3)-labeled cDNA of the sample (0.6 µg) was hybridized onto Agilent SurePrint G3 Mouse Gene Expression Microarray (8x60K) using Agilent’s Gene Expression Hybridization Kit. Hybridization was performed for 17h, rotating at a speed of 10rpm at 65? in an Agilent hybridization oven.

scan_protocol: After hybridization, microarrays were washed for 1 minute at room temperature with Wash Buffer 1 and 1 minute at 37? with Wash buffer 2.  Microarrays were scanned with Agilent Microarray Scanner and the fluorescence intensities were quantified.

data_processing: Array Raw data files were loaded into R version 2.12.1 to process data analysis.

organism: Mus musculus

source_name: Splenic CD4 T cells

label_protocol: 0.1 µg of total RNA was amplified and labeled using Agilent's Low Input Quick Amp Labeling Kits. Dye incorporation and aRNA yield were checked using the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: B5 TCR Tg mice (BALB/cJ) were infected with Plasmodium chabaudi.

extract_protocol: RNA was isolated and processed according to Agilent Array protocol (PhalanxBio, Inc, San Diego, CA).

treatment_protocol: Splenic CD4 T cells from naive or infected B5 TCR Tg mice ( 5- to 12-wks-old) were enriched by EasySep biotin selection kit (Stemcell Technologies, Vancouver, BC, Canada) with a mixture of biotinylated anti-CD8a, B220 (RA3-6B2), CD11b (MI/70), CD11c (N418), F4/80 (BM8), and Ter119 (eBioscience). The negative fraction was then stained with anti-CD4-FITC, CD44-allophycocyanin-Cy7, CD127-PE, anti CD62L PE-TxRd and CD27 APC for the subsets. Cells were sorted on a FACS Aria with FACDiva software (BDbiosciences, San Diego, CA). Effector (CD44int-hi CD127neg) and memory (CD44hi CD127hi) subsets were sorted on d8 and d60 post-infection, respectively.

tag: strain

value: B5 TCR Tg mice (BALB/cJ)

tag: subset group

value: Early Effector (E, CD62Lhi CD27hi)

tag: infection

value: day 8 post P. chabaudi-infection


title: MG1363_Butanol_5min_Rep1

source_name: MG1363, Butanol (10 mg/ml), 5 min, Biological Replica 1

value: Butanol (10 mg/ml), 5 min


title: TRAF6 NULL IR2

city: New York

first: Xian

last: Zhang

address: 580 main st apt 138

institute: MSKCC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Please note that Genepatter, PreprocessData (v5), row normalization function was used to process the data. The software/web server does not indicate the algorithm, however data was processed to eliminate the system variation between samples.
Normalized with housekeeping genes provide in the illumina array. 1.Gene with max expression value smaller than 150 are eliminated, 2. Data are then normalized with house keeping gene value. 3. Genes with max fold change between groups <1.3 is eliminated.

label: biotin

source_name: TRAF6 null_IR_thymus cells

label_protocol: Standard Illumina labeling protocol

growth_protocol: H1299 cells grow in DMEM high glcuose medium

extract_protocol: Standard TRIZOL protocol

treatment_protocol: Mice were treated with IR (15Gy) for 10 hours

tag: strain background

tag: age

value: 2.5 week

tag: genotype/variation

value: TRAF6 null

tag: treated with

value: IR (15Gy) for 10 hours

tag: cell type

value: Thymus cells


title: WT IR1

source_name: WT_IR_thymus cells

value: wild type


title: PP2ACα knockout BMDM (PP2ACαfl/fl;lyM-Cre), biological rep1

city: Ann arbor

first: Lei

last: Sun

state: MI

address: 109 Zina Pitcher Place, BSRB 4478

department: Pediatrics

institute: University of Michigan

description: gene expression data from PP2ACαfl/fl;lyM-Cre (myeloid specific knockout of PP2ACα exon1) bone marrow derived macrophages

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse ST 2.1 Array strips, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment version 3.1.1. RMA was used to fit log2 transformed expression values

source_name: LPS-stimulated PP2ACα knockout BMDM (PP2ACαfl/fl;lyM-Cre)

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Bone marrow derived macrophages were cultured in RPMI medium supplemented with L-cell supernatant in vitro for 6 days

extract_protocol: RNA was isolated with Trizol method and purified with RNeasy Kit (Qiagen).

treatment_protocol: 100 ng/ml LPS for 2 hours

tag: tissue

value: Bone marrow derived macrophages

tag: genotype

value: PP2ACα knockout (PP2ACαfl/fl;lyM-Cre)


title: MG1363_Hexanol_60min_Rep1

source_name: MG1363, Hexanol (2 mg/ml), 60 min, Biological Replica 1

value: Hexanol (2 mg/ml), 60 min


title: P. aeruginosa PA14 WT

state: PA

description: Gene expression data for IPTG induction of cells containing pCA24N (empty).

source_name: PA14 wild-type

value: wildtype


title: Reactive Lymph node LR12

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

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

country: Italy

institute: università di padova

description: Gene expression data from normal reactive lymph node

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

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

organism: Homo sapiens

source_name: Lymph node

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: No growth protocol

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

treatment_protocol: No treatment protocol

tag: alcl subgroup

value: Normal tissue


title: WT IR2


title: WT NO IR

source_name: WT_control_thymus cells


title: control BMDM (PP2ACαfl/fl), biological rep1

description: gene expression data from PP2ACαfl/fl (conditional knockout with floxed exon1) bone marrow derived macrophages

source_name: LPS-stimulated control BMDM (PP2ACαfl/fl)

value: control (PP2ACαfl/fl)


title: Reactive Lymph node LR9


title: Reactive Lymph node LR8


title: Reactive Lymph node LR10


title: Reactive Lymph node LR11


title: TRAF6 NULL IR1


title: Reactive Lymph node LR4


title: control BMDM (PP2ACαfl/fl), biological rep2


title: Reactive Lymph node LR6


title: Reactive Lymph node LR7


title: Reactive Lymph node LR5


title: Reactive Lymph node LR2


title: Reactive Lymph node LR3


title: SOX2_rep3

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Agilent Technologies Scanner G2505C US82003505

data_processing: Data were normalized with Bioconductor software using quantiles

source_name: GSC-11 cell line, siRNA against human Sox2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: GSC11 cells were maintained in Dulbecco's modified Eagle's medium/nutrient mixture F12 supplemented with B27 (Invitrogen, Carlsbad, CA), epidermal growth factor, and basic fibroblast growth factor (20 ng/mL each; Sigma-Aldrich, St Louis, MO.

extract_protocol: Total cellular RNA was isolated from the cultured cells using Trizol reagent (Ambion) according to the manufacturers' protocols

treatment_protocol: To inhibit Sox2 expression, transient transfection  were performed using si-Sox2 or si-scramble (Ambion) according to the manufacturer's instructions using Lipofectamine 2000 (Invitrogen). The cells were then cultured for 72 h after transfections and subjected to RNA extraction

tag: cell line

tag: sirna

value: siRNA against human Sox2


title: SOX2_rep1


title: SOX2_rep4


title: Control_rep4

source_name: GSC-11 cell line, non-targeting control siRNA

value: non-targeting control


title: Reactive Lymph node LR1


title: SOX2_rep2


title: Patient ALCL23

description: Gene expression data from ALCL samples at diagnosis with NPM-ALK translocation

value: ALK high


title: Control_rep2


title: patient no 459 tumor sample at I grade_ biological_rep1

city: Kraków

first: Paulina

last: Marona

state: Lesser

address: Gronostajowa 7

department: Department of General Biochemistry

country: Poland

institute: Jagiellonian University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on Affymetrix HuGene2.1 ST Array Strp. Arrays were washed and stained in the Affymetrix Gene Atlas Fluidics Station.

scan_protocol: Affymetric HuGene2.1 ST Array Strips were scanned using the GeneAtlas Imaging Station (S/N 91001280).

data_processing: The data were normalized with Expression Console Software 1.4.1 with RMA algorithm and analyse using Affymetrix Transcriptom Analysis Console (TAC) Software 3.1 with ANOVA one-way between subjects (unpaired)

source_name: human tumor sample in first stage of cancer

label_protocol: 100 ng of total RNA were used to synthesis and amplification of ss-cDNA, then samples were fragmented and labeled with biotin. Each step was performed according to Affymetrix GeneChip WT PLUS Reagent Kit Manual (2013 Affymetrix, P/N 703174 Rev. 2)

extract_protocol: total RNA was extracted using Eurx Universal RNA Purification Kit (EURx) according to manufacturer protocol. The quantity of ribosomal RNA and DNA contamination was examined using electrophoresis in 1% denaturing formaldehyde gel. Concentration of total RNA was assessed using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific).

value: clear cell renal cell carcinoma

tag: Stage

value: first

tag: gender

value: female


title: Control_rep3


title: Patient ALCL20


title: Control_rep1


title: Patient ALCL21


title: Patient ALCL22

value: ALK low


title: Reh control cells replicate 1

city: Herston

first: Fares

last: Al-Ejeh

state: QLD

address: 300 Herston Road

department: Cancer

country: Australia

institute: QIMR Berghofer

hyb_protocol: Standard Illumina hybridization protocol.

data_processing: Raw data were log2 transformed, normalized and analysed using  BRB-ArrayTools (V4.5, Biometric Research Branch, NCI, MD, USA)

source_name: Cancer cell line_Reh

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion, AMIL1791).

growth_protocol: Cells were maintained in RPMI1640 supplemented with 10% fetal-calf-serum

extract_protocol: Qiagen RNEasy RNA isolation kit according to manufacturer's instructions

treatment_protocol: No treatments. Comparison of control Reh and LK63 cells vs. LK63 with stable knockdown of EphA3

value: Reh


title: Tumor 8800

city: Montreal

first: Tung

last: Bui

state: Quebec

address: 1160 Pine Ave. W, R507

department: Biochemistry

country: Canada

institute: McGill University

description: Gene expression data

hyb_protocol: 3.5µg DNA target was hybridized on GeneChip® Mouse Gene 2.0 ST Array (Affymetrix) and incubated at 45oC in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix)

data_processing: Raw data were first processed to perform gene-level normalization and quality control using Affymetrix Expression Console software (Affymetrix). Processed data were next subjected to Gene Level Differential Expression Analysis using Affymetrix Transcriptome Analysis Console software with filter criteria as following: linear fold change < -2 or > 2 and ANOVA p-value (condition pair) <  0.05.

label: Biotin

source_name: Mammary tumor

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix)

extract_protocol: Rneasy RNA extraction kit Qiagen

value: Ctnnb1 fl/fl


title: LK63-EphA3 knockdown cells replicate 1

source_name: Cancer cell line_LK63_EphA3 knockdown


title: Tumor 5217

description: Gene expression data


title: Tumor 4077

description: Gene expression data


title: Patient ALCL19


title: LK63 control cells replicate 2

source_name: Cancer cell line_LK63


title: Blood Human Sarcoid rep49

city: London

first: Krzysztof

last: Potempa

address: The Ridgeway

country: United Kingdom

institute: National Institute for Medical Research (NIMR)

description:
9682760039_L
replicate 49

data_processing: quantile normalization, background subtraction using Genomestudio

source_name: Blood Human Sarcoid

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

extract_protocol: 1ml added to 2mls Tempus solution. RNA extracted using PerfectPURE RNA Blood kit (5-PRIME), globin RNA reduced using GLOBINclear (Biosystems/Ambion)

value: F

tag: ethnicity

value: White

tag: disease state

value: Sarcoid

value: Blood


title: Patient ALCL18


title: LK63-EphA3 knockdown cells replicate 2


title: Reh control cells replicate 2


title: LK63 control cells replicate 1


title: Blood Human Sarcoid rep47

description:
9682760039_G
replicate 47


title: Patient ALCL17


title: Blood Human Sarcoid rep48

description:
9682760039_K
replicate 48

value: Black


title: Tumor 9870

description: Gene expression data


title: Blood Human Sarcoid rep46

description:
9682760039_E
replicate 46


title: Blood Human Sarcoid rep43

description:
9682760004_K
replicate 43


title: Tumor 2278R1

description: Gene expression data

value: Ctnnb1 fl/wt


title: Blood Human Sarcoid rep41

description:
9682760001_D
replicate 41


title: Blood Human Sarcoid rep44

description:
9682760033_F
replicate 44

value: M


title: Patient ALCL16


title: Tumor 1414R5

description: Gene expression data


title: Tumor 1413L2

description: Gene expression data


title: Blood Human Sarcoid rep39

description:
9665647092_E
replicate 39

value: ISC


title: Tumor 7158L3

description: Gene expression data


title: Blood Human Sarcoid rep42

description:
9682760004_F
replicate 42


title: Patient ALCL12


title: Patient ALCL13


title: Blood Human Sarcoid rep37

description:
9665647088_L
replicate 37


title: Blood Human Sarcoid rep40

description:
9665647092_J
replicate 40


title: Patient ALCL15


title: Patient ALCL10


title: Blood Human Sarcoid rep38

description:
9665647092_D
replicate 38


title: Blood Human Sarcoid rep35

description:
9665647022_H
replicate 35


title: Blood Human Sarcoid rep33

description:
9665647016_G
replicate 33


title: Blood Human Sarcoid rep31

description:
9631032010_J
replicate 31


title: Tumor 007R2/3

description: Gene expression data


title: Patient ALCL14


title: Tumor 8750

description: Gene expression data

value: Ctnnb1 wt/wt


title: Tumor 2617

description: Gene expression data


title: Blood Human Sarcoid rep34

description:
9665647022_F
replicate 34


title: Blood Human Sarcoid rep36

description:
9665647088_I
replicate 36


title: Blood Human Sarcoid rep32

description:
9665647016_F
replicate 32


title: Patient ALCL11


title: Tumor 1653

description: Gene expression data


title: Blood Human Sarcoid rep30

description:
9631032010_F
replicate 30


title: Patient ALCL7


title: Blood Human Sarcoid rep28

description:
9610356056_G
replicate 28


title: Tumor 1651R3

description: Gene expression data


title: CBS_12_C_DD_2

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

description:
SAMPLE 4
one of two biological replicates

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

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

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
matrix_proteinIDs.txt (linked a supplementary file on the Series record) reports RMA signals for protein ID numbers which are similar in both Platform designs as they are based on homologues in the two T. reesei genomes on which the array is based.

organism: Trichoderma reesei

source_name: CBS999.97 MAT1-2 grown on cellulose in constant darkness

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Trichoderma reesei strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1% microcrystalline cellulose as carbon source in constant darkness (DD) for 72 hours.

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.

treatment_protocol: Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.

tag: strain

tag: mating type

tag: growth protocol

value: grown on cellulose in constant darkness


title: Patient ALCL8


title: Patient ALCL9

value: ALK high


title: Blood Human Sarcoid rep29

description:
9631032010_E
replicate 29


title: Blood Human Sarcoid rep24

description:
9610342033_E
replicate 24

value: Other


title: Patient ALCL6


title: Blood Human Sarcoid rep27

description:
9610356056_F
replicate 27


title: Tumor 1093

description: Gene expression data


title: CBS_11_C_DD_2

description:
SAMPLE 2
one of two biological replicates

source_name: CBS999.97 MAT1-1 grown on cellulose in constant darkness


title: Blood Human Sarcoid rep26

description:
9610356056_E
replicate 26


title: Blood Human Sarcoid rep23

description:
9610342028_F
replicate 23


title: CBS_11_C_DD_1

description:
SAMPLE 1
one of two biological replicates


title: CBS_12_C_DD_1

description:
SAMPLE 3
one of two biological replicates


title: Patient ALCL5


title: Blood Human Sarcoid rep20

description:
9610342021_H
replicate 20


title: Blood Human Sarcoid rep21

description:
9610342028_D
replicate 21


title: Blood Human Sarcoid rep19

description:
9610342021_G
replicate 19


title: Blood Human Sarcoid rep25

description:
9610342033_F
replicate 25


title: Patient ALCL4


title: Blood Human Sarcoid rep18

description:
9610342021_F
replicate 18


title: Blood Human Sarcoid rep22

description:
9610342028_E
replicate 22


title: Blood Human Sarcoid rep17

description:
9610342003_L
replicate 17


title: K

data_processing:
Normalized with housekeeping genes provide in the illumina array
Please note that Genepatter, PreprocessData (v5), row normalization function was used to process the data. The software/web server does not indicate the algorithm, however data was processed to eliminate the system variation between samples.

value: Lung cancer cell line

tag: transfected with


title: Patient ALCL3


title: Blood Human Sarcoid rep15

description:
9610342003_G
replicate 15

tag: age


title: Blood Human Sarcoid rep16

description:
9610342003_K
replicate 16


title: W

tag: genotype/variation

value: p53 WT


title: Blood Human Sarcoid rep10

description:
9380252001_G
replicate 10


title: ASE_3

city: Warsaw

first: Mohammed

middle: Imran

last: Khan

address: ul. Szaserów 128

department: Department of Oncology

institute: Military Institute of Medicine

description: Healthy kidney epithelial cells

hyb_protocol: Resulting cRNA was hybridized (Gene Expression Hybridization Kit, Agilent, USA) on Agilent’s Mouse GE 4x44K v2 microarrays  as manufacturer protocol.

scan_protocol: Data were extracted using G2505C Microarray Scanner (Agilent, USA) and Agilent Feature Extraction Software (version 10.7.3.1) (Agilent, USA) on default settings.

data_processing: Microarray data normalization, quality control, principal component analysis, and filtered on flags were performed using GeneSpring GX 13.0 (Agilent, Santa Clara, CA, USA). Statistical analysis of the gene expression microarray data was performed using moderate T-test and multiple testing corrected with Bonferonni FWER algorithm. The statistical significance was assessed at p<0.05 and fold change cut off >2.0 (up-/down-regulated).

label: Cyanine 3 (Cy3)

source_name: Derived from whole kidney

label_protocol: 50 ng of total RNA from each pool was converted to cDNA, then amplified and labeled with cyanine 3 (One-Color Low Input Quick Amp Labeling Kits, Agilent, USA) as manufacturer protocol.

growth_protocol: Human renal carcinoma cell line Caki-2, ACHN and human healthy kidney epithelial cell line (ASE-5063) were maintained in RPMI-1640 + GlutaMAX-I  media with 10% FBS and 1% PenStrep (100 U/mL penicillin and 100μg/mL Streptomycin). Cells were expanded in T-75 flask before sorting of CD105+ cells. Isolation of total RNA of CD105+ cells sorted from Caki-2 and CD105+ cells sorted from ACHN was performed.

extract_protocol: Total RNA was isolated using Total RNA Mini Plus from A&A Biotechnology as described in manufactural protocol. RNA quality and integrity was measured by 2100 Bioanalyzer. The isolated RNA was stored in -80ºC until the microarray experiment was carried out.

treatment_protocol: No treatement

value: Human normal kidney epithelial cells

value: Prenatal

value: kidney


title: ASE_2

description: Healthy kidney epithelial cells


title: Blood Human Sarcoid rep12

description:
9380252030_K
replicate 12


title: Blood Human Sarcoid rep11

description:
9380252030_F
replicate 11

value: F


title: ASE_1

description: Healthy kidney epithelial cells


title: Patient ALCL1


title: Blood Human Sarcoid rep9

description:
9380252001_F
replicate 9

value: White


title: V

value: vector control


title: Patient ALCL2

value: ALK low


title: Blood Human Sarcoid rep13

description:
9380252031_G
replicate 13

value: Sarcoid

value: Blood


title: Blood Human Sarcoid rep14

description:
9610342003_E
replicate 14

value: M

value: Black


title: Blood Human Sarcoid rep7

description:
9380037052_G
replicate 7


title: Blood Human Sarcoid rep4

description:
9380037037_G
replicate 4


title: Blood Human Sarcoid rep6

description:
9380037037_I
replicate 6


title: Blood Human Sarcoid rep8

description:
9380037052_I
replicate 8


title: Blood Human Sarcoid rep5

description:
9380037037_H
replicate 5


title: Tumor 3443

description: Gene expression data

value: Ctnnb1 fl/fl


title: pre-Leptotene_Spo11-/-

city: Tampa

first: John

middle: Lamoine

last: Cleveland

state: FL

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

description:
Gene expression data from FACS sorted meiotic cells from Spo11-/- male mice 10-16 weeks old.
Sorted Spo11-/- pre-Leptotene

hyb_protocol: Fragmentation/hybridization to MOE430v2.0 arrays (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: Imaging was performed on a Hewlett Packard GeneArray Scanner according to standard Affymetrix protocol.

data_processing: The data were analyzed using GeneSpring GX version 12.1 based on GCRMA analysis default settings.

source_name: pre-Leptotene_Spo11-/- (Testis)

label_protocol: Biotin-labeled cRNA probes were prepared as recommended by the manufacturer (Affymetrix), using oligo-dT primers, SuperScript, and BioArray High Yield RNA Transcript kits (Affymetrix).

extract_protocol: For purified meiotic fractions, RNA was prepared using RNAqueous Micro kits (Ambion) according to recommended protocols.

value: testis

tag: stain

value: Hoechst 33342

value: male

tag: meiotic fraction

value: pre-leptotene


title: Spermatogonia_Spo11-/-

description:
Gene expression data from FACS sorted meiotic cells from Spo11-/- male mice 10-16 weeks old.
Sorted Spo11-/- spermatogonia

source_name: Spermatogonia_Spo11-/- (Testis)

tag: tissue

value: spermatogonia


title: Blood Human Sarcoid rep45

description:
9682760033_G
replicate 45


title: Blood Human Sarcoid rep3

description:
9380037014_I
replicate 3


title: Leptotene/Zygotene_Spo11-/-

description:
Gene expression data from FACS sorted meiotic cells from Spo11-/- male mice 10-16 weeks old.
Sorted Spo11-/- Leptotene/Zygotene

source_name: Leptotene/Zygotene_Spo11-/- (Testis)

tag: genotype

value: leptotene/zygotene


title: CD105(Caki-2)_1

description: CD105+ cells derived from primary  renal cell carcinoma cell line Caki-2

source_name: Derived from primary renal cell carcinoma of the kidney

tag: cell type

value: clear cell renal cell carcinoma

value: 69 years


title: CD105(Caki-2)_2

tag: cell line

value: kidney


title: Diplotene rep2

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted Diplotene, biological rep2

source_name: Diplotene (Testis)

tag: generation

value: diplotene


title: Blood Human PTB rep41

description:
9682760004_B
replicate 41

source_name: Blood Human PTB

value: F

value: PTB


title: Blood Human Sarcoid rep2

description:
9380037014_H
replicate 2

value: White

value: Sarcoid


title: Blood Human PTB rep45

description:
9682760039_J
replicate 45

value: Blood


title: Blood Human PTB rep39

description:
9665647088_D
replicate 39

value: M

value: Black


title: CD105(Caki-2)_3


title: CD105(ACHN)_2

description: CD105+ cells derived from metastatic renal cell carcinoma cell line ACHN

source_name: Derived from patient with metastatic renal adenocarcinoma

value: ACHN

value: 22 years


title: Round Spermatids rep4

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted round spermatids, biological rep4

source_name: Round Spermatids (Testis)

value: testis

value: Hoechst 33342

value: male

value: round spermatids


title: CD105(ACHN)_3

value: clear cell renal cell carcinoma


title: Blood Human Sarcoid rep1

description:
9370786041_G
replicate 1


title: Blood Human PTB rep43

description:
9682760004_E
replicate 43

value: ISC


title: Round Spermatids rep1

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted round spermatids, biological rep1


title: Blood Human PTB rep34

description:
9665647016_D
replicate 34


title: Round Spermatids rep2

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted round spermatids, biological rep2


title: Blood Human PTB rep32

description:
9631032010_L
replicate 32


title: Blood Human PTB rep42

description:
9682760004_D
replicate 42


title: Blood Human PTB rep35

description:
9665647016_E
replicate 35


title: Blood Human PTB rep37

description:
9665647022_B
replicate 37


title: mid-Pachytene rep2

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted mid-Pachytene, biological rep2

source_name: mid-Pachytene (Testis)

value: mid-pachytene


title: late-Pachytene

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted late-Pachytene

source_name: late-Pachytene (Testis)

value: late-pachytene


title: Blood Human PTB rep33

description:
9665647016_B
replicate 33


title: Blood Human PTB rep36

description:
9665647016_H
replicate 36

value: Other


title: CD105(ACHN)_1

value: kidney


title: Blood Human PTB rep30

description:
9610342033_K
replicate 30

value: PTB


title: Blood Human PTB rep40

description:
9665647088_H
replicate 40


title: Blood Human PTB rep29

description:
9610342033_I
replicate 29

value: White


title: Blood Human PTB rep38

description:
9665647088_B
replicate 38

value: Blood


title: Diplotene rep1

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted Diplotene, biological rep1

value: diplotene


title: Blood Human PTB rep31

description:
9610356056_J
replicate 31

value: F


title: mid-Pachytene rep1

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted mid-Pachytene, biological rep1


title: Blood Human PTB rep28

description:
9610342028_I
replicate 28

value: M


title: Blood Human PTB rep26

description:
9610342021_K
replicate 26


title: Blood Human PTB rep27

description:
9610342028_H
replicate 27


title: Blood Human PTB rep24

description:
9380252031_K
replicate 24


title: Blood Human PTB rep22

description:
9380252031_A
replicate 22


title: Leptotene/Zygotene rep3

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted Leptotene/Zygotene, biological rep3

source_name: Leptotene/Zygotene (Testis)

value: leptotene/zygotene


title: early-Pachytene

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted early-Pachytene

source_name: early-Pachytene (Testis)

value: testis

value: early-pachytene


title: Leptotene/Zygotene rep2

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted Leptotene/Zygotene, biological rep2

value: Hoechst 33342

value: male


title: Blood Human PTB rep44

description:
9682760033_D
replicate 44


title: Maize-GLS-RILs-193_205

city: Cape Town

first: Shane

last: Murray

address: University Avenue North

department: Dept of Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

description: Pool of three biological replicates of each RIL line

hyb_protocol: Labelled aRNA was hybridized to the Agilent-016047 maize 4×44 K microarrays using the Quadchamber on the Tecan Hybridisation station.  The Agilent Two-Color Microarray-Based Gene Expression protocol was followed.

scan_protocol: The microarrays were scanned using a Tecan LS Re-loaded scanner (Tecan, Mannedorf, Switzerland).  Image acquisition was carried out using automatic gain control settings for Cy3 and Cy5.  Images from both channels were saved as separate tif files.  Spots were flagged as bad if the signal to noise ration was <3 for either the Cy3 or Cy 5 channel.

data_processing: Cy 5 and Cy3 TIF images for each slide were imported into the Genepix Pro 6.1 software (Molecular Devices, Sunnyvale USA), overlaid on top of each other and saved as a single multitif image.  This image was used for all further analysis in Genepix.  Four GPR files were exported per slide.  Normalization was performed in the R-based package limma, with a weighting of zero for flagged spots. Background correction was performed using the normexp method (offset =50). The loess method was used for normalization within arrays and Aquantile for normalization between arrays.  After normalization, 50 datasets of M values (M=log2 Cy5/Cy3) represented the 100 RILs. Back-conversion of the normalized data was required to obtain separate, normalised expression values per reporter for each of the 100 RILs.

organism: Zea mays

source_name: Leaf, Grey leafspot

label_protocol: RNA (1μg) was amplified from each of the 100 RIL samples using the Amino Allyl MessageAmpII aRNA Amplification kit (Ambion, Dallas, USA) and labeled with either Cy3 or Cy5 (100 pmol each) according to the manufacturer's instructions.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, followed by Dnase treatment and Qiagen column purification

tag: ril

value: 103 DAP


title: Maize-GLS-RILs-10_124


title: Leptotene/Zygotene rep1

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted Leptotene/Zygotene, biological rep1

tag: gender


title: pre-Leptotene rep3

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted pre-Leptotene, biological rep3

source_name: pre-Leptotene (Testis)

value: pre-leptotene


title: Round Spermatids rep3

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted round spermatids, biological rep3

value: round spermatids


title: Blood Human PTB rep19

description:
9380252030_A
replicate 19

tag: ethnicity


title: Blood Human PTB rep20

description:
9380252030_B
replicate 20

tag: disease state


title: Blood Human PTB rep17

description:
9380252001_B
replicate 17


title: Blood Human PTB rep15

description:
9380037052_L
replicate 15

value: ISC


title: Blood Human PTB rep18

description:
9380252001_C
replicate 18


title: Blood Human PTB rep25

description:
9610342021_B
replicate 25

value: Black


title: Blood Human PTB rep21

description:
9380252030_C
replicate 21


title: Maize-GLS-RILs-337_186


title: Maize-GLS-RILs-33_268


title: Blood Human PTB rep23

description:
9380252031_C
replicate 23


title: pre-Leptotene rep1

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted pre-Leptotene, biological rep1

tag: strain


title: Blood Human PTB rep16

description:
9380252001_A
replicate 16

value: Other


title: Blood Human PTB rep13

description:
9380037052_A
replicate 13

value: PTB


title: Maize-GLS-RILs-29_110


title: Spermatogonia rep4

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted spermatogonia, biological rep4

source_name: Spermatogonia (Testis)

value: spermatogonia


title: Blood Human PTB rep14

description:
9380037052_K
replicate 14

value: Blood


title: Spermatogonia rep3

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted spermatogonia, biological rep3


title: Blood Human PTB rep12

description:
9380037037_L
replicate 12


title: Maize-GLS-RILs-68_217


title: Spermatogonia rep2

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted spermatogonia, biological rep2


title: Blood Human PTB rep10

description:
9380037037_B
replicate 10


title: Maize-GLS-RILs-43_95


title: Maize-GLS-RILs-66_175


title: Maize-GLS-RILs-70_381


title: Blood Human PTB rep11

description:
9380037037_D
replicate 11


title: Spermatogonia rep1

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted spermatogonia, biological rep1


title: Blood Human PTB rep3

description:
9370786041_C
replicate 3

value: White


title: Maize-GLS-RILs-144_354


title: Blood Human PTB rep9

description:
9380037014_L
replicate 9

value: F


title: Blood Human PTB rep7

description:
9380037014_C
replicate 7


title: Blood Human PTB rep4

description:
9370786041_K
replicate 4

value: M


title: Blood Human PTB rep5

description:
9380037014_A
replicate 5


title: Blood Human PTB rep2

description:
9370786041_B
replicate 2


title: Blood Human PTB rep1

description:
9370786041_A
replicate 1


title: Blood Human PTB rep6

description:
9380037014_B
replicate 6


title: Maize-GLS-RILs-86_107


title: Blood Human PTB rep8

description:
9380037014_D
replicate 8


title: Maize-GLS-RILs-153_109


title: Blood Human Control rep60

description:
9682760039_B
replicate 60

source_name: Blood Human Control

value: HC


title: Maize-GLS-RILs-49_125


title: Blood Human Control rep59

description:
9682760039_A
replicate 59


title: Blood Human Control rep61

description:
9682760039_C
replicate 61


title: Maize-GLS-RILs-333_145


title: Blood Human Control rep57

description:
9682760033_K
replicate 57


title: Maize-GLS-RILs-383_168


title: Blood Human Control rep58

description:
9682760033_L
replicate 58


title: Blood DNA from 3 muscular dystrophy patients

type: genomic

city: Mexico City

first: Juan Carlos

last: Zenteno

state: In the USA or Canada, please select...

address: Chimalpopoca 14

country: Mexico

institute: Institute of Ophthalmology "Conde de Valenciana"

description:
ECC-1994, ETF-1999, DRD-2000
Data from a pool of 3 DNA samples.
Hybridized to Affymetrix 250K_Nsp array.

hyb_protocol: DNA was hybridized to the array according to the manufacturer's instructions. The array was washed using Affymetrix Fluidics Stations.

scan_protocol: The array was scanned using the GeneChip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1.

molecule: genomic DNA

source_name: Blood of 3 patients with muscular dystrophy

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions (Affymetrix).

extract_protocol: Genomic DNA was extracted from leukocytes obtained from peripheral blood at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity were assessed using a NanoDrop Spectrophotometer and agarose gel electrophoresis.

value: Muscular dystrophy (autosomal recessive form)


title: Blood Human Control rep54

description:
9682760033_A
replicate 54


title: Blood Human Control rep56

description:
9682760033_C
replicate 56


title: Blood Human Control rep55

description:
9682760033_B
replicate 55


title: pre-Leptotene rep2

description:
Gene expression data from FACS sorted meiotic cells from C57bl6/JxDBA/2J F1 male mice 10-16 weeks old.
Sorted pre-Leptotene, biological rep2

value: testis


title: Blood Human Control rep51

description:
9682760001_K
replicate 51


title: Maize-GLS-RILs-131_361


title: Blood Human Control rep53

description:
9682760004_J
replicate 53


title: Blood Human Control rep48

description:
9682760001_F
replicate 48


title: Maize-GLS-RILs-150_127


title: Maize-GLS-RILs-322_288


title: Blood Human Control rep50

description:
9682760001_J
replicate 50


title: Blood Human Control rep40

description:
9665647088_E
replicate 40


title: Maize-GLS-RILs-239_160


title: Blood Human Control rep43

description:
9665647092_B
replicate 43


title: Maize-GLS-RILs-387_366


title: Maize-GLS-RILs-194_135


title: Blood Human Control rep47

description:
9682760001_C
replicate 47


title: Maize-GLS-RILs-156_329


title: Blood Human Control rep46

description:
9682760001_B
replicate 46


title: Maize-GLS-RILs-282_31


title: Blood Human Control rep41

description:
9665647088_J
replicate 41


title: Blood Human Control rep52

description:
9682760004_C
replicate 52


title: Blood Human Control rep45

description:
9665647092_L
replicate 45


title: Blood Human Control rep44

description:
9665647092_C
replicate 44


title: Maize-GLS-RILs-238_379


title: Blood Human Control rep39

description:
9665647088_C
replicate 39


title: Maize-GLS-RILs-164_25


title: Blood Human Control rep42

description:
9665647092_A
replicate 42


title: Maize-GLS-RILs-47_121


title: Maize-GLS-RILs-166_382


title: tSBE(6+2)-Vp64 H3K27me3_R2

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

description:
H3K27me3 ChIP-chip
Supplementary files for combined samples (R1, R2) linked to Series record:
tSBE(6+2) H3K27me3 Combined.wig.bedgraph
normalizedlog2ratios_CombinedSamples.txt (column: tSBE(6+2) H3K27me3 Combined)

hyb_protocol: Samples were hybridized and washed according to manufacturer´s protocol. A custom 8x60K mouse tiling array (Agilent Technologies) containing 51,504 probes was used.

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray scanner (Roche) using 100% laser power and 2μm resolution and Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Raw signal intensities were quantified from TIFF images using MS 200 Data Collection software. Microarray data were analyzed in R using the bioconductor packages Beadarray and Limma according to the Epigenesys NimbleGen ChIP-on-chip protocol 43

source_name: H3K27me3 ChIP DNA from 46c ESC

label_protocol: one microgram genomic DNA was prepared and amplified using the Agilent Sample preparation protocol. All the amplified material was labelled with Cy3 or Cy5 by random priming using SureTag DNA Labelling kit according to the Agilent ChIP-chip protocol

growth_protocol: ESCs were cultured in GMEM+ Supplement, transfected using Lipofectamine 2000 reagents or differentiated in NPC using N2B27 protocol

extract_protocol: Nuclei from 3x10e6 mESCs were prepared and resuspended in NB-R (85 mM NaCl, 5.5% Sucrose, 10mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT), Micrococcal nuclease (MNase) digestion and native ChIP were performed as previously described (Eskeland et al. 2010, Pradeepa et al.2012)  Antibody used for ChIP was H3K27me3 (Millipore 07-449).

value: 46c ESCs

tag: transfection

tag: chip antibody

value: H3K27me3 (Millipore 07-449)

source_name: Input DNA from 46c ESCs

tag: tag


title: Blood Human Control rep49

description:
9682760001_G
replicate 49

tag: age


title: WT-TAC 3

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: MOA v2.1 arrays were pre-heated at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridized on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent Microarray Scanner (G2505C) 0.1 XDR protocol and quantify the fluorescence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: heart, transverse aortic constriction

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amersham).

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: The mice were performed the transverse aortic constriction (n=3) or sham operation (n=2) for 28 days.

value: heart

tag: treatment

value: transverse aortic constriction


title: Sham operation 2

description: WT

source_name: heart, sham operation

value: sham operation


title: Maize-GLS-RILs-336_259

value: 103 DAP


title: WT-TAC 2


title: Maize-GLS-RILs-42_346


title: Blood Human Control rep37

description:
9665647022_I
replicate 37


title: Maize-GLS-RILs-275_364


title: tSBE(6+2)-Vp64 H3K27me3_R1


title: Blood Human Control rep38

description:
9665647088_A
replicate 38


title: Maize-GLS-RILs-116_327


title: WT-TAC 1


title: tSBE2-Vp64 H3K27me3_BioRep2_R2

description:
H3K27me3 ChIP-chip
Supplementary files for combined samples (R1, R2) linked to Series record:
tSBE2 H3K27me3 Combined.wig.bedgraph
normalizedlog2ratios_CombinedSamples.txt (column: tSBE2 H3K27me3 Combined)


title: Blood Human Control rep36

description:
9665647022_C
replicate 36


title: tSBE2-Vp64 H3K27me3_BioRep2_R1


title: Sham operation 1


title: Blood Human Control rep34

description:
9665647016_J
replicate 34

value: ISC


title: tSBE6-Vp64 H3K27me3_R2

description:
H3K27me3 ChIP-chip
Supplementary files for combined samples (R1, R2) linked to Series record:
tSBE6 H3K27me3 Combined.wig.bedgraph
normalizedlog2ratios_CombinedSamples.txt (column: tSBE6 H3K27me3 Combined)


title: Blood Human Control rep35

description:
9665647022_A
replicate 35


title: Blood Human Control rep32

description:
9665647016_A
replicate 32


title: Maize-GLS-RILs-349_108


title: tShh-Vp64 H3K27me3_BioRep2_R1

description:
H3K27me3 ChIP-chip
Supplementary files for combined samples (R1, R2) linked to Series record:
tShh H3K27me3 Biorep2 Combined.wig.bedgraph
normalizedlog2ratios_CombinedSamples.txt (column: tShh H3K27me3 Biorep2 Combined)


title: Blood Human Control rep33

description:
9665647016_C
replicate 33


title: tShh-Vp64 H3K27me3_BioRep2_R2


title: Blood Human Control rep31

description:
9631032010_C
replicate 31

value: Black


title: Maize-GLS-RILs-134_230


title: Maize-GLS-RILs-328_57


title: Maize-GLS-RILs-8_165


title: tSBE6-Vp64 H3K27me3_R1


title: Maize-GLS-RILs-362_319


title: Maize-GLS-RILs-59_400


title: Maize-GLS-RILs-40_341


title: NPC H3K27me3_R2

description:
H3K27me3 ChIP-chip
Supplementary files for combined samples (R1, R2) linked to Series record:
NPC H3K27me3 Combined.wig.bedgraph
normalizedlog2ratios_CombinedSamples.txt (column: NPC H3K27me3 Combined)

source_name: H3K27me3 ChIP DNA from 46c NPC

value: 46c NPCs N2B27 differentiation

source_name: Input DNA from 46c NPCs


title: Blood Human Control rep30

description:
9631032010_B
replicate 30


title: Blood Human Control rep28

description:
9610356056_L
replicate 28


title: Blood Human Control rep27

description:
9610356056_K
replicate 27


title: NPC H3K27me3_R1


title: Blood Human Control rep29

description:
9631032010_A
replicate 29


title: Maize-GLS-RILs-138_220


title: eGFP H3K27me3_BioRep2_R2

description:
H3K27me3 ChIP-chip
Supplementary files for combined samples (R1, R2) linked to Series record:
eGFP H3K27me3 Biorep2 Combined.wig.bedgraph
normalizedlog2ratios_CombinedSamples.txt (column: eGFP H3K27me3 Biorep2 Combined)


title: Blood Human Control rep25

description:
9610356056_B
replicate 25


title: Maize-GLS-RILs-141_392

description: Pool of three biological replicates of each RIL line


title: Maize-GLS-RILs-314_317


title: NPC R1

description: nuclear RNA on chip

hyb_protocol: Samples were hybridized and washed according to manufacturer´s protocol. A custom 8x60K mouse tiling array (Agilent Technologies) containing 51,504 probes was used

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray scanner (Roche) using 100% laser power and 2 μm resolution.

data_processing: Raw signal intensities were quantified from TIFF images using MS 200 Data Collection software. Median foreground and background signal intensities from microararys were read into R using the package Limma. Signals were background corrected using normexp method and then quantile normalized to remove techincal variation. Only probes whose signal was 10% above 95 percentile of negative control probes in at least 1 array were kept for further analysis.  Microarray data were analysed in R using the bioconductor packages Beadarray and Limma according to the Epigenesys NimbleGen ChIP-on-chip protocol 43. Scale normalization was used within replicates, to control inter-array variability.

molecule: nuclear RNA

source_name: RNA on chip from 46c NPC

label_protocol: All the amplified material was labelled with Cy3 by random priming using SureTag DNA Labelling kit according to the Agilent ChIP-chip protocol.

growth_protocol: ESCs were cultured in GMEM+ Supplement or differentiated in NPC using N2B27 protocol

extract_protocol: 250 ng of each sample RNA was amplified using WTA2 Complete Whole Transcriptome Amplification kit (Sigma) following manufacturer’s protocol.

treatment_protocol: chromatin from nuclei was first prepared as for Native Chromatin Immunoprecipitation without RNase A and RNA was then extracted using TRIzol® Reagent (ThermoFisher 15596026) following manufacturer’s protocol


title: NPC R2

description: nuclear RNA on chip


title: Day 2, 2.8 mg/kg LPS, Animal 5001

city: Monrovia

first: Claude

middle: J

last: Rogers

state: CA

address: 1225 S. Shamrock Ave.

institute: ChromoLogic

description: 2-5 year old NHP weighing 3.8-6.5 kg was treated with indicated concentration of LPS. Plasma was extracted at indicated time after treatment. Circulating miRNA was extracted and measured via nanoString.

hyb_protocol: Label protocol was performed following manufacturer's standard protocol

data_processing: Raw data came from the NanoString nCounter system. Technical normalization was performed using internal positive controls, as described by NanoString. The data was further processed by quantile normalization of the log2 counts, followed by Z scaling.

organism: Macaca mulatta

source_name: Plasma

extract_protocol: RNA was extracted from 200 µL plasma using Qiagen miRNeasy kit. After lysis, three synthetic oligonucleotides (spike-in oligos) were added. Purified RNA was eluted in 100 µL water and concentrated to 20 µL.

value: Plasma

value: LPS

tag: dose

tag: day

tag: conc

tag: Sex

value: Female


title: ESC R2

description: nuclear RNA on chip

source_name: RNA on chip from 46c ESC

tag: cell type


title: eGFP H3K27me3_BioRep2_R1


title: Maize-GLS-RILs-318_187


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_25)

city: Kiel

first: Anke

middle: Katharina

last: Bergmann

address: Arnold-Heller Str.

country: Germany

institute: University Hospital Schleswig-Holstein

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

scan_protocol: Arrays were scanned using the Illumina iScan using standard recommended Illumina scanner settings

data_processing: GenomeStudio software (version2011.1; Methylation Analysis Module version 1.9.0, Illumina)

source_name: pediatric ALL with KMT2A rearrangement

label_protocol: Standard Illumina Protocol

extract_protocol: Whole genomic DNA was extracted from tumor cell containing bone marrow or peripheral blood in all samples using the Gentra purification kit (Qiagen, Hilden, Germany)

value: pediatric ALL with KMT2A rearrangement

tag: disease condition

value: malignant

value: f

tag: tissue

value: peripheral blood

value: tumor cell

tag: tumor cell content in %


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_26)

tag: gender


title: ESC R1

description: nuclear RNA on chip

value: 46c ESCs


title: Maize-GLS-RILs-203_390

tag: ril


title: Blood Human Control rep23

description:
9610342033_J
replicate 23

hyb_protocol: Standard Illumina hybridization protocol

value: F

tag: ethnicity

value: White

tag: disease state

value: HC

value: Blood


title: Day 0, 2.8 mg/kg LPS, Animal 5001

scan_protocol: Label protocol was performed following manufacturer's standard protocol


title: Blood Human Control rep26

description:
9610356056_C
replicate 26

value: M

value: Other


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_24)


title: Blood Human Control rep22

description:
9610342033_C
replicate 22

value: Black


title: Day 2, 2.8 mg/kg LPS, Animal 5002

label_protocol: Label protocol was performed following manufacturer's standard protocol


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_20)


title: Day 0, 2.8 mg/kg LPS, Animal 5002


title: Day 2, 2.1 mg/kg LPS, Animal 4002


title: Maize-GLS-RILs-298_115

value: 103 DAP


title: Maize-GLS-RILs-190_315


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_23)


title: Blood Human Control rep21

description:
9610342033_B
replicate 21


title: Maize-GLS-RILs-284_112


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_18)

value: m


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_19)


title: Day 0, 2.1 mg/kg LPS, Animal 4002

value: Plasma

value: LPS


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_22)

value: pediatric ALL with KMT2A rearrangement

value: bone marrow


title: Maize-GLS-RILs-207_7


title: Day 2, 2.1 mg/kg LPS, Animal 4001

value: Female


title: Maize-GLS-RILs-140_19


title: Blood Human Control rep18

description:
9610342028_J
replicate 18


title: Blood Human Control rep20

description:
9610342033_A
replicate 20


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_15)

value: malignant

value: peripheral blood


title: Day 0, 2.1 mg/kg LPS, Animal 4001


title: Day 2, 0.7 mg/kg LPS, Animal 2001


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_17)

value: f

value: tumor cell


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_21)


title: Blood Human Control rep17

description:
9610342028_C
replicate 17

value: F

value: White


title: Blood Human Control rep16

description:
9610342028_A
replicate 16

value: HC

value: Blood


title: Day 2, 0.0 mg/kg LPS, Animal 1001


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_16)


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_14)


title: Blood Human Control rep15

description:
9610342021_L
replicate 15

value: ISC


title: Blood Human Control rep14

description:
9610342021_J
replicate 14

value: Other


title: Day 0, 0.0 mg/kg LPS, Animal 1002


title: Day 2, 0.0 mg/kg LPS, Animal 1002


title: Day 0, 0.0 mg/kg LPS, Animal 1001


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_12)


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_13)


title: Blood Human Control rep12

description:
9610342003_C
replicate 12

value: M

value: Black


title: Day 7, 6.5 Gy, Animal 6503

description: 2-5 year old NHP weighing 3.4-5.9 kg was irradiated with indicated dose. Plasma was extracted at indicated time after irradiation. Circulating miRNA was extracted and measured via nanoString.

value: Plasma

value: Radiation

value: Male


title: Blood Human Control rep13

description:
9610342021_C
replicate 13


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_11)

value: pediatric ALL with KMT2A rearrangement

value: bone marrow


title: Blood Human Control rep11

description:
9610342003_B
replicate 11


title: Blood Human Control rep24

description:
9610356056_A
replicate 24


title: Maize-GLS-RILs-320_113

value: 103 DAP


title: Blood Human Control rep9

description:
9380252031_J
replicate 9


title: QM6a_12_C_DD_2

description:
SAMPLE 10
one of two biological replicates

source_name: QM6a grown on cellulose in constant darkness

tag: strain

tag: mating type

tag: growth protocol

value: grown on cellulose in constant darkness


title: Day 7, 6.5 Gy, Animal 6502


title: Blood Human Control rep10

description:
9610342003_A
replicate 10

tag: age


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_8)

value: malignant

value: m

value: peripheral blood


title: Blood Human Control rep8

description:
9380252030_J
replicate 8


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_10)

value: f

value: tumor cell


title: Day 0, 0.7 mg/kg LPS, Animal 2001

tag: treatment

value: LPS

value: Female


title: Day 7, 6.5 Gy, Animal 6003

description: 2-5 year old NHP weighing 3.8-6.5 kg was irradiated with indicated dose. Plasma was extracted at indicated time after irradiation. Circulating miRNA was extracted and measured via nanoString.

tag: dose


title: Blood Human Control rep7

description:
9380252030_D
replicate 7

value: White

value: HC

value: Blood


title: Blood Human Control rep6

description:
9380252001_L
replicate 6

value: F

value: Black


title: Blood Human Control rep19

description:
9610342028_K
replicate 19


title: FF_12_C_DD_C

description:
SAMPLE 8
one of two biological replicates

source_name: FF2b MAT1-2 grown on cellulose in constant darkness


title: Day 7, 3.0 Gy, Animal 4503

value: Plasma

value: Radiation

tag: day

value: Male


title: FF_11_C_DD_C

description:
SAMPLE 6
one of two biological replicates

source_name: FF1b MAT1-1 grown on cellulose in constant darkness


title: Day 7, 3.0 Gy, Animal 4502

tag: conc


title: FF_11_C_DD_B

description:
SAMPLE 5
one of two biological replicates

source_name: FF1a MAT1-1 grown on cellulose in constant darkness


title: FF_12_C_DD_B

description:
SAMPLE 7
one of two biological replicates

source_name: FF2a MAT1-2 grown on cellulose in constant darkness


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_5)

value: pediatric ALL with KMT2A rearrangement

value: bone marrow


title: QM6a_12_C_DD_1

description:
SAMPLE 9
one of two biological replicates

value: grown on cellulose in constant darkness


title: Day 7, 3.0 Gy, Animal 4501

tag: Sex


title: Blood Human Control rep5

description:
9380252001_D
replicate 5

source_name: Blood Human Control

value: Other


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_6)

value: malignant

value: m

tag: cell type


title: Day 7, 3.0 Gy, Animal 4003


title: Blood Human Control rep4

description:
9380037037_F
replicate 4


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_9)

tag: disease condition

value: f

value: tumor cell


title: Blood Human Control rep2

description:
9380037014_K
replicate 2

value: M

tag: tissue


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_4)

value: peripheral blood

tag: tumor cell content in %


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_7)

tag: gender


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_2)


title: Day 7, 1.0 Gy, Animal 2503


title: Maize-GLS-RILs-50_330

source_name: Leaf, Grey leafspot

tag: ril

value: 103 DAP


title: Day 7, 0.0 Gy, Animal 1503


title: Day 7, 1.0 Gy, Animal 2003

value: Female


title: Day 7, 0.0 Gy, Animal 1502


title: Eze5

city: Groningen

first: vincent

last: bloks

country: Netherlands

institute: UMCG

description:
6331302016_G
Biological replicate 5

scan_protocol: Standard Illumina scanning protocol using the Illumina iScan.

data_processing: The data were normalized using quantile normalisation strategies improved with a batch controlling Combat algorithm, PMID 20181233.

source_name: Small intestine, ezetimibe

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems).

extract_protocol: RNA was extracted with TriReagent (Sigma). Quality control was performed with RQS Caliper.

treatment_protocol: 0.005% Ezetimbe (Ezetrol; Pharmacia, UMCG, Groningen) was added to the lab chow.

tag: strain/background

value: male

value: proximal small intestine

value: ezetimibe


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_1)

tag: disease state


title: Day 7, 1.0 Gy, Animal 2502

value: Plasma

value: Radiation


title: Blood Human Control rep3

description:
9380037037_C
replicate 3

scan_protocol: Standard Illumina scanning protocol

value: F

tag: ethnicity

value: ISC

value: HC

value: Blood


title: Blood Human Control rep1

description:
9370786041_L
replicate 1


title: Day 7, 0.0 Gy, Animal 1501

value: Male


title: Day 7, 0.0 Gy, Animal 1003


title: Day 3, 6.5 Gy, Animal 6503


title: Day 3, 6.5 Gy, Animal 6502


title: Blood Human EPTB rep47

description:
9682760039_H
replicate 47

source_name: Blood Human EPTB

value: EPTB


title: Eze3

description:
6331302016_B
Biological replicate 3


title: Control8

description:
6331302016_F
Biological replicate 8

source_name: Small intestine, control

value: control


title: Eze2

description:
6331302005_G
Biological replicate 2


title: Blood Human EPTB rep45

description:
9682760039_D
replicate 45

value: White


title: Blood Human EPTB rep46

description:
9682760039_F
replicate 46

value: Other


title: Blood Human EPTB rep43

description:
9682760033_H
replicate 43

value: M


title: Eze1

description:
6331302005_E
Biological replicate 1


title: Blood Human EPTB rep44

description:
9682760033_I
replicate 44


title: Day 3, 6.5 Gy, Animal 6501


title: Control6

description:
6331302016_C
Biological replicate 6


title: Blood Human EPTB rep41

description:
9682760001_I
replicate 41


title: Day 3, 1.0 Gy, Animal 2502


title: Day 3, 1.0 Gy, Animal 2503


title: Day 3, 3.0 Gy, Animal 4502


title: Day 3, 3.0 Gy, Animal 4003


title: Day 3, 3.0 Gy, Animal 4503 (replicate)


title: Day 3, 3.0 Gy, Animal 4503


title: Blood Human EPTB rep40

description:
9682760001_E
replicate 40


title: Blood Human EPTB rep38

description:
9665647092_K
replicate 38


title: Control5

description:
6331302016_A
Biological replicate 5


title: Eze4

description:
6331302016_E
Biological replicate 4


title: Day 3, 1.0 Gy, Animal 2003


title: Control1

description:
6331302005_A
Biological replicate 1


title: Control4

description:
6331302005_D
Biological replicate 4


title: P28_rep5_array

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 28

hyb_protocol: Hybridization was performed by incubating biotinylated target with the GeneChip® Mouse Exon 1.0 ST array (Affymetrix, Santa Clara, CA) at 45°C for 18–20 hours. The arrays were washed and stained using the Hybridization, Wash and Stain kit per manufacturer’s instructions (Affymetrix).

scan_protocol: Exon chips were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Gene-level core RMA intensity values for each GeneChip® Mouse Exon 1.0 ST array were collected using Expression Console Software v1.3.1.187 (Affymetrix). The resulting number of transcript clusters after RMA summarization was 16,755.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.core.mps

source_name: Nrlp-GFP positive retina cells

label_protocol: Five nanograms of total RNA was used to synthesize sense transcript cDNA (ST-cDNA) using the WT-Ovation RNA Amplification System and WT-Ovation Exon Module, as described by the manufacturer (NuGEN Technologies, San Carlos, CA). Five micrograms of ST-cDNA was fragmented and labeled with the Encore Biotin Module (NuGEN).

growth_protocol: The retina was dissected from Nrlp-GFP mice at different postnatal stages of development in Hank’s Balanced Salt Solution (HBSS; Life Technologies, NY, USA), followed by dissociation in papain (Worthington biochemical, NJ, USA) supplemented with DNase I, superoxidodismutase, catalase, D-alpha-tocopherol acetate, and gentamycin at 28°C for 8 min. After removing cell clumps by filtration, 4 ml of PBS (GIBCO, Life Technologies) was added to dissociated cells. The cells were collected by centrifugation at 800g for 5 min and re-suspended in 1 ml of PBS.

extract_protocol: RNA from GFP-positive cells was purified using RNeasy Mini kit (Qiagen) plus on column DNase I incubation technique.

treatment_protocol: GFP-positive cells were isolated by fluorescence-activated cell sorting (FACS) using FACS Aria II (Becton Dickinson, CA, USA) with a stringent precision setting to maximize the purity of the sorted cells. The purity of isolated GFP-positive cells was evaluated by re-sorting, and only samples with at least 97% of purity were used for analysis. To avoid RNA degradation, GFP-positive cells were collected into RNAProtect (Qiagen, Hilden, Germany).

tag: strain

tag: genotype

value: Nrlp-GFP

tag: post-natal age


title: Control3

description:
6331302005_C
Biological replicate 3

tag: treatment


title: P28_rep3_array


title: P28_rep2_array


title: Blood Human EPTB rep36

description:
9665647088_G
replicate 36

value: Black

tag: age


title: Blood Human EPTB rep34

description:
9665647022_L
replicate 34


title: P28_rep4_array


title: Blood Human EPTB rep33

description:
9665647022_E
replicate 33


title: Control2

description:
6331302005_B
Biological replicate 2

value: male


title: Blood Human EPTB rep39

description:
9682760001_A
replicate 39


title: Blood Human EPTB rep37

description:
9665647092_F
replicate 37


title: Blood Human EPTB rep42

description:
9682760033_E
replicate 42


title: Control7

description:
6331302016_D
Biological replicate 7

value: proximal small intestine


title: Blood Human EPTB rep32

description:
9665647016_L
replicate 32


title: Blood Human EPTB rep35

description:
9665647088_F
replicate 35


title: Day 3, 0.0 Gy, Animal 1503

tag: dose

tag: day


title: pediatric ALL with KMT2A rearrangement (KMT2Ar_3)

value: pediatric ALL with KMT2A rearrangement

value: malignant

value: m

value: peripheral blood

value: tumor cell


title: Day 3, 0.0 Gy, Animal 1501

value: Plasma

value: Radiation

tag: conc

tag: Sex


title: Day 1, 6.5 Gy, Animal 6502

value: Male


title: Day 3, 0.0 Gy, Animal 1003

value: Female


title: Day 3, 0.0 Gy, Animal 1502


title: Day 1, 6.5 Gy, Animal 6503


title: Day 1, 6.5 Gy, Animal 6003


title: Day 1, 5.5 Gy, Animal 5003


title: P21_rep3_array

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 21


title: P21_rep4_array


title: P28_rep1_array


title: Day 7, 6.5 Gy, Animal 6501


title: P21_rep2_array


title: P12_rep1_array

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 12


title: P12_rep2_array


title: P10_rep4_array

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 10


title: Day 1, 6.5 Gy, Animal 6503 (replicate)


title: P21_rep1_array


title: Blood Human EPTB rep29

description:
9631032010_I
replicate 29

value: ISC

value: EPTB

value: Blood


title: Day 1, 3.0 Gy, Animal 4501


title: Blood Human EPTB rep31

description:
9665647016_K
replicate 31

value: F


title: Blood Human EPTB rep30

description:
9665647016_I
replicate 30

value: Other


title: Blood Human EPTB rep28

description:
9631032010_H
replicate 28

value: M


title: P12_rep3_array

value: Nrlp-GFP


title: Blood Human EPTB rep25

description:
9610342033_G
replicate 25


title: P12_rep4_array


title: Blood Human EPTB rep26

description:
9610342033_H
replicate 26


title: Blood Human EPTB rep27

description:
9631032010_D
replicate 27


title: Day 1, 5.5 Gy, Animal 5002


title: Day 1, 3.0 Gy, Animal 4503


title: Day 1, 3.0 Gy, Animal 4003


title: Day 1, 2.0 Gy, Animal 3002


title: P10_rep3_array


title: Day 1, 3.0 Gy, Animal 4002


title: Day 1, 3.0 Gy, Animal 4502


title: Blood Human EPTB rep24

description:
9610342033_D
replicate 24


title: Blood Human EPTB rep23

description:
9610342028_L
replicate 23

value: Black


title: P10_rep2_array


title: P6_rep4_array

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 6


title: P10_rep1_array


title: Blood Human EPTB rep22

description:
9610342021_D
replicate 22


title: Day 1, 1.0 Gy, Animal 2603


title: P6_rep2_array


title: Day 1, 1.0 Gy, Animal 2502


title: P6_rep3_array


title: Blood Human EPTB rep20

description:
9610342003_I
replicate 20


title: P6_rep1_array


title: P4_rep4_array

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 4


title: Blood Human EPTB rep19

description:
9610342003_F
replicate 19


title: Blood Human EPTB rep21

description:
9610342003_J
replicate 21


title: Day 1, 1.0 Gy, Animal 2002


title: Blood Human EPTB rep18

description:
9610342003_D
replicate 18

value: White


title: Blood Human EPTB rep17

description:
9380252031_H
replicate 17


title: Day 1, 0.0 Gy, Animal 1503


title: Day 1, 0.0 Gy, Animal 1502


title: Day 1, 0.0 Gy, Animal 1002


title: P4_rep3_array


title: Blood Human EPTB rep14

description:
9380252031_B
replicate 14


title: P4_rep2_array


title: Blood Human EPTB rep15

description:
9380252031_E
replicate 15


title: P2_rep3_array

description: flow sorted Nrlp-GFP positive cells in wild-type retina at post natal day 2


title: Day 1, 0.0 Gy, Animal 1003


title: P2_rep1_array


title: Day 0, 6.5 Gy, Animal 6501


title: Day 0, 6.5 Gy, Animal 6502


title: Blood Human EPTB rep16

description:
9380252031_F
replicate 16


title: Blood Human EPTB rep13

description:
9380252030_L
replicate 13


title: PM_N3

type: SRA

city: Wuhan

first: Wei

last: Zhang

state: Hubei Province

address: Luoyu

institute: Central China Normal University

library_source: transcriptomic

data_processing:
Illumina CASVA 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence through in-house perl scripts, then mapped to the assembled Unigene sequences using RSEM 1.2.0 with Bowtie allowing  mismatchs of no more than two bases (Bowtie default parameter).
The left files (read1 file) from all samples were pooled into one big left.fq file, and right files (read2 file) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (r2012-10-05) with min_kmer_cov set to 2 by default and all other parameters set defalut.Unigenes was selected from the longest transcript copy of each gene clusters using in-house Perl scripts to avoid redundant transcripts.
Gene expression level for each sample were estimated using the software package RSEM (v 1.2.0) based on the expectation-maximization (EM) algorithm. Firstly, clean reads of each sample were mapped back onto the assembled transcripts. Then, the read count for each gene was obtained from the mapping results. The gene expression level was estimated by calculating the fragments per kb per million reads (FPKM).
Genome_build: Assembly Unigene.fasta
Supplementary_files_format_and_content: xls files include Readcount and FPKM values for each Sample,and fasta file is the assembled Unigene sequence.

organism: Leptobrachium boringii

source_name: Upper jaw skin

extract_protocol:
Tissues of brain, testis and upper jaw skin were removed, and RNA was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: Upper jaw skin

tag: developmental stage

value: Post breeding period


title: P4_rep1_array


title: Blood Human EPTB rep10

description:
9380252001_J
replicate 10

tag: tissue


title: Day 0, 6.5 Gy, Animal 6503


title: P2_rep2_array


title: PM_N2


title: Blood Human EPTB rep11

description:
9380252030_G
replicate 11


title: Blood Human EPTB rep12

description:
9380252030_I
replicate 12


title: Blood Human EPTB rep9

description:
9380037052_J
replicate 9


title: Blood Human EPTB rep7

description:
9380037052_F
replicate 7


title: Blood Human EPTB rep4

description:
9380037014_G
replicate 4


title: Blood Human EPTB rep8

description:
9380037052_H
replicate 8


title: PM_N1


title: Blood Human EPTB rep5

description:
9380037037_A
replicate 5


title: Blood Human EPTB rep3

description:
9380037014_F
replicate 3


title: Day 0, 6.5 Gy, Animal 6003


title: Day 0, 5.5 Gy, Animal 5003


title: M_N2

value: Breeding period


title: Day 0, 5.5 Gy, Animal 5002

value: Plasma


title: M_N1


title: M_N3


title: Day 0, 3.0 Gy, Animal 4502

value: Radiation


title: Day 0, 3.0 Gy, Animal 4501

value: Male


title: PM_T2

source_name: Testis

value: Testis


title: Day 0, 3.0 Gy, Animal 4002

value: Female


title: Day 0, 3.0 Gy, Animal 4003


title: M_T3


title: Blood Human EPTB rep2

description:
9370786041_I
replicate 2

value: EPTB


title: Day 1, 0.0 Gy, Animal 1501


title: Day 0, 2.0 Gy, Animal 3002


title: MG1363_Ethanol_5min_Rep3

city: Kgs. Lyngby

first: Mogens

last: Kilstrup

address: Building 301 room 158

institute: Technical University of Denmark

hyb_protocol: Hydridzation according to Aglient Protocol. Aglient 8x15k custom microarray G2509F

scan_protocol: Aglient technologies scanner G2505C. Aglient’s Feature Extraction Software

data_processing: Quantile normalization

source_name: MG1363, Ethanol (55 mg/ml), 5 min, Biological Replica 3

label_protocol: Labbeling according to aglient protocol using random hexamer and Cy3

extract_protocol: Cells were pelleted by centrifugation and washed in ice cold salin water (0.9% NaCl). RNA was extracted by the hot phenol method

value: Ethanol (55 mg/ml), 5 min


title: Day 1, 1.0 Gy, Animal 2003

source_name: Plasma


title: MG1363_Hexanol_60min_Rep2

source_name: MG1363, Hexanol (2 mg/ml), 60 min, Biological Replica 2

value: Hexanol (2 mg/ml), 60 min


title: Day 0, 1.0 Gy, Animal 2503


title: PM_B3

source_name: Brain

value: Brain


title: Day 0, 1.0 Gy, Animal 2502


title: MG1363_Butanol_60min_Rep2

source_name: MG1363, Butanol (55 mg/ml), 60 min, Biological Replica 2

value: Butanol (55 mg/ml), 60 min


title: MG1363_Hexanol_5min_Rep3

source_name: MG1363, Hexanol (2 mg/ml), 5 min, Biological Replica 3

value: Hexanol (2 mg/ml), 5 min


title: Day 0, 1.0 Gy, Animal 2002


title: MG1363_Butanol_5min_Rep3

source_name: MG1363, Butanol (10 mg/ml), 5 min, Biological Replica 3

value: Butanol (10 mg/ml), 5 min


title: PM_B2


title: PM_B1


title: MG1363_Ethanol_60min_Rep2

source_name: MG1363, Ethahol (55 mg/ml), 60 min, Biological Replica 2

value: Ethahol (55 mg/ml), 60 min


title: Day 0, 1.0 Gy, Animal 2003


title: M_B3

value: wild type


title: M_B2


title: Day 0, 0.0 Gy, Animal 1502


title: Day 0, 0.0 Gy, Animal 1501 (replicate)


title: Day 0, 0.0 Gy, Animal 1503


title: M_B1


title: Day 0, 0.0 Gy, Animal 1501


title: MG1363_Butanol_5min_Rep2

source_name: MG1363, Butanol (10 mg/ml), 5 min, Biological Replica 2


title: Day 0, 0.0 Gy, Animal 1002


title: MG1363_Hexanol_5min_Rep2

source_name: MG1363, Hexanol (2 mg/ml), 5 min, Biological Replica 2


title: MG1363_Ethanol_5min_Rep2

source_name: MG1363, Ethanol (55 mg/ml), 5 min, Biological Replica 2


title: Blood Human EPTB rep1

description:
9370786041_D
replicate 1

value: M

value: ISC

value: Blood


title: HPNE #1 + #3

status: Public on Nov 03 2016

city: Guangzhou

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

description: Comparison between HPNE cells with activated Kras to HPNE cells with activated Kras and inactivated p16

hyb_protocol: Agilent Technologies Scanner G2505C US23502373

scan_protocol: Images were quantified using Agilent Feature Extraction Software (GE2-v5_95).

data_processing: Agilent Feature Extraction Software (GE2-v5_95) was used for background subtraction and LOWESS normalization. The sorting method uses the error-model (p-value) built into the output of Agilent arrays. Agilent has redundant spots on the arrays, and the error-model correlates the signals seen at the various replicate positions to predict the error of the other (non-repeated) probes. This gives an estimate of the p-values for any probe on the array. Gene lists were generated using p-value information from the internal replicates within the microarray. The data with insignificant p-value larger than 0.0001 were considered as insignificant and was deleted. The significant differential expression was defined as p-values <0.0001 as measured with the random variance t-test.

source_name: HPNE/Kras cells

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: HPNE/Kras and HPNE/Kras/shp16 cells were grown in Medium D with a mixture of M3 medium and DMEM containing one volume of M3 Base F culture medium (InCell Corp., San Antonio, USA), three volumes of glucose-free DMEM, 10% FBS, 5.5 mM glucose, 10 ng/ml EGF, and 50 µg/ml gentamycin.

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell line

value: HPNE cells with activated Kras

tag: cell type

value: Pancreatic cells

source_name: HPNE/Kras/shp16 cells


title: Sample NY106: whole liver tissue

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: Sample NY106: whole liver tissue (Normal group)

hyb_protocol: Hybridization was performed on Affymetrix GeneChip miRNA 2.0 arrays using standard protocols available at www.affymetrix.com.

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABD) and RMA Background Adjustment algorithm were performed in order to remove the background value.

source_name: whole liver sample

extract_protocol: RNA was extracted from liver tissues using Trizol and following manufacter’s manual instructions (Life Tecnologies, Carlsbad, CA). miRNA quantification was performed using the commercial kit Mir-X miRNA First-Strand Synthesis Kit doing as manufacter’s manual instructions (Takara Bio Europe/Clontech, Saint-Germain-en-Laye, France).

tag: tissue type

value: normal liver

tag: group

value: Normal


title: HCC cell line SNU423

description: HCC cell line SNU423 (HCC Cell line group)

source_name: HCC cell line

label_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

value: hepatocellular carcinoma

value: HCC Cell line


title: Sample NY108: whole liver tissue

description: Sample NY108: whole liver tissue (Normal group)


title: HCC cell line SNU475

description: HCC cell line SNU475 (HCC Cell line group)


title: HCC cell line SNU449

description: HCC cell line SNU449 (HCC Cell line group)


title: PALMITATE10

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description: treated, biological replicate 1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction,55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100µl were hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed according to manufacturer's intructions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted .  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were normalized using bioconductor and limma package. Briefly, background substraction was performed using the normexp correction with an offset=1, then signals were normalized using quantile normalization. Only spots presenting a signal 10% brighter than the 95th percentile of the negative control are kept for statistical analysis

source_name: C2C12 incubated with EXO-Palm

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

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

value: myoblast


title: BSA5

description: control, biological replicate 3

source_name: C2C12 incubated with Exo-BSA


title: Sample M807: whole liver tissue

description: Sample M807: whole liver tissue (HCC group)

value: HCC


title: HCC cell line SNU182

description: HCC cell line SNU182 (HCC Cell line group)


title: HCC cell line PLC5

description: HCC cell line PLC5 (HCC Cell line group)


title: PALMITATE11

description: treated, biological replicate 2


title: PALMITATE12

description: treated, biological replicate 3


title: BSA6

description: control, biological replicate 4


title: Sample NY101: whole liver tissue

description: Sample NY101: whole liver tissue (Normal group)


title: BSA3

description: control, biological replicate 1


title: Sample NY103: whole liver tissue

description: Sample NY103: whole liver tissue (Normal group)


title: Sample M803: whole liver tissue

description: Sample M803: whole liver tissue (HCC group)


title: Sample M805: whole liver tissue

description: Sample M805: whole liver tissue (HCC group)


title: HCC cell line SNU398

description: HCC cell line SNU398 (HCC Cell line group)


title: Sample M795: whole liver tissue

description: Sample M795: whole liver tissue (HCC group)


title: Sample M797: whole liver tissue

description: Sample M797: whole liver tissue (HCC group)


title: Sample NY104: whole liver tissue

description: Sample NY104: whole liver tissue (Normal group)


title: BSA4

description: control, biological replicate 2


title: Sample NY107: whole liver tissue

description: Sample NY107: whole liver tissue (Normal group)


title: Sample M799: whole liver tissue

description: Sample M799: whole liver tissue (HCC group)


title: HCC cell line SNU387

description: HCC cell line SNU387 (HCC Cell line group)


title: Sample M791: whole liver tissue

description: Sample M791: whole liver tissue (HCC group)


title: Sample M793: whole liver tissue

description: Sample M793: whole liver tissue (HCC group)


title: Sample M789: whole liver tissue

description: Sample M789: whole liver tissue (HCC group)


title: Sample M777: whole liver tissue

description: Sample M777: whole liver tissue (HCC group)


title: Sample M787: whole liver tissue

description: Sample M787: whole liver tissue (HCC group)


title: Sample M785: whole liver tissue

description: Sample M785: whole liver tissue (HCC group)


title: Sample M765: whole liver tissue

description: Sample M765: whole liver tissue (HCC group)


title: Sample M783: whole liver tissue

description: Sample M783: whole liver tissue (HCC group)


title: Sample M773: whole liver tissue

description: Sample M773: whole liver tissue (HCC group)


title: Sample M759: whole liver tissue

description: Sample M759: whole liver tissue (HCC group)


title: Sample M781: whole liver tissue

description: Sample M781: whole liver tissue (HCC group)


title: Sample M769: whole liver tissue

description: Sample M769: whole liver tissue (HCC group)


title: Sample M757: whole liver tissue

description: Sample M757: whole liver tissue (HCC group)


title: Sample M755: whole liver tissue

description: Sample M755: whole liver tissue (HCC group)


title: Sample M751: whole liver tissue

description: Sample M751: whole liver tissue (HCC group)


title: Sample M749: whole liver tissue

description: Sample M749: whole liver tissue (HCC group)


title: Sample M733: whole liver tissue

description: Sample M733: whole liver tissue (HCC group)


title: Sample M743: whole liver tissue

description: Sample M743: whole liver tissue (HCC group)


title: Sample M745: whole liver tissue

description: Sample M745: whole liver tissue (HCC group)


title: Sample M747: whole liver tissue

description: Sample M747: whole liver tissue (HCC group)


title: Sample M771: whole liver tissue

description: Sample M771: whole liver tissue (HCC group)


title: Sample M735: whole liver tissue

description: Sample M735: whole liver tissue (HCC group)


title: Sample M741: whole liver tissue

description: Sample M741: whole liver tissue (HCC group)


title: Sample M719: whole liver tissue

description: Sample M719: whole liver tissue (HCC group)


title: Sample M725: whole liver tissue

description: Sample M725: whole liver tissue (HCC group)


title: Sample M761: whole liver tissue

description: Sample M761: whole liver tissue (HCC group)


title: Sample M723: whole liver tissue

description: Sample M723: whole liver tissue (HCC group)


title: Sample M713: whole liver tissue

description: Sample M713: whole liver tissue (HCC group)


title: Sample M727: whole liver tissue

description: Sample M727: whole liver tissue (HCC group)


title: Blood Human EPTB rep6

city: London

first: Krzysztof

last: Potempa

description:
9380037037_E
replicate 6

data_processing: quantile normalization, background subtraction using Genomestudio

source_name: Blood Human EPTB

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

extract_protocol: 1ml added to 2mls Tempus solution. RNA extracted using PerfectPURE RNA Blood kit (5-PRIME), globin RNA reduced using GLOBINclear (Biosystems/Ambion)

tag: gender

tag: disease state

value: EPTB


title: Sample M715: whole liver tissue

description: Sample M715: whole liver tissue (HCC group)


title: Sample M711: whole liver tissue

description: Sample M711: whole liver tissue (HCC group)


title: Sample M729: whole liver tissue

description: Sample M729: whole liver tissue (HCC group)


title: Sample M709: whole liver tissue

description: Sample M709: whole liver tissue (HCC group)


title: Sample M701: whole liver tissue

description: Sample M701: whole liver tissue (HCC group)


title: Sample M693: whole liver tissue

description: Sample M693: whole liver tissue (HCC group)


title: Sample M691: whole liver tissue

description: Sample M691: whole liver tissue (HCC group)


title: Sample M703: whole liver tissue

description: Sample M703: whole liver tissue (HCC group)


title: Sample M683: whole liver tissue

description: Sample M683: whole liver tissue (HCC group)


title: Sample M685: whole liver tissue

description: Sample M685: whole liver tissue (HCC group)


title: Sample M689: whole liver tissue

description: Sample M689: whole liver tissue (HCC group)


title: Sample M681: whole liver tissue

description: Sample M681: whole liver tissue (HCC group)


title: Sample M697: whole liver tissue

description: Sample M697: whole liver tissue (HCC group)


title: Sample M671: whole liver tissue

description: Sample M671: whole liver tissue (HCC group)


title: Sample M673: whole liver tissue

description: Sample M673: whole liver tissue (HCC group)


title: Sample M679: whole liver tissue

description: Sample M679: whole liver tissue (HCC group)


title: Sample M687: whole liver tissue

description: Sample M687: whole liver tissue (HCC group)


title: Sample M667: whole liver tissue

description: Sample M667: whole liver tissue (HCC group)


title: Sample M665: whole liver tissue

description: Sample M665: whole liver tissue (HCC group)


title: Sample M707: whole liver tissue

description: Sample M707: whole liver tissue (HCC group)


title: Sample M669: whole liver tissue

description: Sample M669: whole liver tissue (HCC group)


title: Sample M661: whole liver tissue

description: Sample M661: whole liver tissue (HCC group)


title: Sample M651: whole liver tissue

description: Sample M651: whole liver tissue (HCC group)


title: Sample M677: whole liver tissue

description: Sample M677: whole liver tissue (HCC group)


title: Sample M657: whole liver tissue

description: Sample M657: whole liver tissue (HCC group)


title: Sample M649: whole liver tissue

description: Sample M649: whole liver tissue (HCC group)


title: Sample M653: whole liver tissue

description: Sample M653: whole liver tissue (HCC group)


title: Sample M675: whole liver tissue

description: Sample M675: whole liver tissue (HCC group)


title: Sample M659: whole liver tissue

description: Sample M659: whole liver tissue (HCC group)


title: Sample M655: whole liver tissue

description: Sample M655: whole liver tissue (HCC group)


title: Sample M647: whole liver tissue

description: Sample M647: whole liver tissue (HCC group)


title: Sample M633: whole liver tissue

description: Sample M633: whole liver tissue (HCC group)


title: Sample M639: whole liver tissue

description: Sample M639: whole liver tissue (HCC group)


title: Sample M635: whole liver tissue

description: Sample M635: whole liver tissue (HCC group)


title: Sample M645: whole liver tissue

description: Sample M645: whole liver tissue (HCC group)


title: Sample M629: whole liver tissue

description: Sample M629: whole liver tissue (HCC group)


title: Sample M631: whole liver tissue

description: Sample M631: whole liver tissue (HCC group)


title: Sample M623: whole liver tissue

description: Sample M623: whole liver tissue (HCC group)


title: Sample M627: whole liver tissue

description: Sample M627: whole liver tissue (HCC group)


title: Sample M621: whole liver tissue

description: Sample M621: whole liver tissue (HCC group)


title: Sample M619: whole liver tissue

description: Sample M619: whole liver tissue (HCC group)


title: Sample M617: whole liver tissue

description: Sample M617: whole liver tissue (HCC group)


title: Sample M609: whole liver tissue

description: Sample M609: whole liver tissue (HCC group)


title: Sample M605: whole liver tissue

description: Sample M605: whole liver tissue (HCC group)


title: Sample M615: whole liver tissue

description: Sample M615: whole liver tissue (HCC group)


title: Sample M597: whole liver tissue

description: Sample M597: whole liver tissue (HCC group)


title: Sample M607: whole liver tissue

description: Sample M607: whole liver tissue (HCC group)


title: Sample M603: whole liver tissue

description: Sample M603: whole liver tissue (HCC group)


title: Sample M599: whole liver tissue

description: Sample M599: whole liver tissue (HCC group)


title: Sample M595: whole liver tissue

description: Sample M595: whole liver tissue (HCC group)


title: Sample M591: whole liver tissue

description: Sample M591: whole liver tissue (HCC group)


title: Sample M593: whole liver tissue

description: Sample M593: whole liver tissue (HCC group)


title: Sample M587: whole liver tissue

description: Sample M587: whole liver tissue (HCC group)


title: Sample M581: whole liver tissue

description: Sample M581: whole liver tissue (HCC group)


title: Sample M585: whole liver tissue

description: Sample M585: whole liver tissue (HCC group)


title: Sample M573: whole liver tissue

description: Sample M573: whole liver tissue (HCC group)


title: Sample M577: whole liver tissue

description: Sample M577: whole liver tissue (HCC group)


title: Sample M613: whole liver tissue

description: Sample M613: whole liver tissue (HCC group)


title: Sample M565: whole liver tissue

description: Sample M565: whole liver tissue (HCC group)


title: Sample M561: whole liver tissue

description: Sample M561: whole liver tissue (HCC group)


title: Sample M579: whole liver tissue

description: Sample M579: whole liver tissue (HCC group)


title: Sample M559: whole liver tissue

description: Sample M559: whole liver tissue (HCC group)


title: Sample M569: whole liver tissue

description: Sample M569: whole liver tissue (HCC group)


title: Sample M551: whole liver tissue

description: Sample M551: whole liver tissue (HCC group)


title: Sample M547: whole liver tissue

description: Sample M547: whole liver tissue (HCC group)


title: Sample M545: whole liver tissue

description: Sample M545: whole liver tissue (HCC group)


title: Sample M557: whole liver tissue

description: Sample M557: whole liver tissue (HCC group)


title: Sample M567: whole liver tissue

description: Sample M567: whole liver tissue (HCC group)


title: Sample M543: whole liver tissue

description: Sample M543: whole liver tissue (HCC group)


title: Sample M571: whole liver tissue

description: Sample M571: whole liver tissue (HCC group)


title: Sample M529: whole liver tissue

description: Sample M529: whole liver tissue (HCC group)


title: Sample M537: whole liver tissue

description: Sample M537: whole liver tissue (HCC group)


title: Sample M553: whole liver tissue

description: Sample M553: whole liver tissue (HCC group)


title: Sample M517: whole liver tissue

description: Sample M517: whole liver tissue (HCC group)


title: Sample M539: whole liver tissue

description: Sample M539: whole liver tissue (HCC group)


title: Sample M519: whole liver tissue

description: Sample M519: whole liver tissue (HCC group)


title: Sample M531: whole liver tissue

description: Sample M531: whole liver tissue (HCC group)


title: Sample M505: whole liver tissue

description: Sample M505: whole liver tissue (HCC group)


title: Sample M511: whole liver tissue

description: Sample M511: whole liver tissue (HCC group)


title: Sample M515: whole liver tissue

description: Sample M515: whole liver tissue (HCC group)


title: Sample M533: whole liver tissue

description: Sample M533: whole liver tissue (HCC group)


title: Sample M535: whole liver tissue

description: Sample M535: whole liver tissue (HCC group)


title: Sample M501: whole liver tissue

description: Sample M501: whole liver tissue (HCC group)


title: Sample M497: whole liver tissue

description: Sample M497: whole liver tissue (HCC group)


title: Sample M499: whole liver tissue

description: Sample M499: whole liver tissue (HCC group)


title: Sample M489: whole liver tissue

description: Sample M489: whole liver tissue (HCC group)


title: Sample M523: whole liver tissue

description: Sample M523: whole liver tissue (HCC group)