title: LIVER_diclofenac_repl5

description: Human liver slices (diameter 4 mm, thickness 250 µm)

hyb_protocol: cRNA was denaturized to prepare for the hybridization on the array. The fragmented cRNA with a concentration of 0.0375 μg/μl was finally utilized for the hybridization on the Affymetrix HT HG U133 plus PM.  The Affymetrix HWS Kit (#901530) was used for the hybridization, washing and staining of the chips.

scan_protocol: Scanning of the Array Plates was performed using the Affymetrix GeneTitan scanner

data_processing: BRB Array Tools software was used to normalize the CEL data using the Robust Multichip Average (RMA) method. Significantly differentially expressed genes (p-value < 0.001) between the various experimental conditions were identified with an ANOVA test followed by calculation according to Benjamini and Hochberg (Benjamini and Hochberg, 1995).

source_name: human liver

label_protocol: The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labeling reactions.

growth_protocol: Human hepatoma HepG2 cells were obtained from American Type Culture Collection (ATCC, Wesel, Germany), cultured in DMEM supplemented with 10% (v/v) FBS, 25 U/mL penicillin and 25 µg/mL streptomycin and used for experiments between passage 5 and 20.

extract_protocol: RNA was isolated using the RNeasy® Plus Mini Kit (Qiagen, Venlo, the Netherlands) and RNA integrity and quality was assessed using the Agilent bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Diclofenac sodium, carbamazepine, nefazodone and ketoconazole were obtained from Sigma (Zwijndrecht, the Netherlands). Methotrexate was from Acros Organics (Geel, Belgium). Human recombinant TNFα was acquired from R&D Systems (Abingdon, United Kingdom).

tag: batch

tag: donor


title: LIVER_CONTROL_repl5

status: Public on Jan 22 2014

type: RNA

city: Leiden

first: Steven

last: Wink

state: Zuid Holland

address: Einsteinweg 55

department: Division of Toxicology

country: Netherlands

institute: LACDR

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: treatment

value: control

tag: tissue

value: Human liver slices (diameter 4 mm, thickness 250 µm)


title: Tumor T_AT_159

city: Modena

first: Erica

last: Villa

address: Via del Pozzo 71

country: Italy

institute: University of Modena and Reggio Emilia

description: Gene expression of tumor liver tissue

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays (44K, Design ID 014850) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

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

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

source_name: Biopsy of tumor tissue

label_protocol: Cyanine-3 (Cy3) Cy3-labeled cRNA was prepared from 0.5 ug RNA using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) or  the Agilent Quick Amp Labeling Kit (Agilent Technologies)  following the manufacturer’s protocol.  Yields of cRNA and the dye-incorporation rate were  measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Total RNA was isolated from non tumor (NT) and tumor (T) liver tissues using Trizol (Invitrogen Corp., Carlsbad, California, USA) protocol. Quality and quantity of the RNA samples was checked on an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and ND-1000 Spectrophotometer (NanoDrop Technologies), respectively.

tag: tissue type

value: Biopsy of tumor tissue

value: Liver

tag: gender

value: male

tag: doubling time (days)

tag: survival time(months)

tag: amplification and labeling kit

value: Agilent Quick Amp Labeling Kit

tag: scanner update

tag: feature extraction software update


title: Tumor T_AR_119

description: Gene expression of tumor liver tissue

value: Agilent Low RNA Input Linear Amp Kit


title: LIVER_CONTROL_repl3


title: Tumor T_AP_146

description: Gene expression of tumor liver tissue


title: Tumor T_AO_138

description: Gene expression of tumor liver tissue

value: female


title: Tumor T_AU_163

description: Gene expression of tumor liver tissue


title: Tumor T_AQ_150

description: Gene expression of tumor liver tissue


title: Tumor T_AS_153

description: Gene expression of tumor liver tissue


title: LIVER_CONTROL_repl4


title: LIVER_diclofenac_repl1

value: diclofenac


title: HepG2 Ketoconazole14hr biological replicate 1 101446-92_Ket - 4

source_name: HepG2 ATCC, Wesel, Germany

tag: cell line

tag: source

value: caucasian male


title: LIVER_diclofenac_repl4


title: LIVER_diclofenac_repl2


title: Tumor_rep1 T_AL_127r

description: Gene expression of tumor liver tissue


title: LIVER_CONTROL_repl1


title: LIVER_diclofenac_repl3


title: Tumor T_AK_117

description: Gene expression of tumor liver tissue


title: LIVER_CONTROL_repl2


title: HepG2 Carbamazepine 8hr + TNFalpha 6h biological replicate 1 101446-91_CBZ 6 h TNF - 4

value: Carbamazepine 8hr + TNFalpha 6h


title: Tumor T_AJ_115

description: Gene expression of tumor liver tissue


title: Tumor T_AN_131

description: Gene expression of tumor liver tissue


title: HepG2 Ketoconazole 8hr + TNFalpha 6h biological replicate 1 101446-96_Ket 6 h TNF - 4

value: Ketoconazole 8hr + TNFalpha 6h


title: Tumor T_AL_127

description: Gene expression of tumor liver tissue


title: Tumor T_AM_129

description: Gene expression of tumor liver tissue


title: HepG2 Ketoconazole 8hr + TNFalpha 1h biological replicate 1 101446-95_Ket 1 h TNF - 4

value: Ketoconazole 8hr + TNFalpha 1h


title: Tumor T_AI_113

description: Gene expression of tumor liver tissue


title: HepG2 Ketoconazole 8hr + BSA 6h biological replicate 1 101446-94_Ket 6 h BSA - 4

value: Ketoconazole 8hr + BSA 6h


title: Tumor T_AH_132

description: Gene expression of tumor liver tissue


title: Tumor_rep1 T_AG_107r

description: Gene expression of tumor liver tissue


title: Tumor T_AG_107

description: Gene expression of tumor liver tissue


title: Tumor T_AF_104

description: Gene expression of tumor liver tissue


title: HepG2 Carbamazepine 14hr biological replicate 1 101446-87_CBZ - 4

value: Carbamazepine 14hr


title: HepG2 Carbamazepine 8hr + BSA 6h biological replicate 1 101446-89_CBZ 6 h BSA - 4

value: Carbamazepine 8hr + BSA 6h


title: HepG2 Ketoconazole 8hr + BSA 1h biological replicate 1 101446-93_Ket 1 h BSA - 4

value: Ketoconazole 8hr + BSA 1h


title: HepG2 Carbamazepine 8hr + TNFalpha 1h biological replicate 1 101446-90_CBZ 1 h TNF - 4

value: Carbamazepine 8hr + TNFalpha 1h


title: HepG2 Carbamazepine 8hr + BSA 1h biological replicate 1 101446-88_CBZ 1 h BSA - 4

value: Carbamazepine 8hr + BSA 1h


title: Tumor T_AD_096

description: Gene expression of tumor liver tissue

value: Biopsy of tumor tissue


title: Tumor T_AA_089

description: Gene expression of tumor liver tissue

value: Liver


title: Tumor T_AB_091

description: Gene expression of tumor liver tissue

value: male


title: HepG2 Diclofenac 8hr + TNFalpha 1h biological replicate 1 101446-85_Dic 1 h TNF - 4

value: Diclofenac 8hr + TNFalpha 1h


title: HepG2 DMSO 8hr + TNFalpha 6h biological replicate 1 101446-81_DMSO 6 h TNF - 4

value: DMSO 8hr + TNFalpha 6h


title: Tumor T_AE_098

description: Gene expression of tumor liver tissue

value: Agilent Low RNA Input Linear Amp Kit


title: Tumor T_AC_105

description: Gene expression of tumor liver tissue

value: female


title: Tumor T_Y_078

description: Gene expression of tumor liver tissue


title: HepG2 DMSO 14hr biological replicate 1 101446-79_DMSO - 4

description: HepG2 DMSO 14hr biological replicate 1

value: DMSO 14hr

value: caucasian male


title: HepG2 Diclofenac 8hr + BSA 1h biological replicate 1 101446-83_Dic 1 h BSA - 4

value: Diclofenac 8hr + BSA 1h


title: HepG2 Diclofenac 8hr + TNFalpha 6h biological replicate 1 101446-86_Dic 6 h TNF - 4

value: Diclofenac 8hr + TNFalpha 6h


title: Tumor T_W_069

description: Gene expression of tumor liver tissue


title: HepG2 Diclofenac 14hr biological replicate 1 101446-82_Dic - 4

value: Diclofenac 14hr


title: Tumor T_Z_080

description: Gene expression of tumor liver tissue


title: Tumor T_X_086

description: Gene expression of tumor liver tissue


title: Tumor T_X_087

description: Gene expression of tumor liver tissue


title: Tumor T_V_065

description: Gene expression of tumor liver tissue


title: HepG2 Nefadozone 8hr + TNFalpha 1h biological replicate 1 101446-77_Nef 1 h TNF - 3

value: Nefadozone 8hr + TNFalpha 1h


title: HepG2 Nefadozone 8hr + TNFalpha 6h biological replicate 1 101446-78_Nef 6 h TNF - 3

value: Nefadozone 8hr + TNFalpha 6h


title: HepG2 DMSO 8hr + TNFalpha 1h biological replicate 1 101446-80_DMSO 1 h TNF - 4

value: DMSO 8hr + TNFalpha 1h


title: HepG2 Diclofenac 8hr + BSA 6h biological replicate 1 101446-84_Dic 6 h BSA - 4

value: Diclofenac 8hr + BSA 6h


title: HepG2 Nefadozone 8hr  + BSA 6h biological replicate 1 101446-76_Nef 6 h BSA - 3

value: Nefadozone 8hr  + BSA 6h


title: HepG2 Methotrexate 8hr + TNFalpha 6h biological replicate 1 101446-74_MTX 6 h TNF - 3

value: Methotrexate 8hr + TNFalpha 6h


title: HepG2 Nefadozone 8hr + BSA 1h biological replicate 1 101446-75_Nef 1 h BSA - 3

value: Nefadozone 8hr + BSA 1h


title: Tumor T_Q_063

description: Gene expression of tumor liver tissue

value: Biopsy of tumor tissue

value: Liver

value: male


title: HepG2 Methotrexate 8hr + BSA 6h biological replicate 1 101446-72_MTX 6 h BSA - 3

value: Methotrexate 8hr + BSA 6h


title: Tumor T_U_060

description: Gene expression of tumor liver tissue

value: Agilent Low RNA Input Linear Amp Kit


title: Tumor T_T_059

description: Gene expression of tumor liver tissue


title: Tumor T_P_049

description: Gene expression of tumor liver tissue


title: Tumor T_R_055

description: Gene expression of tumor liver tissue


title: HepG2 Ketoconazole 8hr + BSA 6h biological replicate 1 101446-68_Ket 6 h BSA - 3

value: Ketoconazole 8hr + BSA 6h


title: HepG2 Ketoconazole 8hr + TNFalpha 6h biological replicate 1 101446-70_Ket 6 h TNF - 3

value: Ketoconazole 8hr + TNFalpha 6h

value: caucasian male


title: HepG2 Methotrexate 8hr + TNFalpha 1h biological replicate 1 101446-73_MTX1 h TNF - 3

value: Methotrexate 8hr + TNFalpha 1h


title: HepG2 Methotrexate 8hr + BSA 1h biological replicate 1 101446-71_MTX 1 h BSA - 3

value: Methotrexate 8hr + BSA 1h


title: Tumor T_S_057

description: Gene expression of tumor liver tissue

value: female


title: Tumor T_N_041

description: Gene expression of tumor liver tissue


title: Tumor_rep1 T_O_047r

description: Gene expression of tumor liver tissue

value: Agilent Quick Amp Labeling Kit


title: Tumor T_M_035

description: Gene expression of tumor liver tissue


title: HepG2 Ketoconazole 8hr + TNFalpha 1h biological replicate 1 101446-69_Ket 1 h TNF - 3

value: Ketoconazole 8hr + TNFalpha 1h


title: HepG2 Ketoconazole14hr biological replicate 1 101446-66_Ket - 3


title: IL1

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

country: USA

institute: Johns Hopkins University

description: About 5 μg total RNA of each sample was used for labeling and array hybridization

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner

data_processing: Scanned images were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

source_name: chronic inflammatory liver

label_protocol: ds-cDNA labeling with NimbleGen one-color DNA labeling kit

growth_protocol: All these fresh tissues were collected in the operating room and processed immediately within 15 minutes. Each sample was frozen and stored at -80°C.

extract_protocol: Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit

treatment_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis

value: liver

tag: condition

value: chronic inflammatory liver

tag: age

value: M

tag: hbsag

value: Positive

tag: hbeag

value: Negative


title: HepG2 Ketoconazole 8hr + BSA 1h biological replicate 1 101446-67_Ket 1 h BSA - 3

value: Ketoconazole 8hr + BSA 1h


title: Tumor T_O_047

description: Gene expression of tumor liver tissue

value: Biopsy of tumor tissue

value: Liver

value: male


title: HepG2 Carbamazepine 8hr + TNFalpha 6h biological replicate 1 101446-65_CBZ 6 h TNF - 3

value: Carbamazepine 8hr + TNFalpha 6h


title: Tumor T_J_025

description: Gene expression of tumor liver tissue

value: Agilent Low RNA Input Linear Amp Kit


title: HepG2 Carbamazepine 8hr + BSA 6h biological replicate 1 101446-63_CBZ 6 h BSA - 3

value: Carbamazepine 8hr + BSA 6h

value: caucasian male


title: HepG2 Carbamazepine 8hr + TNFalpha 1h biological replicate 1 101446-64_CBZ 1 h TNF - 3

value: Carbamazepine 8hr + TNFalpha 1h


title: NL10

source_name: normal liver

value: normal liver


title: Tumor T_I_023

description: Gene expression of tumor liver tissue


title: Tumor T_K_027

description: Gene expression of tumor liver tissue


title: Tumor T_H_021

description: Gene expression of tumor liver tissue


title: NL8


title: NL7


title: Tumor T_L_029

description: Gene expression of tumor liver tissue


title: NL9


title: Tumor T_G_019

description: Gene expression of tumor liver tissue

value: female


title: HepG2 Carbamazepine 8hr + BSA 1h biological replicate 1 101446-62_CBZ 1 h BSA - 3

value: Carbamazepine 8hr + BSA 1h


title: bacteria_160minpostarrest_rep3

city: Dallas

first: Nicole

middle: Janell

last: De Nisco

state: Texas

address: 6000 Harry Hines Blvd, NA5.146, NA5.146

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

hyb_protocol: hyridization was carried out following the standard Agilent protocol

scan_protocol: Scanning was carried out following the standard Agilent protocol

data_processing: The array data were processed using the limma package in R

organism: Sinorhizobium meliloti 1021

source_name: early exponential phase bacteria

label_protocol: cDNA labeling with Cy3 and Cy5 fluorophores was carried out using the Ambion Amino Allyl MessageAmp II cRNA Amplification kit

growth_protocol: S.meliloti was grown at 30C in LB/MC media until early log phase (OD600=0.2). For synchronized samples early log phase bacteria was transferred to minimal MOPS medium for 4.5 hours to arrest and then returned to LB/MC when time points began to be taken starting at t=0 after release from arrest.

extract_protocol: RNA was extracted using the Qiagen RNAeasy plus kit

treatment_protocol: Cells were treated with RNA protect bacterial reagent (Qiagen) prior to freezing at -80C

tag: time

value: 160 min post arrest

tag: cell cycle stage

value: unsynchronized


title: HepG2 Diclofenac 8hr + TNFalpha 6h biological replicate 1 101446-60_Dic 6 h TNF - 3

tag: treatment

value: Diclofenac 8hr + TNFalpha 6h


title: Tumor T_E_009

description: Gene expression of tumor liver tissue

tag: tissue


title: bacteria_160minpostarrest_rep2


title: Tumor T_F_011

description: Gene expression of tumor liver tissue

tag: tissue type


title: bacteria_160minpostarrest_rep1


title: bacteria_140minpostarrest_rep3

value: 140 min post arrest

value: late S phase/G2/M


title: Tumor T_D_007

description: Gene expression of tumor liver tissue

tag: gender


title: bacteria_140minpostarrest_rep2


title: NL5

value: liver

value: M

value: Negative


title: HepG2 Carbamazepine 14hr biological replicate 1 101446-61_CBZ - 3

value: Carbamazepine 14hr


title: HepG2 Diclofenac 8hr + BSA 6h biological replicate 1 101446-58_Dic 6 h BSA - 3

value: Diclofenac 8hr + BSA 6h


title: bacteria_140minpostarrest_rep1


title: HepG2 Diclofenac 8hr + BSA 1h biological replicate 1 101446-57_Dic 1 h BSA - 3

value: Diclofenac 8hr + BSA 1h


title: Tumor T_C_005

description: Gene expression of tumor liver tissue

value: Biopsy of tumor tissue

value: Liver

value: male

tag: doubling time (days)

value: Agilent Low RNA Input Linear Amp Kit


title: Tumor T_B_003

description: Gene expression of tumor liver tissue

tag: survival time(months)


title: bacteria_140minpostarrest_rep4


title: HepG2 Diclofenac 8hr + TNFalpha 1h biological replicate 1 101446-59_Dic 1 h TNF - 3

value: Diclofenac 8hr + TNFalpha 1h

value: caucasian male


title: Tumor T_A_001

description: Gene expression of tumor liver tissue

value: female

tag: amplification and labeling kit


title: NL3

value: normal liver


title: NL4


title: bacteria_120minpostarrest_rep4

value: 120 min post arrest

value: S phase

value: unsynchronized


title: NL2

value: liver


title: HepG2 Diclofenac 14hr biological replicate 1 101446-56_Dic - 3

value: Diclofenac 14hr


title: HepG2 DMSO 8hr + TNFalpha 6h biological replicate 1 101446-55_DMSO 6 h TNF - 3

value: DMSO 8hr + TNFalpha 6h


title: HepG2 DMSO 8hr + TNFalpha 1h biological replicate 1 101446-54_DMSO 1 h TNF - 3

value: DMSO 8hr + TNFalpha 1h


title: HepG2 Nefadozone 8hr + TNFalpha 6h biological replicate 1 101446-52_Nef 6 h TNF - 2

value: Nefadozone 8hr + TNFalpha 6h


title: bacteria_100minpostarrest_rep3

value: 100 min post arrest


title: bacteria_120minpostarrest_rep2


title: bacteria_120minpostarrest_rep3


title: aHCC11

source_name: advanced HCC

value: advanced HCC

value: M

value: Positive


title: bacteria_120minpostarrest_rep1


title: bacteria_100minpostarrest_rep4


title: bacteria_100minpostarrest_rep2


title: bacteria_100minpostarrest_rep1


title: aHCC10

value: Negative


title: HepG2 Nefadozone 8hr  + BSA 6h biological replicate 1 101446-50_Nef 6 h - 2

value: Nefadozone 8hr  + BSA 6h


title: aHCC9


title: aHCC13


title: aHCC12


title: NL1


title: HepG2 Nefadozone 8hr + BSA 1h biological replicate 1 101446-49_Nef 1 h - 2

value: Nefadozone 8hr + BSA 1h

value: caucasian male


title: HepG2 DMSO 14hr biological replicate 1 101446-53_DMSO - 3

description: HepG2 DMSO 14hr biological replicate 1

value: DMSO 14hr


title: HepG2 Nefadozone 8hr + TNFalpha 1h biological replicate 1 101446-51_Nef 1 h TNF - 2

value: Nefadozone 8hr + TNFalpha 1h


title: HepG2 Methotrexate 8hr + TNFalpha 6h biological replicate 1 101446-48_MTX 6 h TNF - 2

value: Methotrexate 8hr + TNFalpha 6h


title: bacteria_80minpostarrest_rep4

value: 80 min post arrest

value: S phase

value: unsynchronized


title: aHCC8

value: liver


title: bacteria_80minpostarrest_rep3


title: bacteria_80minpostarrest_rep2


title: aHCC7


title: bacteria_80minpostarrest_rep1


title: bacteria_60minpostarrest_rep4

value: 60 min post arrest

value: replication initiation


title: aHCC5


title: bacteria_60minpostarrest_rep3


title: aHCC6


title: aHCC4


title: HepG2 Methotrexate 8hr + BSA 1h biological replicate 1 101446-45_MTX 1 h BSA - 2

value: Methotrexate 8hr + BSA 1h


title: HepG2 Methotrexate 14hr  101446-46_MTX 6 h BSA - 2

description: HepG2 Methotrexate 14hr

value: Methotrexate 14hr


title: eHCC13

source_name: early HCC

value: early HCC

value: M


title: bacteria_60minpostarrest_rep2


title: HepG2 Ketoconazole 8hr + TNFalpha 6h biological replicate 1 101446-44_Ket 6 h TNF - 2

value: Ketoconazole 8hr + TNFalpha 6h


title: aHCC3

value: advanced HCC

value: Positive


title: HepG2 Methotrexate 8hr + TNFalpha 1h biological replicate 1 101446-47_MTX1 h TNF - 2

value: Methotrexate 8hr + TNFalpha 1h

value: caucasian male


title: aHCC1

value: Negative


title: bacteria_40minpostarrest_rep4

value: 40 min post arrest

value: end G1/replication initiation


title: eHCC12


title: HepG2 Ketoconazole 8hr + BSA 6h biological replicate 1 101446-42_Ket 6 h BSA - 2

value: Ketoconazole 8hr + BSA 6h


title: aHCC2


title: HepG2 Ketoconazole14hr biological replicate 1 101446-40_Ket - 2


title: Subject C058 [miRNA]

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: normalized miRNA expression data from cord blood

hyb_protocol: Following fragmentation, cRNA was hybridized on Agilent Human miRNA Microarray, v16.0

scan_protocol: Microarrays were scanned using Agilent Microarray Scanner

data_processing: Data were normalized by quantile using Partek® Genomics SuiteTM software (version 6.5)

source_name: Cord blood from newborn, subject C058

label_protocol: Labeled cRNA were prepared with Cyanine 3-Cytidine bisphosphate (pCp) reagent according to the standard Agilent protocol

extract_protocol: This cohort includes residents from Gómez Palacio, located in the state of Durango in the Lagunera region of Northern Mexico. A total of 200 pregnant women residing in Gómez Palacio, State of Durango, Mexico, were recruited at the General Hospital of Gómez Palacio to participate in the BEAR prospective pregnancy cohort. The present study focuses on miRNA expression profiles and utilizes 40 samples obtained from mother-newborn pairs selected from the larger cohort (n=200). Cord blood samples were collected from the newborns immediately after infant delivery. Blood samples were collected using PreAnalytix PaxGene RNA tubes and extracted using the PAXgene RNA Kit, per standard protocol (Qiagen, Valencia, CA). Isolated RNA used for microarray analysis were amplified and labeled using the NuGEN Ovation Pico WTA System V2 and Encore Biotin Module, respectively (NuGEN, San Carlos, CA). RNA isolated from 40 cord blood samples were labeled and hybridized to the Agilent Human miRNA Microarray, based off miRBase v16.0.

tag: mother's age (years)

tag: smoking status

value: Nonsmoker

tag: gestational age (weeks)

tag: newborn weight (grams)

tag: newborn sex

value: female

value: Cord blood from newborn

tag: total urinary arsenic (specific gravity adjusted) (ug/l)

tag: arsenic in drinking water (ug/l)


title: Subject C074 [miRNA]

source_name: Cord blood from newborn, subject C074


title: HepG2 Carbamazepine 8hr + TNFalpha 6h biological replicate 1 101446-39_CBZ 6 h TNF - 2

tag: cell line

value: Carbamazepine 8hr + TNFalpha 6h

tag: source


title: HepG2 Ketoconazole 8hr + TNFalpha 1h biological replicate 1 101446-43_Ket 1 h TNF - 2

value: Ketoconazole 8hr + TNFalpha 1h


title: bacteria_60minpostarrest_rep1

tag: time

value: 60 min post arrest

tag: cell cycle stage

value: replication initiation

value: unsynchronized


title: bacteria_40minpostarrest_rep3


title: HepG2 Carbamazepine 8hr + TNFalpha 1h biological replicate 1 101446-38_CBZ 1 h TNF - 2

tag: treatment

value: Carbamazepine 8hr + TNFalpha 1h


title: eHCC11

tag: tissue

value: liver

tag: condition

value: early HCC

tag: age

value: M

tag: hbsag

tag: hbeag


title: HepG2 Ketoconazole 8hr + BSA 1h biological replicate 1 101446-41_Ket 1 h BSA - 2

value: Ketoconazole 8hr + BSA 1h

value: caucasian male


title: Subject C071 [miRNA]

source_name: Cord blood from newborn, subject C071

tag: mother's age (years)


title: bacteria_40minpostarrest_rep2

value: 40 min post arrest


title: eHCC10

tag: gender

value: Positive

value: Negative


title: bacteria_40minpostarrest_rep1

value: end G1/replication initiation


title: eHCC9


title: eHCC8


title: bacteria_G1arrest_rep3


title: Subject C026 [miRNA]

source_name: Cord blood from newborn, subject C026

tag: smoking status

value: Nonsmoker

tag: gestational age (weeks)

value: female


title: HepG2 Diclofenac 8hr + TNFalpha 1h biological replicate 1 101446-33_Dic 1 h TNF - 2

value: Diclofenac 8hr + TNFalpha 1h


title: eHCC7


title: bacteria_G1arrest_rep4


title: Subject C024 [miRNA]

source_name: Cord blood from newborn, subject C024

tag: newborn weight (grams)

tag: newborn sex

value: Cord blood from newborn


title: HepG2 Carbamazepine 8hr + BSA 6h biological replicate 1 101446-37_CBZ 6 h BSA - 2

value: Carbamazepine 8hr + BSA 6h


title: Subject C003 [miRNA]

source_name: Cord blood from newborn, subject C003

tag: total urinary arsenic (specific gravity adjusted) (ug/l)

tag: arsenic in drinking water (ug/l)


title: Subject C133 [miRNA]

source_name: Cord blood from newborn, subject C133


title: HepG2 Diclofenac 8hr + TNFalpha 6h biological replicate 1 101446-34_Dic 6 h TNF - 2

tag: cell line

value: Diclofenac 8hr + TNFalpha 6h

tag: source


title: Subject C120 [miRNA]

source_name: Cord blood from newborn, subject C120

value: male


title: HepG2 Carbamazepine 14hr biological replicate 1 101446-35_CBZ - 2

value: Carbamazepine 14hr


title: eHCC6

value: liver


title: eHCC5

value: early HCC


title: bacteria_G1arrest_rep1

tag: cell cycle stage

value: unsynchronized


title: Subject C067 [miRNA]

source_name: Cord blood from newborn, subject C067


title: bacteria_G1arrest_rep2


title: HepG2 Diclofenac 8hr + BSA 6h biological replicate 1 101446-32_Dic 6 h BSA - 2

tag: treatment

value: Diclofenac 8hr + BSA 6h


title: HepG2 Carbamazepine 8hr + BSA 1h biological replicate 1 101446-36_CBZ 1 h BSA - 2

value: Carbamazepine 8hr + BSA 1h

value: caucasian male


title: Seedling-HeatStressed_POLYSOMESmRNA_REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Seedling, Heat-stresed, polysome-bound mRNA-REP2

hyb_protocol: Each sample was added to a hybridization solution containing 100 mm 2-(N-morpholino) ethanesulfonic acid, 1M Na+, and 20 mm of EDTA in the presence of 0.01% Tween-20. Hybridization was performed for 16 h at 45°C.

scan_protocol: Each microarray was washed and stained with streptavidin–phycoerythrin in a Fluidics station 450 (Affymetrix) and scanned at 2.5-μm resolution in a GeneChip® Scanner 3000 7G system (Affymetrix).

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor. To quantify the amount of individual mRNAs in the polysomal samples, the RMA data values of POLY-38 samples were further adjusted based on the heavy polysome content (HPC), as previously described. Briefly, the normalization factor was generated from the quantitative measurement of the relative heavy polysome content (HPC38ºC/HPC22ºC) in each biological experiment (0.558 and 0.538, respectively).

label: Biotin

organism: Arabidopsis thaliana

source_name: Seedling Heat-stresed, polysome-bound mRNA

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 seeds were surface sterilized using 0.05% Tween-20 and ethanol for 5 min, sown on MS medium plates (0.9% agar, pH 5.7) and kept at 4º degrees in darkness for 2 days for stratification. Plates were vertically oriented in a growth chamber under a 16 h light and 8 h dark cycle for 7 days at 22ºC.

extract_protocol: Polysomes isolation by differential centrifugation was performed by slight modification of a previously described protocol (Kawaguchi et al., 2004) . Briefly, 2 gr of frozen tissue was thawed in 2 ml of polysome extraction buffer (200 mm Tris (pH 9.0), 200 mm KCl, 26 mm MgCl2, 25 mm EGTA, 100 µm 2-mercaptoethanol, 50 µg ml−1 cycloheximide, 50 µg ml−1 chloramphenicol, 1% (v/v) Triton X-100, 1% (v/v) Tween-20, 1% (v/v) NP-40, 2% (v/v) polyoxyethylene-10-tridecyl-ether, 1% (v/v) deoxycholic acid). The crude cell extract was clarified by centrifugation at 13,500 g for 15 min at 4ºC and the OD260 of the supernatant determined. Approximately 7000 units (OD260) were layered on top of a 10 ml 15-40% (w/v) sucrose gradient and centrifuged at 250,000 g for 3:40 h at 4ºC (SW41Ti rotor, Beckman). 16 fractions of 600 µl were manually collected and RNA extraction was performed using TRIzol reagent (Invitrogen) according to manufacturer’s protocol. The polysome profile (OD260) and the verification of the quality of the polysome preparation by electrophoretic analysis of rRNA distribution were evaluated. Quantitative polysome gradient fractionation was performed using three biological samples.

treatment_protocol: 7-day-old seedlings were subjected to heat-stress by incubation at 38ºC for 45 min. For the control conditions, plates taken directly from the growth chamber were used. Seedlings were quickly frozen in liquid nitrogen, ground to powder and stored at -80ºC.

tag: cultivar/ecotype

tag: tissue

value: seedling

tag: developmental stage


title: Subject C116 [miRNA]

source_name: Cord blood from newborn, subject C116


title: eHCC4

tag: condition

tag: age

value: M

tag: hbsag

value: Positive

value: Negative


title: Seedling-HeatStressed_POLYSOMESmRNA_REP1

description: Seedling, Heat-stresed, polysome-bound mRNA-REP1


title: HepG2 Diclofenac 14hr biological replicate 1 101446-30_Dic - 2

source_name: HepG2 ATCC, Wesel, Germany

value: Diclofenac 14hr


title: eHCC3

tag: gender

tag: hbeag


title: Subject C117 [miRNA]

source_name: Cord blood from newborn, subject C117

tag: mother's age (years)

tag: smoking status

value: Nonsmoker

tag: gestational age (weeks)

value: female


title: Seedling-control_POLYSOMESmRNA_REP2

description: Seedling, control, polysome-bound mRNA-REP2

source_name: Seedling control, polysome-bound mRNA


title: Subject C007 [miRNA]

source_name: Cord blood from newborn, subject C007

tag: newborn weight (grams)

tag: newborn sex

value: Cord blood from newborn

tag: total urinary arsenic (specific gravity adjusted) (ug/l)


title: NL6

source_name: normal liver

value: normal liver


title: HepG2 Diclofenac 8hr + BSA 1h biological replicate 1 101446-31_Dic 1 h BSA - 2

tag: cell line

value: Diclofenac 8hr + BSA 1h

tag: source


title: HepG2 DMSO 8hr + TNFalpha 6h biological replicate 1 101446-29_DMSO 6 h TNF - 2

tag: treatment

value: DMSO 8hr + TNFalpha 6h


title: Seedling-HeatStressed_TOTALmRNA_REP2

description: Seedling, Heat-stresed, total mRNA-REP2

source_name: Seedling Heat-stresed, total mRNA

tag: cultivar/ecotype


title: eHCC1

source_name: early HCC

tag: tissue

value: liver


title: HepG2 DMSO 8hr + TNFalpha 1h biological replicate 1 101446-28_DMSO 1 h TNF - 2

value: DMSO 8hr + TNFalpha 1h


title: Subject C104 [miRNA]

source_name: Cord blood from newborn, subject C104

value: male

tag: arsenic in drinking water (ug/l)


title: HepG2 DMSO 14hr biological replicate 1 101446-27_DMSO - 2

description: HepG2 DMSO 14hr biological replicate 1

value: DMSO 14hr


title: CL10

source_name: cirrhotic livers

tag: condition

value: cirrhotic livers


title: Subject C062 [miRNA]

source_name: Cord blood from newborn, subject C062


title: CL9

tag: age


title: Subject C059 [miRNA]

source_name: Cord blood from newborn, subject C059


title: CL8

tag: hbsag


title: HepG2 Nefadozone 8hr + TNFalpha 6h biological replicate 1 101446-26_Nef 6 h TNF - 1

value: Nefadozone 8hr + TNFalpha 6h

value: caucasian male


title: Seedling-control_TOTALmRNA_REP2

description: Seedling, control, total mRNA-REP2

source_name: Seedling control, total mRNA

value: seedling

tag: developmental stage


title: Subject C079 [miRNA]

source_name: Cord blood from newborn, subject C079


title: HepG2 Nefadozone 8hr + TNFalpha 1h biological replicate 1 101446-25_Nef 1 h TNF - 1

value: Nefadozone 8hr + TNFalpha 1h


title: Seedling-control_TOTALmRNA_REP1

description: Seedling, control, total mRNA-REP1


title: CL7

tag: gender

value: M

value: Positive

tag: hbeag

value: Negative


title: Seedling-HeatStressed_TOTALmRNA_REP1

description: Seedling, Heat-stresed, total mRNA-REP1


title: Subject C129 [miRNA]

source_name: Cord blood from newborn, subject C129

tag: mother's age (years)

tag: smoking status

value: Nonsmoker


title: HepG2 Nefadozone 8hr  + BSA 6h biological replicate 1 101446-24_Nef 6 h BSA - 1

value: Nefadozone 8hr  + BSA 6h


title: Subject C134 [miRNA]

source_name: Cord blood from newborn, subject C134

tag: gestational age (weeks)

tag: newborn weight (grams)

value: Cord blood from newborn


title: CL6


title: HepG2 Nefadozone 8hr + BSA 1h biological replicate 1 101446-23_Nef 1 h BSA - 1

value: Nefadozone 8hr + BSA 1h


title: Prefrontal cortex rat #7 none treated

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) to Affymetrix GeneChip Rat Gene 1.0 ST Arrays (Affymetrix, Inc., Santa Clara, CA)  was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data was extracted, normalized (quantile normalization) and transformed (RMA style background adjustment) using the Affymetrix Power Tool (apt-1.15.1 from Affymetrix http://media.affymetrix.com/Download/updates/apt-1.15.1-i686-intel-win64.zip).

organism: Rattus norvegicus

source_name: prefrontal cortex

label_protocol: Biotinylated cRNA were prepared per the Whole Transcript (WT) Sense Target Labeling Assay protocol (Affymetrix 2006) using 200 ng of total RNA from each sample.

growth_protocol: No cell culture.

extract_protocol:
Blood and tissue sampling: Six male Wistar rats were sacrificed. Blood samples were immediately collected in Paxgene tubes containing a stabilizing agent for RNA (Preanalytix, BD) and rat brains were quickly removed, submerged for 3 minutes in -40°C isopentane (Sigma-Aldrich Co., St. Louis, Missouri). All samples were stored at -80°C. For dissection, brains were sliced in coronal sections of 120 µm in a Leica CM3000 Cryostat (Leica, Bensheim, Germany). The prefrontal cortex (PFC) and hippocampus were punched out, collected into vials and stored at -80°C.
For RNA isolation, punched tissue were lysed in TRIzol ® Reagent (Invitrogen, Karlsruhe, Germany) and homogenized by passing the suspension 30 times through a 22-gauge needle. Total RNA was extracted by adding chloroform. To achieve better separation of organic and aqueous phases, Phase Lock Gel™ Heavy tubes (Eppendorf, Hamburg, Germany) were used. Upper phases were carefully removed by pipetting and total RNA was purified using RNeasy ® Micro Kit (Qiagen, Hilden, Germany). RNA from blood samples was isolated with Paxgene Blood RNA Kit 50 (PreAnalystix, Qiagen) according to the manufacturer's recommendation. Total RNA yield was determined with Quant-iT™ RiboGreen ® RNA Reagent and Kit (Invitrogen) by measuring in a Wallac Victor 2 1420 Multilabel Counter (Perkin Elmer, Jügesheim, Germany). Total RNA purity was evaluated by OD measurements (260 nm/280 nm) in a NanoDrop (peqLab, Erlangen, Germany) and its integrity was determined by RNA integrity number (RIN) measurement using RNA 6000 Nano Assay RNA chips run in an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Ratios of 1.9–2.2 (OD 260/280) and RIN > 8.0 as well as an absence of a peak of genomic DNA contamination in electropherograms were chosen as inclusion criteria.

treatment_protocol: No treatment of the animals.

tag: strain

value: Wistar

value: prefrontal cortex

tag: animal number


title: CL5

value: liver


title: HepG2 Methotrexate 8hr + TNFalpha 6h biological replicate 1 101446-22_MTX 6 h TNF - 1

tag: cell line

value: Methotrexate 8hr + TNFalpha 6h

tag: source


title: Subject C132 [miRNA]

source_name: Cord blood from newborn, subject C132

tag: newborn sex

value: male

tag: total urinary arsenic (specific gravity adjusted) (ug/l)


title: HepG2 Methotrexate 8hr + TNFalpha 1h biological replicate 1 101446-21_MTX1 h TNF - 1

source_name: HepG2 ATCC, Wesel, Germany

tag: treatment

value: Methotrexate 8hr + TNFalpha 1h


title: Subject C081 [miRNA]

source_name: Cord blood from newborn, subject C081

tag: tissue

tag: arsenic in drinking water (ug/l)


title: CL4

tag: condition

value: cirrhotic livers

tag: age

tag: hbsag


title: Hippocampus rat #7 none treated

source_name: hippocampus

tag: gender

value: hippocampus


title: IL10

source_name: chronic inflammatory liver

value: chronic inflammatory liver

tag: hbeag


title: CL3


title: IL8


title: Subject C124 [miRNA]

source_name: Cord blood from newborn, subject C124

tag: mother's age (years)

tag: smoking status

value: female


title: IL9

value: M


title: CL1

value: Positive


title: HepG2 Ketoconazole 8hr + TNFalpha 1h biological replicate 1 101446-17_Ket 1 h TNF - 1

value: Ketoconazole 8hr + TNFalpha 1h

value: caucasian male


title: Subject C111 [miRNA]

source_name: Cord blood from newborn, subject C111

value: Nonsmoker

tag: gestational age (weeks)

tag: newborn weight (grams)


title: Subject C086 [miRNA]

source_name: Cord blood from newborn, subject C086

value: Smoker

value: Cord blood from newborn


title: HepG2 Methotrexate 14hr  101446-20_MTX 6 h - 1

description: HepG2 Methotrexate 14hr

value: Methotrexate 14hr


title: Prefrontal cortex rat #5 none treated

tag: strain

value: Wistar

value: prefrontal cortex

tag: animal number


title: Blood rat #7 none treated

source_name: blood

value: blood


title: Subject C123 [miRNA]

source_name: Cord blood from newborn, subject C123


title: HepG2 Ketoconazole 8hr + BSA 1h biological replicate 1 101446-15_Ket 1 h BSA - 1

tag: cell line

value: Ketoconazole 8hr + BSA 1h

tag: source


title: HepG2 Methotrexate 8hr + BSA 1h biological replicate 1 101446-19_MTX 1 h BSA - 1

value: Methotrexate 8hr + BSA 1h


title: Subject C027 [miRNA]

source_name: Cord blood from newborn, subject C027

tag: newborn sex

value: male

tag: total urinary arsenic (specific gravity adjusted) (ug/l)


title: Muscle_wild-type_80days_rep3

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: Fifteen gastrocnemius muscles from transgenic and wild-type SOD1G93A mouse model by the ages of 40 and 80 days old were used for this study. RNA were extracted with TRIzol Reagent (Invitrogen Life Technologies, USA) according to the manufacturer’s instructions and treated with Ambion® TURBO DNA-free (Invitrogen Life Technologies, USA). A two-round RNA amplification procedure (Gomes et al. 2003) was carried out for all samples. Labeled cDNA was generated in a reverse transcriptase reaction using 7 ug of amplified RNA (aRNA), random hexamer primer (Invitrogen Life Technologies, USA), Alexa Fluor 555- or Alexa Fluor 647-labelled dCTP (Invitrogen Life Technologies, USA).and IMPROM (PROMEGA, USA) using oligo-dT7(24), following manufacture recommendations. Eight µg of test and reference cDNA reverse color Alexa-labeled aRNA targets were competitively hybridized against the cDNA probes in a customized cDNA platform with 4,608 ORESTES representing human genes, 326 of them homolog to mouse. Pre-hybridization and hybridization were performed as described (Maschietto et al. 2008). A pool of RNAs obtained from 15 distinct human cell lines as was used as reference. Signal intensities capture and analysis were performed as described in Maschietto et al (2008).

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Esperma de salmao,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: SSC 2X / Temperature:42 / Time:5 min / Washing Number: 1 Washing - Round 2 - Solution: SSC 0,1X , SDS 0,1% / Temperature:42 / Time:10 min / Washing Number: 2 Washing - Round 3 - Solution: SSC 0,1X / Temperature:42 / Time:5 min / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowess-normalized signal intensity, log2 test/reference

label: Alexa Fluor® 555

organism: Mus musculus

source_name: Gastrocnemius muscle, wild-type, 80 days of age

label_protocol: A two-round RNA amplification procedure was carried out for all samples as described (Maschietto et al., 2008). A pool of human cell lines(Mello et al., 2009) was used as a reference sample. Labeled cDNA was generated in a reverse transcriptase reaction (ImProm-II™riptase, Promega, USA) using 7 µRNA (aRNA), random hexamer primer (Invitrogen Life Technologies, USA), Alexa Fluor 555- or Alexa Fluor 647-labelled dCTP (Invitrogen Life Technologies, USA). Eight micrograms of test and reference cDNA reverse colour Alexa-labelled aRNA targets were hybridized competitively against the cDNA probes in a customized cDNA platform previously described.

extract_protocol: kit Pico Pure RNA Isolation Kit

tag: tissue

value: gastrocnemius muscle

tag: genotype

value: wild type

tag: genetic background

label: Alexa Fluor® 647

source_name: Reference

extract_protocol: Trizol

tag: cell lines

value: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU145 (prostate carcinoma), FaDU (pharynx squamous cell carcinoma), GM637 (fibroblast), H1080 (fibrosarcoma), H146 (small cell lung carcinoma), HB4a (normal mammary luminal epithelium), HEK293 (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma) e T98G (glioblastoma multiform).


title: Hippocampus rat #2 none treated

value: hippocampus

tag: treatment


title: CL2

source_name: cirrhotic livers

value: liver

tag: condition

value: cirrhotic livers

tag: age

tag: gender

value: M

tag: hbsag

value: Positive

value: Negative


title: Prefrontal cortex rat #2 none treated


title: Hippocampus rat #5 none treated


title: IL7

value: chronic inflammatory liver

tag: hbeag


title: HepG2 Ketoconazole 8hr + TNFalpha 6h biological replicate 1 101446-18_Ket 6 h TNF - 1

value: Ketoconazole 8hr + TNFalpha 6h

value: caucasian male


title: IL6


title: Muscle_wild-type_80days_rep2


title: Muscle_wild-type_80days_rep1


title: IL5


title: HepG2 Ketoconazole 8hr + BSA 6h biological replicate 1 101446-16_Ket 6 h BSA - 1

value: Ketoconazole 8hr + BSA 6h


title: Subject C194 [miRNA]

source_name: Cord blood from newborn, subject C194

tag: mother's age (years)

tag: smoking status

value: Nonsmoker

tag: gestational age (weeks)

tag: newborn weight (grams)

value: female

value: Cord blood from newborn

tag: arsenic in drinking water (ug/l)


title: IL4


title: Muscle_wild-type_40days_rep2

source_name: Gastrocnemius muscle, wild-type, 40 days of age

value: male


title: Subject C085 [miRNA]

source_name: Cord blood from newborn, subject C085

tag: newborn sex


title: HepG2 Ketoconazole14hr biological replicate 1 101446-14_Ket - 1

tag: cell line

tag: source


title: Subject C139 [miRNA]

source_name: Cord blood from newborn, subject C139

tag: tissue

tag: total urinary arsenic (specific gravity adjusted) (ug/l)


title: Muscle_wild-type_40days_rep3

value: gastrocnemius muscle

tag: genotype

tag: genetic background

tag: cell lines


title: HepG2 Carbamazepine 8hr + BSA 6h biological replicate 1 101446-11_CBZ 6 h BSA - 1

source_name: HepG2 ATCC, Wesel, Germany

tag: treatment

value: Carbamazepine 8hr + BSA 6h


title: Blood rat #5 none treated

tag: strain

value: Wistar

tag: gender

value: blood

tag: animal number


title: Blood rat #2 none treated


title: HepG2 Carbamazepine 8hr + TNFalpha 1h biological replicate 1 101446-12_CBZ 1 h TNF - 1

value: Carbamazepine 8hr + TNFalpha 1h


title: Subject C151 [miRNA]

source_name: Cord blood from newborn, subject C151

tag: mother's age (years)


title: HepG2 Carbamazepine 8hr + TNFalpha 6h biological replicate 1 101446-13_CBZ 6 h TNF - 1

value: Carbamazepine 8hr + TNFalpha 6h


title: Subject C092 [miRNA]

source_name: Cord blood from newborn, subject C092

tag: smoking status


title: Muscle_wild-type_40days_rep1

value: wild type

tag: age

value: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU145 (prostate carcinoma), FaDU (pharynx squamous cell carcinoma), GM637 (fibroblast), H1080 (fibrosarcoma), H146 (small cell lung carcinoma), HB4a (normal mammary luminal epithelium), HEK293 (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma) e T98G (glioblastoma multiform).


title: eHCC2

source_name: early HCC

value: liver

tag: condition

value: early HCC

value: M

tag: hbsag

value: Positive

tag: hbeag

value: Negative


title: HepG2 Carbamazepine 14hr biological replicate 1 101446-09_CBZ - 1

tag: cell line

value: Carbamazepine 14hr

value: caucasian male


title: Subject C113 [miRNA]

source_name: Cord blood from newborn, subject C113

value: Nonsmoker

tag: gestational age (weeks)

tag: newborn weight (grams)

tag: newborn sex

value: female

value: Cord blood from newborn

tag: arsenic in drinking water (ug/l)


title: HepG2 Carbamazepine 8hr + BSA 1h biological replicate 1 101446-10_CBZ 1 h BSA - 1

value: Carbamazepine 8hr + BSA 1h

tag: source


title: Subject C029 [miRNA]

source_name: Cord blood from newborn, subject C029

tag: tissue

tag: total urinary arsenic (specific gravity adjusted) (ug/l)


title: IL2

source_name: chronic inflammatory liver

value: chronic inflammatory liver


title: Muscle_transgenic_80days_rep3

source_name: Gastrocnemius muscle, transgenic, 80 days of age

value: gastrocnemius muscle

tag: genotype

value: SOD1G93A transgenic

value: male

tag: genetic background

tag: cell lines


title: Muscle_transgenic_80days_rep4

tag: gender


title: IL3


title: Muscle_transgenic_80days_rep2


title: Muscle_transgenic_40days_rep5

source_name: Gastrocnemius muscle, transgenic, 40 days of age


title: Muscle_transgenic_80days_rep1


title: Subject C075 [miRNA]

source_name: Cord blood from newborn, subject C075

tag: mother's age (years)

tag: smoking status


title: Seedling-control_POLYSOMESmRNA_REP1

description: Seedling, control, polysome-bound mRNA-REP1

source_name: Seedling control, polysome-bound mRNA

tag: cultivar/ecotype

value: seedling

tag: developmental stage


title: Muscle_transgenic_40days_rep4

tag: age

source_name: Reference

value: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU145 (prostate carcinoma), FaDU (pharynx squamous cell carcinoma), GM637 (fibroblast), H1080 (fibrosarcoma), H146 (small cell lung carcinoma), HB4a (normal mammary luminal epithelium), HEK293 (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma) e T98G (glioblastoma multiform).


title: HepG2 Diclofenac 8hr + TNFalpha 1h biological replicate 1 101446-07_Dic 1 h TNF - 1

tag: cell line

tag: treatment

value: Diclofenac 8hr + TNFalpha 1h


title: Subject C218 [miRNA]

source_name: Cord blood from newborn, subject C218

tag: gestational age (weeks)

tag: newborn weight (grams)


title: Muscle_transgenic_40days_rep3


title: Subject C097 [miRNA]

source_name: Cord blood from newborn, subject C097

value: Smoker

tag: newborn sex

tag: arsenic in drinking water (ug/l)


title: Subject C094 [miRNA]

source_name: Cord blood from newborn, subject C094

tag: tissue


title: HepG2 Diclofenac 8hr + TNFalpha 6h biological replicate 1 101446-08_Dic 6 h TNF - 1

value: Diclofenac 8hr + TNFalpha 6h

tag: source


title: HepG2 Diclofenac 8hr + BSA 6h biological replicate 1 101446-06_Dic 6 h BSA - 1

value: Diclofenac 8hr + BSA 6h


title: Muscle_transgenic_40days_rep1

tag: genotype


title: HepG2 DMSO 8hr + TNFalpha 1h biological replicate 1 101446-02_DMSO 1 h TNF - 1

value: DMSO 8hr + TNFalpha 1h


title: Muscle_transgenic_40days_rep2

tag: genetic background


title: Subject C095 [miRNA]

source_name: Cord blood from newborn, subject C095

tag: total urinary arsenic (specific gravity adjusted) (ug/l)


title: Subject C115 [miRNA]

source_name: Cord blood from newborn, subject C115


title: HepG2 Diclofenac 8hr + BSA 1h biological replicate 1 101446-05_Dic 1 h BSA - 1

source_name: HepG2 ATCC, Wesel, Germany

value: Diclofenac 8hr + BSA 1h


title: HepG2 DMSO 8hr + TNFalpha 6h biological replicate 1 101446-03_DMSO 6 h TNF - 1

value: DMSO 8hr + TNFalpha 6h

value: caucasian male


title: Subject C221 [miRNA]

source_name: Cord blood from newborn, subject C221

value: Nonsmoker

value: female


title: HepG2 Diclofenac 14hr biological replicate 1 101446-04_Dic - 1

value: Diclofenac 14hr


title: HepG2 DMSO 14hr biological replicate 1 101446-01_DMSO - 1

description: HepG2 DMSO 14hr biological replicate 1

value: DMSO 14hr


title: RA_24h_rep3

status: Public on Jan 21 2014

city: Lanzhou

first: Y

last: Gao

address: Xujiaping 1

country: China

institute: LVRI

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: J1 mESCs_RA_24h

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

growth_protocol: The J1 mESC was gelatin adapted and plated on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF at condition of 37℃ and 5% CO2.

extract_protocol: Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations. Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: The J1 mESCs were treated with a final concentration of RA (1μM), DMSO (1μL), VC (50μg), ddH2O (1μL)

tag: cell type

value: J1 mouse embryonic stem cells

tag: treated with

value: RA (Retinoic acid 1μM) for 24hrs


title: RA_24h_rep1


title: RA_24h_rep2


title: DMSO_24h_rep3

source_name: J1 mESCs_DMSO_24h

value: DMSO (1μL) for 24hrs


title: Subject C128 [miRNA]

source_name: Cord blood from newborn, subject C128

tag: mother's age (years)

tag: smoking status

value: male

value: Cord blood from newborn


title: DMSO_24h_rep1


title: DMSO_24h_rep2


title: PT-1590_primary single-cell WGA_single cell 1_PCR-T2_25probes

type: genomic

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

description:
PT-1590 single-cell Primary WGA; single-cell 1 (25 probes)
Raw data file:
252206023802_201111081305_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 1_PCR-T2
sample used to demonstrate the ability of the new single-cell aCGH protocol to detect single-cell heterogeneity in vitro. aCGH profiles of this sample are depicted in the Fig. 3 and S4.

hyb_protocol: Array CGH was performed on oligonucleotide-based SurePrint G3 Human CGH 4x180K microarray slides (design code: 022060) according the protocol provided by the manufacturer (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.1, December 2011). Slight modifications were introduced WGA products processed with the PCR-based labeling approaches. Here, the hybridization mix consisted of 5.0 µg of Cot1-DNA (Roche Diagnostics), 12 µl of 10x Blocking Reagent (Agilent Technologies), 60 µl of 2x Hi RPM Hybridization Buffer, 1% (v/v) of both Tween20 and Igepal and 19 µl of both test and reference DNA. For each hybridization 100 µl of the hybridization mix was applied on the array and hybridized at 65◦C for 24 h. Following the hybridization, the slides were washed sequentially: twice for 2:30 min in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technologies) at room temperature, twice for 30 sec min in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technologies) at 37◦C. Washed slides were immersed in acetonitrile to remove all remaining traces of the wash buffers.

scan_protocol: Scanned on an Agilent G2565CA scanner (Dye channel: R+G; Scan resolution: 2.5µm, double pass; Tiff file dynamic range: 16 Bit; Red PMT gain: 100%; Green PMT gain: 100%; No XDR)

data_processing: Microarray TIFF image files were processed with the Agilent Genomic Feature Extraction Software (version 10.7.3.1). The resulting text files were imported and analyzed with Agilent Genomic Workbench Software (version 6.5.0.18 Lite). Aberrant regions were recognized using ADM-2 algorithm with threshold set to 6.5. Centralization algorithm was set to a threshold of 6.0 and bin size of 10. To avoid false positive calls, aberration filters were applied to define the minimum log2 ratio (minimum absolute average log ratio for region = 0.3) and the minimum number of probes in an aberrant interval (minimum number of probes in region = 10 for unamplified DNA and freshly picked cells or minimum number of probes in region = 25 for WGA products generated with immunostained cells and FFPE samples).  The log2 ratios were obtained using the Agilent Genomic Workbench 6.5.0.18.

molecule: genomic DNA

source_name: PT-1590 esophageal cancer cell line

label_protocol:
Random-primed DNA labeling approach (RP labeling):
Test and reference DNA samples were labeled using SureTag DNA Labeling Kit (Agilent Technologies) according to the instruction provided by the supplier (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.1, December 2011). Briefly, 1.5 - 2.0 µg of the purified input DNA (WGA product or unamplified genomic DNA) was supplemented with 5 µl of Random Primer Mix and filled up with H2O to 31 µl. Unamplified DNA and WGA products samples were denatured at 95◦C for 10 or 3 minutes, respectively. Sample tubes were transferred on ice and incubated for 5 min. The labeling reaction with exo-Klenow fragment consisted of the following ingredients: 31 µl of denatured DNA, 10 µl of 5x Reaction Buffer, 5.0 µl of 10x dNTP Mix, 3.0 µl of Cy5-dUTP (test) or Cy3-dUTP (reference) and 1.0 µl of Exo(-) Klenow fragment. Labeling reaction was run at 37◦C for two hours, followed by an inactivation step at 65◦C for 10 minutes. Labeled DNA was purified using Ultra 0.5 purification system with a size cut-off of 30 kDa. DNA yields and dye incorporation rates were quantified using the NanoDrop ND-1000 instrument.
PCR-based labeling using dye-conjugated universal primer (PCR-T1):
Placement of the dye on the universal primer provides the advantage that all restriction digestion fragments present in the WGA product irrespectively of their size will be labeled with the same amount of dye. To avoid cross-hybridization of adapter sequences flanking amplicons in the WGA products, test and reference samples were labeled using different PCR-adapters. Test samples were labeled with the PCR-adapter incorporated in the Ampli1™ WGA kit, while all the reference DNA samples were amplified using the following adapters: MIB5 (5’-TGAGCTGGTCATTGCGCATGGT-3’) and ddMse XI (5’-TAACCATGCGC-3’). Universal primers used in the labeling reaction were directly conjugated with either Cy5 in the case of Ampli1™ universal primer [5’-TAGTGGGATTCCTGCTGTCAGT-3’] or Cy3 in the cases of MIB5 primer [5’-TGAGCTGGTCATTGCGCATGGT-3’] (underscores indicate the placement of the dye). The labeling PCR was run in a total volume of 50 µl reaction composed of 5 µl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 µM of dye-conjugated LIB1 or MIB5 primer (for test and reference sample, respectively), 350 µM of dNTPs, 0.5 µl BSA (Roche), 3.75 U of Expand-Long-Template DNA Polymerase (Roche Diagnostics) and 1.0 µl of the template DNA. The PCR was programmed as follows: 10 cycle of 94◦C for 15 sec, 51◦C for 30 sec and 65◦C for 3:30 min, 2 cycles of 94◦C for 15 sec, 51◦C for 30 sec and 65◦C for 3:30 min (extended by 10 sec every cycle), followed by a final elongation step of 7 min at 65◦C. Products were purified using the Amicon Ultra 0.5 System (cut-off size 100 kDa) and quantified with the NanoDrop ND-1000 instrument.
PCR-based labeling using incorporation of dye-conjugated dNTPs (PCR-T2):
WGA products were labeled by PCR in the presence of Cy5 or Cy3 conjugated dCTP and dUTP. Incorporation of the fluorescent dyes using the dNTPs provided the advantage that adapters flanking each amplicon in the WGA product could be removed prior to aCGH hybridization, thereby avoiding unspecific cross-hybridization of test sample with reference DNA and oligonucleotide probes on the array. For each sample two 50µl PCR reactions were run in parallel each comprising 5 µl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 µM of the universal primer (LIB1 or MseLig-21, depending on the adapter sequence incorporated in the WGA product), 350 µM of dATP and dGTP, 315 µM of dCTP and dTTP, 35 µM of Cy5/Cy3-dCTP and Cy5/Cy3-dUTP (GE Healthcare), 0.5 µl of BSA (Roche Diagnostics), 7.5 U of Expand-Long-Template DNA Polymerase (Roche) and 0.5 µl of the template DNA. Labeling products were pooled and purified using the Amicon Ultra 0.5 System (100 kDa cut-off). DNA yields and dye incorporation rates were quantified using the NanoDrop ND-1000 Instrument.

growth_protocol: Esophageal cancer cell lines (PT-1590 and OE-19) were grown in RPMI 1640 medium (PAN-Biotech) supplemented with 10% fetal calf serum (FCS)(PAN-Biotech), 2mM L-Glutamic acid (PAN-Biotech) and 1% of Penicillin/Streptomycin solution (PEN STREP) (PAN-Biotech). Breast cancer cell lines SKBR3, MDA-MB-453 and MDA-MB-361 were cultured in DMEM (PAN-Biotech) medium supplemented with 10% FCS (PAN-Biotech), 2mM L-Glutamic acid (PAN-Biotech) and  1% PEN STREP (PAN-Biotech). BT-474 was grwon in RPMI 1640 medium supplemented with 10% FCS, 2mM L-Glutamic acid, 1% P/S and 1mM sodium pyruvate.

extract_protocol: Total genomic DNA (bulk DNA) was extracted using the Dbeasy Blood & Tissue Kit (QIAgen) following manufacture's instructions. All single cells, cell pools (few hundred cells) and microdissected specimens from formalin fixed paraffin embedded (FFPE) tumor tissue were amplified using the Ampli1™ WGA Kit (Silicon Biosystems).

tag: cell line/clinical sample

value: cell line (University Medical Center Hamburg-Eppendorf)

tag: tumor sample/healthy donor

value: tumor sample

tag: amplified/unamplified dna

value: amplified - Ampli1 WGA

tag: primary/reamplified wga

value: primary WGA

tag: labeling protocol

tag: gender

tag: bulk dna/cell pool wga/single-cell wga

value: single-cell WGA

source_name: Healthy donor: cord blood; cell pool WGA (WGA product obtained from large number of cells)

value: Clinical sample

value: healthy donor

value: cell pool WGA


title: YT cells

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

country: Taiwan

institute: National Taiwan University

description: Total RNA were extracted from YT cells.

hyb_protocol: Hybridization and washing of the arrays was done according to GeneChip Expression Analysis Technical Manual from Affymetrix

scan_protocol: The arrays were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).

data_processing: The data were extracted with Affymetrix Microarray suite (MAS) software.

source_name: YT

label_protocol: The Affymetrix chip, Human Genome U133 plus 2.0, was used. First-strand cDNAs were synthesized from 10 ug total RNAs with a T7-ptomoter-oligo(dT) primer. After second-strand synthesis, biotin-labeled cRNAs were transcribed from the T7 promoter. The quality of cRNAs was checked by gel electrophoresis with an Agilent 6000 Bioanalyzer (Agilent Technologies, Foster City, CA). The cRNAs were fragmented into sizes from 35 to 200 nucleotides, and labeled with streptavidin-PE. The fragmented cRNAs were mixed with control RNAs (bioB, bioC, bioD, and cre) and hybridized with the membrane.

growth_protocol: YT cells were grown in 80% IMDM plus 20% fetal bovine serum (FBS), NK92 cells were grown in 75% α-MEM, 12.5% FBS, 12.5% horse serum, 2 mM L-glutamate, and 10 ng/mL IL-2.

extract_protocol: Total RNA sample was extracted by TRIzol® reagent (Invitrogen )

tag: cell line

value: YT, an EBV-positive human natural killer-like leukemic cell line


title: Healthy female donor 3_single-cell 1_reamplified single-cell WGA_PCR-T2_25probes

description:
Healthy female donor #3, single-cell #1 (25 probes)
Raw data file:
US94700331_252206026490_S01_CGH_107_Sep09_1_2.txt
Healthy female donor 3_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to assess the reliability of the new single-cell aCGH protocol comining: (1) PCR-T2 labeling, (2) reamplified WGA products, (3) single-cell based reference. Profile of the samples is depicted in the Fig. S3C of the manuscript.

source_name: Single cell collected from the cord blood of a healthy female donor

value: clinical sample

value: reamplified WGA

value: female

source_name: Healthy donor: cord blood; a pool of 4 single-cell WGA products from the same donor


title: PC_DCC_male 2_single cell 1_reamplified single-cell WGA_RP labeling_25probes

description:
Prostate cancer patient; DCC; male #2, single cell #1 (25 probes)
Raw data file:
252206026328_201206221218_S01_CGH_107_Sep09_1_2.txt
PC_DCC_male 2_single cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7C.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7C.

source_name: Disseminated cancer cell obtained from bone marrow

value: RP-labeling

value: single-cell WGA (2.0µg)


title: Healthy male donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2_25probes

description:
Healthy male donor #1, single-cell #1 (25 probes)
Raw data file:
US94700331_252206026399_S01_CGH_107_Sep09_1_3.txt
Healthy male donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6B.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6B.

source_name: Single cell collected from the cord blood of a healthy male donor


title: Healthy male donor 1_single-cell 1_reamplified single-cell WGA_RP labeling_25probes

description:
Healthy male donor #1, single-cell #1 (25 probes)
Raw data file:
US94700331_252206026493_S01_CGH_107_Sep09_1_3.txt
Healthy male donor 1_single-cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6A.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6A.

value: single-cell WGA (1.5µg)


title: Healthy female donor 2_single-cell 1_reamplified single-cell WGA_RP labeling_25probes

description:
Healthy female donor #2, single-cell #1 (25 probes)
Raw data file:
US94700331_252206026493_S01_CGH_107_Sep09_1_2.txt
Healthy female donor 2_single-cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6C.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6C.


title: Healthy female donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2_25probes

description:
Healthy female donor #1, single-cell #1 (25 probes)
Raw data file:
US94700331_252206026490_S01_CGH_107_Sep09_1_3.txt
Healthy female donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6F.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6F.


title: Healthy female donor 1_single-cell 1_reamplified single-cell WGA_RP labeling_25probes

description:
Healthy female donor #1, single-cell #1 (25 probes)
Raw data file:
US94700331_252206026480_S01_CGH_107_Sep09_1_3.txt
Healthy female donor 1_single-cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6E.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6E.


title: PC_DCC_male 2_single cell 1_reamplified single-cell WGA_PCR-T2_25probes

description:
Prostate cancer patient; DCC; male #2, single cell #1 (25 probes)
Raw data file:
252206026327_201206221155_S01_CGH_107_Sep09_1_2.txt
PC_DCC_male 2_single cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7D.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7D.

value: male


title: PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 2_25probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 2 (25 probes)
Raw data file:
252206023805_201202061537_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 2
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2A


title: PC_DCC_male 1_single cell 1_reamplified single-cell WGA_PCR-T2_25probes

description:
Prostate cancer patient; DCC; male #1, single cell #1 (25 probes)
Raw data file:
252206026327_201206221155_S01_CGH_107_Sep09_1_1.txt
PC_DCC_male 1_single cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7B. Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7B. This sample was used to compare the performance of aCGH with cCGH - Fig. 8 of the manuscript.


title: SKBR3_bulk gDNA_25probes

description:
SKBR3 genomic DNA; bulk DNA (25 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_3.txt
SKBR3_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

source_name: SKBR3 breast cancer cell line

value: cell line (DSMZ)

value: unamplified

value: bulk DNA (1.5µg)

source_name: Healthy donor: cord blood bulk gDNA


title: PT-1590_primary single-cell WGA_single cell 3 vs. Single-cell ref_repetition 2_25probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 4 (25 probes)
Raw data file:
252206025376_201202211517_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 3 vs. Single-cell ref_repetition 2
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2B

value: cell line (University Medical Center Hamburg-Eppendorf)

value: tumor sample

value: amplified - Ampli1 WGA


title: Healthy female donor 2_single-cell 1_reamplified single-cell WGA_PCR-T2_25probes

description:
Healthy female donor #2, single-cell #1 (25 probes)
Raw data file:
US94700331_252206026399_S01_CGH_107_Sep09_1_2.txt
Healthy female donor 2_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6D.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6D.

value: single-cell WGA

value: Clinical sample


title: MDA-MB-453_bulk gDNA_25probes

description:
MDA-MB-453 genomic DNA; bulk DNA (25 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_2.txt
MDA-MB-453_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

source_name: MDA-MB-453 breast cancer cell line

value: cell line (ATCC)

value: healthy donor


title: PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 1_25probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 1 (vs. cell pool) (25 probes)
Raw data file:
252206023806_201202061600_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 1
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2A

value: primary WGA

value: cell pool WGA


title: PC_DCC_male 1_single cell 1_reamplified single-cell WGA_RP labeling_25probes

description:
Prostate cancer patient; DCC; male #1, single cell #1 (25 probes)
Raw data file:
252206026328_201206221218_S01_CGH_107_Sep09_1_1.txt
PC_DCC_male 1_single cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7A. Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7A.

value: clinical sample

value: reamplified WGA


title: BT-474_bulk gDNA_25probes

description:
BT-474 genomic DNA; bulk DNA (25 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_4.txt
BT-474_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

source_name: BT-474 breast cancer cell line

value: RP-labeling

value: female


title: PT-1590_primary single-cell WGA_single cell 3 vs. single-cell ref_repetition 1_25probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 3 (25 probes)
Raw data file:
252206023806_201202061600_S01_CGH_107_Sep09_1_2.txt
PT-1590_primary single-cell WGA_single cell 3 vs. single-cell ref_repetition 1
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2B and Fig. 3.

value: male


title: MDA-MB-361_bulk gDNA_25probes

description:
MDA-MB-361 genomic DNA; bulk DNA (25 probes)
s
US94700331_252206026492_S01_CGH_107_Sep09_1_1.txt
MDA-MB-361_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

source_name: MDA-MB-361 breast cancer cell line


title: BT-474_reamplified single-cell WGA_PCR-T2_25probes

description:
BT-474 genomic DNA; single-cell WGA; reamplified WGA (25 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_4.txt
BT-474_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

value: cell line (DSMZ)


title: PT-1590_primary single-cell WGA_single-cell 2_PCR-T2_25probes

description:
PT-1590 single-cell Primary WGA; single-cell 2; processed with PCR-T2 (25 probes)
Raw data file:
252206021209_201109201521_S01_CGH_107_Sep09_1_3.txt
PT-1590_primary single-cell WGA_single-cell 2_PCR-T2
sample were used to compate the performance of two custom developed PCR-based labeling protocols [PCR-T1; incorporating of dye using labeled primers] vs. PCR-T2; incorporating of dye using labeled dNTPs]). aCGH profile of this sample is depicted in Fig. S1 and S4 of the manuscript


title: SKBR3_reamplified single-cell WGA_PCR-T2_25probes

description:
SKBR3 genomic DNA; single-cell WGA; reamplified WGA (25 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_3.txt
SKBR3_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.


title: MDA-MB-361_reamplified single-cell WGA_PCR-T2_25probes

description:
MDA-MB-361 genomic DNA; single-cell WGA; reamplified WGA (25 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_2.txt
MDA-MB-361_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.


title: MDA-MB-453_reamplified single-cell WGA_PCR-T2_25probes

description:
MDA-MB-453 genomic DNA; single-cell WGA; reamplified WGA (25 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_1.txt
MDA-MB-453_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.


title: ABC_DCC_time point 4_single cell 1_25probes

description:
Advanced breast cancer patient; DCC; time point #4; single cell #1 (25 probes)
Raw data file:
252206033108_201303131446_S01_CGH_107_Sep09_1_1.txt
ABC_DCC_time point 4_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

tag: time

value: time point 4


title: ABC_DCC_time point 3_single cell 2_25probes

description:
Advanced breast cancer patient; DCC; time point #3; single cell #2 (25 probes)
Raw data file:
252206033108_201303131446_S01_CGH_107_Sep09_1_4.txt
ABC_DCC_time point 3_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 3


title: ABC_DCC_time point 4_single cell 2_25probes

description:
Advanced breast cancer patient; DCC; time point #4; single cell #2 (25 probes)
Raw data file:
252206033108_201303131446_S01_CGH_107_Sep09_1_2.txt
ABC_DCC_time point 4_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript


title: ABC_DCC_time point 3_single cell 1_25probes

description:
Advanced breast cancer patient; DCC; time point #3; single cell #1 (25 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_4.txt
ABC_DCC_time point 3_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript


title: PT-1590_primary single-cell WGA_single-cell 2_PCR-T1_25probes

description:
PT-1590 single-cell Primary WGA; single-cell 2; processed with PCR-T1 (25 probes)
Raw data file:
US94700331_252206021171_S01_CGH_107_Sep09_1_2.txt
PT-1590_primary single-cell WGA_single-cell 2_PCR-T1
sample were used to compate the performance of two custom developed PCR-based labeling protocols [PCR-T1; incorporating of dye using labeled primers] vs. PCR-T2; incorporating of dye using labeled dNTPs]. aCGH profile of this sample is depicted in Fig. S1 of the manuscript

value: cell line (University Medical Center Hamburg-Eppendorf)


title: PT-1590_bulk gDNA_25probes

description:
PT-1590 genomic DNA; bulk DNA (25 probes)
Raw data file:
US94700331_252206021174_S01_CGH_107_Sep09_1_3.txt
PT-1590_bulk gDNA
sample used as benchmark for comparison with the corresponding single-cell WGA samples to evaluate the performance of the PCR-based labeling approaches for WGA products (PCR-T1 vs- PCR-T2). Profiles of the sampels are depicted in the in the Fig.3, S1 and S4 of the manuscript

value: tumor sample

value: unamplified

value: bulk DNA (1.0µg)


title: ABC_DCC_time point 2_single cell 1_25probes

description:
Advanced breast cancer patient; DCC; time point #2; single cell #1 (25 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_2.txt
ABC_DCC_time point 2_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 2

value: amplified - Ampli1 WGA

value: single-cell WGA

value: Clinical sample


title: ABC_DCC_time point 2_single cell 2_25probes

description:
Advanced breast cancer patient; DCC; time point #2; single cell #2 (25 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_3.txt
ABC_DCC_time point 2_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: healthy donor


title: ABC_primary tumor_FFPE_PCR-2_25probes

description:
Advanced breast cancer patient; Primary Tumor; FFPE tissue (25 probes)
Raw data file:
252206026513_201304171359_S01_CGH_107_Sep09_1_4.txt
ABC_primary tumor_FFPE_PCR-2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

source_name: Primary breast tumor, microdissected FFPE sample

value: clinical sample

value: WGA FFPE


title: ABC_DCC_time point 1_single cell 2_25probes

description:
Advanced breast cancer patient; DCC; time point #1; single cell #2 (25 probes)
Raw data file:
252206033109_201303131509_S01_CGH_107_Sep09_1_4.txt
ABC_DCC_time point 1_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 1

value: reamplified WGA


title: OE-19_reamplified single-cell WGA_RP-labeling_25probes

description:
OE-19 genomic DNA; single-cell WGA; reamplified WGA (25 probes)
Raw data file:
252206026310_201205101421_S01_CGH_107_Sep09_1_4.txt
OE-19_reamplified single-cell WGA_RP-labeling
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. S3 of the manuscript

source_name: OE-19 esophageal cancer cell line

value: cell line (European Collection of Cell Cultures)

value: RP-labeling

value: male

value: single-cell WGA (2.0µg)


title: ABC_lymph node metastasis_FFPE_PCR-2_25probes

description:
Advanced breast cancer patient; Lymph Node Metastasis; FFPE tissue sample (25 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_1.txt
ABC_lymph node metastasis_FFPE_PCR-2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

source_name: Lymph node metastasis, microdissected FFPE sample

value: female


title: OE-19_primary single-cell WGA_RP-labeling_25probes

description:
OE-19 genomic DNA; single-cell WGA; primary WGA (25 probes)
Raw data file:
252206026310_201205101421_S01_CGH_107_Sep09_1_3.txt
OE-19_primary single-cell WGA_RP-labeling
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. 2 of the manuscript

value: tumor sample

value: primary WGA


title: Healthy female donor 3_single-cell 1_reamplified single-cell WGA_PCR-T2_10probes

description:
Healthy female donor #3, single-cell #1 (10 probes)
Raw data file:
US94700331_252206026490_S01_CGH_107_Sep09_1_2.txt
Healthy female donor 3_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to assess the reliability of the new single-cell aCGH protocol comining: (1) PCR-T2 labeling, (2) reamplified WGA products, (3) single-cell based reference. Profile of the samples is depicted in the Fig. S3C of the manuscript.


title: ABC_DCC_time point 1_single cell 1_25probes

description:
Advanced breast cancer patient; DCC; time point #1; single cell #1 (25 probes)
Raw data file:
252206033109_201303131509_S01_CGH_107_Sep09_1_3.txt
ABC_DCC_time point 1_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript


title: Healthy female donor 2_single-cell 1_reamplified single-cell WGA_RP labeling_10probes

description:
Healthy female donor #2, single-cell #1 (10 probes)
Raw data file:
US94700331_252206026493_S01_CGH_107_Sep09_1_2.txt
Healthy female donor 2_single-cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6C.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6C.

value: single-cell WGA (1.5µg)


title: OE-19_primary single-cell WGA_PCR-T2_25probes

description:
OE-19 genomic DNA; single-cell WGA; primary WGA (25 probes)
Raw data file:
252206025381_201203291502_S01_CGH_107_Sep09_1_1.txt
OE-19_primary single-cell WGA_PCR-T2
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. 2 of the manuscript


title: Healthy female donor 2_single-cell 1_reamplified single-cell WGA_PCR-T2_10probes

description:
Healthy female donor #2, single-cell #1 (10 probes)
Raw data file:
US94700331_252206026399_S01_CGH_107_Sep09_1_2.txt
Healthy female donor 2_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6D.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6D.


title: OE-19_ bulk gDNA_25probes

description:
OE-19 genomic DNA; bulk DNA (25 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_1.txt
OE-19_ bulk gDNA
sample used as benchmark for comparison with the corresponding single-cell WGA samples: profiles of the sampels included in the Fig.2 and Fig.S3 of the manuscript

value: unamplified

value: bulk DNA (1.5µg)


title: PT-1590_primary single-cell WGA_single cell 1_PCR-T2_10probes

description:
PT-1590 single-cell Primary WGA; single-cell 1 (10 probes)
Raw data file:
252206023802_201111081305_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 1_PCR-T2
sample used to demonstrate the ability of the new single-cell aCGH protocol to detect single-cell heterogeneity in vitro. aCGH profiles of this sample are depicted in the Fig. 3 and S4.

value: cell line (University Medical Center Hamburg-Eppendorf)

value: amplified - Ampli1 WGA

value: single-cell WGA

value: cell pool WGA


title: OE-19_reamplified single-cell WGA_PCR-T2_25probes

description:
OE-19 genomic DNA; single-cell WGA; reamplified WGA (25 probes)
Raw data file:
252206025381_201203291502_S01_CGH_107_Sep09_1_2.txt
OE-19_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. S3 of the manuscript

value: Clinical sample

value: healthy donor


title: PC_DCC_male 2_single cell 1_reamplified single-cell WGA_PCR-T2_10probes

description:
Prostate cancer patient; DCC; male #2, single cell #1 (10 probes)
Raw data file:
252206026327_201206221155_S01_CGH_107_Sep09_1_2.txt
PC_DCC_male 2_single cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7D.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7D.

value: clinical sample

value: reamplified WGA


title: Healthy female donor 1_single-cell 1_reamplified single-cell WGA_RP labeling_10probes

description:
Healthy female donor #1, single-cell #1 (10 probes)
Raw data file:
US94700331_252206026480_S01_CGH_107_Sep09_1_3.txt
Healthy female donor 1_single-cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6E.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6E.

value: RP-labeling


title: Healthy male donor 1_single-cell 1_reamplified single-cell WGA_RP labeling_10probes

description:
Healthy male donor #1, single-cell #1 (10 probes)
Raw data file:
US94700331_252206026493_S01_CGH_107_Sep09_1_3.txt
Healthy male donor 1_single-cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6A.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6A.

value: male


title: Healthy male donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2_10probes

description:
Healthy male donor #1, single-cell #1 (10 probes)
Raw data file:
US94700331_252206026399_S01_CGH_107_Sep09_1_3.txt
Healthy male donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6B.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6B.


title: Healthy female donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2_10probes

description:
Healthy female donor #1, single-cell #1 (10 probes)
Raw data file:
US94700331_252206026490_S01_CGH_107_Sep09_1_3.txt
Healthy female donor 1_single-cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S6F.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S6F.


title: PC_DCC_male 2_single cell 1_reamplified single-cell WGA_RP labeling_10probes

description:
Prostate cancer patient; DCC; male #2, single cell #1 (10 probes)
Raw data file:
252206026328_201206221218_S01_CGH_107_Sep09_1_2.txt
PC_DCC_male 2_single cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7C.  Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7C.

value: single-cell WGA (2.0µg)


title: PT-1590_primary single-cell WGA_single cell 3 vs. Single-cell ref_repetition 2_10probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 4 (10 probes)
Raw data file:
252206025376_201202211517_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 3 vs. Single-cell ref_repetition 2
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2B


title: PC_DCC_male 1_single cell 1_reamplified single-cell WGA_PCR-T2_10probes

description:
Prostate cancer patient; DCC; male #1, single cell #1 (10 probes)
Raw data file:
252206026327_201206221155_S01_CGH_107_Sep09_1_1.txt
PC_DCC_male 1_single cell 1_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7B. Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7B. This sample was used to compare the performance of aCGH with cCGH - Fig. 8 of the manuscript.


title: BT-474_bulk gDNA_10probes

description:
BT-474 genomic DNA; bulk DNA (10 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_4.txt
BT-474_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

value: cell line (DSMZ)

value: female


title: PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 2_10probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 2 (10 probes)
Raw data file:
252206023805_201202061537_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 2
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2A

value: tumor sample

value: primary WGA


title: PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 1_10probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 1 (vs. cell pool) (10 probes)
Raw data file:
252206023806_201202061600_S01_CGH_107_Sep09_1_1.txt
PT-1590_primary single-cell WGA_single cell 3 vs. cell pool ref_repetition 1
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2A


title: MDA-MB-361_bulk gDNA_10probes

description:
MDA-MB-361 genomic DNA; bulk DNA (10 probes)
Raw data file:
US94700331_252206026492_S01_CGH_107_Sep09_1_1.txt
MDA-MB-361_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

value: cell line (ATCC)

value: unamplified


title: PT-1590_primary single-cell WGA_single cell 3 vs. single-cell ref_repetition 1_10probes

description:
PT-1590 single-cell Primary WGA; single-cell 3; repetition 3 (10 probes)
Raw data file:
252206023806_201202061600_S01_CGH_107_Sep09_1_2.txt
PT-1590_primary single-cell WGA_single cell 3 vs. single-cell ref_repetition 1
sample used to demonstarate the reproducibility of the new single-cell aCGH protocol. Genomic profiles of this samples is depicted in the Fig. S2B and Fig. 3.

value: cell line (University Medical Center Hamburg-Eppendorf)


title: MDA-MB-453_bulk gDNA_10probes

description:
MDA-MB-453 genomic DNA; bulk DNA (10 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_2.txt
MDA-MB-453_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

value: bulk DNA (1.5µg)


title: ABC_DCC_time point 4_single cell 1_10probes

description:
Advanced breast cancer patient; DCC; time point #4; single cell #1 (10 probes)
Raw data file:
252206033108_201303131446_S01_CGH_107_Sep09_1_1.txt
ABC_DCC_time point 4_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 4

value: amplified - Ampli1 WGA

value: single-cell WGA


title: SKBR3_bulk gDNA_10probes

description:
SKBR3 genomic DNA; bulk DNA (10 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_3.txt
SKBR3_bulk gDNA
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

value: Clinical sample

value: healthy donor


title: PT-1590_primary single-cell WGA_single-cell 2_PCR-T2_10probes

description:
PT-1590 single-cell Primary WGA; single-cell 2; processed with PCR-T2 (10 probes)
Raw data file:
252206021209_201109201521_S01_CGH_107_Sep09_1_3.txt
PT-1590_primary single-cell WGA_single-cell 2_PCR-T2
sample were used to compate the performance of two custom developed PCR-based labeling protocols [PCR-T1; incorporating of dye using labeled primers] vs. PCR-T2; incorporating of dye using labeled dNTPs]). aCGH profile of this sample is depicted in Fig. S1 and S4 of the manuscript

value: cell pool WGA


title: PC_DCC_male 1_single cell 1_reamplified single-cell WGA_RP labeling_10probes

description:
Prostate cancer patient; DCC; male #1, single cell #1 (10 probes)
Raw data file:
252206026328_201206221218_S01_CGH_107_Sep09_1_1.txt
PC_DCC_male 1_single cell 1_reamplified single-cell WGA_RP labeling
sample used to compare the performance of two labeling approaches (PCR-T2 vs. RP-labeling) - Fig. S7A. Additionaly sample was used demonstrate the necessity of applying aberration filters with a minumum of 25 probes per abrrant interval - Fig. S7A.

value: clinical sample

value: reamplified WGA

value: RP-labeling


title: MDA-MB-453_reamplified single-cell WGA_PCR-T2_10probes

description:
MDA-MB-453 genomic DNA; single-cell WGA; reamplified WGA (10 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_1.txt
MDA-MB-453_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.


title: BT-474_reamplified single-cell WGA_PCR-T2_10probes

description:
BT-474 genomic DNA; single-cell WGA; reamplified WGA (10 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_4.txt
BT-474_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

value: cell line (DSMZ)


title: PT-1590_primary single-cell WGA_single-cell 2_PCR-T1_10probes

description:
PT-1590 single-cell Primary WGA; single-cell 2; processed with PCR-T1 (10 probes)
Raw data file:
US94700331_252206021171_S01_CGH_107_Sep09_1_2.txt
PT-1590_primary single-cell WGA_single-cell 2_PCR-T1
sample were used to compate the performance of two custom developed PCR-based labeling protocols [PCR-T1; incorporating of dye using labeled primers] vs. PCR-T2; incorporating of dye using labeled dNTPs]. aCGH profile of this sample is depicted in Fig. S1 of the manuscript

value: male


title: ABC_DCC_time point 4_single cell 2_10probes

description:
Advanced breast cancer patient; DCC; time point #4; single cell #2 (10 probes)
Raw data file:
252206033108_201303131446_S01_CGH_107_Sep09_1_2.txt
ABC_DCC_time point 4_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: tumor sample

value: female


title: ABC_DCC_time point 3_single cell 1_10probes

description:
Advanced breast cancer patient; DCC; time point #3; single cell #1 (10 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_4.txt
ABC_DCC_time point 3_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 3


title: ABC_DCC_time point 1_single cell 2_10probes

description:
Advanced breast cancer patient; DCC; time point #1; single cell #2 (10 probes)
Raw data file:
252206033109_201303131509_S01_CGH_107_Sep09_1_4.txt
ABC_DCC_time point 1_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 1


title: ABC_DCC_time point 2_single cell 2_10probes

description:
Advanced breast cancer patient; DCC; time point #2; single cell #2 (10 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_3.txt
ABC_DCC_time point 2_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 2


title: PT-1590_bulk gDNA_10probes

description:
PT-1590 genomic DNA; bulk DNA (10 probes)
Raw data file:
US94700331_252206021174_S01_CGH_107_Sep09_1_3.txt
PT-1590_bulk gDNA
sample used as benchmark for comparison with the corresponding single-cell WGA samples to evaluate the performance of the PCR-based labeling approaches for WGA products (PCR-T1 vs- PCR-T2). Profiles of the sampels are depicted in the in the Fig.3, S1 and S4 of the manuscript

value: cell line (University Medical Center Hamburg-Eppendorf)

value: unamplified

value: bulk DNA (1.0µg)


title: ABC_DCC_time point 3_single cell 2_10probes

description:
Advanced breast cancer patient; DCC; time point #3; single cell #2 (10 probes)
Raw data file:
252206033108_201303131446_S01_CGH_107_Sep09_1_4.txt
ABC_DCC_time point 3_single cell 2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: amplified - Ampli1 WGA

value: single-cell WGA


title: MDA-MB-361_reamplified single-cell WGA_PCR-T2_10probes

description:
MDA-MB-361 genomic DNA; single-cell WGA; reamplified WGA (10 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_2.txt
MDA-MB-361_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

value: cell line (ATCC)

value: Clinical sample

value: healthy donor