title: NA21105 Replicate 1


title: NA21104 Replicate 1

status: Public on Jul 01 2015

type: genomic

city: Farmington

first: Charles

last: Lee

state: CT

address: 10 Discovery Dr.

country: USA

institute: Jackson Laboratory for Genomic Medicine

hyb_protocol: Labeled samples were purified using Agilent SureTag Purification columns. Test and reference samples were combined with Agilent Oligo aCGH/ChIP-on-Chip Blocking Agent, Agilent Hi-RPM Hybridization Buffer and Cot-1 DNA and applied to microarrays enclosed in Agilent Hybridization Chamber. After 40 hour incubation at 67 °C, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 and 2.

scan_protocol: Slides were scanned on an Agilent G2505C scanner (version A.8.5.1).

data_processing: Images were processed using Agilent Feature Extraction Software (version 10.5.1.1)

molecule: genomic DNA

organism: Homo sapiens

label_protocol: 1 to 1.5 ug of genomic DNA was digested using AluI and RsaI for 2 hours at 37 °C followed by a 20 minute enzyme-inactivation step at 65 °C. DNA was then labeled with Cyanine-3-dUTP (Reference samples) or Cyanine-5-dUTP (Test samples) at 37 °C for 2 hours followed by a 10 minute enzyme-inactivation step at 65 °C.

growth_protocol: We did not perform the growth in house. We received DNA samples from Coriell. This is the information available on their website for the cell culture of NA10851: Split ratio 1:2, Temperature: 37C, Percent CO2: 5%, Percent O2: Ambient, Medium: Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, Serum: 15% fetal bovine serum Not Inactivated

extract_protocol: We did not perform the extraction in house. We received DNA samples from Coriell. This is the information available on their website for DNA extraction: gDNA is purified from fresh blood, immortalized lymphocyctes or fibroblasts using the Qiagen Autopure LS instrument according to the manufacturer’s instructions or manually by modified Miller’s Salting out procedures.

treatment_protocol: We, nor Coriell, did not perform any treatment on the samples. We received DNA samples from Coriell.

tag: coriell cell line


title: VUMC-Rb-64

type: RNA

city: Amsterdam

first: Irsan

last: Kooi

state: Noord-Holland

address: van der Boechorstraat 7

department: Clininical Genetics

country: Netherlands

institute: VU university medical centre

description: fresh frozen Rb material from a randomly selected cohort

hyb_protocol: Per sample, 7.5 µg cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 µg/µl on the Affymetrix [HT HG U133 + PM96] (Affymetrix, Santa Clara, CA, U.S.A.). After an automated process of washing and staining by the GeneTitan machine (Affymetrix, Santa Clara, CA, U.S.A) using the Affymetrix HWS Kit for GeneTitan (part nr. 901530), absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v3.2 software.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The affy package from Bioconductor was used for this analysis.

label: biotin

molecule: total RNA

source_name: primary Rb tissue

label_protocol: Biotinylated cRNA was prepared using the Affymetrix 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s specifications with an input of 100 ng of total RNA

extract_protocol: Frozen tumour samples were homogenized in Trizol Reagent (Invitrogen, Carlsbad, Canada) with a rotor-stator homogenizer, and RNA was extracted following the manufacturer's instructions. Trizol extracted RNA was treated with rDNase (Macherey-Nagel, Düren, Germany) to digest any contaminating DNA and subsequently purified with the NucleoSpin RNA Clean-up XS kit (Macherey-Nagel)

tag: tissue

value: primary Rb tissue

tag: uhc-subgroup

value: group 3


title: VUMC-Rb-45


title: VUMC-Rb-49


title: NA21108 Replicate 1


title: VUMC-Rb-44


title: NA21102 Replicate 1


title: NA21101 Replicate 1


title: NA21100 Replicate 1


title: NA21103 Replicate 1


title: NA21106 Replicate 1


title: VUMC-Rb-38


title: VUMC-Rb-40

value: group 1


title: VUMC-Rb-42


title: VUMC-Rb-37


title: NA21099 Replicate 1


title: VUMC-Rb-41


title: VUMC-Rb-39


title: VUMC-Rb-35


title: VUMC-Rb-36


title: VUMC-Rb-33


title: NA21098 Replicate 1


title: NA21097 Replicate 1


title: NA21093 Replicate 1


title: VUMC-Rb-30


title: VUMC-Rb-32


title: VUMC-Rb-31


title: VUMC-Rb-29


title: VUMC-Rb-26

value: group 2


title: VUMC-Rb-28


title: NA21090 Replicate 1


title: NA21091 Replicate 1


title: VUMC-Rb-27


title: NA21095 Replicate 1


title: NA21094 Replicate 1


title: VUMC-Rb-25


title: VUMC-Rb-51


title: VUMC-Rb-24


title: NA21088 Replicate 1


title: NA20911 Replicate 1


title: VUMC-Rb-46


title: NA21087 Replicate 1


title: NA21086 Replicate 1


title: NA21089 Replicate 1


title: NA21092 Replicate 1


title: NA20910 Replicate 1


title: NA20908 Replicate 1


title: VUMC-Rb-21


title: VUMC-Rb-22


title: VUMC-Rb-17


title: VUMC-Rb-20


title: NA20906 Replicate 1


title: NA20905 Replicate 1


title: NA20904 Replicate 1


title: VUMC-Rb-23


title: VUMC-Rb-15


title: NA20903 Replicate 1


title: NA20900 Replicate 1


title: NA20901 Replicate 1


title: NA20898 Replicate 1


title: VUMC-Rb-18


title: NA20897 Replicate 1


title: NA20895 Replicate 1


title: NA21135 Replicate 1


title: NA20896 Replicate 1


title: NA20902 Replicate 1


title: VUMC-Rb-16


title: NA20899 Replicate 1


title: VUMC-Rb-11


title: VUMC-Rb-100


title: VUMC-Rb-14


title: NA20893 Replicate 1


title: VUMC-Rb-08


title: VUMC-Rb-12


title: VUMC-Rb-10


title: VUMC-Rb-09


title: VUMC-Rb-102


title: VUMC-Rb-13


title: NA20892 Replicate 1


title: NA20891 Replicate 1


title: NA20890 Replicate 1


title: NA20889 Replicate 1


title: NA20888 Replicate 1


title: NA20894 Replicate 1


title: NA20886 Replicate 1


title: NA20885 Replicate 1


title: NA20884 Replicate 1


title: NA20882 Replicate 1


title: NA20881 Replicate 1


title: VUMC-Rb-05


title: VUMC-Rb-04


title: FSH Vs 6 H R4b

city: Quebec

first: Daulat Raheem

last: Khan

state: QC

address: 2425, rue de l'Agriculture, Pavillon Paul-Comtois

department: Sciences Animales

country: Canada

institute: Université Laval

description: Array 6

hyb_protocol: hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Auto-gain scanning with Tecan technology (PowerScanner) Auto-gain scanning with Tecan technology (PowerScanner)

data_processing: LOESS normalized within array, background subtracted and quantile normalized between array data obtained from log2 of processed Red signal/processed Green signal. Flexarray 1.6.1. (http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e) was used.

organism: Bos taurus

label_protocol: labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol:
Control COCs were aspirated (10 cc syringe, 18G 1 1/2) from slaughterhouse Holstein cow’s ovaries. After 3 washes in TLH (HEPES-buffered Tyrode’s Lactate)/10% bovine serum/0.2 mM pyruvate, groups of up to 10 selected COCs (quality 1-3, Blondin & Sirard, 1995) with at least 5 cumulus layers were cultured and matured at 38.5°C/5% CO2/20% O2/100% humidity/22-24h in TCM-199 (Gibco)/10% FCS (HyClone, ThermoScientific)/1 μg/ml estradiol/0.33 mM pyruvate/50 μg/ml gentamicin.
FSH supplementation group was treated the same way as acotrol except supplementation of in vitro maturation medium with rFSH (0.5µg/mL).

extract_protocol: amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices).The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: breed

value: Holstein

value: ovaries

tag: cell type

value: cumulus cells derived from cumulus oocyte complexes (COCs)

tag: compound added

source_name: CC-rFSH

value: rFSH


title: VUMC-Rb-07


title: NA20878 Replicate 1


title: NA20877 Replicate 1


title: FSH Vs 6 H R4

description: Array 5


title: FSH Vs 6 H R3b

description: Array 4


title: FSH Vs 6 H R3

description: Array 3


title: VUMC-Rb-06


title: VUMC-Rb-03


title: FSH Vs 6 H R2b

description: Array 2


title: VUMC-Rb-02


title: NA20887 Replicate 1


title: 6 H Vs 0 H R3

description: Array 5

scan_protocol: Auto-gain scanning with Tecan technology (PowerScanner)

growth_protocol: COCs were aspirated (10 cc syringe, 18G 1 1/2) from slaughterhouse Holstein cow’s ovaries. COCs were either subjected to mechanical separation of cumulus cells (Ct-0H) or were subjected to maturation after 3 washes in TLH (HEPES-buffered Tyrode’s Lactate)/10% bovine serum/0.2 mM pyruvate, groups of up to 10 selected COCs (quality 1-3, Blondin & Sirard, 1995) with at least 5 cumulus layers were cultured and matured at 38.5°C/5% CO2/20% O2/100% humidity/22-24h in TCM-199 (Gibco)/10% FCS (HyClone, ThermoScientific)/1 μg/ml estradiol/0.33 mM pyruvate/50 μg/ml gentamicin.

extract_protocol:
total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples.
amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices).The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: time point

value: before maturation (Ct-0H)

value: after 6 hrs of in vitro matutaion(Ct-6H)


title: 6 H Vs 0 H R1b

description: Array 2


title: 6 H Vs 0 H R2b

description: Array 4


title: FSH Vs 6 H R2

description: Array 1


title: NA20875 Replicate 1


title: NA20874 Replicate 1


title: NA20871 Replicate 1


title: NA20872 Replicate 1


title: NA20876 Replicate 1


title: NA20870 Replicate 1


title: NA20869 Replicate 1


title: 6 H Vs 0 H R2

description: Array 3


title: NA20868 Replicate 1


title: 6 H Vs 0 H R1

description: Array 1


title: 6 H Vs 0 H R3b

description: Array 6


title: FID Vs 6 H R4

description: Array 5

source_name: CC-FID

growth_protocol:
Control COCs were aspirated (10 cc syringe, 18G 1 1/2) from slaughterhouse Holstein cow’s ovaries. After 3 washes in TLH (HEPES-buffered Tyrode’s Lactate)/10% bovine serum/0.2 mM pyruvate, groups of up to 10 selected COCs (quality 1-3, Blondin & Sirard, 1995) with at least 5 cumulus layers were cultured and matured at 38.5°C/5% CO2/20% O2/100% humidity/22-24h in TCM-199 (Gibco)/10% FCS (HyClone, ThermoScientific)/1 μg/ml estradiol/0.33 mM pyruvate/50 μg/ml gentamicin.
FID supplementation group was treated the same way as acotrol except supplementation of in vitro maturation medium with forskolin (100µM), IBMX (500µM) and dipyridamole (50µM).

value: Forskolin-Dipyridamole-IBMX (FID)


title: FID Vs 6 H R2b

description: Array 4

value: Forskolin-Dipyridamole-IBMX


title: NA20867 Replicate 1


title: NA20864 Replicate 1


title: FID Vs 6 H R1b

description: Array 2


title: NA20866 Replicate 1


title: NA20863 Replicate 1


title: FID Vs 6 H R4b

description: Array 6


title: FID Vs 6 H R2

description: Array 3


title: NA20862 Replicate 1


title: FID Vs 6 H R1

description: Array 1


title: DMSO treated hESC derived EB, replicate 1 [miRNA]

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
miRNA expression data from hESC derived EBS treated with DMSO
SetI_Control

hyb_protocol: The labeled samples were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water. The hybridization mixture [10X GE blocking agent (4.5 ul), 2X Hi-RPM hybridization buffer (22.5ul)] along with labeled miRNA sample was heated for 5 min at 100 °C and immediately kept on ice. Each 45 ul sample was hybridized onto a microarray at 55 °C for 20 h. Slides were washed 5 min in GE wash buffer 1 at RT and again for 5 min in GE wash buffer 2 at 37 °C

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX 11.5 Software. 90th Percentile Shift Normalization.

source_name: DMSO treated hESC derived EB

label_protocol: miRNA labeling was performed as described in Agilent miRNA microarray protocol version 2.0 using Agilent miRNA labeling kit. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. Denaturation was performed by adding DMSO and incubating at 100°C for 7 min and immediately transferred to ice water bath. Ligation was performed with pCp-Cy3 at 16 °C for 2 hr.

growth_protocol: The embryoid body formation was initiated with an ES cell count of 1million cells per ml. The ES cells were resuspended in conditioned medium (Globalstem) containing 1% PVA (Sigma). This suspension was added to low attachment petri plates (Tarsons) and incubated at 37°C for 48 hours without disturbing the plates. The EBs were allowed to grow in size and were visualized at regular intervals under the light microscope. Once the clumping of cells was clearly evident, the EBs were transferred to DMEM medium (Invitrogen) supplemented with 20% KSR (Invitrogen) and 10% FBS (Biological Industries) onto 0.1% gelatin pre-coated dishes

extract_protocol: Trizol method as per manufacturer's instructions

treatment_protocol: Media changes were given every 5-7 days with the differentiation media. Compound treatment was generally given between the day 2 and day 4 of EB formation for 48 hours time point.

tag: source cell line

tag: source cell type

value: Human ES cell line (hESC)

value: hESC-derived embryoid body (EB)

tag: treated with

value: DMSO


title: DMSO treated hESC derived EB, replicate 2 [miRNA]

description:
miRNA expression data from hESC derived EBS treated with DMSO
SetII_Control


title: NA20859 Replicate 1


title: NA20861 Replicate 1


title: NA20858 Replicate 1


title: NA20856 Replicate 1


title: NA20854 Replicate 1


title: TBBD treated hESC derived EB, replicate1 [miRNA]

description:
miRNA expression data from hESC derived Ebs treated with TBBD
SetI_Test

source_name: TBBD treated hESC derived EB

value: 10uM TBBD for 48 h


title: NA20853 Replicate 1


title: NA20852 Replicate 1


title: TBBD treated hESC derived EB, replicate 2 [miRNA]

description:
miRNA expression data from hESC derived Ebs treated with TBBD
SetII_Test


title: NA20851 Replicate 1


title: NA20850 Replicate 1


title: NA20849 Replicate 1


title: NA20847 Replicate 1


title: NA20846 Replicate 1


title: NA20845 Replicate 1


title: NA20832 Replicate 1


title: IFN/IL6 (4) rep2

city: Stanford

first: Zach

middle: Klapholz

last: O'Brown

state: CA

address: 279 Campus Drive West

department: Developmental Biology

institute: Stanford

hyb_protocol: A total of 750 ng of cRNA was hybridized for each array using standard Illumina protocols with streptavidin-Cy3 being used for detection

scan_protocol: Slides were scanned on an Illumina Beadstation and analyzed using BeadStudio (Illumina, Inc).

data_processing: Rank invariant normalization

source_name: HK-2 cells

label_protocol: Each RNA sample was amplified using the Ambion Illumina RNA amplification kit with biotin UTP labeling. The Ambion Illumina RNA amplification kit uses T7 oligo(dT) primer to generate single stranded cDNA followed by a second strand synthesis to generate double-stranded cDNA, which is then column purified. In vitro transcription was done to synthesize biotin-labeled cRNA using T7 RNA polymerase. The cRNA was then column purified. The cRNA was then measured and  total of 750 ng of cRNA was hybridized for each array using standard Illumina protocols with streptavidin-Cy3 being used for detection.

growth_protocol: HK-2 cells were grown in keratinocyte serum-free medium (Life technologies)

extract_protocol: TRIZOL reagent

treatment_protocol: HK-2 cells were treated with either IFN-gamma, IL6/IFN-gamma, IFN-gamma/TNF or all three cytokines in combination, or PBS control treatment

tag: cell line

tag: treatment

value: HK-2 cells treated with 100 ng/ml IFN-gamma and 200 ng/ml IL6 for 90 minutes


title: IFN/TNF/IL6 (4) rep3

value: HK-2 cells treated with 100 ng/ml IFN-gamma, 100 ng/ml TNF and 200 ng/ml IL6 for 90 minutes


title: Control rep4

city: Los Angeles

first: Sylvie

last: Bradesi

address: 10833 Le Conte Avenue

department: Digestive Diseases

institute: UCLA

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: Agilent standard protocol

organism: Rattus norvegicus

source_name: spinal cord, control

label_protocol: Agilent standard protocol

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

value: spinal cord

value: control

tag: gender

value: male

tag: age

value: 12 weeks old


title: Control (4) rep1

value: HK-2 cells treated with PBS vehicle control for 90 minutes


title: Vehicle control for TNF 72 hr (3) rep2

treatment_protocol: HK-2 cells were treated with either TNF/IL6 in combination for 90 minutes, TNF-alpha for 72 hours the appropriate vehicle control treatment (PBS equal volume)

value: 72 hrs of PBS vehicle control treatment


title: IFN/IL6 (4) rep1


title: NA20828 Replicate 1


title: IFN/IL6 (4) rep3


title: IFN/TNF (4) rep2

value: HK-2 cells treated with 100 ng/ml IFN-gamma and 100 ng/ml TNF for 90 minutes


title: Control (4) rep2


title: Control rep2


title: Vehicle control for TNF 72 hr (3) rep3


title: Control rep1


title: IFN (4) rep2

value: HK-2 cells treated with 100 ng/ml IFN-gamma for 90 minutes


title: IFN/TNF (4) rep3


title: IFN/TNF/IL6 (4) rep1


title: IFN/TNF/IL6 (4) rep2


title: Control rep3


title: IFN (4) rep1


title: IFN/TNF (4) rep1


title: TNF 72 hr (3) rep2

value: 72 hrs of 100 ng/mL TNF-alpha treatment


title: TNF 72 hr (3) rep3


title: NA20827 Replicate 1


title: IFN (4) rep3


title: TNF 72 hr (3) rep1


title: Vehicle control for TNF 72 hr (3) rep1


title: Vehicle control for TNF/IL6 (3) rep3

value: 90 minutes of PBS vehicle control treatment


title: NA20826 Replicate 1


title: Water avoidance stres rep 4

source_name: spinal cord, stress

value: stress


title: Vehicle control for TNF/IL6 (3) rep2


title: NA20822 Replicate 1


title: NA20821 Replicate 1


title: NA20819 Replicate 1


title: NA20818 Replicate 1


title: NA20815 Replicate 1


title: Water avoidance stress rep 3


title: Water avoidance stress rep1


title: NA20814 Replicate 1


title: Water avoidance stress rep2


title: TNF (2) rep3

treatment_protocol: HK-2 cells were treated with either IL6, TNF-alpha, or the appropriate vehicle control (PBS equal volume).

value: 90 minutes 100 ng/ml TNF


title: TNF (2) rep1


title: TNF (2) rep2


title: Vehicle control for TNF/IL6 (3) rep1


title: Untreated control for TNF (2) rep2

value: 90 minutes TNF vehicle control


title: NA20813 Replicate 1


title: Untreated control for IL6 (2) rep2

value: 90 minutes IL6 vehicle control


title: TNF/IL6 (3) rep2

value: 90 minutes of 100 ng/mL TNF-alpha and 200 ng/mL IL6


title: TNF/IL6 (3) rep1


title: Untreated control for IL6 (2) rep3


title: NA20812 Replicate 1


title: TNF/IL6 (3) rep3


title: Untreated control for TNF (2) rep3


title: E11 scale mesenchyme, biological rep3

city: Taipei City

first: Shau-Ping

last: Lin

address: No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from differentiated metatarsal scale skin mesenchyme

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were read, analyzed, and normalized with RMA in the affy package in default setting under R statististical computing software environment.

organism: Gallus gallus

source_name: Chicken embryonic metatarsal scale skin mesenchyme, differentiated, pooled

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

growth_protocol: Fertilized egg incubated at 39oC, 50~60% humidity

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

treatment_protocol: Chick skins were dissected in HBSS. Skins were then treated with 2X CMF in 0.25% EDTA, pH 7.5 for 10 min on ice to separate the epidermis and dermis.

value: embryonic skin

value: white leghorn

value: Embryonic Day 11 (E11)


title: Untreated control for IL6 (2) rep1


title: IL6 (2) rep3

value: 90 minutes 200 ng/mL  IL6


title: Mef2d KO P14 retina

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

country: Japan

institute: Osaka Bioscience Institute

hyb_protocol: The labeled cDNA samples were hybridized using Gene Expression Hybridization Kit to the SurePrint G3 Mouse Gene Expression 8x60K microarray (Agilent Technology).

scan_protocol: Hybridized arrays were scanned using an Agilent DNA Microarray Scanner (G2565CA).

data_processing: Microarray analysis was performed by Takara Bio. The data analyses were performed using Feature Extraction software (Agilent Technology).

organism: Mus musculus

source_name: Mef2d KO P14 retina

label_protocol: The isolated total RNA was amplified and labeled with Cy3 using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Total RNA was purified using QIAzol reagent (Invitrogen).

treatment_protocol: Mouse retinas at P14 were dissected using fine forceps.

value: retina

tag: developmental stage

tag: genotype/variation

value: Mef2d KO


title: NA20811 Replicate 1


title: IL6 (2) rep2


title: WT P14 retina

source_name: WT P14 retina

value: wild-type


title: IL6 (2) rep1


title: Untreated control for TNF (2) rep1


title: NA20809 Replicate 1


title: S3I-201 rep3

treatment_protocol: HK-2 cells were either treated with IL6, PBS control or a combination of IL6 and the STAT3 inhibitor S3I-201 as described in the characteristics column indicated for each sample.

value: 90 minutes 50 uM S3I-201


title: NA20808 Replicate 1


title: E11 scale mesenchyme, biological rep1


title: E11 scale epithelium, biological rep3

description: Gene expression data from differentiated metatarsal scale skin epithelium

source_name: Chicken embryonic metatarsal scale skin epithelium, differentiated, pooled


title: NA20807 Replicate 1


title: S3I-201 rep2


title: S3I-201 rep1


title: E11 scale epithelium, biological rep1


title: Control rep2

value: 90 minutes 200 ng/ml IL6 and 50 uM S3I-201


title: NA20810 Replicate 1


title: E11 scale mesenchyme, biological rep2


title: E9 scale mesenchyme, biological rep2

description: Gene expression data from undifferentiated metatarsal scale skin mesenchyme

source_name: Chicken embryonic metatarsal scale skin mesenchyme, undifferentiated, pooled

value: Embryonic Day 9 (E9)


title: NA20806 Replicate 1


title: S3I-201 + IL6 rep3

value: 90 minutes control (PBS)


title: Control rep3


title: S3I-201 + IL6 rep1


title: E11 scale epithelium, biological rep2


title: NA20805 Replicate 1


title: NA20804 Replicate 1


title: S3I-201 + IL6 rep2


title: NA20803 Replicate 1


title: IL6 rep1

value: 90 minutes 200 ng/mL IL6


title: Control rep1


title: E9 scale mesenchyme, biological rep1


title: h1ESC dorsomorphin induced 72h rep 4

city: Shanghai

first: Gang

last: Liu

address: 320 Yueyang Rd, Shanghai

country: China

institute: Shanghai Institutes for Biological Sciences

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with package beadarray in R

source_name: H1 cell line

label_protocol: Label performed under HumanHT-12 v4 BeadArrays (Illumina) manufacturer's instructions.

growth_protocol: For neural differentiation, H1 hESCs were cultured on Matrigel with mTeSR medium to eliminate variations introduced by the MEF feeders. hESCs were gently dissociated into single-cell suspension with 1 mg/ml accutase for 5–7 minutes at 37°C. The dissociated cells were plated on Matrigel at high density (106/cm2) and cultured to confluency in mTeSR medium before induction of differentiation. For compound C-induced neural conversion, mTeSR medium was replaced with DMEM/F12 containing 20% KSR, 1 mM glutamine, 1% nonessential amino acid, and 0.1 mM β-mercaptoethanol, medium was replaced every day.

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) by the protocol provided. DNA contamination was eliminated with DNase I digestion, and the RNA was purified with RNeasy mini kit (QIAGEN);

tag: treatment/time period

value: dorsomorphin induced 72h


title: h1ESC dorsomorphin induced 48h rep 4

description: replicate 4

value: dorsomorphin induced 48h


title: E9 scale epithelium, biological rep1

description: Gene expression data from undifferentiated metatarsal scale skin epithelium

source_name: Chicken embryonic metatarsal scale skin epithelium, undifferentiated, pooled


title: IL6 rep2


title: NA20802 Replicate 1

tag: coriell cell line


title: h1ESC dorsomorphin induced 48h rep 3

description: replicate 3


title: E9 feather mesenchyme, biological rep3

description: Gene expression data from differentiated dorsal feather skin mesenchyme

source_name: Chicken embryonic dorsal feather skin mesenchyme, differentiated, pooled

tag: tissue


title: NA20801 Replicate 1


title: E9 scale epithelium, biological rep2


title: h1ESC dorsomorphin induced 12h rep 4

description: replicate 4

value: dorsomorphin induced 12h


title: h1ESC dorsomorphin induced 36h rep 4

description: replicate 4

value: dorsomorphin induced 36h


title: NA20800 Replicate 1


title: E9 feather mesenchyme, biological rep2


title: h1ESC dorsomorphin induced 0h rep 4

description: replicate 4

value: dorsomorphin induced 0h


title: h1ESC dorsomorphin induced 72h rep 3

description: replicate 3


title: NA20799 Replicate 1


title: h1ESC dorsomorphin induced 36h rep 3

description: replicate 3


title: h1ESC dorsomorphin induced 0h rep 3

description: replicate 3


title: NA20798 Replicate 1


title: E9 feather epithelium, biological rep3

description: Gene expression data from differentiated dorsal feather skin epithelium

source_name: Chicken embryonic dorsal feather skin epithelium, differentiated, pooled

value: embryonic skin


title: h1ESC dorsomorphin induced 24h rep 3

description: replicate 3

value: dorsomorphin induced 24h


title: E9 feather epithelium, biological rep2

value: white leghorn


title: h1ESC dorsomorphin induced 12h rep 3

description: replicate 3


title: NA20797 Replicate 1


title: h1ESC dorsomorphin induced 0h rep 2

description: replicate 2


title: E7 feather mesenchyme, biological rep2

description: Gene expression data from undifferentiated dorsal feather skin mesenchyme

source_name: Chicken embryonic dorsal feather skin mesenchyme, undifferentiated, pooled

value: Embryonic Day 7 (E7)


title: NA20796 Replicate 1


title: NA20795 Replicate 1


title: h1ESC dorsomorphin induced 48h rep 2

description: replicate 2


title: h1ESC dorsomorphin induced 12h rep 2

description: replicate 2


title: h1ESC dorsomorphin induced 24h rep 2

description: replicate 2


title: E9 feather epithelium, biological rep1


title: E9 feather mesenchyme, biological rep1


title: h1ESC dorsomorphin induced 48h rep 1

description: replicate 1


title: h1ESC dorsomorphin induced 36h rep 2

description: replicate 2


title: h1ESC dorsomorphin induced 24h rep 4

description: replicate 4


title: E7 feather epithelium, biological rep2

description: Gene expression data from undifferentiated dorsal feather skin epithelium

source_name: Chicken embryonic dorsal feather skin epithelium, undifferentiated, pooled


title: h1ESC dorsomorphin induced 24h rep 1

description: replicate 1


title: h1ESC dorsomorphin induced 72h rep 1

description: replicate 1


title: h1ESC dorsomorphin induced 36h rep 1

description: replicate 1


title: NA20792 Replicate 1


title: E7 feather mesenchyme, biological rep1


title: h1ESC dorsomorphin induced 72h rep 2

description: replicate 2


title: NA20790 Replicate 1


title: NA20787 Replicate 1


title: E7 feather epithelium, biological rep1


title: h1ESC dorsomorphin induced 12h rep 1

description: replicate 1


title: Sp-GSC-derived xenograft L

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Glioblastoma

hyb_protocol: Biotinylated cRNA was hybridized to the Illumina array per manufacturer's instructions

data_processing: The data were analyzed with Partek Genomics suite 6.6 and  in STATA/SE 11.2.

label: Biotin

source_name: Xenograft tumor tissue of GBM6 cells grown as Sp-GSCs

label_protocol: Biotinylated cRNA was prepared according to the standard Illumina protocol

growth_protocol: not applicable

extract_protocol: Trizol

treatment_protocol: Cells were cultured under normal adherent conditon (Bulk tumor cells), non-adherent plates with stem cell medium (Sp-GSC) or laminin-coated plates with stem cell medium (Ad-GSC). Xenografts were generated in NSG mice by subcutaneous inoculation.

tag: subgroup

value: GSph

value: xenograft tumor


title: NA20786 Replicate 1


title: h1ESC dorsomorphin induced 0h rep 1

description: replicate 1


title: Sp-GSC-derived xenograft K

description: Glioblastoma


title: Ad-GSC-derived xenograft J

description: Glioblastoma

source_name: Xenograft tumor tissue of GBM6 cells grown as Ad-GSCs

value: GLam


title: Roots at Nano BS treatment, biological rep 3

city: Lexington

first: Chun

last: Chen

state: Kentucky

address: 1100 Nicholasville Road, University of Kentucky

department: Plant and Soil Science

institute: University of Kentucky

description: Gene expression data from roots of Medicago following 30 days exposure to metal nanoparticle mixture added biosolids amended soil

hyb_protocol: Following fragmentation, 13.6 ug of biotinylated cRNA were hybridized for 16 hr at 45C on Medicago Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G Scanner.

data_processing: The data were analyzed using Partek Genomics Suite software version 6.6. Raw expression data (Affymetrix CEL files) were normalized with the RMA (Robust multiarray average) algorithm.

organism: Medicago truncatula

source_name: Medicago_roots_nano 3.CEL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express kit protocol from 100 ng total RNA.

growth_protocol: Twelve pots replicates of each treatment (control BS, Bulk BS and Nano BS) were randomly placed in a plant growth chamber with a 14 h light/10 h dark photoperiod at 20 ℃ and 70 % relative humidity, and were grown for 30 days.

extract_protocol: The pooled shoots and roots samples were selected respectively to isolate the total RNA using the RNeasy® Plant Mini Kit (Qiagen, Chatsworth, CA), and then purified after DNase I treatment (Qiagen)  according to the manufacturer’s protocol.

treatment_protocol: Take plant shoots and place in a 4 mL cryogenic tube and fill tube with liquid nitrogen. Place the tube in styrofoam cooler on bench top filled with dry ice. And then transfer these tubes to minus 80 freezer. For roots samples, dump out pot onto the bench paper. Gently remove the roots from the pot. Gently rinse the roots with DI water to remove soil particles as well as possible. And transfer the roots to a clearn 50 mL tube. Add DI water in the tube. Put the tube on the flat shaker for 10 mins. Rinse the roots and gently dry it with paper towel. Place the roots in 15 mL tube and fill tube with liquid nitrogen, and transfer tubes to minus 80 freezer.

value: roots

tag: exposure treatments

value: nano biosolids amended soil (Nano BS)


title: Roots at Nano BS treatment, biological rep 2

source_name: Medicago_roots_nano 2.CEL


title: Ad-GSC-derived xenograft I

description: Glioblastoma


title: Bulk Tumor xenograft G

description: Glioblastoma

source_name: Xenograft tumor tissue of GBM6 cells grown in Serum

value: GMono


title: Sp-GSCs F

description: Glioblastoma

source_name: GBM6 cells grown as Sp-GSCs

value: GBM6 cells


title: NA20785 Replicate 1


title: Ad-GSCs D

description: Glioblastoma

source_name: GBM6 cells grown as Ad-GSCs


title: Roots at Nano BS treatment, biological rep 1

source_name: Medicago_roots_nano 1.CEL


title: Sp-GSCs E

description: Glioblastoma


title: Bulk Tumor xenograft H

description: Glioblastoma


title: Ad-GSCs C

description: Glioblastoma


title: NA20778 Replicate 1


title: NA20783 Replicate 1


title: NA20775 Replicate 1


title: NA20774 Replicate 1


title: Bulk tumor cells B

description: Glioblastoma

source_name: GBM6 cells grown in Serum


title: NA20773 Replicate 1


title: NA20772 Replicate 1


title: RNA obtained from a. Patient replicate 158_2 SOX2

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

description:
Tracheal basal cell-line treated with a SOX2 lentiviral vector
Sample 8

scan_protocol: Standard Illumina scanning protocol (Genome Studio Version 2011.1)

data_processing: The data were normalised using quantile normalisation in Genespring (version 12.1) followed by median centered normalization

source_name: patient derived primary tracheal basal cell line

label_protocol: Biotinylated cDNA were prepared with the Illumina 96 RNA prep Kit (LifeTech)

growth_protocol: Primary tracheal basal cells were grown in LHC9 media on type I collagen-coated Petri dishes.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser using RNA Nano Kit (Agilent).

treatment_protocol: Cells were treated with either empty lentiviral vector, Lenti-SOX2 and Lenti-SOX2 with 2.5 uM BMK120.

tag: patient

value: Patient 158 derived line 2

value: SOX2-lentiviral vector

tag: cell type

value: primary tracheal basal cell line


title: Roots at Bulk BS treatment, biological rep 2

description: Gene expression data from roots of Medicago following 30 days exposure to bulk metals added biosolids amended soil

source_name: Medicago_roots_bulk 2.CEL

value: bulk biosolids amended soil (Bulk BS)


title: RNA obtained from a. Patient replicate 158 SOX2

description:
Tracheal basal cell-line treated with a SOX2 lentiviral vector
Sample 5

value: Patient 158 derived line 1


title: Roots at Bulk BS treatment, biological rep 1

source_name: Medicago_roots_bulk 1.CEL


title: shoots at Nano BS treatment, biological rep 3

description: Gene expression data from shoots of Medicago following 30 days exposure to metal nanoparticle mixture added biosolids amended soil

source_name: Medicago_shoots_nano 3.CEL

value: shoots


title: Roots at control BS treatment, biological rep 3

description: Gene expression data from roots of Medicago following 30 days exposure to control biosolids amended soil

source_name: Medicago_roots_control 3.CEL

value: control biosolids amended soil (control BS)


title: NA20771 Replicate 1


title: RNA obtained from a. Patient replicate 158_2 SOX2_BKM120

description:
Tracheal basal cell-line treated with a SOX2 lentiviral vector and a PI3K inhibitor (BMK120)
Sample 9

value: SOX2-lentiviral vector and a PI3K inhibitor (BKM120)


title: Roots at Bulk BS treatment, biological rep 3

source_name: Medicago_roots_bulk 3.CEL


title: RNA obtained from a. Patient replicate 35 SOX2_BKM120

description:
Tracheal basal cell-line treated with a SOX2 lentiviral vector and a PI3K inhibitor (BMK120)
Sample 3

value: Patient 35


title: RNA obtained from a. Patient replicate 158 PMA

description:
Tracheal basal cell-line treated with an empty lentiviral vector
Sample 4

value: empty lentiviral vector


title: RNA obtained from a. Patient replicate 158 SOX2_BKM120

description:
Tracheal basal cell-line treated with a SOX2 lentiviral vector and a PI3K inhibitor (BMK120)
Sample 6


title: Roots at control BS treatment, biological rep 2

source_name: Medicago_roots_control 2.CEL


title: RNA obtained from a. Patient replicate 35 SOX2

description:
Tracheal basal cell-line treated with a SOX2 lentiviral vector
Sample 2


title: shoots at Nano BS treatment, biological rep 2

source_name: Medicago_shoots_nano 2.CEL


title: Roots at control BS treatment, biological rep 1

source_name: Medicago_roots_control 1.CEL


title: Hut78 CTCL cell line treated with a vehicle control  Control_4

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

description: replicate 4

data_processing: The data were normalised using the default quantile normalisation with R/bioconductor package lumi version 2.15.1

source_name: Cultured cells of CTCL cell line isolated from a patient with Sézary Syndrome

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

growth_protocol: Hut78 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2mM glutamine, 100U/mL penicillin, 100mg/mL streptomycin, and 2.5 mg/mL amphotericin B. Cells were maintained in a 37°C incubator at 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The cells were treated with a combination of Enzastaurin (4μM) and AR-A014418 (5μM), each compound alone, and a vehicle control (note: both compounds are diluted in DMSO).

tag: tumor

value: Cutaneous T-Cell Lymphoma

value: vehicle control


title: Bulk tumor cells A

description: Glioblastoma


title: RNA obtained from a. Patient replicate 35 PMA

description:
Tracheal basal cell-line treated with an empty lentiviral vector
Sample 1


title: RNA obtained from a. Patient replicate 158_2 PMA

description:
Tracheal basal cell-line treated with an empty lentiviral vector
Sample 7


title: Hut78 CTCL cell line treated with DMSO DMSO_4

description: replicate 4

value: DMSO


title: Hut78 CTCL cell line treated with Enzastaurin (4μM)  Enz_4

description: replicate 4

value: Enzastaurin (4μM)


title: NA20769 Replicate 1


title: NA20770 Replicate 1


title: NA20767 Replicate 1


title: shoots at Bulk BS treatment, biological rep 3

description: Gene expression data from shoots of Medicago following 30 days exposure to bulk metals added biosolids amended soil

source_name: Medicago_shoots_bulk 3.CEL


title: NA20768 Replicate 1


title: shoots at Nano BS treatment, biological rep 1

source_name: Medicago_shoots_nano 1.CEL

value: nano biosolids amended soil (Nano BS)


title: Hut78 CTCL cell line treated with AR-A014418 (5μM) ARA_4

description: replicate 4


title: NA20766 Replicate 1


title: NA20765 Replicate 1


title: Hut78 CTCL cell line treated with Enzastaurin (4μM)  Enz_3

description: replicate 3


title: Hut78 CTCL cell line treated with DMSO DMSO_3

description: replicate 3


title: shoots at Bulk BS treatment, biological rep 2

source_name: Medicago_shoots_bulk 2.CEL


title: Hut78 CTCL cell line treated with Enzastaurin (4μM) and AR-A014418 (5μM) Enz+ARA_3

description: replicate 3

value: Enzastaurin (4μM) and AR-A014418 (5μM)


title: Hut78 CTCL cell line treated with Enzastaurin (4μM) and AR-A014418 (5μM) Enz+ARA_2

description: replicate 2


title: NA20764 Replicate 1


title: Hut78 CTCL cell line treated with AR-A014418 (5μM) ARA_3

description: replicate 3


title: Hut78 CTCL cell line treated with a vehicle control  Control_3

description: replicate 3


title: Hut78 CTCL cell line treated with Enzastaurin (4μM) and AR-A014418 (5μM) Enz+ARA_4

description: replicate 4


title: shoots at control BS treatment, biological rep 3

description: Gene expression data from shoots of Medicago following 30 days exposure to control biosolids amended soil

source_name: Medicago_shoots_control 3.CEL


title: shoots at control BS treatment, biological rep 2

source_name: Medicago_shoots_control 2.CEL


title: shoots at Bulk BS treatment, biological rep 1

source_name: Medicago_shoots_bulk 1.CEL


title: shoots at control BS treatment, biological rep 1

source_name: Medicago_shoots_control 1.CEL


title: Hut78 CTCL cell line treated with DMSO DMSO_2

description: replicate 2


title: Hut78 CTCL cell line treated with Enzastaurin (4μM)  Enz_1

description: replicate 1


title: Hut78 CTCL cell line treated with a vehicle control  Control_2

description: replicate 2


title: ES2i_GFP_IP_3

city: Utrecht

first: Niels

last: Geijsen

address: Uppsalalaan 8

institute: Hubrecht Institute

description: immunoprecipitated RNA

hyb_protocol: hybridization was done following the Agilent protocols in Agilent hybridization chambers and incubator

scan_protocol: Slides were scanned in Agilent scanner following manufacturer's protocols

data_processing: Data were analyzed with GeneSifter online tools

source_name: mouse Dazl-GFP ES in 2i condition, RNA-IP with anti-GFP antibody

label_protocol: RNA was labeled and amplififed following Agilent One-Color protocols

growth_protocol: A re-derived transgenic mouse ES cell lines Dazl-GFP cultured on γ-irradiated feeder MEFs in DMEM containing 15% FBS supplemented with leukemia inhibitory factor (LIF) and 2i inhibitors 1µM MEK inhibitor PD0325901 (Axon Medchem), and 3 µM GSK3β inhibitor CHIR99021. Cells were harvested and subjected to native RNA-IP with anti-PABP1 antibodies or anti-GFP antibodies

extract_protocol: total and immunoprecipitated RNA was extracte with TRIZOL reagent following manufacturer's protocols

value: Dazl-GFP (a re-derived transgenic ES cell line)

tag: growth protocol

value: cultured on γ-irradiated feeder MEFs in DMEM containing 15% FBS supplemented with LIF and 2i inhibitors (MEK inhibitor PD0325901 and GSK3β inhibitor CHIR99021)

tag: rip antibody

value: anti-GFP antibody


title: ES2i_GFP_IP_2

description: immunoprecipitated RNA


title: Hut78 CTCL cell line treated with DMSO DMSO_1

description: replicate 1


title: Hut78 CTCL cell line treated with a vehicle control  Control_1

description: replicate 1


title: Hut78 CTCL cell line treated with Enzastaurin (4μM)  Enz_2

description: replicate 2


title: ES2i_GFP_IP_1

description: immunoprecipitated RNA


title: Hut78 CTCL cell line treated with AR-A014418 (5μM) ARA_2

description: replicate 2


title: NA20762 Replicate 1


title: NA20763 Replicate 1


title: Hut78 CTCL cell line treated with Enzastaurin (4μM) and AR-A014418 (5μM) Enz+ARA_1

description: replicate 1


title: NA20761 Replicate 1


title: Hut78 CTCL cell line treated with AR-A014418 (5μM) ARA_1

description: replicate 1


title: NA20760 Replicate 1


title: NA20759 Replicate 1


title: NA20758 Replicate 1


title: NA20757 Replicate 1


title: NA20756 Replicate 1


title: HepG2_PBLD_3

city: Guangzhou

first: Aimin

last: Li

state: Guangdong

address: Department of Gastroenterology and Hepatology, Guangzhou First Municipal People's Hospital, Guangzhou Medical University

department: Gastroenterology

institute: Guangzhou Medical University

description: PBLD

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. The  expression values for all the probes for each sample were scaled to have median 256 (28) and then log (base 2) transformed before performing statistical analysis.

source_name: HepG2 cells

label_protocol: Total RNA was labled with the Ambion TotalPrep RNA Amplification Kit according to manufacturers suggested protocols.

extract_protocol: Cells were collected and were immediately lysed in Trizol reagent (Invitrogen, Carlsbad, California). Additional purification was performed on RNeasy columns (Qiagen, Valencia, CA 913555, cat. no. 74104).  The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: PBLD overexpressed


title: HepG2_PBLD_1

description: PBLD


title: ES2i_Input_3

source_name: mouse Dazl-GFP ES in 2i condition input for RNA-IP

value: none (input)


title: HepG2_control_2

description: control

value: control


title: VUMC-Rb-19

description: fresh frozen Rb material from a randomly selected cohort

source_name: primary Rb tissue

value: primary Rb tissue

tag: uhc-subgroup

value: group 3


title: ES2i_PABP1_IP_1

description: immunoprecipitated RNA

source_name: mouse Dazl-GFP ES in 2i condition, RNA-IP with anti-PABP1 antibody

tag: cell line

value: anti-PABP1 antibody


title: HepG2_control_1

description: control


title: HepG2_PBLD_2

description: PBLD


title: NA20755 Replicate 1


title: HepG2_control_3

description: control


title: WT_salt_12h_rep1

city: Taipei

first: Pei-Shan

last: Chien

address: 128 Academia Road, Section 2, Nankang

department: ABRC

institute: Academia Sinica

description: Gene expression of wild-type Ler after 125mM NaCl treatment for 12 h

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Arabidopsis V4 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing the microarrays are scanned with an Agilent microarray scanner G2565CA (Agilent Technologies, USA) at 535 nm for Cy3. The array image was analyzed by the Feature Extraction software version 10.7.1.1 using the default setting.

data_processing: Raw data of hybridization were imported into microarray analysis software GeneSpring 11.5 (Agilent Technologies), and the data of Ler subjected to medium alone was used as a control for normalization.

organism: Arabidopsis thaliana

source_name: WT (Ler), 125mM NaCl, 12h, replicate 1

label_protocol: Cy3 labeling (CyDye, Agilent Technologies, USA) was performed  during the in vitro transcription process. 1.65 μg of Cy3-labled cRNA was fragmented at 60°C for 30 minutes.

growth_protocol: Seeds were surface sterilized with 30% bleach (CLOROX) for 8 minutes and then washed with sterilized ddH2O 5 times. Seeds were germinated on half-strength Murashige and Skoog (1/2 MS) medium under a 16 h photoperiod (80-100 μmol•m−2•s−1 illumination) at 22°C.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s recommendations followed by DNase treatments at 37°C for 15 minutes with RQ1 RNase-free DNase (Promega, Madison, WI, USA) to remove the contamination of genomic DNA. Equal volume of Phenol:Chloroform:Isoamyl Alcohol (25:24:1; Sigma, St. Louis, MO, USA) was added to remove the contaminants of protein and DNA, and total RNA was precipitated by ethanol. Quality control of total RNA was determined by Agilent Bioanalyzer 2100 (Agilent Technologies, St. Clara, CA, USA). Total RNA (0.2 μg) was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies).

treatment_protocol:
125mM NaCl treatment for 12 h
Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: whole seedlings

tag: genotype

value: wild type

tag: strain

value: Landsberg erecta


title: ES2i_PABP1_IP_2

description: immunoprecipitated RNA


title: WT_salt_12h_rep3

source_name: WT (Ler), 125mM NaCl, 12h, replicate 3

tag: age


title: proatcape1_salt_12h_rep1

description: Gene expression of proatcape1 mutant  after 125mM NaCl treatment for 12 h

source_name: proatcape1, 125mM NaCl, 12h, replicate 1

value: proatcape1 mutant


title: proatcape1_control_rep3

description: Gene expression of proatcape1 mutant without salt treatment

source_name: proatcape1, 1/2 MS treatment, 0h, replicate 3

treatment_protocol:
no salt
Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.


title: proatcape1_salt_12h_rep3

source_name: proatcape1, 125mM NaCl, 12h, replicate 3


title: NA20754 Replicate 1

extract_protocol: We did not perform the extraction in house. We received DNA samples from Coriell. This is the information available on their website for DNA extraction: gDNA is purified from fresh blood, immortalized lymphocyctes or fibroblasts using the Qiagen Autopure LS instrument according to the manufacturer’s instructions or manually by modified Miller’s Salting out procedures.


title: BNDazlD10

data_processing:
Data were analyzed with GeneSifter online tools
Background subtracted signals were uploaded into Genesifter and normalized to median values. Genesifter output is available on the series record.

source_name: mouse ES in 2i condition, Day 10

growth_protocol: Two independent mouse ES cell lines, Dazl-GFP and Stella-GFP, were cultured on γ-irradiated feeder MEFs in DMEM containing 15% FBS or serum-free B27N2 medium both supplemented with leukemia inhibitory factor (LIF) (Ying 2008). For the 2i experiments, 1µM MEK inhibitor PD0325901 (Axon Medchem), and 5 µM GSK3β inhibitor Kenpaullone (Tocris), were used. Cells were harvest at 0, 3 and 10 days in each condition for expression microarray analysis.

extract_protocol: Total RNA was extracte with TRIZOL reagent following manufacturer's protocols

value: ES cells

tag: gfp-construct

value: Dazl-GFP


title: proatcape1_salt_12h_rep2

source_name: proatcape1, 125mM NaCl, 12h, replicate 2


title: NA20753 Replicate 1

data_processing: Images were processed using Agilent Feature Extraction Software (version 10.5.1.1)


title: proatcape1_control_rep1

source_name: proatcape1, 1/2 MS treatment, 0h, replicate 1


title: BNDazlD3

source_name: mouse ES in 2i condition, Day 3


title: BNDazlD0

source_name: mouse ES in 2i condition, Day 0


title: WT_salt_12h_rep2

source_name: WT (Ler), 125mM NaCl, 12h, replicate 2


title: WT_control_rep3

description: Gene expression of wild-type Ler without salt treatment

source_name: WT (Ler), 1/2 MS treatment, 0h, replicate 3


title: NA20752 Replicate 1


title: ES2i_Input_2


title: WT_control_rep2

source_name: WT (Ler), 1/2 MS treatment, 0h, replicate 2


title: WT_control_rep1

source_name: WT (Ler), 1/2 MS treatment, 0h, replicate 1


title: BNStellaD10

value: Stella-GFP


title: NA20589 Replicate 1


title: proatcape1_control_rep2

source_name: proatcape1, 1/2 MS treatment, 0h, replicate 2


title: NA20588 Replicate 1


title: BNStellaD3


title: NA20587 Replicate 1


title: NA20586 Replicate 1


title: FBSDazlD10

source_name: mouse ES in FBS condition, Day 10


title: BNStellaD0


title: NA20585 Replicate 1


title: FBSDazlD3

source_name: mouse ES in FBS condition, Day 3


title: buk_solventogenesis_rep3

city: Toulouse

first: Philippe

last: Soucaille

address: 135 avenue de Rangueil

country: France

institute: INSA Toulouse

hyb_protocol: Hybridization followed a one-color microarray-based gene expression analysis protocol (Agilent)

scan_protocol: The slides were scanned using a Tecan MS200 scanner.

data_processing: The scanned slides were analyzed using Feature Extraction V.11.5.1.1.

organism: Clostridium acetobutylicum ATCC 824

source_name: Chemostat culture

label_protocol: The RNAs were labeled with a Low Input Quick Amp Labeling kit (Agilent)

growth_protocol: The culture conditions described previously by Vasconcelos et al. (Vasconcelos I, et al. J Bacteriol. 1994; 176, 1443-1450.) and Girbal et al. (Girbal L, Soucaille P.  J Bacteriol. 1995; 176,6433-6438.) were used for the phosphate-limited continuous culture of C. acetobutylicum, fed with a constant total carbon amount of 995 mM. The cultures were maintained under acidogenesis (pH 6.3, 995 mM of carbon from glucose), solventogenesis (pH 4.4, 995 mM of carbon from glucose) and alcohologenesis (pH 6.3, 498 mM of carbon from glucose and 498 mM of carbon from glycerol).

extract_protocol: RNA was extracted using an RNeasy Midi kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions with supplementation of DNase treatment using RNase-Free DNase Set (Qiagen). RNA quantity and quality evaluations were performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France) and a NanoDrop ND-1000 spectrophotometer (Labtech France, Paris, France) at 260 nm and 280 nm.

treatment_protocol: Immediately frozen in liquid nitrogen

tag: genotype/variation

value: Δbuk

tag: condition

value: solventogenesis


title: adhE1_alcohologenesis_rep3

value: alcohologenesis


title: adhE2_alcohologenesis_rep3


title: ES2i_Input_1

source_name: mouse Dazl-GFP ES in 2i condition input for RNA-IP

value: Dazl-GFP (a re-derived transgenic ES cell line)

value: cultured on γ-irradiated feeder MEFs in DMEM containing 15% FBS supplemented with LIF and 2i inhibitors (MEK inhibitor PD0325901 and GSK3β inhibitor CHIR99021)


title: ctrl_acidogenesis_rep3

value: ctrl

value: acidogenesis


title: buk_acidogenesis_rep3


title: adhE1_acidogenesis_rep3


title: ctrl_alcohologenesis_rep3


title: ctrl_solventogenesis_rep3


title: Control leaf vs transgenic NROB  leaf  Replicate 1

city: wuhan

first: Hong

middle: li

last: Yang

state: Hubei

address: xudong 2 road

department: Oil Crops Research Institute

institute: Chinese Academy of Agricultural Sciences

description: Biological replicate 1 of 2.

hyb_protocol: Each Slide was hybridized with 0.825μg Cy3‐labeled cRNA and 0.825μg Cy‐5  labeled cRNA using Gene Expression Hybridization Kit (Cat#5188‐5242, Agilent  technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent  technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.  After 17 hours hybridization, slides were washed in staining dishes (Cat#121, ThermoShandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188‐5327,  Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution  (Cat#5185‐5979, Agilent technologies, Santa Clara, CA, US) followed the  manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent  technologies, Santa Clara, CA, US) with default settings, Dye channel:  Red&Green ,Scan resolution=3μm, 20bit. and Feature Extraction software 10.7  (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by  Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software  11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Arabidopsis thaliana Columbia-0 control leaf

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,  Two‐Color (Cat#5190‐2306, Agilent technologies, Santa Clara, CA, US), followed the  manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit  (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Transgenic Arabidopsis plants, WT (wild type) were in the Arabidopsis thaliana Columbia-0 (Col-0) background and were grown in a standard greenhouse with a continuous artificial light period of 16h (22℃) and a dark period of 8h (20℃) at a photon flux density of 100–120 µmol m-2 s.-1

extract_protocol: Total RNA was extracted using the RNeasy plant mini kit (Qiagen)

value: wildtype

tag: cultivar

value: leaf

value: Day after growth 30

source_name: Arabidopsis thaliana Columbia-0 transgenic leaf

value: 35S:NROB #2


title: FBSDazlD0

source_name: mouse ES in FBS condition, Day 0


title: NA20581 Replicate 1

city: Farmington

first: Charles

last: Lee

address: 10 Discovery Dr.

institute: Jackson Laboratory for Genomic Medicine

label_protocol: 1 to 1.5 ug of genomic DNA was digested using AluI and RsaI for 2 hours at 37 °C followed by a 20 minute enzyme-inactivation step at 65 °C. DNA was then labeled with Cyanine-3-dUTP (Reference samples) or Cyanine-5-dUTP (Test samples) at 37 °C for 2 hours followed by a 10 minute enzyme-inactivation step at 65 °C.

growth_protocol: We did not perform the growth in house. We received DNA samples from Coriell. This is the information available on their website for the cell culture of NA10851: Split ratio 1:2, Temperature: 37C, Percent CO2: 5%, Percent O2: Ambient, Medium: Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, Serum: 15% fetal bovine serum Not Inactivated

tag: coriell cell line


title: adhE2_solventogenesis_rep3


title: adhE1_solventogenesis_rep3


title: buk_acidogenesis_rep2


title: FBSStellaD3


title: adhE1_acidogenesis_rep2


title: NA20582 Replicate 1


title: ctrl_solventogenesis_rep2


title: FBSStellaD10


title: FBSStellaD0


title: Control leaf vs transgenic NROB  leaf  Replicate 2

description: Biological replicate 2 of 2.

tag: tissue


title: adhE2_acidogenesis_rep3


title: ctrl_alcohologenesis_rep2


title: control_UNBS_9h_rep4

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: Biological replicate 4 of 4.  untreated vs UNBS-treated U937 cells at time point 9 hrs

hyb_protocol: 750ng of each cRNA were fragmented in the fragmentation buffer, in presence of blocking agent. Subsequently, samples were hybridized with hybridization buffer on microarrays slides in a Surhyb gasket for 17h at 65°C

scan_protocol: Slides were scanned by an Axon 4100A microarray scanner. Images analysis and fluorescence quantification were performed using Axon GenePix Pro software version 6.1

data_processing: Data were processed in the R statistical environement using the Limma package. Background correction was performed using the normexp method and normalization was performed using Loess. Between-array normalization was performed using Aquantile method.

source_name: U397, control, 9h

label_protocol: Labeling was perfomed according to the manufacturer’s protocol, using 200ng of total RNA for the preparation of cDNA probes and Cy5- and Cy3-labeled cRNA probes (Low RNA Input Linear Amplification Kit, PLUS, Two-Color).

growth_protocol: U937 cells (human histiocytic lymphoma, DSMZ) were cultured in RPMI 1640 medium containing 10% (v/v) of fetal calf serum, 1% (v/v) of antibiotic-antimycotic and 2mM of L-glutamine at 37°C, 5% CO2.

extract_protocol: Total RNA was extracted from a batch of 2x106 to 5x106 cells by TRIzol and cleanup was performed with the RNeasy Mini Kit (Qiagen). Quantification of RNA was assessed by using Nanodrop.  RNA integrity value was verified using an Agilent Bioanalyzer 2100.

treatment_protocol: Treatments with 20 nM UNBS1450 were started in the exponential growth phase, 24 h after seeding with 2x106 cells. The stop of cell treatment were performed after 0, 3, 6 and 9 h; a control sample was performed for each time point.

tag: agent

tag: time

source_name: U397, treated, 9h

value: UNBS


title: ctrl_acidogenesis_rep2


title: NA20543 Replicate 1

scan_protocol: Slides were scanned on an Agilent G2505C scanner (version A.8.5.1).


title: NA20542 Replicate 1


title: NA20541 Replicate 1


title: NA20544 Replicate 1


title: ctrl_acidogenesis_rep1


title: control_UNBS_3h_rep4

description: Biological replicate 4 of 4.  untreated vs UNBS-treated U937 cells at time point 3 hrs

source_name: U397, control, 3h

source_name: U397, treated, 3h


title: adhE2_acidogenesis_rep2


title: NA20539 Replicate 1


title: control_UNBS_6h_rep4

description: Biological replicate 4 of 4.  untreated vs UNBS-treated U937 cells at time point 6 hrs

source_name: U397, control, 6h

source_name: U397, treated, 6h


title: NA20538 Replicate 1


title: control_UNBS_0h_rep4

description: Biological replicate 4 of 4.  untreated vs UNBS-treated U937 cells at time point 0 hrs

source_name: U397, control, 0h

source_name: U397, treated, 0h


title: IkBa-SR NGPS Fibroblasts

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Gene 2.0 ST Array according to the protocols recommended by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix, Inc.).

data_processing:
After scanning, raw data (Affymetrix CEL files) were processed with Affymetrix Expression Console using default settings.
"Full" exons were included in the analysis.

source_name: Ikappa B alpha-transduced NGPS fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fibroblasts were grown at 37 ºC, 5% CO2, under standard conditions.

treatment_protocol: Cells were treated with 0.2 mM sodium salicylate for 96 h before RNA extraction.

tag: disease state

value: Nestor-Guillermo Progeria Syndrome (NGPS)

tag: cell type

value: fibroblasts

tag: treatment

value: Ikappa B alpha-transduced


title: ctrl_solventogenesis_rep1


title: NA20535 Replicate 1

hyb_protocol: Labeled samples were purified using Agilent SureTag Purification columns. Test and reference samples were combined with Agilent Oligo aCGH/ChIP-on-Chip Blocking Agent, Agilent Hi-RPM Hybridization Buffer and Cot-1 DNA and applied to microarrays enclosed in Agilent Hybridization Chamber. After 40 hour incubation at 67 °C, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 and 2.

treatment_protocol: We, nor Coriell, did not perform any treatment on the samples. We received DNA samples from Coriell.


title: NA20540 Replicate 1


title: control_UNBS_9h_rep3

description: Biological replicate 3 of 4.  untreated vs UNBS-treated U937 cells at time point 9 hrs


title: buk_alcohologenesis_rep3


title: buk_alcohologenesis_rep2


title: Untreated NGPS Fibroblasts

source_name: Untreated NGPS fibroblasts


title: NaS NGPS Fibroblasts

source_name: Sodium salicylate-treated NGPS fibroblasts

value: sodium salicylate


title: adhE1_acidogenesis_rep1


title: UNBS_control_9h_rep2

description: Biological replicate 2 of 4. UNBS-treated vs. untreated U937 cells at time point 9 hrs


title: control_UNBS_6h_rep3

description: Biological replicate 3 of 4.  untreated vs UNBS-treated U937 cells at time point 6 hrs


title: NA20534 Replicate 1


title: control_UNBS_3h_rep3

description: Biological replicate 3 of 4.  untreated vs UNBS-treated U937 cells at time point 3 hrs


title: adhE2_alcohologenesis_rep1


title: NA20533 Replicate 1


title: adhE2_alcohologenesis_rep2


title: control_UNBS_0h_rep3

description: Biological replicate 3 of 4.  untreated vs UNBS-treated U937 cells at time point 0 hrs


title: adhE1_alcohologenesis_rep2


title: UNBS_control_6h_rep2

description: Biological replicate 2 of 4. UNBS-treated vs. untreated U937 cells at time point 6 hrs


title: NA20532 Replicate 1


title: UNBS_control_3h_rep2

description: Biological replicate 2 of 4. UNBS-treated vs. untreated U937 cells at time point 3 hrs


title: NA20531 Replicate 1


title: NA20530 Replicate 1


title: NA20529 Replicate 1


title: NA20528 Replicate 1


title: UNBS_control_9h_rep1

description: Biological replicate 1 of 4. UNBS-treated vs. untreated U937 cells at time point 9 hrs


title: adhE2_acidogenesis_rep1


title: UNBS_control_0h_rep2

description: Biological replicate 2 of 4. UNBS-treated vs. untreated U937 cells at time point 0 hrs


title: adhE1_solventogenesis_rep2


title: NA20527 Replicate 1


title: UNBS_control_3h_rep1

description: Biological replicate 1 of 4. UNBS-treated vs. untreated U937 cells at time point 3 hrs


title: buk_solventogenesis_rep2


title: adhE1_alcohologenesis_rep1


title: NA20526 Replicate 1


title: buk_solventogenesis_rep1


title: buk_acidogenesis_rep1


title: UNBS_control_6h_rep1

description: Biological replicate 1 of 4. UNBS-treated vs. untreated U937 cells at time point 6 hrs


title: postnatal day 1 (p1), biological rep3

first: Xinjun

last: He

address: 1425 San Pablo St

department: BROAD CIRM Center

institute: University of Southern California

hyb_protocol: Following fragmentation, 25ul of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned with GeneChip Scanner 3000 (Affymetrix) to generate image and CEL files, using Affymetrix default analysis settings and global scaling as normalization method

data_processing: Data analysis was performed by loading CEL files into the statistical computing language R software, and probes were normalized using robust multi-array average (RMA) (CDF: MoGene10stv1_Mm_REFSEQ_14.1.0)

source_name: postnatal day 1 (p1)_Rib Chondrocyte

label_protocol: Three hundred ng of total RNA were labeled for each sample using the GeneChip WT cDNA Synthesis and Amplification Kit and WT Terminal Labeling Kit (900673 and 900671; Affymetrix)

growth_protocol: Neonatal ICR wild-type mice embryonic day 17.5 nasal septum or postnatal day 1 rib

extract_protocol: Embryonic day 17.5 (E17.5) nasal septum or postnatal day 1 (p1) rib chondrocytes isolated from wild-type ICR mice were subject to Trizol total RNA isolation.  Isolated RNAs were digested with DNAse I.

treatment_protocol: Wild type, not treated

value: ICR

tag: developmental stage/age

value: postnatal day 1

value: Rib Chondrocyte


title: UNBS_control_0h_rep1

description: Biological replicate 1 of 4. UNBS-treated vs. untreated U937 cells at time point 0 hrs


title: NA20525 Replicate 1


title: postnatal day 1 (p1), biological rep1


title: buk_alcohologenesis_rep1

source_name: Chemostat culture

value: Δbuk

value: alcohologenesis


title: Embryonic day 17.5 (E17.5) Nasal Septum, biological rep3

source_name: Embryonic day 17.5_Nasal Septum

value: embryonic day 17.5

value: Nasal chondrocyte


title: Mac_MCF7-patient4-sample2

city: Goettingen

first: Annalen

last: Bleckmann

address: Robert-Koch-Straße 40

department: Hematology/Oncology

country: Germany

institute: University Medical Center Goettingen

description: Macrophage from patient 4 after co-culture with MCF-7, second sample

hyb_protocol: 1.65µg of each labeled cDNA sample were fragmented and applied onto Human GE 4x44K v2 (#G4112F, Agilent) microarrays. Hybridizations were performed for 17 hours at 10 rpm and 65°C in a hybridization oven (Agilent). Hybridizations were performed for 20 hours at 10 rpm and 65°C in a hybridization oven (Agilent).

scan_protocol: Cy3 intensities were detected by one-color scanning using the G2505B Agilent DNA microarray scanner at 5µm or 3µm resolution.

data_processing: Raw Median signal intensities were log2-transformed and quantile normalized.

source_name: Macrophage

label_protocol: Global gene expression analyses utilized the “Human GE 4x44K v2 Microarray Kit” (Agilent, Böblingen, Germany) and the QuickAmp Labeling Kit Cy3 One-Color (Agilent) as well as the RNA Spike-In Kit (Agilent). 500ng of total RNA were used as starting material for the synthesis of cDNA. Following in-vitro transcription, the quality and quantity of labeled RNA was determined using the NanoDrop D-1000 UV-VIS Spectrophotometer (Peqlab, Erlangen, Germany). For human miRNA microarray analyses, 200ng of total RNA were labeled using the miRNA Complete Labeling and Hyb Kit (Agilent).

extract_protocol: Total RNA for array experiments was isolated using TRIZOL reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Samples used for microarray experiments exhibited a RIN number greater than 7.5. Each RNA sample was then split into two aliquots that were either processed for the miRNA or the mRNA microarray.

treatment_protocol: The ER+ and PR+ human breast cancer cell line MCF-7 was purchased from DSMZ and maintained in RPMI-1640 medium (PAA Laboratories Inc., Cölbe, Germany) supplemented with 10% fetal calf serum (FCS, Invitrogen, Karlsruhe, Germany). Human macrophages were derived from mononuclear peripheral blood cells. Briefly, monocytes were obtained from buffy coats of healthy donors through double-density-gradient isolation. Macrophages were differentiated by culturing monocytes in fluorinated ethylene propylene-coated cell culture bags (CellGenix, Freiburg, Germany) in the presence of M-CSF (Immunotools, Friesoythe, Germany) for 7 days. For indirect co-culture experiments, macrophages were seeded in hanging cell culture inserts (0.4µm pore size, PET; Millipore, Billerica, MA, USA) and co-cultured with MCF-7 cells at a ratio of 2:1 under normoxia for 24 hours.

tag: coculture

value: coculture with MCF-7

tag: patient


title: NA20522 Replicate 1


title: NA20524 Replicate 1


title: adhE2_solventogenesis_rep2

value: solventogenesis


title: NA20521 Replicate 1


title: Embryonic day 17.5 (E17.5) Nasal Septum, biological rep2

city: Los Angeles


title: adhE1_solventogenesis_rep1


title: adhE2_solventogenesis_rep1


title: Mac_MCF7-patient2-sample1

description: Macrophage from patient 2 after co-culture with MCF-7, first sample


title: Mac_MCF7-patient1-sample1

description: Macrophage from patient 1 after co-culture with MCF-7, first sample


title: NA20520 Replicate 1


title: Embryonic day 17.5 (E17.5) Nasal Septum, biological rep1


title: NA20517 Replicate 1


title: Mac-patient4-sample1

description: Untreated macrophage from patient 4, first sample

value: control


title: NA20519 Replicate 1


title: NA20516 Replicate 1


title: NA20518 Replicate 1


title: NA20514 Replicate 1


title: postnatal day 1 (p1), biological rep2


title: NA20515 Replicate 1


title: NA20513 Replicate 1


title: Mac-patient1-sample1

description: Untreated macrophage from patient 1, first sample


title: NA20509 Replicate 1


title: NA20510 Replicate 1


title: NA20508 Replicate 1


title: NA20507 Replicate 1


title: NA20504 Replicate 1


title: NA20506 Replicate 1


title: NA20505 Replicate 1


title: NA20502 Replicate 1


title: NA20362 Replicate 1


title: NA20503 Replicate 1


title: NA20412 Replicate 1


title: NA20357 Replicate 1


title: NA20355 Replicate 1


title: NA20359 Replicate 1


title: NA20351 Replicate 1


title: NA20356 Replicate 1


title: NA20344 Replicate 1


title: NA20346 Replicate 1


title: NA20342 Replicate 1


title: NA20340 Replicate 1


title: NA20512 Replicate 1


title: NA20341 Replicate 1


title: NA20511 Replicate 1


title: NA20336 Replicate 1


title: NA20322 Replicate 1


title: NA20332 Replicate 1


title: NA20321 Replicate 1


title: NA20334 Replicate 1


title: NA20320 Replicate 1


title: NA20318 Replicate 1


title: NA20314 Replicate 1


title: NA20299 Replicate 1


title: NA20348 Replicate 1


title: NA20317 Replicate 1


title: NA20298 Replicate 1


title: NA20294 Replicate 1


title: NA20287 Replicate 1


title: NA20282 Replicate 1


title: NA20281 Replicate 1


title: NA20291 Replicate 1


title: NA20339 Replicate 1


title: NA20274 Replicate 1


title: NA20276 Replicate 1


title: NA20278 Replicate 1


title: NA20126 Replicate 1


title: NA20127 Replicate 1


title: NA19984 Replicate 1


title: NA19982 Replicate 1


title: NA19985 Replicate 1


title: NA19923 Replicate 1


title: NA19920 Replicate 1


title: NA19921 Replicate 1


title: NA20296 Replicate 1


title: NA19916 Replicate 1


title: NA20289 Replicate 1


title: NA19917 Replicate 1


title: NA20536 Replicate 1


title: NA19908 Replicate 1


title: NA19904 Replicate 1


title: NA19914 Replicate 1


title: NA19922 Replicate 1


title: NA19909 Replicate 1


title: NA19900 Replicate 1


title: NA19835 Replicate 1


title: NA19834 Replicate 1


title: NA19901 Replicate 1


title: NA19913 Replicate 1


title: NA19819 Replicate 1


title: NA19795 Replicate 1


title: NA19818 Replicate 1


title: NA19794 Replicate 1


title: NA19789 Replicate 1


title: NA19792 Replicate 1


title: NA19788 Replicate 1


title: NA19785 Replicate 1


title: NA19783 Replicate 1


title: NCI-H1975 parental cells vs pooled DNA 10 individuals

city: Amsterdam

first: Elena

last: Galvani

address: De Boelelaan 1117

department: Medical Oncology

institute: VU University Medical Center

description: Control NCI-H1975 cells, untreated, harvested for DNA extraction 3 passages after thawing vs pooled DNA 10 individuals

hyb_protocol: Agilent SurePrint G3 Human CGH Microarray Kit for the 4x180K Agilent platform (Agilent Technologies, Santa Clara, CA) was used for DNA hybridization

scan_protocol: Images were scanned using an Agilent microarray scanner G2565AA and quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and normalization.

source_name: NCI-H1975 (CRL-5908) parental cells

label_protocol: Enzo’s CGH Labeling Kit for Oligo Arrays (Enzo Life Sciences, Farmingdale, NY) was used following manufacturer's instructions

growth_protocol: NCI-H1975, H1975CR and H1975CRv2cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% Pen/strep (50 IU/ml penicillin, 50 µg/ml streptomycin) in a humidified atmosphere of 5% CO2 and 95% air at 37 °C

extract_protocol: Genomic DNA was extracted using Ambion®-RecoverAll kit (Life Technologies, Breda, The Netherlands) following manufacturer's istructions

tag: cell line

value: lung cells

source_name: healthy volunteers

tag: sample type

value: reference DNA 10 individuals


title: CNX-2006-resistant cells variant 1 (H1975CR) vs pooled DNA 10 individuals

description: H1975CR cells, untreated for 3 passages before DNA extraction vs pooled DNA 10 individuals

source_name: NCI-H1975 (CRL-5908) CNX-2006-resistant cells variant 1 (H1975CR)


title: NA19782 Replicate 1


title: NA19780 Replicate 1


title: NA19786 Replicate 1


title: Zyxin-null VSMCs, stretched, biological rep3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from stretched Zyxin-null VSMCs

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with JMP Genomics V. 6 from SAS. Gene expression profiling was performed using arrays of from Affymetrix. A Custom CDF with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

label_protocol: Fifteen μl (corresponding to 5-10 μg total RNA) of each biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Primary mouse aortic vascular smooth muscle cells were grown on flexible membranes in presence of DMEM medium supplemented with 15% FCS in an incubator at 37 degree C and 5% CO2.

extract_protocol: Total RNA was isolated using a kit from Qiagen and tested for quality.   sample were delivered for microarray analysis.

treatment_protocol: Cells were stretched to 10% cyclic elongation for 6 hours at a frequency of 0.5 Hertz. Static, unstretched cells were used as a control.

tag: genotype

value: zyxin KO

value: vascular smooth muscle cells

value: stretched

tag: genetic background


title: Zyxin-null VSMCs, stretched, biological rep2


title: NA19779 Replicate 1


title: Wild type VSMCs, stretched, biological rep3

description: Gene expression data from stretched wild type VSMCs

value: WT


title: NA19777 Replicate 1


title: Zyxin-null VSMCs, stretched, biological rep1


title: CNX-2006-resistant cells variant 2 (H1975CRv2) vs pooled DNA 10 individuals

description: H1975CRv2 cells, untreated for 3 passages before DNA extraction vs poled DNA 10 individuals

source_name: NCI-H1975 (CRL-5908)CNX-2006-resistant cells variant 2 (H1975CRv2)


title: Wild type VSMCs, stretched, biological rep2


title: NA19776 Replicate 1


title: NA19774 Replicate 1


title: NA19773 Replicate 1


title: Wild type VSMCs, stretched, biological rep1


title: NA19771 Replicate 1


title: Wild type VSMCs, static, biological rep3

description: Gene expression data from static wild type VSMCs

value: normal


title: NA19770 Replicate 1


title: Wild type VSMCs, static, biological rep1


title: Wild type VSMCs, static, biological rep2


title: NA19764 Replicate 1


title: Zyxin-null VSMCs, static, biological rep3

description: Gene expression data from static Zyxin-null VSMCs


title: NA19762 Replicate 1


title: Mac-patient2-sample1

description: Untreated macrophage from patient 2, first sample


title: Zyxin-null VSMCs, static, biological rep1


title: ctrl_alcohologenesis_rep1

tag: genotype/variation

value: ctrl


title: NA19761 Replicate 1


title: NA19759 Replicate 1


title: NA19758 Replicate 1


title: NA19756 Replicate 1


title: Patient17_Normal

city: Kaohsiung

first: Chun-Wei

last: Tung

address: No. 100, Shih-Chuan 1st Rd.

institute: Kaohsiung Medical University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm power 100 ) and quantify the fluoresence intensity.

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

source_name: adjacent normal tissues

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

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

tag: gender

value: Male


title: NA19755 Replicate 1


title: Patient16_Tumor

source_name: esophageal squamous cell carcinoma

value: esophageal squamous cell carcinoma


title: Patient16_Normal


title: NA19752 Replicate 1


title: Patient17_Tumor


title: Patient15_Tumor


title: NA19749 Replicate 1


title: FASR replicate 1

city: Darlinghurst

last: Zotenko

state: NSW

address: 384 Victoria St.

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Raw data was processed and normalized using Bioconductor's  minfi  package. Background correction was performed using preprocessIllumina(..., bg.correct = TRUE, normalize = controls, reference=1) function.

label: Cy5 and Cy3

source_name: FASR cell line

label_protocol: Standard Illumina protocol

growth_protocol: MCF-7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF-7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF-7 (TAM-R) cells were generated by the long-term culture of MCF-7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Fulvestrant-resistant MCF-7 (FAS-R) cells were generated by the long-term culture of MCF-7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and fulvestrant (1×10－7 M) (FAS). Long-term estrogen deprived MCF7 (MCF7X) cells were generated by the long-term culture of MCF-7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS. Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge/ estrogen deprivation exposure. All cell lines were  authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit according to manufacturer’s instructions.

tag: resistant phenotype

value: resistant

value: FASR cell line


title: Patient15_Normal


title: FASR replicate 2


title: NA19747 Replicate 1

tag: coriell cell line


title: NA19750 Replicate 1


title: NA19746 Replicate 1


title: Patient14_Tumor


title: Su(H) BG3 egta vs Input rep3

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

hyb_protocol: 34 µg labeled sample DNA and 34 µg labeled control DNA were combined, dried in a speed vac with medium heat and resuspended in 12.3 µl water.  For each hybridisation 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) were combined and 31.7µl added to each hybridisation sample. Samples were incubated at +95°C for 5 minutes, 42°C for 5 minutes and 41 µl loaded onto the array. The hybridisation was performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 18 hours. Post hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains. Signal for Cy3 and Cy5 channels are balanced using the histogram view in the GenePix software. Images are saved as Single-image TIFF.

data_processing:
Images are processed with NimbleScan software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Loess spatial correction was performed using the NimbleScan software, followed by quantile normalise between the arrays. The *.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package. The bed files were created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.
BG3_Ectrl_loess_quant-all_Ringo_hw300v5.sgr, BG3_Hctrl_loess_quant-all_Ringo_hw300v5.sgr, BG3_Ectrl_loess_quant-all_Ringo_normalNullzero_hw300v5g200FDR1_filtered.bed, BG3_Hctrl_loess_quant-all_Ringo_normalNullzero_hw300v5g200FDR1_filtered.bed
The *Ringo_hw300v5.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 2.14). The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

organism: Drosophila melanogaster

source_name: Su(H) BG3 egta replicate 3

label_protocol: Amplify the entire yield of ChIP and 10ng input by GenomePlex® Complete Whole Genome Amplification Kit (WGA2, Sigma) using two rounds of amplification (14 and 6 cycles). In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

growth_protocol: BG3 cells were cultured at 25 OC in Shields and Sang M3 insect medium, supplemented with 10% FBS (Sigma, F4135), 10 mg/L insulin (Sigma, I9278), and also 1x Antibiotic-Antimycotic.

extract_protocol: 1x10^7 cells treated with 4mM EGTA in HBSS (egta) or HBSS only (hbss) for 30min were fixed with 1% formaldehyde in culture medium for 12 min at 25C followed by quenching with 0.125 M glycine for 2 min. The cells were washed twice with ice-cold PBS and lysed in 500ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 20 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 150mM NaCl, Roche Complete inhibitor) and pre-cleared with 25 µl protein G agarose beads (pre-absorbed with BSA) and 2ug IgG for 2h at 4C. Protein G agarose beads (50 µl) were pre-bound with 2 µg of purified antibody for 6h at 4C. The chromatin supernatant with beads/antibody was then incubated overnight at 4C, the immune complexes were collected by centrifugation and washed for 5min at 4C with the following buffers: dilution buffer, IP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 50mM NaCl) (two washes), IP wash buffer 2 (1% NP-40 substitute, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.0, 250mM LiCl) (two washes) and TE (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted from the beads in 200 µl of fresh elution buffer (1% SDS, 100 mM NaHCO3) at 65C for 2 h with rotation and de-crosslinked by overnight incubation at 65C with addition of 10 ul 5M NaCl. Following the treatment with 1ul RNase A (10mg/ml) for 2h at 37C and 5ul proteinase K (10mg/ml) for 4h at 45C, genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by QiaQuick PCR purification (Qiagen).

treatment_protocol: BG3 cells were treated with 4mM EGTA in HBSS for 30min

tag: chip antibody

value: anti-Su(H) (Santa Cruz, sc-15813)

source_name: Total Input Su(H) BG3 egta replicate 3

value: none, input DNA


title: TAMR replicate 2

source_name: TAMR cell line

value: TAMR cell line


title: Patient14_Normal


title: MCF7X replicate 1

source_name: MCF7X cell line

value: MCF7X cell line


title: K56ac Kc egta vs Input rep1

data_processing:
Images are processed with NimbleScan software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Loess spatial correction was performed using the NimbleScan software, followed by quantile normalise between the arrays. For the K56ac Kc pbs experiment the quantile normalisation was perfromed across the sample and control channels separate and then the log ratio calculated. The *.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package. The bed files were created assuming a normalNull distribution centred around the mode and the resulting p-values were adjusted for multiple testing using the fdr method.
Kcr12_e_k56ac.sm_quant-sep_Ringo_hw300v5.sgr, Kcr12_h_k56ac.sm_quant-sep_Ringo_hw300v5.sgr, Kcr1_e_k56ac_quant-sep_normalNullmode_hw300v5g200FDR1.bed, Kcr1_h_k56ac_quant-sep_normalNullmode_hw300v5g200FDR1.bed, Kc_EGTA-Pbs-quantNorm.wig, Kc_EGTA-Pbs-2kb-peaks-FDR1.bed
The *Ringo_hw300v5.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 2.14). The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method. The difference between wildtype and N-activation H3K56ac signal was calculated as the subtraction of quantile normalised ChIP signal files (*quantNorm.wig). The *-2kb-peaks-FDR1.bed files were calculated as follows. All ChIP signal files were averaged over a 2kb window (in 200bp increments), and the noise distribution based on two replicates estimated. This noise distribution is used to call differentially enriched 2kb regions at 1% FDR, with overlapping 2kb regions merged together.

source_name: K56ac Kc egta replicate 1

label_protocol: Amplify 10ng of ChIP and input by GenomePlex® Complete Whole Genome Amplification Kit (WGA2, Sigma) using 14 cycles. In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

growth_protocol: Kc cells were cultured at 25 OC in Shields and Sang M3 insect medium (Sigma, S3652), supplemented with 5% FBS (Sigma, F9665), 1 g/L yeast extract (Oxoid, LP0021), 2.5 g/L bacto-peptone (BD Biosciences, 211677) and 1x Antibiotic-Antimycotic (Gibco, 15240-062).

extract_protocol: 5x10^6 cells treated with 4mM EGTA in PBS (egta) or PBS only (pbs) for 30min were fixed with 1% formaldehyde in culture medium for 12 min at 25C followed by quenching with 0.125 M glycine for 2 min. The cells were washed twice with ice-cold PBS and lysed in 500ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 20 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 150mM NaCl, Roche Complete inhibitor) and pre-cleared with 25 µl protein A agarose beads (pre-absorbed with BSA) and 2ug IgG for 2 h at 4C. The chromatin supernatant was then incubated overnight with 2 µg of purified antibody at 4C. After incubation with protein A agarose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed for 5min at 4C with the following buffers: dilution buffer, IP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 50mM NaCl) (two washes), IP wash buffer 2 (1% NP-40 substitute, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.0, 250mM LiCl) (two washes) and TE (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted from the beads in 200 µl of fresh elution buffer (1% SDS, 100 mM NaHCO3) at 65C for 2 h with rotation and de-crosslinked by overnight incubation at 65C with addition of 10 ul 5M NaCl. Following the treatment with 1ul RNase A (10mg/ml) for 2h at 37C and 5ul proteinase K (10mg/ml) for 4h at 45C, genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by QiaQuick PCR purification (Qiagen).

treatment_protocol: Kc cells treated with 4mM EGTA in PBS for 30min

value: anti-H3K56ac (Active Motif, 39281)

source_name: Total Input K56ac Kc egta replicate 1


title: MCF7 replicate 2

source_name: MCF7 cell line

value: responsive

value: MCF7 cell line


title: Su(H) BG3 egta vs Input rep1

source_name: Su(H) BG3 egta replicate 1

source_name: Total Input Su(H) BG3 egta replicate 1


title: Su(H) BG3 hbss vs Input rep1

source_name: Su(H) BG3 hbss replicate 1

treatment_protocol: BG3 cells were treated with HBSS for 30min

source_name: Total Input Su(H) BG3 hbss replicate 1


title: MCF7X replicate 2


title: Patient13_Tumor


title: NA19740 Replicate 1


title: TAMR replicate 1


title: Su(H) BG3 egta vs Input rep2

source_name: Su(H) BG3 egta replicate 2

source_name: Total Input Su(H) BG3 egta replicate 2


title: MCF7 replicate 1


title: NA19741 Replicate 1


title: K56ac BG3 hbss vs Input rep1

data_processing:
Images are processed with NimbleScan software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Loess spatial correction was performed using the NimbleScan software, followed by quantile normalise between the arrays. The *.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package. The bed files were created assuming a normalNull distribution centred around the mode and the resulting p-values were adjusted for multiple testing using the fdr method.
BG3r12_e56.sm_quant-all_Ringo_hw300v5.sgr, BG3r12_h56.sm_quant-all_Ringo_hw300v5.sgr, BG3r12_h56_quant-all_normalNullmode_hw300v5g200FDR1.bed, BG3r12_e56_quant-all_normalNullmode_hw300v5g200FDR1.bed, BG3_EGTA-Hbss-quantNorm.wig, BG3_EGTA-Hbss-2kb-peaks-FDR1.bed
The *Ringo_hw300v5.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 2.14). The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method. The difference between wildtype and N-activation H3K56ac signal was calculated as the subtraction of quantile normalised ChIP signal files (*quantNorm.wig). The *-2kb-peaks-FDR1.bed files were calculated as follows. All ChIP signal files were averaged over a 2kb window (in 200bp increments), and the noise distribution based on two replicates estimated. This noise distribution is used to call differentially enriched 2kb regions at 1% FDR, with overlapping 2kb regions merged together.

source_name: K56ac BG3 hbss replicate 1

extract_protocol: 5x10^6 cells treated with 4mM EGTA in HBSS (egta) or HBSS only (hbss) for 30min were fixed with 1% formaldehyde in culture medium for 12 min at 25C followed by quenching with 0.125 M glycine for 2 min. The cells were washed twice with ice-cold PBS and lysed in 500ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 20 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 150mM NaCl, Roche Complete inhibitor) and pre-cleared with 25 µl protein A agarose beads (pre-absorbed with BSA) and 2ug IgG for 2 h at 4C. The chromatin supernatant was then incubated overnight with 2 µg of purified antibody at 4C. After incubation with protein A agarose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed for 5min at 4C with the following buffers: dilution buffer, IP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 50mM NaCl) (two washes), IP wash buffer 2 (1% NP-40 substitute, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.0, 250mM LiCl) (two washes) and TE (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted from the beads in 200 µl of fresh elution buffer (1% SDS, 100 mM NaHCO3) at 65C for 2 h with rotation and de-crosslinked by overnight incubation at 65C with addition of 10 ul 5M NaCl. Following the treatment with 1ul RNase A (10mg/ml) for 2h at 37C and 5ul proteinase K (10mg/ml) for 4h at 45C, genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by QiaQuick PCR purification (Qiagen).

source_name: Total input K56ac BG3 hbss replicate 1


title: NA19735 Replicate 1


title: Patient13_Normal

source_name: adjacent normal tissues


title: NA19734 Replicate 1


title: Su(H) BG3 hbss vs Input rep2

source_name: Su(H) BG3 hbss replicate 2

source_name: Total Input Su(H) BG3 hbss replicate 2