title: OCI-LY3, Geldanamycin, 0.032 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Geldanamycin treatment with 0.032 uM concentration


title: OCI-LY3, Etoposide, 0.812 uM, 24hrs, Replicate3

status: Public on Sep 25 2014

type: RNA

city: New York

first: Mukesh

last: Bansal

state: NY

address: 1130 St. Nicholas Ave. Room 908

country: USA

institute: Columbia University

description: OCI-LY3 cell line profiled at 24hrs following Etoposide treatment with 0.812 uM concentration

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized on HG-U219 arrays in 120ul volume/well. The GeneTitan Hybridization, Wash and Stain kit (Affymetrix) was used for preparing hybridization mixes and automated processing of 96-array plates on the GeneTitan Instrument (Affymetrix).

scan_protocol: HG-U219 Array Plates were scanned on the GeneTitan instrument (Affymetrix) imaging device according to manufacturer's instructions.

data_processing: Determination of the signal values were obtained with GeneChip Command Console Software (AGCC) (Affymetrix). Raw data were normalized with the Robust Multichip Analysis (RMA) algorithm using BioConductor Affy Package.  Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm of the BioConductor Affy Package.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: cRNA synthesis and biotin-labelling was performed starting with 300 ng of total RNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) following manufacterer's protocol.

growth_protocol: OCI-LY3 cells were cultured under standard conditions in IMDM supplemented with 10% FCS.

extract_protocol: Total RNA was isolated from each well on an automated liquid handling system using the RNAqueous-96 Automated Kit (Ambion) following the manufacturer’s instructions. RNA quantification was performed by NanoDrop 8000 spectrophotometer and itd integrity evaluated by Agilent Bioanalyser.

treatment_protocol: Cells were seeded at 5x10^4 cells/well in 96-well culture plates and 12 hrs post-plating were treated with the specified drug. Samples were harvested in triplicate at 6, 12 and 24 hours post compound addition. In each experiment, vehicle (DMSO)-treated samples were used as controls.

tag: drug

value: Etoposide

tag: concentration

tag: time point

tag: replicate


title: OCI-LY3, Mitomycin C, 2.56 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Mitomycin C treatment with 2.56 uM concentration

value: Mitomycin C


title: OCI-LY3, Etoposide, 0.811 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Etoposide treatment with 0.811 uM concentration


title: OCI-LY3, Cycloheximide, 0.264 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Cycloheximide treatment with 0.264 uM concentration

value: Cycloheximide


title: OCI-LY3, Etoposide, 0.812 uM, 24hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 24hrs following Etoposide treatment with 0.812 uM concentration


title: OCI-LY3, Cycloheximide, 0.264 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Cycloheximide treatment with 0.264 uM concentration


title: OCI-LY3, Rapamycin, 22 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Rapamycin treatment with 22 uM concentration

value: Rapamycin

value: 22 uM


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following DMSO treatment with 0.01 concentration

value: DMSO


title: OCI-LY3, Etoposide, 0.811 uM, 24hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 24hrs following Etoposide treatment with 0.811 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Aclacinomycin A treatment with 0.036 uM concentration

value: Aclacinomycin A


title: OCI-LY3, Geldanamycin, 0.032 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Geldanamycin treatment with 0.032 uM concentration

value: Geldanamycin


title: OCI-LY3, Etoposide, 0.811 uM, 24hrs, Replicate1


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Doxorubicin hydrochloride treatment with 0.03 uM concentration

value: Doxorubicin hydrochloride


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 24hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 24hrs following Doxorubicin hydrochloride treatment with 0.03 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Aclacinomycin A treatment with 0.105 uM concentration


title: OCI-LY3, Cycloheximide, 0.264 uM, 24hrs, Replicate1


title: OCI-LY3, Cycloheximide, 5 uM, 24hrs, Replicate1

description: OCI-LY3 cell line profiled at 24hrs following Cycloheximide treatment with 5 uM concentration

value: 5 uM


title: OCI-LY3, Cycloheximide, 5 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Cycloheximide treatment with 5 uM concentration


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Doxorubicin hydrochloride treatment with 0.101 uM concentration


title: OCI-LY3, Camptothecin, 0.01 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Camptothecin treatment with 0.01 uM concentration

value: Camptothecin


title: OCI-LY3, Methotrexate, 100 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Methotrexate treatment with 100 uM concentration

value: Methotrexate


title: OCI-LY3, Blebbistatin, 10 uM, 24hrs, Replicate3

description: OCI-LY3 cell line profiled at 24hrs following Blebbistatin treatment with 10 uM concentration

value: Blebbistatin

value: 10 uM


title: OCI-LY3, Media, 24hrs, Replicate1

description: OCI-LY3 cell line profiled at 24hrs after growing them in Media

value: Media


title: OCI-LY3, Cycloheximide, 5 uM, 24hrs, Replicate2


title: OCI-LY3, Camptothecin, 0.31 uM, 24hrs, Replicate2

description: OCI-LY3 cell line profiled at 24hrs following Camptothecin treatment with 0.31 uM concentration


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 24hrs, Replicate1


title: OCI-LY3, Camptothecin, 0.01 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Camptothecin treatment with 0.01 uM concentration


title: OCI-LY3, Camptothecin, 0.31 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Camptothecin treatment with 0.31 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Aclacinomycin A treatment with 0.036 uM concentration


title: OCI-LY3, Camptothecin, 0.01 uM, 24hrs, Replicate1


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Aclacinomycin A treatment with 0.105 uM concentration


title: OCI-LY3, Blebbistatin, 100 uM, 24hrs, Replicate1

description: OCI-LY3 cell line profiled at 24hrs following Blebbistatin treatment with 100 uM concentration


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 24hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, Blebbistatin, 10 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Blebbistatin treatment with 10 uM concentration


title: OCI-LY3, Blebbistatin, 10 uM, 24hrs, Replicate2


title: OCI-LY3, Camptothecin, 0.31 uM, 24hrs, Replicate1


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Doxorubicin hydrochloride treatment with 0.101 uM concentration


title: OCI-LY3, Blebbistatin, 100 uM, 24hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 24hrs following Blebbistatin treatment with 100 uM concentration


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 24hrs, Replicate3


title: A04 OCI-LY3 cell line, Methotrexate, 100 uM, 24hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 24hrs following Methotrexate treatment with 100 uM concentration


title: OCI-LY3, DMSO, 1%, 24hrs, Replicate1


title: A03 OCI-LY3 cell line, Methotrexate, 100 uM, 24hrs, Replicate3


title: A02 OCI-LY3 cell line, Methotrexate, 100 uM, 24hrs, Replicate2


title: A05 OCI-LY3 cell line, Methotrexate, 100 uM, 24hrs, Replicate2


title: A01 OCI-LY3 cell line, Methotrexate, 100 uM, 24hrs, Replicate1


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following H-7, Dihydrochloride treatment with 12.4 uM concentration

value: H-7, Dihydrochloride


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following H-7, Dihydrochloride treatment with 20.2 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following H-7, Dihydrochloride treatment with 12.4 uM concentration


title: OCI-LY3, Monastrol, 50 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Monastrol treatment with 50 uM concentration

value: Monastrol

value: 50 uM


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 24hrs, Replicate3


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate8

description: OCI-LY3 cell line profiled at 12hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, Monastrol, 100 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Monastrol treatment with 100 uM concentration


title: OCI-LY3, Monastrol, 50 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Monastrol treatment with 50 uM concentration


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate7

source_name: OCI-LY3 cell line profiled at 12hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, Vincristine, 0.005 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Vincristine treatment with 0.005 uM concentration

value: Vincristine


title: OCI-LY3, Monastrol, 100 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Monastrol treatment with 100 uM concentration


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate6


title: OCI-LY3, Vincristine, 0.01 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Vincristine treatment with 0.01 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following H-7, Dihydrochloride treatment with 20.2 uM concentration


title: OCI-LY3, Trichostatin A, 0.114 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Trichostatin A treatment with 0.114 uM concentration

value: Trichostatin A


title: OCI-LY3, Monastrol, 50 uM, 12hrs, Replicate1


title: OCI-LY3, Vincristine, 0.005 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following Vincristine treatment with 0.005 uM concentration


title: OCI-LY3, Vincristine, 0.005 uM, 12hrs, Replicate2


title: OCI-LY3, Trichostatin A, 0.114 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following Trichostatin A treatment with 0.114 uM concentration


title: OCI-LY3, Trichostatin A, 0.114 uM, 12hrs, Replicate3


title: OCI-LY3, Trichostatin A, 0.143 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Trichostatin A treatment with 0.143 uM concentration


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate5


title: OCI-LY3, Blebbistatin, 100 uM, 24hrs, Replicate2


title: OCI-LY3, Rapamycin, 13.8 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Rapamycin treatment with 13.8 uM concentration

value: Rapamycin


title: OCI-LY3, Monastrol, 100 uM, 12hrs, Replicate1


title: OCI-LY3, Rapamycin, 13.8 uM, 12hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 12hrs following Rapamycin treatment with 13.8 uM concentration


title: OCI-LY3, Rapamycin, 13.8 uM, 12hrs, Replicate1


title: HUES8-stage6-2

city: Cambridge

first: Jeffrey

middle: Robert

last: Millman

state: Massachusetts

address: 7 Divinity Ave

department: HSCRB

institute: Harvard University

hyb_protocol: 750 ng cRNA from each sample was hybridized to Human HT-12 Expression BeadChips (Illumina). The Whole- Genome Expression Direct Hybridization kit (Illumina) was used according to manufacturer's instructions.

scan_protocol: Illumina Beadstation 500

data_processing: GenomeStudio (Illumina, V2011.1). Raw data were adjusted by background subtraction and quantile normalization. The p- values for differences between mean signals were calculated in GenomeStudio by t-test and corrected for multiple hypotheses testing by the Benjamini-Hochberg method in combination with the Illumina custom false discovery rate (FDR) model.

source_name: HUES8 cell differentiated to stage 6 containing insulin-expressing SC-beta cells

label_protocol: The Illumina TotalPrep RNA Amplification kit (Ambion) was using according to manufacturer's instructions.

growth_protocol: hES cells were grown in suspension in mTesr prior to differentiation.

extract_protocol: MARIS was used to extract total RNA after flow cytometry sorting. Detailed protocol is described in the paper: Generation of functional human pancreatic  cells in vitro

treatment_protocol: Differentiation methods are available in the paper: Generation of functional human pancreatic  cells in vitro

tag: cell type

value: stage 6 Nkx6.1+/Ins+ cells

tag: cell line


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 12hrs, Replicate3


title: OCI-LY3, Rapamycin, 22 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Rapamycin treatment with 22 uM concentration

value: 22 uM


title: Pio_24_Rep2

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: Pioglitazone treated 24hr rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Slides were scanned using Illumina HiScan SQ

data_processing: The data were extracted with GenomeStudio using Illumina default analysis settings. Data is background corrected and quantile normalized.

source_name: NCI-H2347 cell line, Pioglitazone treated 24hr rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA

growth_protocol: NCI-H2347 cells were cultured in RPMI medium with 5% FBS.

extract_protocol: Total RNA was extracted from cells using the RNAeasy (Qiagen) Kit.

treatment_protocol: 1x10^6 cells were plated for each experiment. 24 hours after plating complete media was replaced with 5% FBS RPMI medium containing pioglitazone (50 µM) or vehicle (DMSO). Cells were harvested for RNA extraction after 12, 24 or 48 hours.

value: lung cancer


title: OCI-LY3, Mitomycin C, 0.553 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Mitomycin C treatment with 0.553 uM concentration

value: Mitomycin C


title: Veh_24_Rep2

description: Vehicle 24hr rep2

source_name: NCI-H2347 cell line, Vehicle 24hr rep2


title: OCI-LY3, Vincristine, 0.01 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Vincristine treatment with 0.01 uM concentration


title: OCI-LY3, Trichostatin A, 0.143 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Trichostatin A treatment with 0.143 uM concentration


title: Veh_24_Rep3

description: Vehicle 24hr rep3

source_name: NCI-H2347 cell line, Vehicle 24hr rep3


title: HUES8-stage6-1


title: Pio_24_Rep3

description: Pioglitazone treated 24hr rep3

source_name: NCI-H2347 cell line, Pioglitazone treated 24hr rep3


title: OCI-LY3, Mitomycin C, 2.56 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Mitomycin C treatment with 2.56 uM concentration


title: OCI-LY3, Mitomycin C, 0.553 uM, 12hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 12hrs following Mitomycin C treatment with 0.553 uM concentration


title: OCI-LY3, Vincristine, 0.01 uM, 12hrs, Replicate1


title: Pio_48_Rep3

description: Pioglitazone treated 48hr rep3

source_name: NCI-H2347 cell line, Pioglitazone treated 48hr rep3


title: Pio_48_Rep2

description: Pioglitazone treated 48hr rep2

source_name: NCI-H2347 cell line, Pioglitazone treated 48hr rep2


title: Pio_24_Rep1

description: Pioglitazone treated 24hr rep1

source_name: NCI-H2347 cell line, Pioglitazone treated 24hr rep1


title: Veh_48_Rep3

description: Vehicle 48hr rep3

source_name: NCI-H2347 cell line, Vehicle 48hr rep3


title: Veh_48_Rep2

description: Vehicle 48hr rep2

source_name: NCI-H2347 cell line, Vehicle 48hr rep2


title: Veh_24_Rep1

description: Vehicle 24hr rep1

source_name: NCI-H2347 cell line, Vehicle 24hr rep1


title: Pio_48_Rep1

description: Pioglitazone treated 48hr rep1

source_name: NCI-H2347 cell line, Pioglitazone treated 48hr rep1


title: Veh_48_Rep1

description: Vehicle 48hr rep1

source_name: NCI-H2347 cell line, Vehicle 48hr rep1


title: OCI-LY3, Geldanamycin, 0.001 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Geldanamycin treatment with 0.001 uM concentration

value: Geldanamycin


title: Pio_12_Rep2

description: Pioglitazone treated 12hr rep2

source_name: NCI-H2347 cell line, Pioglitazone treated 12hr rep2


title: OCI-LY3, Trichostatin A, 0.143 uM, 12hrs, Replicate1


title: OCI-LY3, Geldanamycin, 0.001 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Geldanamycin treatment with 0.001 uM concentration


title: OCI-LY3, Mitomycin C, 0.553 uM, 12hrs, Replicate1


title: Pio_12_Rep3

description: Pioglitazone treated 12hr rep3

source_name: NCI-H2347 cell line, Pioglitazone treated 12hr rep3


title: Pio_12_Rep1

description: Pioglitazone treated 12hr rep1

source_name: NCI-H2347 cell line, Pioglitazone treated 12hr rep1


title: OCI-LY3, Geldanamycin, 0.001 uM, 12hrs, Replicate1


title: Veh_12_Rep2

description: Vehicle 12hr rep2

source_name: NCI-H2347 cell line, Vehicle 12hr rep2


title: Veh_12_Rep3

description: Vehicle 12hr rep3

source_name: NCI-H2347 cell line, Vehicle 12hr rep3


title: OCI-LY3, Rapamycin, 22 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Rapamycin treatment with 22 uM concentration


title: OCI-LY3, Rapamycin, 22 uM, 12hrs, Replicate1


title: OCI-LY3, Etoposide, 0.812 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Etoposide treatment with 0.812 uM concentration

value: Etoposide


title: OCI-LY3, Etoposide, 0.812 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following Etoposide treatment with 0.812 uM concentration


title: OCI-LY3, Media, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs after growing them in Media


title: OCI-LY3, Cycloheximide, 0.264 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Cycloheximide treatment with 0.264 uM concentration

value: Cycloheximide


title: OCI-LY3, Etoposide, 0.812 uM, 12hrs, Replicate3


title: OCI-LY3, Geldanamycin, 0.032 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Geldanamycin treatment with 0.032 uM concentration


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate4

source_name: OCI-LY3 cell line profiled at 12hrs following DMSO treatment with 0.01 concentration

value: DMSO


title: OCI-LY3, Geldanamycin, 0.032 uM, 12hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 12hrs following Geldanamycin treatment with 0.032 uM concentration


title: OCI-LY3, Geldanamycin, 0.032 uM, 12hrs, Replicate1


title: OCI-LY3, Mitomycin C, 2.56 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following Mitomycin C treatment with 2.56 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Aclacinomycin A treatment with 0.036 uM concentration

value: Aclacinomycin A


title: OCI-LY3, Mitomycin C, 2.56 uM, 12hrs, Replicate2


title: OCI-LY3, Cycloheximide, 0.264 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Cycloheximide treatment with 0.264 uM concentration


title: Veh_12_Rep1

description: Vehicle 12hr rep1

source_name: NCI-H2347 cell line, Vehicle 12hr rep1


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Aclacinomycin A treatment with 0.036 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following H-7, Dihydrochloride treatment with 20.2 uM concentration


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, Etoposide, 0.811 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Etoposide treatment with 0.811 uM concentration


title: OCI-LY3, Etoposide, 0.811 uM, 12hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 12hrs following Etoposide treatment with 0.811 uM concentration


title: OCI-LY3, Etoposide, 0.811 uM, 12hrs, Replicate1


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Doxorubicin hydrochloride treatment with 0.03 uM concentration

value: Doxorubicin hydrochloride


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Aclacinomycin A treatment with 0.105 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 12hrs, Replicate1


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Aclacinomycin A treatment with 0.105 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 12hrs, Replicate1


title: OCI-LY3, Camptothecin, 0.01 uM, 12hrs, Replicate2

description: OCI-LY3 cell line profiled at 12hrs following Camptothecin treatment with 0.01 uM concentration

value: Camptothecin


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 12hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 12hrs following Doxorubicin hydrochloride treatment with 0.03 uM concentration


title: OCI-LY3, Cycloheximide, 5 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Cycloheximide treatment with 5 uM concentration

value: 5 uM


title: OCI-LY3, Cycloheximide, 5 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following Cycloheximide treatment with 5 uM concentration


title: OCI-LY3, Camptothecin, 0.01 uM, 12hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 12hrs following Camptothecin treatment with 0.01 uM concentration


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Doxorubicin hydrochloride treatment with 0.101 uM concentration


title: OCI-LY3, Cycloheximide, 0.264 uM, 12hrs, Replicate1


title: OCI-LY3, Cycloheximide, 5 uM, 12hrs, Replicate2


title: OCI-LY3, Blebbistatin, 10 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Blebbistatin treatment with 10 uM concentration

value: Blebbistatin

value: 10 uM


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following Doxorubicin hydrochloride treatment with 0.101 uM concentration


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 12hrs, Replicate1


title: OCI-LY3, Methotrexate, 100 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Methotrexate treatment with 100 uM concentration

value: Methotrexate


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 12hrs, Replicate2


title: OCI-LY3, Blebbistatin, 10 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Blebbistatin treatment with 10 uM concentration


title: OCI-LY3, Camptothecin, 0.31 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Camptothecin treatment with 0.31 uM concentration


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate2


title: OCI-LY3, Camptothecin, 0.01 uM, 12hrs, Replicate1


title: OCI-LY3, Media, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs after growing them in Media

value: Media


title: A02 OCI-LY3 cell line, Methotrexate, 100 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Methotrexate treatment with 100 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following H-7, Dihydrochloride treatment with 12.4 uM concentration

value: H-7, Dihydrochloride


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following H-7, Dihydrochloride treatment with 12.4 uM concentration


title: OCI-LY3, Camptothecin, 0.31 uM, 12hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 12hrs following Camptothecin treatment with 0.31 uM concentration


title: OCI-LY3, Camptothecin, 0.31 uM, 12hrs, Replicate1


title: OCI-LY3, Blebbistatin, 10 uM, 12hrs, Replicate1


title: OCI-LY3, DMSO, 1%, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, Blebbistatin, 100 uM, 12hrs, Replicate3

description: OCI-LY3 cell line profiled at 12hrs following Blebbistatin treatment with 100 uM concentration


title: A04 OCI-LY3 cell line, Methotrexate, 100 uM, 12hrs, Replicate1


title: A03 OCI-LY3 cell line, Methotrexate, 100 uM, 12hrs, Replicate3


title: A06 OCI-LY3 cell line, Methotrexate, 100 uM, 12hrs, Replicate2


title: OCI-LY3, Blebbistatin, 100 uM, 12hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 12hrs following Blebbistatin treatment with 100 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 12.4 uM, 6hrs, Replicate1


title: OCI-LY3, Blebbistatin, 100 uM, 12hrs, Replicate2


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following H-7, Dihydrochloride treatment with 20.2 uM concentration


title: OCI-LY3, Monastrol, 50 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Monastrol treatment with 50 uM concentration

value: Monastrol

value: 50 uM


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following H-7, Dihydrochloride treatment with 20.2 uM concentration


title: OCI-LY3, Monastrol, 100 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Monastrol treatment with 100 uM concentration


title: OCI-LY3, Monastrol, 50 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Monastrol treatment with 50 uM concentration


title: OCI-LY3, Vincristine, 0.005 uM, 6hrs, Replicate1

description: OCI-LY3 cell line profiled at 6hrs following Vincristine treatment with 0.005 uM concentration

value: Vincristine


title: OCI-LY3, Vincristine, 0.005 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Vincristine treatment with 0.005 uM concentration


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate7

description: OCI-LY3 cell line profiled at 6hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, Monastrol, 100 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Monastrol treatment with 100 uM concentration


title: OCI-LY3, H-7, Dihydrochloride, 20.2 uM, 6hrs, Replicate1


title: OCI-LY3, Vincristine, 0.01 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Vincristine treatment with 0.01 uM concentration


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate8

source_name: OCI-LY3 cell line profiled at 6hrs following DMSO treatment with 0.01 concentration


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate6


title: OCI-LY3, Monastrol, 50 uM, 6hrs, Replicate2


title: OCI-LY3, Trichostatin A, 0.114 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Trichostatin A treatment with 0.114 uM concentration

value: Trichostatin A


title: OCI-LY3, Trichostatin A, 0.114 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Trichostatin A treatment with 0.114 uM concentration


title: OCI-LY3, Mitomycin C, 0.553 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Mitomycin C treatment with 0.553 uM concentration

value: Mitomycin C


title: OCI-LY3, Trichostatin A, 0.114 uM, 6hrs, Replicate1


title: OCI-LY3, Vincristine, 0.01 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Vincristine treatment with 0.01 uM concentration


title: OCI-LY3, Mitomycin C, 0.553 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Mitomycin C treatment with 0.553 uM concentration


title: OCI-LY3, Rapamycin, 13.8 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Rapamycin treatment with 13.8 uM concentration

value: Rapamycin


title: OCI-LY3, Rapamycin, 13.8 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Rapamycin treatment with 13.8 uM concentration


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate5


title: OCI-LY3, Monastrol, 100 uM, 6hrs, Replicate1


title: OCI-LY3, Rapamycin, 13.8 uM, 6hrs, Replicate1


title: OCI-LY3, Vincristine, 0.01 uM, 6hrs, Replicate2


title: OCI-LY3, Trichostatin A, 0.143 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Trichostatin A treatment with 0.143 uM concentration


title: OCI-LY3, Rapamycin, 22 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Rapamycin treatment with 22 uM concentration

value: 22 uM


title: OCI-LY3, Mitomycin C, 0.553 uM, 6hrs, Replicate1


title: OCI-LY3, Geldanamycin, 0.001 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Geldanamycin treatment with 0.001 uM concentration

value: Geldanamycin


title: OCI-LY3, Trichostatin A, 0.143 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Trichostatin A treatment with 0.143 uM concentration


title: OCI-LY3, Mitomycin C, 2.56 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Mitomycin C treatment with 2.56 uM concentration


title: OCI-LY3, Media, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs after growing them in Media


title: OCI-LY3, Geldanamycin, 0.001 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Geldanamycin treatment with 0.001 uM concentration


title: OCI-LY3, Geldanamycin, 0.001 uM, 6hrs, Replicate2


title: A01 OCI-LY3 cell line, Methotrexate, 100 uM, 12hrs, Replicate1

description: OCI-LY3 cell line profiled at 12hrs following Methotrexate treatment with 100 uM concentration


title: OCI-LY3, Trichostatin A, 0.143 uM, 6hrs, Replicate1


title: OCI-LY3, Rapamycin, 22 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Rapamycin treatment with 22 uM concentration


title: OCI-LY3, Etoposide, 0.812 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Etoposide treatment with 0.812 uM concentration

value: Etoposide


title: OCI-LY3, Rapamycin, 22 uM, 6hrs, Replicate2


title: OCI-LY3, Etoposide, 0.812 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Etoposide treatment with 0.812 uM concentration


title: OCI-LY3, Etoposide, 0.812 uM, 6hrs, Replicate2


title: OCI-LY3, Mitomycin C, 2.56 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Mitomycin C treatment with 2.56 uM concentration


title: OCI-LY3, Geldanamycin, 0.032 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Geldanamycin treatment with 0.032 uM concentration


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate3

value: DMSO


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate4


title: OCI-LY3, Mitomycin C, 2.56 uM, 6hrs, Replicate1


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Aclacinomycin A treatment with 0.036 uM concentration

value: Aclacinomycin A


title: OCI-LY3, Cycloheximide, 0.264 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Cycloheximide treatment with 0.264 uM concentration

value: Cycloheximide


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Aclacinomycin A treatment with 0.036 uM concentration


title: OCI-LY3, Etoposide, 0.811 uM, 6hrs, Replicate1

description: OCI-LY3 cell line profiled at 6hrs following Etoposide treatment with 0.811 uM concentration


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Doxorubicin hydrochloride treatment with 0.03 uM concentration

value: Doxorubicin hydrochloride


title: OCI-LY3, Etoposide, 0.811 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Etoposide treatment with 0.811 uM concentration


title: OCI-LY3, Geldanamycin, 0.032 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Geldanamycin treatment with 0.032 uM concentration


title: OCI-LY3, Etoposide, 0.811 uM, 6hrs, Replicate2


title: OCI-LY3, Geldanamycin, 0.032 uM, 6hrs, Replicate3


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Doxorubicin hydrochloride treatment with 0.03 uM concentration


title: OCI-LY3, Cycloheximide, 0.264 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Cycloheximide treatment with 0.264 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 6hrs, Replicate1

description: OCI-LY3 cell line profiled at 6hrs following Aclacinomycin A treatment with 0.105 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.036 uM, 6hrs, Replicate1


title: OCI-LY3, Camptothecin, 0.01 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Camptothecin treatment with 0.01 uM concentration

value: Camptothecin


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Aclacinomycin A treatment with 0.105 uM concentration


title: OCI-LY3, Cycloheximide, 5 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Cycloheximide treatment with 5 uM concentration

value: 5 uM


title: OCI-LY3, Camptothecin, 0.01 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Camptothecin treatment with 0.01 uM concentration


title: OCI-LY3, Aclacinomycin A, 0.105 uM, 6hrs, Replicate3


title: OCI-LY3, Blebbistatin, 10 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Blebbistatin treatment with 10 uM concentration

value: Blebbistatin

value: 10 uM


title: OCI-LY3, Cycloheximide, 0.264 uM, 6hrs, Replicate1


title: OCI-LY3, Cycloheximide, 5 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Cycloheximide treatment with 5 uM concentration


title: OCI-LY3, Doxorubicin hydrochloride, 0.03 uM, 6hrs, Replicate1


title: WT-Ser5kinase_Spt6-MYC_Rpb3vsInput_rep2

type: genomic

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

description: Biological replicate 2 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in WT-Ser5kinase_Spt6-MYC tagged cells, after 15 min with 6uM NA-PP1.

hyb_protocol: Hybridization: Resuspend colored pellet in 110uL hybridization buffer (100uL DIGEasy Buffer, 5uL 10mg/mL Salmon Sperm DNA, 5uL 8mg/mL yeast tRNA). Put at 95?C for 5 minutes. Put at 42?C for 10 min (Keep samples at 42?C while waiting for hybridization). Follow standard Agilent chamber hybridization protocols. Incubate overnight (16-24h) at 42?C in Agilent hybridization oven at 20 rpm rotation speed.  Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Stripping: Stripping is done in 1L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. 1. Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations.  Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 5 ml of this 1M solution in 1L Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180K  Set the scan as follow:  pixel size = 2Âµm;  speed = 20;  Scan Mode = Normal;  Acquisition Mode = Simultaneous;  Focus = Auto.    Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing: Correction = Foreground-Background  Normalisation = limma loess (subgrid)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice. Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C.    Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly.    Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C.    Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.    Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O).  PCR cycling conditions:  1) 5:00 at 55C  2) 5:00 at 72C  3) 2:00 at 95C  4) 0:30 at 95C  5) 0:30 at 55C  6) 1:00 at 72C  7) Repeat steps 4-6 31 more times.  8) 4:00 at 72C  9) Forever at 4C    Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness.    Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour.    Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness.      Phosphate Wash Buffer (100mL):  0.5mL 1M KPO4, pH 8.5  15.25mL ddH2O  84.25mL 95% EtOH  Solution will be cloudy upon mixing.    Phosphate Elution Buffer (10mL):  0.04mL 1M KPO4, pH 8.5  9.96mL ddH2O    1M KPO4, pH 8.5 (10mL):  9.5mL 1M K2HPO4  0.5mL 1M KH2PO4    1M Sodium Carbonate Buffer, pH 9.0 (100mL):  10.8g Na2CO3  80mL ddH2O  pH to 9.0 with concentrated HCl  Adjust volume to 100mL with ddH2O  DILUTE 1:10 WHEN USING!  Solution will change composition over time. Use only if less than a month old.

growth_protocol: For chromatin immunoprecipitation, saturated overnight cultures were subcultured in 100 ml of synthetic complete (SC) media lacking isoleucine/valine and were grown to A600 between 0.5 and 0.6. The cultures were treated with 0.65 μg/ml of sulfometuron methyl (SM) for 25 minutes to induce Gcn4. Analog sensitive Ser5 kinase mutants (kin28as/bur2Δ) were treated with 6 μM of NA-PP1 for 15 minutes prior to Gcn4 induction by SM as described previously (Bataille et al., 2012; Govind et al., 2010).

extract_protocol: Chromatin immunoprecipitation experiments were performed as described previously (Govind et al., 2012). Briefly, 100 ml of cells (A600 = 0.6) were cross-linked with 1% formaldehyde for 15 minutes at ambient temperature and quenched with glycine. Chromatin was isolated and fragmented by sonication (Branson450) to an average size of 300-400 base pairs. The soluble fraction of chromatin was used for ChIP using the appropriate antibodies.

treatment_protocol: 6uM NA-PP1_15 min

tag: strain

tag: antibody

value: Rpb3 (W0012 neoclone)


title: OCI-LY3, Cycloheximide, 5 uM, 6hrs, Replicate1


title: WT-Ser5kinase_Spt6-MYC_Rpb3vsInput_rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in WT-Ser5kinase_Spt6-MYC tagged cells, after 15 min with 6uM NA-PP1.


title: WT-HDAC_Spt6-202del-MYCvsInput_rep2

description: Biological replicate 2 of 2. spt6-202del-MYC tagged mutant occupancy, using the anti-MYC antibody, measured by the ratio of ChIP versus Input DNA in tagged WT-HDAC cells.

growth_protocol: For chromatin immunoprecipitation, saturated overnight cultures were subcultured in 100 ml of synthetic complete (SC) media lacking isoleucine/valine and were grown to A600 between 0.5 and 0.6. The cultures were treated with 0.65 μg/ml of sulfometuron methyl (SM) for 25 minutes to induce Gcn4.

value: 9E10 (lab stock by AF)


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Doxorubicin hydrochloride treatment with 0.101 uM concentration


title: WT-Ser5kinase_Spt6-MYCvsUntagged_rep2

description: Biological replicate 2 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged WT-Ser5kinase strain versus the ChIP in the untagged strain, after 15 min with 6uM NA-PP1.


title: kin28as-bur2D_Spt6-MYC_Rpb3vsInput_rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in kin28as-bur2D_Spt6-MYC tagged cells, after 15 min with 6uM NA-PP1.


title: OCI-LY3, Media, 6hrs, Replicate1

description: OCI-LY3 cell line profiled at 6hrs after growing them in Media

value: Media


title: WT-Ser5kinase_Spt6-MYCvsUntagged_rep1

description: Biological replicate 1 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged WT-Ser5kinase strain versus the ChIP in the untagged strain, after 15 min with 6uM NA-PP1.


title: rpd3D-hos2D_Spt6-202del-MYCvsInput_rep1

description: Biological replicate 1 of 2. spt6-202del-MYC tagged mutant occupancy, using the anti-MYC antibody, measured by the ratio of ChIP versus Input DNA in tagged rpd3D-hos2D cells.


title: OCI-LY3, Vincristine, 0.005 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Vincristine treatment with 0.005 uM concentration

value: Vincristine


title: OCI-LY3, Camptothecin, 0.31 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Camptothecin treatment with 0.31 uM concentration


title: OCI-LY3, Camptothecin, 0.31 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Camptothecin treatment with 0.31 uM concentration


title: rpd3D-hos2D_Spt6-202del-MYCvsInput_rep2

description: Biological replicate 2 of 2. spt6-202del-MYC tagged mutant occupancy, using the anti-MYC antibody, measured by the ratio of ChIP versus Input DNA in tagged rpd3D-hos2D cells.


title: OCI-LY3, Methotrexate, 100 uM, 6hrs, Replicate3

description: OCI-LY3 cell line profiled at 6hrs following Methotrexate treatment with 100 uM concentration

value: Methotrexate


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following Doxorubicin hydrochloride treatment with 0.101 uM concentration


title: WT-HDAC_Spt6-202del-MYCvsInput_rep1

description: Biological replicate 1 of 2. spt6-202del-MYC tagged mutant occupancy, using the anti-MYC antibody, measured by the ratio of ChIP versus Input DNA in tagged WT-HDAC cells.


title: WT-HDAC_Spt6-MYCvsUntagged_rep7

description: Biological replicate 2 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged WT-HDAC strain versus the ChIP in the untagged strain.


title: WT-Ser2kinases_Spt6-MYCvsUntagged_rep6

description: Biological replicate 1 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged WT-Ser2kinases strain versus the ChIP in the untagged strain, after 60 min with 6uM 3MB-PP1.

growth_protocol: For chromatin immunoprecipitation, saturated overnight cultures were subcultured in 100 ml of synthetic complete (SC) media lacking isoleucine/valine and were grown to A600 between 0.5 and 0.6. The cultures were treated with 0.65 μg/ml of sulfometuron methyl (SM) for 25 minutes to induce Gcn4. Analog sensitive Ser2 kinase mutants (bur1as/ctk1Δ) were treated with 6 μM of 3MB-PP1 one hour prior to addition of SM as described previously (Qiu et al., 2009).

treatment_protocol: 6uM 3MB-PP1_60 min


title: OCI-LY3, Doxorubicin hydrochloride, 0.101 uM, 6hrs, Replicate1


title: kin28as-bur2D_Spt6-MYC_Rpb3vsInput_rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in kin28as-bur2D_Spt6-MYC tagged cells, after 15 min with 6uM NA-PP1.


title: kin28as-bur2D_Spt6-MYCvsUntagged_rep2

description: Biological replicate 2 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged kin28as-bur2D strain versus the ChIP in the untagged strain, after 15 min with 6uM NA-PP1.


title: OCI-LY3, Camptothecin, 0.01 uM, 6hrs, Replicate1

description: OCI-LY3 cell line profiled at 6hrs following Camptothecin treatment with 0.01 uM concentration


title: WT-Ser2kinases_Spt6-MYCvsUntagged_rep7

description: Biological replicate 2 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged WT-Ser2kinases strain versus the ChIP in the untagged strain, after 60 min with 6uM 3MB-PP1.


title: kin28as-bur2D_Spt6-MYCvsUntagged_rep1

description: Biological replicate 1 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged kin28as-bur2D strain versus the ChIP in the untagged strain, after 15 min with 6uM NA-PP1.


title: rpd3D-hos2D_Spt6-Myc_Rpb3vsInput_rep4

description: Biological replicate 2 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in rpd3D-hos2D_Spt6-MYC tagged cells.


title: WT-HDAC_Spt6-MYCvsUntagged_rep6

description: Biological replicate 1 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged WT-HDAC strain versus the ChIP in the untagged strain.


title: rpd3D-hos2D_Spt6-MYC_Rpb3vsInput_rep3

description: Biological replicate 1 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in rpd3D-hos2D_Spt6-MYC tagged cells.


title: OCI-LY3, Camptothecin, 0.31 uM, 6hrs, Replicate1


title: rpd3D-hos2D_Spt6-MYCvsUntagged_rep7

description: Biological replicate 2 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged rpd3D-hos2D strain versus the ChIP in the untagged strain.


title: rpd3D-hos2D_Spt6-MYCvsUntagged_rep6

description: Biological replicate 1 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged rpd3D-hos2D strain versus the ChIP in the untagged strain.


title: bur1as-ctk1D_Spt6-MYCvsUntagged_rep7

description: Biological replicate 2 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged bur1as-ctk1D strain versus the ChIP in the untagged strain, after 60 min with 6uM 3MB-PP1.


title: WT-Ser2kinases_Spt6-MYC_Rpb3vsInput_rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in WT-Ser2kinases_Spt6-MYC tagged cells, after 60 min with 6uM 3MB-PP1.


title: Macrophage WT 2

first: Stephen

last: Eichhorn

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Affy standard hyb protocol

scan_protocol: Affy scan protocol

data_processing: GCOS and RMAExpress software

label: Biotin

organism: Mus musculus

source_name: primary macrophage

label_protocol: Affy standard labeling protocol

growth_protocol: Samples were isolated from a mouse and cultured according to standard protocols

extract_protocol: Tri Reagent (Ambion) followed by RNeasy Plus (Qiagen)

value: primary macrophage

tag: genotype/variation

value: wild type

tag: age

value: 3 months

tag: Sex

value: male


title: OCI-LY3, Blebbistatin, 10 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Blebbistatin treatment with 10 uM concentration


title: WT-Ser2kinases_Spt6-MYC_Rpb3vsInput_rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in WT-Ser2kinases_Spt6-MYC tagged cells, after 60 min with 6uM 3MB-PP1.


title: bur1as-ctk1D_Spt6-MYC_Rpb3vsInput_rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in bur1as-ctk1D_Spt6-MYC tagged cells, after 60 min with 6uM 3MB-PP1.


title: bur1as-ctk1D_Spt6-MYCvsUntagged_rep6

description: Biological replicate 1 of 2. Spt6-MYC tagged occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged bur1as-ctk1D strain versus the ChIP in the untagged strain, after 60 min with 6uM 3MB-PP1.


title: Macrophage KO 2

value: knock out


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate1

description: OCI-LY3 cell line profiled at 6hrs following DMSO treatment with 0.01 concentration

value: DMSO


title: Macrophage WT 1


title: B cell KO

source_name: primary b cell

value: primary b cell


title: B cell WT


title: Neutrophil KO 2

source_name: primary neutrophil

value: primary neutrophil


title: OCI-LY3, Blebbistatin, 100 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Blebbistatin treatment with 100 uM concentration


title: Macrophage KO 1


title: OCI-LY3, Blebbistatin, 10 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Blebbistatin treatment with 10 uM concentration


title: OCI-LY3, Blebbistatin, 100 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Blebbistatin treatment with 100 uM concentration


title: bur1as-ctk1D_Spt6-MYC_Rpb3vsInput_rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in bur1as-ctk1D_Spt6-MYC tagged cells, after 60 min with 6uM 3MB-PP1.


title: OCI-LY3, Blebbistatin, 100 uM, 6hrs, Replicate3


title: WT-HDAC_Spt6-MYC_Rpb3vsInput_rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in WT-HDAC_Spt6-MYC tagged cells.


title: IPS2, grown feeder-free in 3D culture for > 20 passages

city: Manhattan

first: Mark

middle: Louis

last: Weiss

state: KS

address: 1600 Denison Ave, 228 coles hall

department: Anatomy and Physiology

institute: Kansas State University

description:
SAMPLE 72 & 73
Sample 73 is a technical replicate of Sample 72. The non-normalized_data.txt file contains raw data for both replicates.
induce pluripotent stem cells

data_processing:
The normalized data of the duplicate samples were averaged.  Normalization and all the data analysis were performed according to the manufacturers instructions using RT-PCR profiler instruction manual.
For the normalization, the housekeeping gene was  (geometric mean of GAPDH, LDHA)
Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
An excel spreadsheet was used to calculate deltaCt, fold change, etc.
Matrix normalized against housekeeping gene.  Averaged data from the replicates is provided.
Fold Change ratio is calculated as  2(-delta delta Ct).
The non-normalized data, normalized data and fold-change data are all available on the series record.

label: SYBR Green

organism: Rattus norvegicus

source_name: Fischer 344 embryonic fibroblasts

label_protocol: RT-PCR assays using a customized RT-PCR Profiler array (SABiosciences- Qiagen, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1000 ng total RNA using the RT2 First Strand Kit (SA Biosciences). The focused array was run using Qiagen's RT2 qPCR Mastermix for the BioRad iQ5 thermal cycler (loading control dye).  Quantitative real-time PCR were performed on a BioRad iCQ5 iCycler using Biorad iCycler IQ software version 3.1.7050. PCR program: 950C for 10 min,  40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. Followed by melt point analysis.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit.  Followed by DNase I treatment.  First strand synthesis using the Qiagen's RT2 first strand kit. Samples stored at -80C until use

value: Fischer 344

value: induced pluripotent stem cells, grown feeder-free in 3D culture for > 20 passages

tag: differentiation status

value: undifferentiated


title: Neutrophil KO 1


title: DA52, grown feeder free in 3D culture for > 20 passages

description:
SAMPLE 70 & 71
Sample 71 is a technical replicate of Sample 70. The non-normalized_data.txt file contains raw data for both replicates.
embryonic stem cells

source_name: 4.5 days post coitus Dark Agouti rat embryo

value: Dark Agouti

value: embryonic stem cells, grown feeder-free in 3D culture for > 20 passages


title: Agrobacterium tumefaciens C58_in_AB5.5_with_low_Fe_rep1

city: Ames

first: Hui-Hsien

last: Chou

state: IA

address: 503 Science II

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: This sample is the first one which is grown under low pH and low Fe condition

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization kit and 4-Chip Workstation following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by GenePix 4100A, following their standard operating protocol. See http://www.moleculardevices.com/systems/microarray-scanners/genepix-4100a-microarray-scanner.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleGen Deva software, version 1.2 (Roche NimbleGen, Inc.).

organism: Agrobacterium fabrum str. C58

source_name: Agrobacterium tumefaciens C58 AB5.5 low pH and low Fe

label_protocol: Labeling was performed by NimbleGen Labelling kit following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Agrobacterium tumefaciens C58 low pH and no Fe was grown untill reach to quarter of O.D.600nm of Standard sample at 28°C in AB5.5 without Fe media(AB5.5 Fe-).

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA  concentration was measured by SpectorPhotometer(NonoDrop).
cDNA were synthesized from the reverse transcription of Total RNA using the Life Technologies SuperScript II Double-Strand Synthesis Kit

tag: treatment

value: Low pH & Low Fe


title: Agrobacterium tumefaciens_under_Oxidative_Stress_rep2

description: This sample is the second one which is exposed to Oxidative stress

growth_protocol: Agrobacterium tumefaciens C58 Oxidative Stress was grown untill reach to half of O.D.600nm of Standard sample at 28°C in 40ml YEM media with 130μl 1% Hydrogen peroxide.

value: Oxidative stress


title: A02 OCI-LY3 cell line, Methotrexate, 100 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Methotrexate treatment with 100 uM concentration


title: Neutrophil WT 1


title: Agrobacterium tumefaciens C58_in_AB5.5_with_HeatShock_rep1

description: This sample is the first one which is grown under low pH condition and expose to heat shock at the same time

source_name: Agrobacterium tumefaciens C58 AB5.5 low pH and Heat Shock

growth_protocol: Agrobacterium tumefaciens C58 low pH and Heat Shock was grown at 40°C for 11 hour then grown untill reach to quarter of O.D.600nm of Standard sample at 28°C in AB5.5 media.

value: Low pH & Heat Shock


title: OCI-LY3, DMSO, 1%, 6hrs, Replicate2

source_name: OCI-LY3 cell line profiled at 6hrs following DMSO treatment with 0.01 concentration


title: A03 OCI-LY3 cell line, Methotrexate, 100 uM, 6hrs, Replicate3

source_name: OCI-LY3 cell line profiled at 6hrs following Methotrexate treatment with 100 uM concentration

value: Methotrexate


title: Agrobacterium tumefaciens_in_low_Fe_rep2

description: This sample is the second one which is grown under low Fe condition

source_name: Agrobacterium tumefaciens C58 AB7 No Fe

growth_protocol: Agrobacterium tumefaciens C58 low Fe was grown to mid-log phase (O.D.600nm 0.6~0.8) at 28°C in AB7 without Fe media (AB7 Fe-).

value: Low Fe


title: Agrobacterium tumefaciens C58_under_ColdShock_and_oxidative_stress_rep2

description: This sample is the second one which is exposed to Cold shock and Oxidative stress at the same time

growth_protocol: Agrobacterium tumefaciens C58 Cold Shock and Oxidative Stress was grown at 17°C for 13 hour then grown untill reach to quarter of O.D.600nm of Standard sample at 28°C in 40ml YEM media with 130μl 1% Hydrogen.

value: Cold Shock & Oxidative Stress


title: Agrobacterium tumefaciens C58_in_AB5.5_with_HeatShock_rep2

description: This sample is the second one which is grown under low pH condition and expose to heat shock at the same time


title: Agrobacterium tumefaciens C58_in_AB5.5_with_low_Fe_rep2

description: This sample is the second one which is grown under low pH and low Fe condition

source_name: Agrobacterium tumefaciens C58 AB5.5 low pH and no Fe


title: Agrobacterium tumefaciens C58_in_AB5.5_with_ColdShock_rep2

description: This sample is the second one which is grown under low pH condition and expose to cold shock at the same time

source_name: Agrobacterium tumefaciens C58 AB5.5 low pH and Cold Shock

growth_protocol: Agrobacterium tumefaciens C58 low pH and Cold Shock was grown at 17°C for 13 hour then grown untill reach to quarter of O.D.600nm of Standard sample at 28°C in AB5.5 media.

value: Low pH & Cold Shock


title: Agrobacterium tumefaciens_under_Oxidative_Stress_rep1

description: This sample is the first one which is exposed to Oxidative stress

source_name: Agrobacterium tumefaciens C58 Oxidative Stress


title: Agrobacterium tumefaciens C58_in_AB5.5_with_ColdShock_rep1

description: This sample is the first one which is grown under low pH condition and expose to cold shock at the same time


title: Agrobacterium tumefaciens C58_under_ColdShock_and_oxidative_stress_rep1

description: This sample is the first one which is exposed to Cold shock and Oxidative stress at the same time

source_name: Agrobacterium tumefaciens C58 Cold Shock and Oxidative Stress


title: A01 OCI-LY3 cell line, Methotrexate, 100 uM, 6hrs, Replicate1


title: Neutrophil WT 2

value: wild type

value: 3 months

value: male


title: Agrobacterium tumefaciens_in_low_Fe_rep1

description: This sample is the first one which is grown under low Fe condition


title: Agrobacterium tumefaciens_in_AB5.5_rep2

description: This sample is the second one which is grown under low pH condition

source_name: Agrobacterium tumefaciens C58 AB5.5 low pH

growth_protocol: Agrobacterium tumefaciens C58 low pH was grown to mid-log phase (O.D.600nm 0.6~0.8) at 28°C in AB5.5 media.

value: Low pH


title: WT-HDAC_Spt6-MYC_Rpb3vsInput_rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using anti-Rpb3 subunit antibody, measured by the ratio of ChIP versus Input DNA in WT-HDAC_Spt6-MYC tagged cells.

value: Rpb3 (W0012 neoclone)


title: Agrobacterium tumefaciens_in_AB5.5_rep1

description: This sample is the first one which is grown under low pH condition


title: Agrobacterium tumefaciens C58_standard_condition_rep1

description: This sample is the first one which is grown under standard condition

source_name: Agrobacterium tumefaciens C58 Standard

growth_protocol: Agrobacterium tumefaciens C58 Standard was grown to mid-log phase (O.D.600nm 0.6~0.8) at 28°C in YEM media.

value: Standard


title: Agrobacterium tumefaciens C58_under_ColdShock_rep2

description: This sample is the second one which is exposed to cold shock

growth_protocol: Agrobacterium tumefaciens C58 Cold Shock was grown at 17°C for 13 hour then grown untill reach to half of O.D.600nm of Standard sample at 28°C in YEM media.

value: Cold Shock


title: Agrobacterium tumefaciens C58_under_HeatShock_rep2

description: This sample is the second one which is exposed to heat shock

growth_protocol: Agrobacterium tumefaciens C58 Heat Shock was grown at 40°C for 11 hour then grown untill reach to half of O.D.600nm of Standard sample at 28°C in YEM media.

value: Heat Shock


title: Agrobacterium tumefaciens C58_under_ColdShock_rep1

description: This sample is the first one which is exposed to cold shock

source_name: Agrobacterium tumefaciens C58 Cold Shock


title: Agrobacterium tumefaciens C58_standard_condition_rep2

description: This sample is the second one which is grown under standard condition


title: Agrobacterium tumefaciens C58_under_HeatShock_rep1

description: This sample is the first one which is exposed to heat shock

source_name: Agrobacterium tumefaciens C58 Heat Shock


title: A05 OCI-LY3 cell line, Methotrexate, 100 uM, 6hrs, Replicate2

description: OCI-LY3 cell line profiled at 6hrs following Methotrexate treatment with 100 uM concentration

growth_protocol: OCI-LY3 cells were cultured under standard conditions in IMDM supplemented with 10% FCS.


title: Acne non lesional_Pt11

city: SOPHIA-ANTIPOLIS

first: Johannes

last: Voegel

address: 2400 route des colles

department: Research Department

country: France

institute: Galderma R&D

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

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Expression Console (Affymetrix, v.1.3.0.187) with RMA normalization.

source_name: non-lesional skin of acne patients

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA).

extract_protocol: miRNeasy (Qiagen) RNA extraction was performed according to the manufacturer's instructions.

tag: patient id#

tag: tissue

value: whole skin

tag: tissue subgroup

value: non-lesional skin


title: Acne non lesional_Pt12


title: Acne lesion_Pt12

source_name: lesional skin of acne patients

value: lesional skin


title: MSC cultured in human MSC media, MSC-34

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

description: healthy sample

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

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

data_processing: R-bioconductor/minfi

label: Cy3, Cy5

source_name: human mesenchymal stem cell, 12-year-old female

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: mesenchymal stem cells (MSCs)

value: 12 years

tag: gender

value: female

tag: disease state

value: healthy


title: MSC cultured in human MSC media, MSC-32

description: healthy sample

source_name: human mesenchymal stem cell, 14-year-old female

value: 14 years


title: MSC cultured in human MSC media, MSC-30

description: healthy sample

source_name: human mesenchymal stem cell, 6-year-old female

value: 6 years


title: Acne non lesional_Pt10


title: Acne lesion_Pt10


title: MSC cultured in human MSC media, MSC-31

description: healthy sample

source_name: human mesenchymal stem cell, 3-year-old female

value: 3 years


title: MSC cultured in human MSC media, MSC-33

description: healthy sample

source_name: human mesenchymal stem cell, 10-year-old female

value: 10 years


title: Acne non lesional_Pt9


title: Acne lesion_Pt11


title: MSC cultured in human MSC media, MSC-24

description: healthy sample

source_name: human mesenchymal stem cell, 89-year-old female

value: 89 years


title: Acne lesion_Pt9


title: Acne non lesional_Pt8


title: MSC cultured in human MSC media, MSC-27

description: healthy sample

source_name: human mesenchymal stem cell, 92-year-old female

value: 92 years


title: Whole blood twin 57A

description:
ITR 057A
Healthy sample

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to the Illumina Human Methylation450 BeadChip using standard Illumina protocol.

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

data_processing: Subset-quantile Within Array Normalization (SWAN) using the R-Bioconductor/minfi package.

source_name: human whole blood, 21.08-year-old male

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Total DNA was isolated by standard procedures.

value: whole blood

value: male

value: 21.08 years

tag: twin pair


title: MSC cultured in human MSC media, MSC-25

description: healthy sample

source_name: human mesenchymal stem cell, 86-year-old female

value: 86 years


title: Whole blood twin 57B

description:
ITR 057B
Healthy sample


title: Whole blood twin 52B

description:
ITR 052B
Healthy sample

source_name: human whole blood, 66-year-old male

value: 66 years


title: Whole blood twin 6B

description:
ITR 006B
Healthy sample

source_name: human whole blood, 60.05-year-old female

value: 60.05 years


title: A04 OCI-LY3 cell line, Methotrexate, 100 uM, 6hrs, Replicate1

source_name: OCI-LY3 cell line profiled at 6hrs following Methotrexate treatment with 100 uM concentration

tag: drug

value: Methotrexate

tag: concentration

tag: time point


title: Whole blood twin 54B

description:
ITR 054B
Healthy sample

source_name: human whole blood, 58.41-year-old female

value: 58.41 years


title: Whole blood twin 54A

description:
ITR 054A
Healthy sample


title: Whole blood twin 6A

description:
ITR 006A
Healthy sample


title: RR IgG ChIP

city: Edmonton

first: Raymond

last: Lai

state: Alberta

address: 5-142 Katz Building, University of Alberta

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

description: IgG ChIP-chip DNA from MCF7 RR cells

hyb_protocol: Hybridization was performed according to Nimblegen protocols by Roche Nimblegen. http://www.nimblegen.com/support/dna-microarray-support.html

scan_protocol: Scanning was performed according to Nimblegen protocols by Roche Nimblegen. http://www.nimblegen.com/support/dna-microarray-support.html

data_processing: Data processing was performed according to Nimblegen protocols using NImbleScan by Roche Nimblegen. http://www.nimblegen.com/support/dna-microarray-support.html

source_name: IgG ChIP DNA from RR cells

label_protocol: Labelling was performed according to Nimblegen protocols by Roche Nimblegen. http://www.nimblegen.com/support/dna-microarray-support.html

growth_protocol: Cells were grown on regular tissue culture plastic in high glucose DMEM supplemented with 10% FBS, 1 μg/mL puromycin, 1% pen/strep

extract_protocol: The starting materials was scaled up 4x, such that starting materials are 4x 15 cm plates of both MCF7 RU and RR cells, and 4 identical IPs were performed for each con+B30dition (MCF7 RU and RR, IgG and Sox2 IPs). MCF7 RU and RR cells were cultured in 15 cm plates in 10% FBS DMEM high glucose supplemented with 1 μg/ml of puromycin and 1% pen/strep. At about 80% confluency, cells with fixed for 20 minutes with 1% formaldehyde (in culture media). Cells were pelleted and lysed with SDS lysis buffer (1% SDS, 10mM EDTA), rocking at 4ºC. The chromatin was sonicated on ice using a Fisher Scientific Sonic Dismembrator Ultrasonic Processor Model 705 (Fisher Scientific) at 25% power with 10 pulses of 20 seconds sonication and 30 seconds rest to give optimized DNA fragments between 200 bp and 1 kb. The degree of shearing and the amount of input DNA were evaluated and equal. Aliquots of input chromatin were saved for extraction of input DNA later. The chromatin was first diluted in ChIP Dilution Buffer (0.01% SDS, 1.2 mM EDTA, 167 mM NaCl, 1.1% TritonX-100, 16.7 mM Tris-HCl, pH 8.1) and precleared with Protein G Plus/Protein A agarose suspension (Calbiochem, Darmstadt, Germany) equilibrated in RIPA buffer for 2 hours at 4°C. Then the chromatin was incubated with 5 μg of either normal rabbit IgG (Cell Signaling) or anti-Sox2 antibody (Santa Cruz) overnight at 4°C. Next, the same equilibrated Protein G Plus/Protein A agarose beads were subsequently incubated with the chromatin and Sox2 or rabbit IgG antibody for 2 hours at 4°C. The immunoprecipitated material bound to agarose beads was then washed once in the Low Salt Wash Buffer (0.1% SDS, 2 mM EDTA, 150 mM NaCl, 1% TritonX-100, 20 mM Tris-HCl, pH8.1), High Salt Wash Buffer (0.1% SDS, 2mM EDTA, 500mM NaCl, 1% TritonX-100, 20 mM Tris-HCl, pH 8.1), LiCl Wash Buffer (0.25M LiCl, 1% deoxycholate, 10 mM Tris-HCl, pH 8.1, 1% Nonidet P-40, 1 mM EDTA), and twice in the freshly prepared TE Buffer (1 mM EDTA, 10mM Tris-HCl, pH 8.1). To elute the immunoprecipitated material from the beads, the beads-bound chromatin was then incubated with the ChIP Elution Buffer. Along with the previously aliquoted input chromatin, the DNA/protein formaldehyde crosslinks were then reversed with 5M NaCl at 65ºC overnight. Finally, protein was degraded with Proteinase K (Ambion, Invitron, Burlington, ON, Canada) at 55ºC for 2 hours and DNA extracted by phenol/chloroform extraction. The resulting DNA was further purified using the QIAquick PCR Purification Kit (Qiagen Canada, Toronto, ON, Canada), lyophilized, and reconstituted in 10 µL of UltraPure DNase/RNase-free distilled water (Life Technologies, Burlington, ON, Canada). The DNA was subsequently amplified twice using the Sigma GenomePlex Complete Whole Genome Amplification Kit (#WGA2, Sigma-Aldrich Canada) using a published adapted protocol. ChIP-PCR was performed as previously described. ChIP input DNA was run on an agarose gel to check for microarray optimized DNA fragments of 200 to 1200 bp. DNA samples were sent in 2 replicates to Roche Nimblegen ChIP-chip Microarray Services for quality assessment, and full service ChIP-chip microarray service and analysis.

treatment_protocol: RR cells were purified by virally infecting Sox2 transcription activity reporter into MCF7 parental cells and FACS sorting for GFP+ cells

tag: cell type

value: Breast cancer cells, estrogen receptor positive

tag: cell line

tag: purified subset

value: Reporter responsive (RR)

tag: chip antibody

value: IgG

source_name: Input DNA from RR cells

value: None, input DNA


title: Acne non lesional_Pt6

source_name: non-lesional skin of acne patients

value: whole skin

value: non-lesional skin


title: Whole blood twin 50A

description:
ITR 050A
Healthy sample

source_name: human whole blood, 21.02-year-old female

value: female

tag: age

value: 21.02 years

value: healthy


title: Acne non lesional_Pt5


title: Acne lesion_Pt8

source_name: lesional skin of acne patients

value: lesional skin


title: Whole blood twin 52A

description:
ITR 052A
Healthy sample

value: whole blood

value: male


title: Acne lesion_Pt7


title: RU Sox2 ChIP Rep 2

description: Sox2 ChIP-chip DNA from MCF7 RU cells - Replicate 2

source_name: Sox2 ChIP DNA from RU cells

treatment_protocol: RU cells were purified by virally infecting Sox2 transcription activity reporter into MCF7 parental cells and FACS sorting for GFP- cells

value: Reporter unresponsive (RU)

source_name: Input DNA from RU cells


title: Acne lesion_Pt6


title: Whole blood twin 40A

description:
ITR 040A
Healthy sample

source_name: human whole blood, 22.3-year-old male

value: 22.3 years


title: Whole blood twin 40B

description:
ITR 040B
Healthy sample


title: IgG-IP sample 4

city: Toronto

first: Freda

middle: D

last: Miller

state: Ontario

address: 686 Bay Street

institute: Hospital for Sick Children

description: RNA enriched in IgG immunoprecipitates from embryonic E12-13 mouse cortices

hyb_protocol: Samples were hybridized with Mouse Gene 2.0 ST Arrays (Affymetrix) and scanned at the HSC Microarray Facility.

scan_protocol: The hybridized microarray image was scanned with the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw probe intensity values were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) algorithm at the gene level in the Affymetrix Expression Console program.

source_name: E12-13 cortices_IgG-IP

label_protocol: cDNA was generated and amplified with the NuGEN Pico protocol (NuGEN) and then labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Pregnant CD1 mouse were purchased from Charles River.

extract_protocol: IgG or 4ET-bound RNA were purified with the Magna RIP RNA-Binding Protein Immunoprecipitation Kit as per manufacturer's instructions (Millipore). Total RNA was isolated, extracted with phenol/chloroform, and quality checked on a BioAnalyzer (Agilent).

treatment_protocol: E12-13 mouse embryos were dissected and cortices were freshly collected for RNA purification and extraction.

tag: strain

value: embryonic cortices

tag: molecule subtype

value: IgG-bound RNA


title: RU Sox2 ChIP Rep 1

description: Sox2 ChIP-chip DNA from MCF7 RU cells - Replicate 1


title: Acne lesion_Pt5


title: input sample 4

description: total RNA from embryonic E12-13 mouse cortices

source_name: E12-13 cortices_input

value: total RNA


title: Whole blood twin 28B

description:
ITR 028B
Healthy sample

source_name: human whole blood, 22.02-year-old male

value: 22.02 years


title: Acne non lesional_Pt4


title: Acne lesion_Pt4


title: IgG-IP sample 3


title: RR Sox2 ChIP Rep 2

description: Sox2 ChIP-chip DNA from MCF7 RR cells - Replicate 2

source_name: Sox2 ChIP DNA from RR cells

value: Breast cancer cells, estrogen receptor positive

value: Reporter responsive (RR)


title: Whole blood twin 23B

description:
ITR 023B
Healthy sample

source_name: human whole blood, 21.08-year-old female

value: 21.08 years


title: 4ET-IP sample 3

description: RNA enriched in 4ET immunoprecipitates from embryonic E12-13 mouse cortices

source_name: E12-13 cortices_4ET-IP

value: 4ET-bound RNA


title: Whole blood twin 50B

description:
ITR 050B
Healthy sample


title: RR Sox2 ChIP Rep 1

description: Sox2 ChIP-chip DNA from MCF7 RR cells - Replicate 1

value: None, input DNA


title: RU IgG ChIP

description: IgG ChIP-chip DNA from MCF7 RU cells

source_name: IgG ChIP DNA from RU cells

value: IgG


title: Acne non lesional_Pt7

value: whole skin

value: non-lesional skin


title: input sample 3


title: Acne non lesional_Pt3


title: Whole blood twin 23A

description:
ITR 023A
Healthy sample

value: female

value: healthy


title: Whole blood twin 14A

description:
ITR 014A
Healthy sample

source_name: human whole blood, 21.46-year-old female

value: whole blood

value: 21.46 years


title: Whole blood twin 20A

description:
ITR 020A
Healthy sample

source_name: human whole blood, 58.55-year-old female

value: 58.55 years


title: Acne lesion_Pt3

value: lesional skin


title: Whole blood twin 28A

description:
ITR 028A
Healthy sample

value: male


title: Whole blood twin 20B

description:
ITR 020B
Healthy sample


title: Acne lesion_Pt2


title: Whole blood twin 14B

description:
ITR 014B
Healthy sample


title: input sample 2

value: embryonic cortices

value: total RNA


title: Whole blood twin 11A

description:
ITR 011A
Healthy sample

source_name: human whole blood, 59.63-year-old female

value: 59.63 years


title: Acne non lesional_Pt2


title: Whole blood twin 7B

description:
ITR 007B
Healthy sample

source_name: human whole blood, 60.14-year-old male

value: 60.14 years


title: 4ET-IP sample 2


title: Whole blood twin 11B

description:
ITR 011B
Healthy sample


title: input sample 1


title: Acne non lesional_Pt1

source_name: non-lesional skin of acne patients


title: Acne lesion_Pt1


title: 4ET-IP sample 1


title: Whole blood twin 7A

description:
ITR 007A
Healthy sample


title: NOI002

city: Wuhan

first: Zhao

middle: Lian

last: Zhong

address: Shizishan Street

country: China

institute: Huazhong Agriculture University

hyb_protocol: The samples were hybridized with the miRCURY™ LNA (locked nucleic acid) Array (v.11.0)

scan_protocol: Hybridizations between RNA samples and the spotted probes were performed with an Automated Hybridization Station (Lucidea Slide Processor; GE Healthcare, Piscataway, NJ). Signal scanning was performed with the Axon GenePix 4000B.

data_processing:
Microarray Scanner and raw image intensities were read with GenePix Pro software, V6.0.
The signal intensity values obtained were normalized to per-chip median values and then applied to obtain geometric means and standard deviations for each miRNA

label_protocol: The samples were labelled using the miRCURY™ Hy3™/Hy5™ Array Power Labelling Kit.

growth_protocol: Human lung epithelial cells (A549)  were cultured in F12 with 10%FBS

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) and further purified with the RNeasy Mini Kit (Qiagen, Valencia, CA), following the manufacturer’s instructions.

treatment_protocol: Cells were grown in T-flasks (25 cm2) and identically processed by removing their growth medium, washed three times with PBS before adding serum-free medium containing hm/06 virus of 103 TCID50 for 36 h. The uninfected cells group as the mock simulated the procedure for virus infection.

value: human lung epithelial cells

tag: infected with

value: none (uninfected control)


title: HNI001

value: H5N1 Influenza A Virus (hm/06)


title: HNI002


title: NOI001


title: HNI003


title: NOI003


title: MSC cultured in human MSC media, MSC-19

description: Healthy sample

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

source_name: human mesenchymal stem cells, 79-year-old female

value: mesenchymal stem cells (MSCs)

value: 79 years


title: MSC cultured in human MSC media, MSC-18

description: Healthy sample

source_name: human mesenchymal stem cells, 87-year-old male

value: 87 years


title: MSC cultured in human MSC media, MSC-17

description: Healthy sample

source_name: human mesenchymal stem cells, 70-year-old female

value: female

value: 70 years


title: MSC cultured in human MSC media, MSC-16

description: Healthy sample

source_name: human mesenchymal stem cells, 61-year-old female

value: 61 years

value: healthy


title: MSC cultured in human MSC media, MSC-15

description: Healthy sample

source_name: human mesenchymal stem cells, 91-year-old female

value: 91 years


title: MSC cultured in human MSC media, MSC-14

description: Healthy sample

source_name: human mesenchymal stem cells, 87-year-old female


title: MSC cultured in human MSC media, MSC-12

description: Healthy sample

source_name: human mesenchymal stem cells, 22-year-old male

value: 22 years


title: MSC cultured in human MSC media, MSC-8

description: Healthy sample

source_name: human mesenchymal stem cells, 9-year-old female

value: 9 years


title: MSC cultured in human MSC media, MSC-7

description: Healthy sample

source_name: human mesenchymal stem cells, 2-year-old female

value: 2 years


title: MSC cultured in human MSC media, MSC-9

description: Healthy sample

source_name: human mesenchymal stem cells, 19-year-old male

value: male

value: 19 years


title: MSC cultured in human MSC media, MSC-11

description: Healthy sample


title: MSC cultured in human MSC media, MSC-13

description: Healthy sample

source_name: human mesenchymal stem cells, 18-year-old male

value: 18 years


title: IgG-IP sample 2

source_name: E12-13 cortices_IgG-IP

value: embryonic cortices

value: IgG-bound RNA


title: Genomic DNA from LC63

status: Public on Sep 24 2014

city: Iowa City

first: Robert

middle: Alan

last: Philibert

address: 500 Newton Rd

institute: University of Iowa

description:
Sample 92
LC63
Control LC sample.

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 BeadChip using the standard Illumina protocol.

data_processing: Genome Studios V2011.1.

label: Cy5 and Cy3

source_name: Control

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from LC samples using the QIAmp DNA Blood Mini Kit according to standard instructions.

value: lymphocyte cells (LC)

tag: sample type

value: control

tag: individual


title: Genomic DNA from LC58

description:
Sample 86
LC58
Control LC sample.


title: MSC cultured in human MSC media, MSC-5

description: Healthy sample

source_name: human mesenchymal stem cells, 10-year-old female

value: mesenchymal stem cells (MSCs)

value: 10 years


title: Genomic DNA from LC57 at T1

description:
Sample 84
LC57-1
Case at T1 LC sample.

source_name: Case at T1

value: alcohol consumption

value: case


title: MSC cultured in human MSC media, MSC-3

description: Healthy sample

value: female


title: Genomic DNA from LC57 at T2

description:
Sample 85
LC57-2
Case at T2 LC sample.

source_name: Case at T2


title: Genomic DNA from LC59 at T1

description:
Sample 87
LC59-1
Case at T1 LC sample.


title: Genomic DNA from LC61 at T1

description:
Sample 90
LC61-1
Case at T1 LC sample.


title: MSC cultured in human MSC media, MSC-1

description: Healthy sample

source_name: human mesenchymal stem cells, 6-year-old female

value: 6 years

value: healthy


title: MSC cultured in human MSC media, MSC-2

description: Healthy sample

source_name: human mesenchymal stem cells, 3-year-old female

value: 3 years


title: MSC cultured in human MSC media, MSC-6

description: Healthy sample

source_name: human mesenchymal stem cells, 10-year-old male


title: Genomic DNA from LC62 at T1

description:
Sample 91
LC62-1
Case at T1 LC sample.


title: Genomic DNA from LC51 at T2

description:
Sample 78
LC51-2
Case at T2 LC sample.


title: Genomic DNA from LC59 at T2

description:
Sample 88
LC59-2
Case at T2 LC sample.


title: Genomic DNA from LC60

description:
Sample 89
LC60
Control LC sample.


title: Genomic DNA from LC53

description:
Sample 80
LC53
Control LC sample.


title: Genomic DNA from LC56

description:
Sample 83
LC56
Control LC sample.


title: MSC cultured in human MSC media, MSC-10

description: Healthy sample

value: 22 years


title: Genomic DNA from LC54 at T1

description:
Sample 81
LC54-1
Case at T1 LC sample.


title: Genomic DNA from LC52 at T1

description:
Sample 79
LC52-1
Case at T1 LC sample.


title: MSC cultured in human MSC media, MSC-20

description: Healthy sample

source_name: human mesenchymal stem cells, 77-year-old female

value: 77 years


title: MSC cultured in human MSC media, MSC-4

description: Healthy sample

source_name: human mesenchymal stem cells, 12-year-old female

value: 12 years


title: Genomic DNA from LC55

description:
Sample 82
LC55
Control LC sample.

value: male


title: Genomic DNA from LC50

description:
Sample 76
LC50
Control LC sample.


title: Genomic DNA from LC49 at T1

description:
Sample 74
LC49-1
Case at T1 LC sample.


title: Genomic DNA from LC51 at T1

description:
Sample 77
LC51-1
Case at T1 LC sample.


title: A375

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

scan_protocol: Standard Illumina scanning protocol

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

source_name: culture cells

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

growth_protocol: The cells were maintained in DMEM medium supplemented with 10% (v/v) FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin under 5% CO2 with 100% humidity at 37 degree

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: The suspended cells were derived from adherent cells by plating  onto sterile plastic dishes at the density of 4x10^5 cells per 10 ml under the same culture medium as adherent culture did. Reattached cells were prepared by inoculating suspended cells onto culture dish with fresh culture medium for attachment in 1 day.

value: adherent A375 cells

value: melanoma


title: A375s

value: suspended A375 cells


title: Genomic DNA from LC43 at T2

description:
Sample 66
LC43-2
Case at T2 LC sample.

value: lymphocyte cells (LC)


title: Genomic DNA from LC48

description:
Sample 73
LC48
Control LC sample.

value: control


title: Genomic DNA from LC47 at T2

description:
Sample 72
LC47-2
Case at T2 LC sample.


title: Genomic DNA from LC49 at T2

description:
Sample 75
LC49-2
Case at T2 LC sample.


title: Genomic DNA from LC46

description:
Sample 70
LC46
Control LC sample.


title: Genomic DNA from LC45 at T1

description:
Sample 68
LC45-1
Case at T1 LC sample.


title: Genomic DNA from LC43 at T1

description:
Sample 65
LC43-1
Case at T1 LC sample.


title: Genomic DNA from LC38

description:
Sample 58
LC38
Control LC sample.


title: Genomic DNA from LC41 at T1

description:
Sample 62
LC41-1
Case at T1 LC sample.


title: Genomic DNA from LC65 at T2

description:
Sample 54
LC65-2
Case at T2 LC sample.


title: Genomic DNA from LC45 at T2

description:
Sample 69
LC45-2
Case at T2 LC sample.


title: Genomic DNA from LC44

description:
Sample 67
LC44
Control LC sample.


title: Genomic DNA from LC39 at T1

description:
Sample 60
LC39-1
Case at T1 LC sample.


title: A375r

value: reattached A375 cells


title: Genomic DNA from LC65 at T1

description:
Sample 53
LC65-1
Case at T1 LC sample.


title: Genomic DNA from LC37 at T1

description:
Sample 56
LC37-1
Case at T1 LC sample.


title: Genomic DNA from LC66

description:
Sample 55
LC66
Control LC sample.


title: Genomic DNA from LC41 at T2

description:
Sample 63
LC41-2
Case at T2 LC sample.


title: Genomic DNA from LC33 at T2

description:
Sample 51
LC33-2
Case at T2 LC sample.


title: Genomic DNA from LC39 at T2

description:
Sample 59
LC39-2
Case at T2 LC sample.


title: Genomic DNA from LC37 at T2

description:
Sample 57
LC37-2
Case at T2 LC sample.


title: Genomic DNA from LC40

description:
Sample 61
LC40
Control LC sample.


title: Genomic DNA from LC35 at T1

description:
Sample 49
LC35-1
Case at T1 LC sample.


title: Genomic DNA from LC64

description:
Sample 52
LC64
Control LC sample.


title: Genomic DNA from LC32

description:
Sample 46
LC32
Control LC sample.


title: Genomic DNA from LC36

description:
Sample 50
LC36
Control LC sample.


title: Genomic DNA from LC33 at T1

description:
Sample 47
LC33-1
Case at T1 LC sample.


title: Genomic DNA from LC31 at T1

description:
Sample 44
LC31-1
Case at T1 LC sample.


title: Genomic DNA from LC31 at T2

description:
Sample 45
LC31-2
Case at T2 LC sample.


title: Genomic DNA from LC28

description:
Sample 41
LC28
Control LC sample.


title: Genomic DNA from LC27 at T1

description:
Sample 40
LC27-1
Case at T1 LC sample.


title: mhz4_Shoot_ET, biological rep1

city: Los Angeles

first: Xiang

last: Lu

state: CA

address: 10833 Le Conte Ave

department: Department of Molecular and Medical Pharmaacology

institute: University of California, Los Angeles

description: ethylene treatment in etiolated seedling

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Oryza sativa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with Microarray Suite using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa

source_name: Shoot

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: The seeds were soaked in tap-water and germinated at 37°C in the dark for two days (change the water daily).

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

treatment_protocol: For ethylene treatment, we reduced the amount of water to 1.5-1.7cm below the seeds.Three-day old seedlings were treated with ethylene (10 ppm) for 8 hours at 28°C in the dark. Seedling grown in the air was used as control.

tag: treatment

value: ethylene treatment

tag: tissue

value: Shoot

tag: genotype


title: mhz4_Shoot_AT, biological rep1

description: air treatment in etiolated seedling

value: air treatment


title: mhz5_Shoot_AT, biological rep1

description: air treatment in etiolated seedling


title: Genomic DNA from LC29 at T1

description:
Sample 42
LC29-1
Case at T1 LC sample.

tag: gender

tag: disease state

value: alcohol consumption

value: case


title: WT_Root_ET mb, biological rep1

source_name: Root

value: Root

value: WT


title: Genomic DNA from LC47 at T1

description:
Sample 71
LC47-1
Case at T1 LC sample.


title: WT_Shoot_ET, biological rep1


title: mhz5_Root_ET, biological rep1


title: Genomic DNA from LC34

description:
Sample 48
LC34
Control LC sample.


title: WT_Shoot_AT, biological rep1

description: air treatment in etiolated seedling


title: Genomic DNA from LC25 at T2

description:
Sample 38
LC25-2
Case at T2 LC sample.

value: female


title: Genomic DNA from LC23 at T2

description:
Sample 35
LC23-2
Case at T2 LC sample.


title: Genomic DNA from LC30

description:
Sample 43
LC30
Control LC sample.


title: mhz4_Root_ET, biological rep1


title: mhz1_Root_ET, biological rep1


title: Genomic DNA from LC21 at T2

description:
Sample 32
LC21-2
Case at T2 LC sample.


title: WT_Root_AT mb, biological rep1

description: air treatment in etiolated seedling


title: mhz5_Root_AT, biological rep1

description: air treatment in etiolated seedling


title: Genomic DNA from LC22

description:
Sample 33
LC22
Control LC sample.


title: mhz8_Root_ET, biological rep1


title: Genomic DNA from LC26

description:
Sample 39
LC26
Control LC sample.


title: WT_Root_ET, biological rep1


title: Genomic DNA from LC21 at T1

description:
Sample 31
LC21-1
Case at T1 LC sample.


title: mhz5_Shoot_ET, biological rep1


title: mhz4_Root_AT, biological rep1

description: air treatment in etiolated seedling


title: Genomic DNA from LC23 at T1

description:
Sample 34
LC23-1
Case at T1 LC sample.


title: mhz1_Root_AT, biological rep1

description: air treatment in etiolated seedling


title: mhz2_Root_AT, biological rep1

description: air treatment in etiolated seedling


title: mhz8_Root_AT, biological rep1

description: air treatment in etiolated seedling


title: Genomic DNA from LC25 at T1

description:
Sample 37
LC25-1
Case at T1 LC sample.


title: Genomic DNA from LC20

description:
Sample 30
LC20
Control LC sample.


title: mhz2_Root_ET, biological rep1


title: Os-74, biological rep1

description: Gene expression data from 14-day-old rice seedlings

source_name: truncated OsSIK2-overexpression line

growth_protocol: Seeds of rice (O. sativa ssp. japonica cv. TP309 and O. sativa ssp. japonica cv. Nipponbare) were sown in pots (8 X 8 X 10 cm) containing 180 g vermiculite soaked with water. All plants were grown under white fluorescent light (600 photons/m2s, 12-h light/12-h dark) at 28ºC and 75% relative humidity.

treatment_protocol: The aerial parts of 14-day-old rice seedlings were harvested for total RNA isolation using TRNzol reagent (Tiangen).

tag: development stage

value: 14-day-old seedlings

tag: genetic background

value: truncated OsSIK2-overexpression line

value: seedling


title: Genomic DNA from LC16

description:
Sample 24
LC16
Control LC sample.

tag: cell type


title: WT_Root_AT, biological rep1

description: air treatment in etiolated seedling


title: Genomic DNA from LC42

description:
Sample 64
LC42
Control LC sample.

value: male


title: TP309, biological rep1

source_name: control of OsSIK2-overexpression line

value: O. sativa ssp. japonica cv. TP309 and O. sativa ssp. japonica cv. Nipponbare

value: wt control of OsSIK2-overexpression line


title: Genomic DNA from LC24

description:
Sample 36
LC24
Control LC sample.

value: lymphocyte cells (LC)


title: Os-72, biological rep1


title: Os-17, biological rep1

source_name: OsSIK2-overexpression line

value: OsSIK2-overexpression line


title: Nip, biological rep1

source_name: control of OsSIK2 mutant

value: wt control of OsSIK2 mutant


title: Genomic DNA from LC18

description:
Sample 27
LC18
Control LC sample.

value: control


title: Genomic DNA from LC15 at T2

description:
Sample 23
LC15-2
Case at T2 LC sample.

tag: time point


title: Genomic DNA from LC17 at T2

description:
Sample 26
LC17-2
Case at T2 LC sample.


title: Genomic DNA from LC19 at T1

description:
Sample 28
LC19-1
Case at T1 LC sample.


title: Genomic DNA from LC19 at T2

description:
Sample 29
LC19-2
Case at T2 LC sample.


title: Os-15, biological rep1


title: iPS-MSC_M5C1_d35

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: Affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: iPSC-derived MSCs (iPS-MSCs)

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was isolated with the NucleoSpin® miRNA Isolation Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: MSCs were isolated from bone marrow (tibia plateau) after written consent using guidelines approved by the Ethic Committee of the Use of Human Subjects at the University of Aachen (permit number: EK128/09). MSCs from three donors were infected with pMXs based retroviruses (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4, and c-MYC genes. Established iPSCs were maintained on MEFs in DMEM/F12 medium supplemented with Glutamax, 20% knockout serum replacer, 1% nonessential amino acids, 1x penicillin/streptomycin, 1x L-glutamine, 0.1 mM β-Mercaptoethanol, and 50 ng/ml basic fibroblast growth factor (Peprotech, Hamburg, Germany). To exclude contamination of feeder layer cells, iPSCs were adjusted to a feeder-free system on matrigel (BD Biosciences, San Jose, CA, USA) in mTeSR™1 medium (Stemcell Technologies, Vancouver, BC, Canada) for at least three passages. Cells were passaged every 5-6 days enzymatically with dispase (1 g/ml, Stemcell Technologies). For re-differentiation of iPSC towards iPS-MSCs medium was simply exchanged for MSC standard medium supplemented with 10% human platelet lysate (hPL) for 7 days, and cells were then further passaged in culture wells coated with 0.1% gelatin (Sigma-Aldrich, St. Louis, CA, USA).

tag: donor

value: donor 5; clone 1

value: iPS-MSC

tag: passage

value: passage 4


title: iPS-MSC_M2C6_d35

value: donor 2; clone 6


title: Genomic DNA from LC14

description:
Sample 21
LC14
Control LC sample.

source_name: Control


title: iPS-MSC_M2C6_d28

value: passage 3


title: Genomic DNA from LC13 at T1

description:
Sample 19
LC13-1
Case at T1 LC sample.

value: alcohol consumption

value: case


title: Genomic DNA from LC11 at T2

description:
Sample 17
LC11-2
Case at T2 LC sample.


title: sik2, biological rep1

source_name: OsSIK2 mutant

value: 14-day-old seedlings

value: OsSIK2 mutant


title: Genomic DNA from LC17 at T1

description:
Sample 25
LC17-1
Case at T1 LC sample.

source_name: Case at T1


title: Genomic DNA from LC11 at T1

description:
Sample 16
LC11-1
Case at T1 LC sample.


title: iPS-MSC_M4C4_d35

value: donor 4; clone 4