title: mycelia_BI-added-24hrs_sampled-48hrs_rep3

city: Åbo

first: Elina

last: Palonen

address: Artillerigatan 6

department: Biochemistry, Faculty of Science and Engineering

institute: Åbo Akademi University

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E3_48hrs

scan_protocol: According to Agilent protocol: One-Color Microarray-Based Gene Expression Analysis, Version 5.5. The used scanner was Agilent Microarray Scanner G2565BA

data_processing: The data was extracted using Agilent Feature Extraction Software version 9.5.3.1 with default parameters of protocol GE1-v5_95_Feb07. The following steps were performed using R/Bioconductor (version 2.14.1) limma package. The raw FE data was loaded into R using function read.maimages with default parameters with “gIsFound” parameter included. Since the eArray probe design had been modified in the middle of the labelling and hybridisation process, by constructing four additional gene probes, the signal intensities of them had to be removed directly after the feature extraction in order to enable the comparability between all of the arrays. Thus the two loaded FE data sets that originated from the original and modified array designs, have been combined utilising the “ProbeName” column. The background correction and normalisation was performed thereafter using R/Bioconductor (version 2.14.1) limma package, with functions backgroundCorrect (parameters method=“normexp” and normexp.method=“saddle”) and normalizeBetweenArrays (parameter method=“quantile”).

organism: Aspergillus terreus

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 24 hours, sampled at 48 hours p.i.

label_protocol: According to Agilent protocols: One-Color Microarray-Based Gene Expression Analysis, Version 5.5 and Agilent Low RNA Input Linear Amplification Kit PLUS One-Color, version 4.0. Agilent One Color RNA Spike-In Kit was also included in the labeling.

growth_protocol: A. terreus MUCL38669 was cultured under submerged growth conditions with GPY-L production medium at 27 °C for 216 hours and sampled at six time points post inoculation (24 hrs, 48 hrs, 96 hrs, 120 hrs, 144 hrs and 216 hrs).

extract_protocol: The total RNA was isolated from snap-frozen A. terreus mycelia, sampled at the six time points, according to Qiagen RNeasy Plant Mini Kit protocol with following modifications: The frozen mycelia was ground to fine powder under liquid nitrogen using RNase-free mortar and pestle. RLC Buffer was added to the ground mycelia and the isolation was continued as instructed.

tag: tissue

value: mycelia


title: mycelia_BI-added-24hrs_sampled-120hrs_rep3

status: Public on May 08 2017

type: RNA

country: Finland

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E3_120hrs

hyb_protocol: According to Agilent protocol: One-Color Microarray-Based Gene Expression Analysis, Version 5.5

molecule: total RNA

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 24 hours, sampled at 120 hours p.i.

tag: strain


title: mycelia_BI-added-24hrs_sampled-96hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E2_96hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 24 hours, sampled at 96 hours p.i.


title: mycelia_BI-added-24hrs_sampled-144hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E3_144hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 24 hours, sampled at 144 hours p.i.


title: mycelia_BI-added-24hrs_sampled-216hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E3_216hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 24 hours, sampled at 216 hours p.i.


title: mycelia_BI-added-24hrs_sampled-96hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E3_96hrs


title: mycelia_BI-added-24hrs_sampled-48hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E2_48hrs


title: mycelia_BI-added-24hrs_sampled-216hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E2_216hrs


title: mycelia_BI-added-24hrs_sampled-144hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E2_144hrs


title: mycelia_BI-added-24hrs_sampled-120hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E2_120hrs


title: mycelia_BI-added-24hrs_sampled-120hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E1_120hrs


title: mycelia_BI-added-24hrs_sampled-144hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E1_144hrs


title: mycelia_BI-added-24hrs_sampled-216hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E1_216hrs


title: mycelia_BI-added-24hrs_sampled-48hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E1_48hrs


title: mycelia_BI-added-24hrs_sampled-96hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: E1_96hrs


title: mycelia_BI-added-120hrs_sampled-96hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D3_96hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 120 hours, sampled at 96 hours p.i.


title: mycelia_BI-added-120hrs_sampled-120hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D3_120hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 120 hours, sampled at 120 hours p.i.


title: mycelia_BI-added-120hrs_sampled-144hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D3_144hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 120 hours, sampled at 144 hours p.i.


title: mycelia_BI-added-120hrs_sampled-216hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D3_216hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 120 hours, sampled at 216 hours p.i.


title: mycelia_BI-added-120hrs_sampled-48hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D2_48hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 120 hours, sampled at 48 hours p.i.


title: mycelia_BI-added-120hrs_sampled-96hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D1_96hrs


title: mycelia_BI-added-120hrs_sampled-96hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D2_96hrs


title: mycelia_BI-added-120hrs_sampled-144hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D2_144hrs


title: cell_isolated_E4_rep3

status: Public on May 09 2017

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

country: USA

institute: Iowa State University

description: Gene expression data from a single developing chick retinal cell

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip Chicken arrays using standard Affymetrix protocols at either the GeneChip Facility at Iowa State University or the University of Iowa.

scan_protocol: Affymetrix GeneChip Chicken arrays were scanned using standard protocols at either the GeneChip Facility at Iowa State University or the University of Iowa.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: biotin

molecule: polyA RNA

organism: Gallus gallus

source_name: E4 chicken retina

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

growth_protocol: Retinas were dissected and disocciated with papain at different timepoints. There was no culture or time for growth.

extract_protocol: Individual chicken retinal cells were harvested using a pulled glass pipette and were expelled into cold lysis buffer. The total single cell RNA was reverse transcribed using Superscript III combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

treatment_protocol: Single cells were isolated and immediately placed into cell lysis buffer.

value: dissociated retina

tag: time point


title: mycelia_BI-added-120hrs_sampled-216hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D2_216hrs


title: mycelia_BI-added-120hrs_sampled-216hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D1_216hrs


title: mycelia_BI-added-120hrs_sampled-48hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D1_48hrs


title: mycelia_no-BI-added_sampled-144hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: A1_144hrs

source_name: A. terreus submerged culture mycelia, no added butyrolactone I, sampled at 144 hours p.i.


title: mycelia_no-BI-added_sampled-48hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: A1_48hrs

source_name: A. terreus submerged culture mycelia, no added butyrolactone I, sampled at 48 hours p.i.


title: mycelia_BI-added-120hrs_sampled-120hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D1_120hrs


title: mycelia_BI-added-24hrs_sampled-24hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: E3_24hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 24 hours, sampled at 24 hours p.i.


title: mycelia_BI-added-120hrs_sampled-144hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D1_144hrs


title: mycelia_no-BI-added_sampled-216hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: A1_216hrs

source_name: A. terreus submerged culture mycelia, no added butyrolactone I, sampled at 216 hours p.i.


title: mycelia_no-BI-added_sampled-96hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: A1_96hrs

source_name: A. terreus submerged culture mycelia, no added butyrolactone I, sampled at 96 hours p.i.


title: mycelia_BI-added-120hrs_sampled-120hrs_rep2

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D2_120hrs


title: Ep300-knockdown sample 2

city: Baltimore

first: Ling

last: He

state: MD

address: 600 North Wolfe St

department: Department of Pediatrics-Division of Endocrinology

institute: The Johns Hopkins University School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Affiymetrix GeneChip scanner 3000 with G7 upgrade (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

data_processing:
Raw gene expression data, Affymetrix exon CEL files, were extracted and RMA (Robust Multi-array Average) (Bolstad BM et al 2003, Irizarry RA et al. 2003) normalized using Partek Genomics Suite analytic platform (Parteck Inc. St. Louis, MO)
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

organism: Mus musculus

source_name: Liver tissue of 4 months old Male C57BL/6 mice (6h fasting)

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: 14 weeks old C57BL/6 mice were fed on a regular chow diet. One week after the viral injection, mice were fed on high-fat diet (60% calorie from fat) for another week before the termination of experiment.

extract_protocol: RNA was purified by using Trizol, followed by Qiagen RNeasy kit.

treatment_protocol: 15 weeks old C57BL/6 mice were injected with AAV-shSCR or shP300 (1x10^13 GC/mouse) through jugular vein.  Dissected liver was snap-frozen in liquid nitrogen, and stored at  80°C until extraction.

value: Liver

tag: gender

value: Male

tag: age

value: 4 months

tag: shRNA treatment

value: AAV-shRNA Ep300 knockdown


title: mycelia_BI-added-120hrs_sampled-24hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: D2_24hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 120 hours, sampled at 24 hours p.i.


title: mycelia_no-BI-added_sampled-120hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: A1_120hrs

source_name: A. terreus submerged culture mycelia, no added butyrolactone I, sampled at 120 hours p.i.


title: mycelia_BI-added-120hrs_sampled-24hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: D3_24hrs


title: Ep300-knockdown sample 3


title: mycelia_no-BI-added_sampled-24hrs_rep1

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: A1_24hrs

source_name: A. terreus submerged culture mycelia, no added butyrolactone I, sampled at 24 hours p.i.


title: mycelia_BI-added-24hrs_sampled-24hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: E2_24hrs


title: Ep300-knockdown sample 4


title: mycelia_BI-added-24hrs_sampled-24hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: E1_24hrs


title: mycelia_BI-added-96hrs_sampled-24hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C3_24hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 96 hours, sampled at 24 hours p.i.


title: mycelia_BI-added-96hrs_sampled-48hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C3_48hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 96 hours, sampled at 48 hours p.i.


title: Ep300-knockdown sample 1


title: Control replicate 2

value: AAV-shRNA scrambled control


title: mycelia_BI-added-120hrs_sampled-24hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: D1_24hrs


title: mycelia_BI-added-96hrs_sampled-216hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C3_216hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 96 hours, sampled at 216 hours p.i.


title: mycelia_BI-added-96hrs_sampled-144hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C3_144hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 96 hours, sampled at 144 hours p.i.


title: mycelia_BI-added-120hrs_sampled-48hrs_rep3

description:
Modified array design with four additional probes (add. probe name CUST_XXXXX_PI390722834), 41600 gene probes, 43017 probes in total. The four additional probe signal intensities were removed directly after feature extraction step to enable normalisation between all of the arrays.
Sample name: D3_48hrs


title: mycelia_BI-added-96hrs_sampled-96hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C3_96hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 96 hours, sampled at 96 hours p.i.


title: Control replicate 1


title: Control replicate 3


title: Control replicate 4


title: mycelia_BI-added-96hrs_sampled-24hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C2_24hrs


title: mycelia_BI-added-96hrs_sampled-216hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C2_216hrs


title: mycelia_BI-added-96hrs_sampled-48hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C2_48hrs


title: mycelia_BI-added-96hrs_sampled-120hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C2_120hrs

source_name: A. terreus submerged culture mycelia, butyrolactone I was added at 96 hours, sampled at 120 hours p.i.


title: mycelia_BI-added-96hrs_sampled-120hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C3_120hrs


title: Con Young_8784129023_B

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

value: male

value: 2 months

tag: treated with

value: vehicle (ethanol:cremophor:saline 1:1:18) for 28 days

value: Hippocampus


title: mycelia_BI-added-96hrs_sampled-96hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C2_96hrs


title: RECS1 HKO 3

city: Wuhan

first: Hongliang

last: Li

state: Hubei

address: JieFang Road 238, Wuhan

department: Department of Cardiology

country: China

institute: Renmin Hospital of Wuhan University

description: Gene expression data from RECS1 HKO mice treated with HFD for 8 weeks

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃.

scan_protocol: GeneChips were scanned using the Scanner 7G.

data_processing: The data were analyzed The data were analyzed with R/Bioconductor. RMA analysis was employed to normalize and evaluate the gene expression. The differentially expressed genes (DEGs) were obtained by limma R package with the standard that fold > 2 & P < 0.05.

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA

growth_protocol: The mice were exposed to a 12-h light/dark cycle with controlled temperature and humidity. Food and water were provided ad libitum.

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

treatment_protocol: Mice were treated with HFD for 8 weeks, the livers were dissected and immediately put in RNA later reagent.

tag: genotype

value: liver

tag: diet

value: high fat diet (HFD)

tag: background strain

value: 16 weeks


title: Con Old_8784129023_F

value: 12 months


title: mycelia_BI-added-96hrs_sampled-144hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C2_144hrs


title: Con Young_8784129009_F


title: mycelia_BI-added-96hrs_sampled-96hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C1_96hrs


title: THC Old_8784129014_D

value: 3 mg/kg/day Δ9-THC for 28 days


title: mycelia_BI-added-96hrs_sampled-48hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C1_48hrs


title: THC Old_8784129014_C


title: THC Old_8784129023_D


title: Con Old_8784129009_C


title: THC Young_8784129023_E


title: mycelia_BI-added-96hrs_sampled-216hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C1_216hrs


title: THC Young_8784129014_A


title: Con Old_8784129009_D


title: RECS1 HKO 2


title: mycelia_BI-added-96hrs_sampled-24hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C1_24hrs


title: RECS1 HKO 1


title: Con Old_8136594043_D


title: mycelia_no-BI-added_sampled-216hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A3_216hrs


title: Con Young_8136594043_B


title: mycelia_BI-added-96hrs_sampled-120hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C1_120hrs


title: mycelia_no-BI-added_sampled-120hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A3_120hrs


title: mycelia_no-BI-added_sampled-24hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A3_24hrs


title: THC Old_8136594043_C


title: Con Old_8136594043_F


title: Control 3

description: Gene expression data from control mice treated with HFD for 8 weeks


title: mycelia_no-BI-added_sampled-144hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A3_144hrs


title: mycelia_no-BI-added_sampled-96hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A3_96hrs


title: THC Old_8784129014_B


title: THC Young_8784129009_B


title: mycelia_BI-added-96hrs_sampled-144hrs_rep1

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: C1_144hrs


title: KO_18h_2

status: Public on May 07 2017

type: SRA

city: Boston

first: Kai

middle: W

last: Wucherpfennig

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

description:
Processed data file: STAR_Gene_Counts.csv
Processed data file: Cuff_Gene_Counts.csv

library_source: transcriptomic

data_processing:
Illumina Bcl2fastq v2.18.
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5).
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks v2.2.1.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: STAR_Gene_Counts.csv: Comma-separated text file includes raw gene counts for each sample.
Supplementary_files_format_and_content: Cuff_Gene_Counts.csv: Comma-separated text file includes normalized RPKM counts for each sample.

source_name: Spleen and lymph nodes

growth_protocol: CD8 T cells were isolated form spleens and lymph nodes by negative selection (EasySep CD8+ negative selection kit, Stem Cell) and cultured in RMPI-1640 supplemented with 10% fetal calf serum, 50 units/ml Penicillin-Streptomycin, 10 mM HEPES, 2 mM L-glutamine, and 55 microM beta-mercaptoethanol. Cells were activated using CD3/CD28 Dynabeads (Thermo Fisher) for 2 days, then cultured in supplemented RPMI-1640 with 10ng/mL IL-2 (Biolegend) for a further 5 days.

extract_protocol:
RNA was isolated from cells at each time point (0, 4, 18h) using Direct-zol RNA miniprep kit (Zymo) as per the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After 7 days activation, cells were stimulated with 20ng/mL IFN-beta (Biolegend) for 0, 4, or 18h.

tag: strain/background

tag: genotype/variation

value: miR-31 knockout

tag: cell type

value: CD8 T cell

tag: activation

value: anti-CD3/CD28 beads for 2d, IL-2 for 5d

tag: treatment

value: IFN-beta

tag: treatment duration


title: WT_18h_3

value: wild-type


title: mycelia_no-BI-added_sampled-24hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A2_24hrs

value: mycelia


title: KO_18h_3


title: WT_18h_1


title: WT_18h_2


title: KO_18h_1


title: mycelia_no-BI-added_sampled-48hrs_rep3

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A3_48hrs


title: KO_4h_3


title: KO_4h_2


title: Control 1


title: WT_4h_2


title: KO_4h_1


title: WT_4h_1


title: mycelia_no-BI-added_sampled-48hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A2_48hrs


title: KO_0h_1


title: WT_0h_1


title: WT_0h_2


title: mycelia_no-BI-added_sampled-144hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A2_144hrs

source_name: A. terreus submerged culture mycelia, no added butyrolactone I, sampled at 144 hours p.i.


title: mycelia_no-BI-added_sampled-120hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A2_120hrs


title: mycelia_no-BI-added_sampled-96hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A2_96hrs


title: mycelia_no-BI-added_sampled-216hrs_rep2

description:
Original array design with 41596 gene probes (Probe name CUST_XXXXX_PI351404640), 43013 probes in total.
Sample name: A2_216hrs


title: Control 2


title: KO_0h_2


title: B-2

status: Public on May 06 2017

city: Nanning

first: Wang

last: Yikui

address: north road

institute: Institute Of Vegetable Research, Guangxi Academy Of Agricultural Sciences

hyb_protocol: Chip hybridization was performed overnight using a microcirculation pump (Atactic Technologies, China). The hybridization temperatures of each probe were balanced by chemical modifications of the detection probes. Hybridization was performed in 100 μL 6X SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices, China) and digitized using Array-Pro image analysis software (Media Cybernetics, China).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (locally weighted regression). For signal-color experiments, the ratio of the two sets of detected signals (log2-transformed and balanced) and P-values of the t-test were calculated; P-value < 0.05 and fold change > 2 were considered to indicate differential expression.

organism: Solanum virginianum

source_name: pistil

label_protocol: small RNA samples (S- and L-morph) were hybridized separately. Microarray was performed by LC Sciences Company. Five micrograms of total RNA was size-fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the low-molecular-weight RNAs (<300 nt) were 3′-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later staining with a fluorescent dye; two different tags were used for the two RNA samples in dual-sample experiments.

growth_protocol: The long purple eggplant ‘B3-3’, having two morphologically different types of flowers (termed distylous) on the same plant, which is cultivated mainly in South China, was used in the present study. In one morph, termed thrum or brevistylous flower (S-morph), the stamens are long and the pistils are short, whereas in the other morph, termed pin or longistylous flower (L-morph), the stamens are short and the pistils are long. The B3-3 line was maintained in the Guangxi Academy of Agricultural Sciences and cultivated in a field using conventional methods. The L-morph and S-morph pistils were collected, respectively, starting from the budding stage to blooming.

extract_protocol: Total RNA was isolated from each sample using an RNA Extraction Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions.

treatment_protocol: The tissues were immediately frozen in liquid N2 after excision and stored at -80°C until the RNA was extracted. We divided the period of the flower development into five phases, 1-3, 3-6, 7-9, 10-12 and 13-15 days after budding, respectively. The pistil samples of S-morph and L-morph flower were prepared; each sample consisted of a mixture of pistils harvested in phase 1 and 2,.

tag: developmental stage

value: flower development 3-6 days after budding

value: pistil

tag: tissue morph

value: L-morph pistil


title: B-3

description: long purple eggplant ‘B3-3’, having two morphologically different types of flowers (termed distylous) on the same plant, which is cultivated mainly in South China

tag: tissue


title: Ortice_test_rep3

city: Rende

first: Fabrizio

last: Carbone

state: CS

address: C.da Li Rocchi Vermicelli

department: Research Centre for Olive, Citrus and Tree Fruit

country: Italy

institute: Council for Agricultural Research and Economics (CREA)

description: Arrays include around 20.000 quality control spots

hyb_protocol: The fragmented Cy5-cRNAs were added to the hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% formamide, 100 ng/μl salmon sperm DNA, 0.04% SDS) and poured in the hybridization chambers of the pre-hybridized microarrays, following the CombiMatrix Hybridization protocol. After an overnight incubation at 45°C in a rotating rotisserie oven, microarrays were treated with six washing steps: firstly in 6X SSPE and 0.05% Tween-20 for 5’ at 45°C, then with 3X and 0.5X SSPE and 0.05% Tween-20 for 1’ at room temperature, with 2X PBS and 0.1% Tween-20 and finally twice with 2X PBS for 1’ at room temperature.

scan_protocol: Microarray slides were scanned with the GenePix Pro microarray scanner (Axon Instruments) and data processed with the CombiMatrix Microarray Imager software (CombiMatrix). A maximum threshold of 0.20 for the coefficient of variance (of the spots corresponding to identical probes) was applied to control intra-chip hybridization variability. The correlation among the three technical replicates for each experimental condition was assured by a minimum Pearson coefficient (R) of 0.99.

data_processing: Raw values were normalized on the median of the intensities by the CombiMatrix Probe Weaver software using the quantile algorithm. Pairwise analysis of differential expression was assessed with a Welch's t-test, followed by a Bonferroni-Hochberg FDR adjustment with a cut off p-value of 0.05, using R. To filter lowly expressed sequences, we calculated the average and standard deviation of the expression value of all empty and negative controls and set as threshold the mean value plus two times the standard deviation. Of the filtered significantly differentially expressed probes, only those with greater than 2-fold increase or 2-fold decrease in expression compared to the control condition were used for further analysis.

organism: Olea europaea

source_name: drupe

label_protocol: Two μg of total RNA were retrotranscribed using the RNA ampULSe Amplification and Labeling Kit for CombiMatrix arrays (Kreatech Biotechnology). cRNA labeling was carried out with the Cy5-ULS (Cyanine-Universal Linkage System). Unincorporated dye was removed with KREApure purification columns (Agilent). Labeling yield and quality were assessed using a NanoDrop 1000 (Thermo Scientific). cRNAs were fragmented for 20 min at 95°C in 200 mM Tris Acetate (pH 8.1), 500 mM potassium acetate and 150 mM molybdenum acetate

extract_protocol: Total RNA was isolated from 200 mg of finely ground plant tissue. A purification step was performed in a 1:1:2(v/v/v) solution of phenol, chloroform and RNA Extraction Buffer (1 M Tris-HCl pH 8.5, 5M NaCl, 0.5 M EDTA pH 8.0, 10% SDS) twice, followed by a chloroform purification. RNA was isolated from the aqueous phase using the RNeasy plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

tag: cultivar

value: Ortice

value: damaged


title: A-2

value: flower development 1-3 days after budding

value: S-morph pistil


title: Ruveia_control_rep2

value: Ruveia

value: undamaged


title: A-1


title: Ruveia_control_rep3


title: Ortice_test_rep2


title: Ortice_test_rep1


title: Ruveia_test_rep2


title: Ruveia_test_rep1


title: Ortice_control_rep3


title: Ruveia_test_rep3


title: Ortice_control_rep2


title: Ortice_control_rep1


title: A-3


title: B-1


title: Ruveia_control_rep1


title: Patient 4_8wksPH_keratinocytes

status: Public on May 05 2017

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

description:
Pt4_8wksPH_kera
Illumina Chip Bar Code: 9255013078
patient age not available

data_processing: The data were normalised using CubicSpline with background subtraction using Illumina Genome Studio (V2010.3)

organism: Homo sapiens

source_name: Human skin biopsy

label_protocol: cDNA were synthesized  using NuGEN pico kits from the extracted total RNA and biotinylated cDNA were prepared using a NuGEN labeling kit for Illumina arrays (Ref8_v4)

extract_protocol: RNA from laser captured cells was extracted with Arturus PicoPure RNA isolation kits in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: patient number

tag: cell marker

value: skin

value: Laser captured keratinocytes

tag: sample type

value: 8 weeks post-healed_shedding


title: Patient 1_control_keratinocytes

description:
Pt1_ctrl_kera
Illumina Chip Bar Code: 9255013078
patient age not available

value: contra-lateral control


title: Patient 1_lesion_keratinocytes

description:
Pt1_lesion_kera
Illumina Chip Bar Code: 9255013078
patient age not available

value: lesion


title: Patient 4_control_keratinocytes

description:
Pt4_ctrl_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: Patient 1_8wksPH_shedding_keratinocytes

description:
Pt1_8wksPH_shedding_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: Patient 2_control_keratinocytes

description:
Pt2_ctrl_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: human myotubes, mifepristone plus aldosterone treated, biological rep 3

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

hyb_protocol: Labeled cDNA targets were hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0 for 16 h at 45⁰C rotating at 60 rpm.

scan_protocol: The arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000.

data_processing: For gene expression analysis, arrays were normalized using RMA algorithm in Expression Console and comparisons made in Transcriptome Analysis Console (Affymetrix, Santa Clara, CA).

source_name: normal primary human myotubes

label_protocol: 5.5 µg of cDNA was labeled and fragmented using the GeneChip® WT PLUS reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's instructions.

growth_protocol: grown in skeletal muscle cell growth medium (SkGM-2 bullet kit; Lonza), containing: 1% bovine serum albumin (BSA), 1% fetuin, 1% insulin, 0.1% human epidermal growth factor (hEGF), 0.1% dexamethasone and 0.1% gentamicin/amphotericin B (GA) and cultured at 37⁰C in 5% CO2.  When cells reached ~80% confluence, they were serum restricted in differentiation media (DMEM supplemented with 2% horse serum (Invitrogen) and 100 U/mL penicillin-streptomycin) for 6 days.

extract_protocol: RNA was isolated using TRIzol reagent (Life Technologies), according to manufacturer’s instructions. RNA concentration was determined spectrophotometrically using a Nanodrop ND-100 (Nanodrop Technologies).  Samples were DNAse treated using RQ1 DNAse (Promega) for 30 minutes at 37⁰C, reaction was stopped with a 25:24:1 phenol: chloroform: isoamyl alcohol mixture (Malinckrodt, Fischer, Sigma) and centrifuged 5 minutes (14,000 x g; room temperature).  A chloroform phase separation was performed; the aqueous layer was removed and ethanol (Fisher) precipitated.  The pellet was washed (75% ethanol), centrifuged (14,000 x g, 10 minutes, 4⁰C), air dried (5 minutes) and re-suspended in autoclaved millipore filtered water.  DNAse treated RNA concentration was determined spectrophotometrically and samples were stored at -80⁰C.  Samples for microarray analysis were further purified using the RNeasy mini kit (Qiagen) RNA cleanup protocol and final RNA concentrations were determined. RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  A 100 ng aliquot of total mRNA was linearly amplified.

treatment_protocol: Myotubes were treated for 24 hours with aldosterone (100 nM; Sigma), spironolactone (10 µM; Sigma) plus aldosterone (100 nM), eplerenone (10 µM; Pfizer compound transfer program) plus aldosterone (100 nM), or mifepristone (1 µM; Caymen Chemical) plus aldosterone (100 nM) (dissolved in 100% DMSO unless specified otherwise).  Drugs were added directly to existing differentiation media.

tag: Sex

value: male

value: myotubes


title: human myotubes, mifepristone plus aldosterone treated, biological rep 2


title: Patient 2_8wksPH_shedding_keratinocytes

description:
Pt2_8wksPH_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: Patient 2_lesion_keratinocytes

description:
Pt2_lesion_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: Patient 3_4wksPH_keratinocytes

description:
Pt3_4wksPH_kera
Illumina Chip Bar Code: 9255013078
patient age not available

value: 4 weeks post-healed_shedding


title: Patient 3_8wksPH_keratinocytes

description:
Pt3_8wksPH_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: Patient 3_lesion_keratinocytes

description:
Pt3_lesion_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: Patient 3_control_keratinocytes

description:
Pt3_arm_kera
Illumina Chip Bar Code: 9255013078
patient age not available


title: human myotubes, eplerenone plus aldosterone treated, biological rep 3


title: human myotubes, mifepristone plus aldosterone treated, biological rep 1


title: ZIKV BR 10*8 F5

first: MALIKA

last: AID

address: 3 blackfan street

institute: BIDMC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Analysis of the genome array output data was conducted using the statistical language R (http://www.r-project.org/) and the Linear Models for Microarray Data (LIMMA) statistical package from Bioconductor (http://bioconductor.org/) (Gentleman et al., 2004).  First, arrays displaying unusually low median intensity, low variability, or low correlation relative to the bulk of the arrays were tagged as outliers and were discarded from the rest of the analysis.  Quantile normalization, followed by a log2 transformation using the Bioconductor package LIMMA, was applied to process microarrays.  The LIMMA package was used to fit a linear model to each probe and to perform a moderated Student’s t test on various differences of interest between time points.  For data mining and functional analyses, genes that satisfied a p value < 0.05 were selected.  Probes that did not map to annotated genes and control probes were removed.  When indicated, the expected proportions of false positives (FDR) were estimated from the unadjusted p value.  Transcriptomic data and correlations with virologic and immunologic data were analyzed by regression linear models using R language.  Pearson correlation was used to assess the significant genes that correlated to virologic and immunologic data.  Enriched biological pathways were performed using gene set enrichment analyses (GSEA) (Subramanian et al., 2005).  Gene interaction networks were generated using GeneMANIA (Mostafavi and Morris, 2010; Mostafavi et al., 2008) and pathway module analyses was performed using cytoscape (Merico et al., 2010).

organism: Macaca mulatta

source_name: NHP

label_protocol: standard Affymetrix protocol

extract_protocol: Cells were isolated from peripheral blood and stored in RNAlater.  Total RNA extraction was performed using the automated RNeasy HT Qiacube kit according to manufacturer’s instructions (Qiagen).  Reverse transcription reactions were performed to obtain cDNAs, and proper cDNA amplification was confirmed using Agilent 2100 Bioanalyzer (Agilent Technologies).  cDNA was hybridized to Rhesus Genome rheMac2 platform (Affymetrix) at the Microarray Core of the Boston University.

tag: time


title: ZIKV BR 10*19 F8


title: human myotubes, eplerenone plus aldosterone treated, biological rep 1


title: human myotubes, eplerenone plus aldosterone treated, biological rep 2


title: ZIKV BR 10*6 F2


title: ZIKV BR 10*7 F4


title: ZIKV BR 10*8 F6


title: ZIKV BR 10*9 F7


title: human myotubes, spironolactone plus aldosterone treated, biological rep 2


title: ZIKV BR 10*8 E6


title: ZIKV BR 10*6 F1


title: ZIKV BR 10*19 E8


title: ZIKV BR 10*8 E5


title: ZIKV BR 10*7 F3


title: human myotubes, spironolactone plus aldosterone treated, biological rep 3


title: human myotubes, prednisolone treated, biological rep 3

growth_protocol: grown in skeletal muscle cell growth medium (SkGM-2 bullet kit; Lonza), containing: 1% bovine serum albumin (BSA), 1% fetuin, 1% insulin, 0.1% human epidermal growth factor (hEGF), 0.1% dexamethasone and 0.1% gentamicin/amphotericin B (GA) and cultured at 37⁰C in 5% CO2.  When cells reached ~80% confluence, they were serum restricted in differentiation media (DMEM supplemented with 2% horse serum (Invitrogen) and 100 U/mL penicillin-streptomycin) for 5 days.

treatment_protocol: Myotubes were treated for 48 hours with aldosterone (10 µM; Sigma), spironolactone (10 µM; Sigma), DMSO/vehicle (untreated; Sigma); eplerenone (10 µM; Pfizer compound transfer program), mifepristone (1 µM; Caymen Chemical), or prednisolone (1 µM; Sigma) (dissolved in 100% DMSO unless specified otherwise).  Drugs were added directly to existing differentiation media.


title: ZIKV BR 10*7 E4


title: human myotubes, aldosterone treated, biological rep 2a


title: human myotubes, aldosterone treated, biological rep 1a


title: CUX1_5mCG

type: protein

city: BETHESDA

first: Syed

middle: Khund

last: Sayeed

state: maryland

address: Building 37, NIH

department: Center for Cancer Research

institute: National Cancer Institute

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_14

hyb_protocol: The protein binding reactions were carried out as described in Genome Res. 2013 Jun;23(6):988-97. Briefly, the double-stranded microarrays were blocked with 4% nonfat dried milk in 1xPBS (Sigma) for 1 h. Microarrays were then washed once with PBS with 0.1% (vol/vol) Tween-20 for 5 min and once with PBS with 0.01% Triton X-100 for 2 min.  DBDs with GST tag were expressed using PURExpress® In Vitro Protein Synthesis Kit (NEB) as per manufacturers instructions.  25 μl of IVT reactions were added to make a total volume of 150 μl protein binding reaction containing PBS with 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), and 0.2 μg/μl bovine serum albumin (NEB), and incubated for 1 h at 20°C. Preincubated protein binding mixtures were applied to individual chambers of 40K arrays and incubated for 1 h at 20°C. Microarrays were washed in a Coplin jar once with 0.5% (vol/vol) Tween-20 in PBS for 3 min, once with 0.01% Triton X-100 in PBS for 2 min, and then finally washed with PBS. Alexa Fluor 647-conjugated GST antibody (Invitrogen) was applied to each chamber and incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS with 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa Fluor 647-conjugated anti-GST at 640 nm using an Agilent Surrescan scanner.  Agilent microarray scanner was set at 2 micron resolution.

data_processing: Microarray images were analyzed using ImaGene (BioDiscovery Inc.), and the extracted data were used for further analysis. To estimate the relative preference for each 8-mer, the Z-score was calculated from the average signal intensity across the 16 or 32 spots containing each 8-merthe Z-score was calculated from the average signal intensity across the 16 or 32 spots containing each 8-mer

label: Alexa 647

molecule: protein

organism: synthetic construct

source_name: human transcription factor DNA-binding domain

label_protocol: DBD sequences of the TFs were expressed as GST fusion proteins. Alexa 647 conjugated Anti-GST antibody was used to label protein bound on microarray.

extract_protocol: Extracted molecule: Protein.   We used 180 ng of plasmid DNA in a 25 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor.

treatment_protocol: The double stranded arrays were either methylated (M) or unmethylated (UM). The methylation of the double stranded microarray were performed using 10 μl of M.SssI (New England Biolabs)in a total volume of 150μl at 37 °C for 3 hrs. The arrays were washed three times with PBS/0.5% Tween-20 and once with PBS.

tag: transcription factor


title: CUX2_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_15


title: human myotubes, spironolactone plus aldosterone treated, biological rep 1


title: human myotubes, prednisolone treated, biological rep 2


title: human myotubes, aldosterone treated, biological rep 3a


title: MAX_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_11

value: MAX


title: ZIKV BR 10*6 E1


title: ZIKV BR 10*6 E2


title: ZIKV BR 10*9 E7


title: ZIKV BR 10*7 E3


title: ZIKV BR 10*9 D7


title: MAX_5mCG

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_12


title: CUX1_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_13


title: CUX2_5mCG

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_16


title: NFATC2_5mCG

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_10


title: ZIKV BR 10*8 D6


title: human myotubes, mifepristone treated, biological rep 2


title: NFATC2_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_9


title: POU5F1_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_7


title: ZIKV BR 10*19 D8


title: human myotubes, mifepristone treated, biological rep 3


title: human myotubes, prednisolone treated, biological rep 1


title: ZIKV BR 10*7 D3


title: ZIKV BR 10*8 D5


title: POU5F1_5mCG

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_8


title: ZIKV BR 10*6 D2


title: human myotubes, eplerenone treated, biological rep 2


title: DLX3_5mCG

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_6


title: human myotubes, eplerenone treated, biological rep 3


title: ZIKV BR 10*7 D4


title: human myotubes, eplerenone treated, biological rep 1


title: ZIKV BR 10*9 C7


title: ZIKV BR 10*6 D1


title: ZIKV BR 10*19 C8


title: DLX3_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_5


title: NKX2.5_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_3


title: human myotubes, untreated/vehicle-treated, biological rep 2


title: LHX9_5mCG

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_2


title: human myotubes, mifepristone treated, biological rep 1


title: ZIKV BR 10*8 C6


title: human myotubes, untreated/vehicle-treated, biological rep 3


title: NKX2.5_5mCG

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_4


title: ZIKV BR 10*8 C5


title: LHX9_Cytosine

description:
Protein Binding Microarray with cytosine and 5mCG
PBM_1


title: human myotubes, aldosterone treated, biological rep 3


title: human myotubes, untreated/vehicle-treated, biological rep 1


title: human myotubes, aldosterone treated, biological rep 1


title: human myotubes, spironolactone treated, biological rep 3


title: ZIKV BR 10*19 B8


title: ZIKV BR 10*7 C4


title: ZIKV BR 10*7 C3


title: ZIKV BR 10*6 C2


title: ZIKV BR 10*6 C1


title: human myotubes, aldosterone treated, biological rep 2


title: ZIKV BR 10*8 B6


title: human myotubes, spironolactone treated, biological rep 2


title: ZIKV BR 10*9 B7


title: ZIKV BR 10*7 B4


title: ZIKV BR 10*8 B5


title: BMSC_d07_ctcf_R1

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
mouse primary MSC osteogenic differentiation d07
ChIP

library_source: genomic

data_processing:
Remove adapter reads (Cutadapt v1.6)
Trim low quality base calls from both ends.  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
Concatenate replicates.
Align reads with Bowtie 1.2.8
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in logFE mode.
Convert logFE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of log fold enrichment over input from bdgcmp function of MACS2. Bigwig files are available in tar archives on the series record.

molecule: genomic DNA

source_name: bone marrow_day7_CTCF

growth_protocol: Primary MSCs were isolated from femurs and tibias of 6 - 8 weeks old SMAA-mCherry mice. Bone marrow stromal cells attached to plate surface after 72 hours were kept and cultured for additional 4 days before enriching for SMAA-mCherry positive cell by FACS. SMAA-positive MSCs were plated at 1.5 x 10^5 cells per 10 cm culture plate for the expansion in the MSC growth media. BMSCs of passage 6 to 10 were used for all the experiments in this study. All animal work was reviewed and approved by UMASS and/or UVM IACUC (protocol number JL-512).

extract_protocol:
Chromatin were prepared and sheared as previously described [12]. Sheared chromatin was used for immunoprecipitation with Runx2 antibody (M-70, Santa Cruz), Ctcf (07-729, Millipore, Billerica, MA, USA), Smc1a (A300-055A, Bethyl Laboratories, Montgomery, TX, USA), H3K4me (ab8895, Abcam, Cambridge, MA, USA), H3K4me3 (ab1012, Abcam), H3K9me3 (Ab8898, Abcam), H3K9ac (39137, Active Motif), H3K27me3 (07-449, Millipore), H3K27ac (07-360, Millipore), H3K36me3 (ab9050, Abcam), ap300 (sc-585 X, Santa Cruz) or Ezh2 (A304-196A, Bethyl Laboratories) or immunoglobulin G (IgG) (12-370, Millipore) followed by purification using Protein-G Dynabeads (Invitrogen).
Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range. Libraries were sequenced on an Illumina GA-II or Hiseq1500 and single-end 36-base (SE36) sequencing was performed at the NEMO facility at Umass Medical School

treatment_protocol: At day 0, 7, 14, and 21 of differentiation, approximately 5x10^7 MSCs were washed with PBS and then fixed on plate with 1% formaldehyde for 10 minutes at room temperature to crosslink DNA-protein complexes.

value: bone marrow

value: mesenchymal stromal cell

tag: markers

value: SMAA-mCherry+

tag: age

value: 6-8 weeks


title: ZIKV BR 10*7 B3


title: ZIKV BR 10*6 B2


title: ZIKV BR 10*8 A6


title: ZIKV BR 10*9 A7


title: MCF7 cells transfected with Par4 overexpression vector (MCF7 over PAR4) and Docetaxel treated Replicate 1

status: Public on May 04 2017

city: São Paulo

first: Simone

middle: Aparecida

last: de Bessa Garcia

state: São Paulo

address: Av. Dr. Arnaldo, 251

department: Radiologia e Oncologia

country: Brazil

institute: ICESP

description: Biological replicate 1 of 2. MCF7 cells, PAR4 overexpression vector transfected, 100nM docetaxel treated, harvested after 24h of drug exposure.

hyb_protocol: 825ng of labeled cRNAs were hybridized with the Human GE 4X44K V2 slides for 17 hours at 65°C. The slides were washed with the GE Wash Buffer 1 and GE Wash Buffer 2 (Agilent), following manufacturer´s instructions.

scan_protocol: Scanned on an Agilent G2600D scanner using the GE2_107_Sep09 protocol.

data_processing: The data quantification and the quality control were performed using the Agilent Feature Extration (v 11.5.1.1) Software.

source_name: MCF7 cell line PAR4 overexpression vector transfected and 100nM docetaxel treated

label_protocol: 162 ng of total RNA (human reference RNA and samples) were primed with 0.8 µl of T7 promoter primer (Agilent) at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of AffinityScript RNA Block Mix (Agilent), and 1 mM of dNTP mix (Agilent). Human RNA reference was labled with Cy3 and samples were labled with  Cy5 at 40°C for 2 h in the presence of T7 RNA polymerase blend (Agilent). The cRNAs were purified using the Qiagen RNeasy mini kit according manufacturer instructions and quantified using NanoDrop (ND-1000).

growth_protocol: MCF7 cells were stably transfected with plasmid pcCMV6-XL6-PAR4 expressing the full length PAR4 cDNA or with empty vector (pcCMV6-XL6-NEO), both acquired from OriGene (Rockville, MD, USA). Transfection assays were performed using TurboFectin 8.0 transfection reagent according to the manufacturer´s recommendations (OriGene, Rockville, MD, USA). Twenty-four hours after transfection, MCF7 cells were selected with G418 (Gibco, Gaithersburg, MD, USA). The stably transfected MCF7 cells were kept in RPMI 1640 medium supplemented with 10% fetal bovine serum and 800ug/ml G418.

extract_protocol: Total RNA extracted using guanidinium thiocyanate-phenol-chloroform method  according Chomczynsky and Sacchi (1987).

treatment_protocol: MCF7 Neo and MCF7 over PAR4 cells were treated with 100nM of Docetaxel for a period of 24 hours.

tag: cell line

value: MCF7 (ATCC® HTB-22™)

value: female breast adenocarcinoma

tag: molecular classification

value: Luminal A (Estrogen Receptor positive)

tag: transfection

value: PAR4 overexpression vector

value: 100nM docetaxel

source_name: Agilent's Universal Human Reference RNA

value: total RNA from 10 human cell lines


title: MCF7 cells transfected with Par4 overexpression vector (MCF7 over PAR4) and Docetaxel treated Replicate 2

description: Biological replicate 2 of 2. MCF7 cells, PAR4 overexpression vector transfected, 100nM docetaxel treated, harvested after 24h of drug exposure.

tag: treatment


title: MCF7 cells transfected with Par4 overexpression vector (MCF7 over PAR4) and without treatment Replicate 1

description: Biological replicate 1 of 1. MCF7 cells, PAR4 overexpression vector transfected, untreated.

source_name: MCF7 cell line PAR4 overexpression vector transfected and without treatment


title: ZIKV BR 10*6 B1


title: ZIKV BR 10*8 A5


title: MCF7 cells transfected with the empty vector (MCF7 Neo) and Docetaxel treated Replicate 2

description: Biological replicate 2 of 2. MCF7 cells, empty vector transfected (Neo), 100nM docetaxel treated, harvested after 24h of drug exposure.

source_name: MCF7 cell line empty vector transfected and 100nM docetaxel treated

value: empty vector (MCF7 Neo)


title: ZIKV BR 10*6 A1


title: ZIKV BR 10*19 A8


title: ZIKV BR 10*6 A2


title: ZIKV BR 10*7 A4


title: MCF7 cells transfected with the empty vector (MCF7 Neo) and Docetaxel treated Replicate 1

description: Biological replicate 1 of 2. MCF7 cells, empty vector transfected (Neo), 100nM docetaxel treated, harvested after 24h of drug exposure.


title: MCF7 cells transfected with the empty vector (MCF7 Neo) and without treatment Replicate 1

description: Biological replicate 1 of 1. MCF7 cells, empty vector transfected (Neo), untreated.

source_name: MCF7 cell line empty vector transfected and without treatment


title: human myotubes, spironolactone treated, biological rep 1

tag: cell type


title: 583_normal

type: genomic

first: Caroline

middle: Moraes

last: Beltrami

state: SP

address: Rua Taguá 440

department: International Research Center - CIPE

institute: A C Camargo Cancer Center

description:
583N
9374342084_R01C02

hyb_protocol: Bisulphite modified DNA was amplified, fragmented and hybridised in the Illumina Hybridization Oven according the standard Illumina protocol.

scan_protocol: Arrays were imaged using the HiScan system (Illumina).

data_processing: Methylation data were analyzed as β values. Probes were also filtered, using WateRmelon package, for low bead count (<3) and low quality (p detection >0.05). Samples having 1% of sites with a detection p-value > 0.05 were also removed. Data was adjusted for color bias, inter-sample normalization and corrected using BMIQ normalization. A linear regression analysis was performed adjusting data for gender and age. The batch effects were corrected using sva package.

label: cy3, cy5

source_name: non-neoplastic adjacent tissue

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Tumor and non-neoplastic adjacent tissues were macro-dissected and genomic DNA extracted using a standard phenol/chloroform method.

treatment_protocol: Genomic DNA samples were bisulfite-modified using EZ DNA Methylation Gold kit D5006 (Zymo Research, Irvine, CA, USA) according to the Illumina recommendation.

tag: subject status

value: papillary thyroid cancer (PTC) patient

tag: gender

value: Female

tag: race

value: Caucasian

tag: variant

tag: multicentricity

tag: invasion

tag: tissue type

value: non-neoplastic adjacent tissue


title: 369_normal

description:
369N
9374342148_R01C02


title: 347_normal

description:
347N
9373551130_R05C02


title: 5049_tumor

description:
5049T
9374342084_R01C01

source_name: tumor tissue

value: Classic

value: tumor tissue


title: 358_normal

description:
358N
9373551157_R02C02

value: No Info


title: 400_normal

description:
400N
9374342148_R06C02


title: 328_tumor

description:
328T
9374342143_R02C01

value: Male

value: Follicular


title: 369_tumor

description:
369T
9374342148_R01C01

value: Perineural


title: 346_normal

description:
346N
9373551130_R01C02


title: 328_normal

description:
328N
9374342143_R02C02


title: 343_tumor

description:
343T
9373551157_R05C01


title: 343_normal

description:
343N
9373551157_R05C02


title: 347_tumor

description:
347T
9373551130_R05C01

value: Folicular + oncocític


title: 507_tumor

description:
507T
9374342105_R05C01


title: 358_tumor

description:
358T
9373551157_R02C01


title: 365_normal

description:
365N
9373551161_R04C02


title: 400_tumor

description:
400T
9374342148_R06C01


title: 379_normal

description:
379N
9373551157_R03C02


title: 365_tumor

description:
365T
9373551161_R04C01


title: 379_tumor

description:
379T
9373551157_R03C01


title: 346_tumor

description:
346T
9373551130_R01C01


title: 367_normal

description:
367N
9374342105_R04C02


title: 367_tumor

description:
367T
9374342105_R04C01


title: 416_normal

description:
416N
9374342084_R04C02


title: ZIKV BR 10*7 A3


title: 416_tumor

description:
416T
9374342084_R04C01


title: 522_tumor

description:
522T
9373551161_R02C01

value: Non Caucasian


title: 522_normal

description:
522N
9373551161_R02C02


title: 332_normal

description:
332N
9374342084_R03C02


title: 507_normal

description:
507N
9374342105_R05C02


title: 586_normal

description:
586N
9374342084_R02C02


title: 332_tumor

description:
332T
9374342084_R03C01


title: 329_tumor

description:
329T
9374342105_R03C01


title: 348_normal

description:
348N
9373551130_R02C02


title: 4955_tumor

description:
4955T
9374342084_R02C01


title: 339_normal

description:
339N
9374342105_R02C02


title: 333_normal

description:
333N
9374342143_R03C02


title: 348_tumor

description:
348T
9373551130_R02C01


title: 316_normal

description:
316N
9374342143_R04C02


title: 329_normal

description:
329N
9374342105_R03C02


title: 333_tumor

description:
333T
9374342143_R03C01


title: 316_tumor

description:
316T
9374342143_R04C01

value: Mucossecretor + classic


title: 318_tumor

description:
318T
9373551157_R01C01


title: 373_tumor

description:
373T
9374342143_R05C01


title: 521_normal

description:
521N
9374342148_R04C02


title: 339_tumor

description:
339T
9374342105_R02C01


title: 423_normal

description:
423N
9374342105_R06C02


title: 318_normal

description:
318N
9373551157_R01C02


title: 521_tumor

description:
521T
9374342148_R04C01


title: 5441_tumor

description:
5441T
9373551161_R03C01


title: 585_normal

description:
585N
9373551161_R03C02


title: 423_tumor

description:
423T
9374342105_R06C01


title: 354_tumor

description:
354T
9373551157_R06C01


title: 373_normal

description:
373N
9374342143_R05C02


title: 386_tumor

description:
386T
9374342148_R05C01


title: tPTL myometrial epigenome

city: San Antonio

first: Kohzoh

last: Mitsuya

state: Texas

address: 7703 Floyd Curl Drive

department: Center for Pregnancy and Newborn Research

institute: University of Texas Health Science Center San Antonio

description: 5mC MeDIP myometrium of women with twin gestations preterm laboring (tPTL); London

hyb_protocol: Equal amounts (34 ug) of Cy5- and Cy3-labeled samples were combined and hybridized to each Human DNA Methylation 2.1M v2 genome tilling array (Roche NimbleGen) for 16-20 h at 42˚C using NimbleGen hybridization System 4. After washing, the hybridized arrays were dried using ArrayIt high-speed microarray centrifuge.

scan_protocol: Arrays were scanned on NimbleGen MS 200 microarray scanner using NimbleGen Data Collection software.

data_processing:
Arrays were processed using the standard protocol (NimbleGen Arrays User’s Guide for DNA methylation analysis v1.0.
log2 (MeDIP/input) ratio in gff files.

label_protocol: Fragmented genomic DNA (10 ug) was denatured and immunoprecipitated using the mouse monoclonal antibody against 5-methylcytosine (clone 33D3, Eurogentec). A portion of the fragmented DNA (20%) was left untreated to serve as input control. Immunoprecipitated and input DNA were amplified using GenomePlex Complete Whole Genome Amplification (WGA2) Kit (Sigma-Aldrich). After cleanup with QIAquick PCR Purification columns (Qiagen), immunoprecipitated and input DNA were denatured and differentially labeled with fluorescent Cy5 and Cy3 dyes, respectively, using Dual-Color DNA Labeling Kit (Roche NimbleGen).

extract_protocol: Myometrial tissue was collected from the upper margin of a lower segment uterine incision at cesarean section as we have previously described. Any decidua and serosa were removed, and the remaining myometrium was flash frozen in liquid nitrogen and stored at -80°C before analysis. Labor was defined as the presence of regular uterine contractions (every 3–4 min), resulting in cervical effacement and dilation. The myometrial epigenome was compared in six groups of women: term laboring (TL, n = 11); term no labor consisting of two sets of tissues, one collected in San Antonio (TNL-san, n = 10) and one collected in London (TNL-lon, n = 9); preterm no labor (PTNL, n = 10); idiopathic preterm laboring (iPTL, n = 6); and twin gestations with preterm laboring (tPTL, n = 7). Genomic DNA was isolated from each myometrial tissue sample using DNeasy spin columns (Qiagen). Following isolation, DNA quality and quantity of all the isolations were measured using NanoDrop 2000 (Thermo Fisher Scientific) and each DNA sample was routinely examined by agarose gel electrophoresis with ethidium bromide staining to verify the absence of contaminating RNA and to determine the extent of genomic DNA degradation. Genomic DNA samples in each of the six groups were combined, resulting in six pools of DNA that were then subjected to methylated DNA immunoprecipitation (MeDIP) analysis.

tag: pregnancy

value: twin gestations with preterm laboring (tPTL)

tag: tissue

value: myometrium

tag: term length

value: preterm

tag: with or without labor

value: laboring

tag: antibody

value: 5-methylcytosine (5mC) mAb (Eurogentec)

source_name: Input myometrium of women with twin gestations preterm laboring (tPTL); London


title: 395_tumor

description:
395T
9373551161_R01C01

value: papillary thyroid cancer (PTC) patient

value: Female

tag: age


title: 360_tumor

description:
360T
9374342143_R01C01

value: Caucasian


title: 386_normal

description:
386N
9374342148_R05C02

value: non-neoplastic adjacent tissue


title: 366_tumor

description:
366T
9374342143_R06C01

value: Tall Cell

value: tumor tissue


title: 384_tumor

description:
384T
9373551161_R06C01

value: Classic

value: No Info


title: iPTL myometrial epigenome

description: 5mC MeDIP myometrium of women with idiopathic preterm laboring (iPTL); London

value: idiopathic preterm laboring (iPTL)

source_name: Input myometrium of women with idiopathic preterm laboring (iPTL); London


title: 384_normal

description:
384N
9373551161_R06C02


title: 395_normal

description:
395N
9373551161_R01C02


title: 354_normal

description:
354N
9373551157_R06C02


title: 360_normal

description:
360N
9374342143_R01C02


title: PTNL myometrial epigenome

description: 5mC MeDIP myometrium of women with preterm no lobor (PTNL); London

value: preterm no labor (PTNL)

value: no labor

source_name: Input myometrium of women with preterm no lobor (PTNL); London


title: 350_normal

description:
350N
9373551130_R03C02


title: 350_tumor

description:
350T
9373551130_R03C01


title: TNL-l myometrial epigenome

description: 5mC MeDIP myometrium of women with term no labor (TNL); London

value: term no labor (TNL)

value: full-term

source_name: Input myometrium of women with term no labor (TNL); London


title: TNL-s myometrial epigenome

description: 5mC MeDIP myometrium of women with term no labor (TNL); San Antonio

value: myometrium

source_name: Input myometrium of women with term no labor (TNL); San Antonio


title: TL myometrial epigenome

description: 5mC MeDIP myometrium of women with term laboring (TL); London

value: term laboring (TL)

source_name: Input myometrium of women with term laboring (TL); London


title: 382_tumor

description:
382T
9373551161_R05C01


title: 382_normal

description:
382N
9373551161_R05C02


title: Tu-End.cells_16.113_120h_TcellnoIFNγ_rep1

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

description: Gene expression data from tumor endothelial cells 120h after transfer of IFNγ-/- T cells

hyb_protocol: Fragmented cDNA (3.8 μg) was hybridized to MOGENE 2.0 ST arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Affymetrix GeneChip Command Console Version 4.0. The image data were normalized and quality controlled with the Affymetrix Expression Console™ Software Version 1.4. CEL files were processed with R/Bioconductor “oligo” and “limma” packages.

source_name: 16.113 Tumor endo-cells 120h TcellnoIFNγ

label_protocol: cDNA was synthesized from ~500 pg total RNA according to the standard Affymetrix protocol GeneChip® WT Pico Kit by using the Affymetrix T7 RNA polymerase promoter which is attached to random primers. Pre-IVT was performed with 12 amplification cycles. Then, ss-cDNA was fragmented and biotin-labelled according to Affymetrix recommendations.

growth_protocol: Tumors (MCA313-IFNγ-IND, or J558L-IFNγ-GFP-IND or 16.113) were grown to a size of ca. 1 cm in diamater and either induced for 24h to 48h to produce IFNγ (MCA313-IFNγ-IND), or for 24h with IFNγ-GFP (J558L-IFNγ-GFP-IND tumors) or were treated for 5 days with T cells that could or could not produce IFNγ (16.113 tumors). Controls are tumors not treated with IFNγ (MCA313-IFNγ-IND) designated as 0h, not treated with IFNγ-GFP (J558L-IFNγ-GFP-IND) designated 0h, or for 5 days with T cells from IFNγ-deficient mice.

extract_protocol: RNAzol extraction of total RNA from 5000 to 15000 FACS sorted endothelial was performed according to the manufacturer's instructions.

treatment_protocol: Tumors (MCA313-IFNγ-IND, or J558L-IFNγ-GFP-IND or 16.113) were were resected, digested with collagenase, DNAse and Dispase and tumour endothelial cells (CD31+/CD146+) were isolated by fluorescence-activated cell sorting into RNAzol.

tag: time point

tag: protocol

value: IFNγ deficient tumor specific T cell transfer

value: tumor endothelial cells

tag: Sex

value: female

tag: genotype

value: mice with ubiquitous IFNγR expression but lacking mature T cells and B cells ( Rag-/-)

value: 3-4 month


title: lean epigenome, 5-hydroxymethylcytosine (5hmC) by hMeDIP

description:
uncomplicated pregnancies
hMeDIP 5hmC human normal epigenome

data_processing: Arrays were processed using the standard protocol (NimbleGen Arrays User’s Guide for DNA methylation analysis v1.0; scaled, log2 (MeDIP/input) or (hMeDIP/input) ratio in gff files).

source_name: 5hmC hMeDIP placental gDNA from lean pregnancies

label_protocol: Fragmented genomic DNA (10 ug) was denatured and immunoprecipitated using the mouse monoclonal antibody against 5-methylcytosine (clone 33D3, Eurogentec) or rabbit polyclonal antibody against 5-hydroxymethylcytosine (Diagenode). A portion of the fragmented DNA (20%) was left untreated to serve as input control. Immunoprecipitated and input DNA were amplified using GenomePlex Complete Whole Genome Amplification (WGA2) Kit (Sigma-Aldrich). After cleanup with QIAquick PCR Purification columns (Qiagen), immunoprecipitated and input DNA were denatured and differentially labeled with fluorescent Cy5 and Cy3 dyes, respectively, using Dual-Color DNA Labeling Kit (Roche NimbleGen).

extract_protocol: Genomic DNA was extracted from each tissue sample using DNeasy Tissue and Blood Kit (Qiagen) according to the manufacturer’s instructions, followed by ethanol reprecipitation. The quality and concentration of isolated genomic DNA was evaluated using NanoDrop 2000 (Thermo Fisher Scientific) and each DNA sample was routinely assessed by agarose gel electrophoresis with ethidium bromide staining to ascertain the absence of contaminating RNA and to determine the extent of degradation of genomic DNA preparations. Villous placental genomic DNA samples derived from 10 obese (prepregnancy or first trimester BMI with a mean and SD values of 34.0 ± 2.9) and 10 healthy weight (BMI of 23.4 ± 2.3) women with uncomplicated pregnancy were combined, resulting in two pools of DNA (each 5 male and 5 female placentas) that were subjected to methylated/hydroxymethylated DNA immunoprecipitation (MeDIP/hMeDIP) assays.

tag: condition

value: lean (healthy weight) pregnancies with a mean BMI of 23.4

tag: pregnancy complications

tag: blood pressure

value: normotensive

tag: neonatal outcome

value: normal

value: full-term placenta

value: 5-hydroxymethylcytosine (5-hmC) pAb (Diagenode)


title: Tu-End.cells_16.113_120h_TcellnoIFNγ_rep2

tag: cell type


title: Tu-End.cells_16.113_120h_TcellnoIFNγ_rep3


title: obese epigenome, 5-methylcytosine (5mC) by MeDIP

description:
uncomplicated pregnancies
MeDIP 5mC human obese epigenome

source_name: 5mC MeDIP placental gDNA from obese mothers

value: obese pregnancies with a mean BMI of 34.0

value: 5-methylcytosine (5-mC) mAb (Eurogentec)


title: lean epigenome, 5-methylcytosine (5mC) by MeDIP

description:
uncomplicated pregnancies
MeDIP 5mC human normal epigenome

source_name: 5mC MeDIP placental gDNA from lean mothers


title: obese epigenome, 5-hydroxymethylcytosine (5hmC) by hMeDIP

description:
uncomplicated full-term pregnancies
hMeDIP 5hmC human obese epigenome

source_name: 5hmC hMeDIP placental gDNA from obese mothers


title: Tu-End.cells_16.113_120h_TcellnoIFNγ_rep5


title: 366_normal

description:
366N
9374342143_R06C02

tag: subject status

value: papillary thyroid cancer (PTC) patient

tag: gender

value: Female

tag: race

value: Caucasian

tag: variant

tag: multicentricity

tag: invasion

value: non-neoplastic adjacent tissue


title: 473_normal

description:
473N
9374342084_R06C02

value: Male

tag: tissue type


title: Tu-End.cells_16.113_120h_Tcell-IFNγ_rep3

description: Gene expression data from tumor endothelial cells 120h after transfer of IFNγ+/+ T cells

source_name: 16.113 Tumor endo-cells 120h Tcell-IFNγ

value: IFNγ competent tumor specific T cell transfer

tag: age


title: 473_tumor

description:
473T
9374342084_R06C01

value: Follicular

value: Blood

value: tumor tissue


title: 4810_tumor

description:
4810T
9374342084_R05C01

value: Classic


title: 376_tumor

description:
376T
9374342148_R02C01


title: Tu-End.cells_16.113_120h_Tcell-IFNγ_rep2

tag: time point

value: tumor endothelial cells

value: female

value: mice with ubiquitous IFNγR expression but lacking mature T cells and B cells ( Rag-/-)

value: 3-4 month


title: 516_normal

description:
516N
9374342148_R03C02


title: 510_normal

description:
510N
9374342084_R05C02


title: Tu-End.cells_16.113_120h_Tcell-IFNγ_rep1

tag: protocol


title: Tu-End.cells_16.113_120h_TcellnoIFNγ_rep4

value: IFNγ deficient tumor specific T cell transfer

tag: Sex


title: 376_normal

description:
376N
9374342148_R02C02


title: 337_tumor

description:
337T
9373551130_R04C01


title: 337_normal

description:
337N
9373551130_R04C02


title: 77_normal

description:
77
9373551157_R04C02


title: 516_tumor

description:
516T
9374342148_R03C01

value: No Info


title: 334_tumor

description:
334T
9374342105_R01C01


title: Pdcd1 knockout, biological replicate 2

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

description:
Mouse were stimulated with IL33 for 3 days
Pdcd1KO_2

hyb_protocol: Affymetrix (WT) Array hybridization protocol

scan_protocol: Data were collected using Affymetrix AGCC software.

data_processing: The R/Bioconductor package “oligo” was used for preprocessing and normalization of the microarray data using RMA algorithm.The normalized expression values are log2-scaled.

source_name: Pdcd1 knockout, ILC2

label_protocol: Affymetrix (WT) Pico labelling kit

extract_protocol: RNA extracted with TrizolRNA extraction protocol and then Affymetrix WTPico labelling kit was used

treatment_protocol: Murine recipients were treated with IL-33 for 3 days and then lungs were isolated and ILC2s were flow sorted

tag: genotype/variation

value: Pdcd1 knockout

tag: tissue

value: Lung


title: Tu-End.cells_J558L_24h_IFNγGFP_rep3

description: Gene expression data from tumor endothelial cells 24h after IFNγGFP induction

source_name: J558L tumor endo-cells 24h IFNγGFP

value: IFNγGFP induction

tag: genotype

value: 4-6 month


title: 27169_tumor

description:
27169
9373551157_R04C01

value: papillary thyroid cancer (PTC) patient

value: Caucasian


title: Ki-End.cells_J558L_24h_IFNγGFP_rep2

description: Gene expression data from kidney endothelial cells 24h after IFNγGFP induction

source_name: J558L kidney endo-cells 24h IFNγGFP

value: kidney endothelial cells


title: Pdcd1 knockout, biological replicate 3

description:
Mouse were stimulated with IL33 for 3 days
Pdcd1KO_3


title: 334_normal

description:
334N
9374342105_R01C02

source_name: non-neoplastic adjacent tissue

value: Male

value: non-neoplastic adjacent tissue


title: Ki-End.cells_J558L_24h_IFNγGFP_rep3


title: Ki-End.cells_J558L_24h_IFNγGFP_rep1


title: Ki-End.cells_J558L_0h_IFNγGFP_rep3

description: Gene expression data from kidney endothelial cells 0h after IFNγGFP induction

source_name: J558L kidney endo-cells 0h IFNγGFP


title: Tu-End.cells_J558L_24h_IFNγGFP_rep2


title: Pdcd1 knockout, biological replicate 1

description:
Mouse were stimulated with IL33 for 3 days
Pdcd1KO_1


title: Tu-End.cells_J558L_0h_IFNγGFP_rep2

description: Gene expression data from tumor endothelial cells 0h after IFNγGFP induction

source_name: J558L tumor endo-cells 0h IFNγGFP


title: wildtype, biological replicate 3

description:
Mouse were stimulated with IL33 for 3 days
WT_3

source_name: wildtype, ILC2

value: wildtype


title: wildtype, biological replicate 1

description:
Mouse were stimulated with IL33 for 3 days
WT_1


title: wildtype, biological replicate 2

description:
Mouse were stimulated with IL33 for 3 days
WT_2


title: Ki-End.cells_J558L_0h_IFNγGFP_rep1


title: Tu-End.cells_MCA313_48h_IFNγ_rep2

description: Gene expression data from tumor endothelial cells 48h after IFNγ induction

source_name: MCA313 tumor endo-cells 48h IFNγ

value: IFNγ induction

value: transgenic mice with exclusive IFNγR expression in endothelial cells (PIG-Pdgfb-Cre-IFNγ-del mice)


title: Tu-End.cells_J558L_0h_IFNγGFP_rep1

value: tumor endothelial cells

value: female


title: Tu-End.cells_J558L_24h_IFNγGFP_rep1

value: mice with ubiquitous IFNγR expression but lacking mature T cells and B cells ( Rag-/-)


title: Tu-End.cells_MCA313_48h_IFNγ_rep1


title: Tu-End.cells_MCA313_0h_IFNγ_rep1

description: Gene expression data from tumor endothelial cells without IFNγ exposure

source_name: MCA313 tumor endo-cells 0h IFNγ

value: wo treatment


title: Tu-End.cells_MCA313_0h_IFNγ_rep3


title: Tu-End.cells_MCA313_0h_IFNγ_rep2


title: Tu-End.cells_MCA313_24h_IFNγ_rep1

description: Gene expression data from tumor endothelial cells 24h after IFNγ induction

source_name: MCA313 tumor endo-cells 24h IFNγ


title: Tu-End.cells_MCA313_24h_IFNγ_rep2


title: Ki-End.cells_J558L_0h_IFNγGFP_rep2


title: 114_4 R848_6991001048_F

status: Public on May 03 2017

city: Heidelberg

first: Mariel

last: Eberle

address: Im Neuenheimer Feld 324

department: Department of Hygiene and Microbiology

institute: University Hospital Heidelberg

description: replicate 2

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

source_name: human blood monocytes

label_protocol: cRNA was labeled with Biotin-16-UPT (Roche Applied Sciences) using the MessageAmp II aRNA Amplification kit (Ambion, Austin, Texas)

growth_protocol: Cells were isolated via AutoMACS (possel) and seeded in 24-well plate format. To obtain immature DCs, cells were supplemented with 10 ng/ml rhGM-CSF and 20 ng/ml rhIL-4. After 6 days of culture, cells were harvested, lysed and RNA was isolated.

extract_protocol: Total RNA was extracted using the High Pure RNA Isolation kit (Roche, Mannheim, Germany). At least 500 ng/ml of purified RNA was used for array analysis and quality (purity and concentration) was determined by means of Agilent Bioanalyzer (RNA gel analysis).

treatment_protocol: TLR-APCs were generated by addition of 1 µg/ml R848, 30 ng/ml LPS or 50 µg/ml PIC to the culture.

value: blood

tag: isolated cell-type

value: CD14+ monocytes

tag: age of cells in culture

value: 6 days

tag: phenotype

value: CD1a- CD14+

tag: treatment


title: 114_1 PIC_6991001048_D

description: replicate 1

value: PIC


title: 114_5 G4_6991001048_I

description: replicate 3

value: untreated


title: 114_4 PIC_6991001048_H

description: replicate 2


title: 114_4 LPS_6991001048_G

description: replicate 2

value: LPS


title: 114_5 LPS_6991001048_K

description: replicate 3


title: 114_5 R848_6991001048_J

description: replicate 3


title: 114_5 PIC_6991001048_L

description: replicate 3


title: 114_4 G4_6991001048_E

description: replicate 2


title: 114_1 LPS_6991001048_C

description: replicate 1


title: 114_1 G4_6991001048_A

description: replicate 1


title: NO_981

city: Taipei

first: Wen-Chien

last: Chou

address: No. 7, Chung-Shan S. Rd.

department: Department of Laboratory Medicine

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: cRNA was hybridized to Illumina HumanHT-12 v4 Expression BeadChip according to the manufacturer’s instructions.

scan_protocol: After 14–20 hours hybridization, the BeadChips were stained by Cy3 and were then washed. Intensities of bead fluorescence were detected by Illumina BeadArray Reader, and the results were transformed to numeric values using GenomeStudio v2010.1 software (Illumina).

data_processing: Expression values were processed with log2 transformation and quantile normalization.

source_name: de novo acute myeloid leukemia

label_protocol: cDNA was amplified (in vitro transcription) to generate biotin labeled cRNA (Ambion) according to manufacturer's instructions.

extract_protocol: RNA was extracted by TriZol reagent according to manufacturer's instructions.

tag: npm1 mutation status

value: wild type

tag: disease

value: AML

value: bone marrow


title: NO_976


title: NO_977


title: NO_980


title: NO_975


title: NO_970


title: NO_971


title: NO_978


title: NO_973


title: NO_969


title: NO_979


title: NO_966


title: NO_968


title: 114_1 R848_6991001048_B

description: replicate 1


title: NO_974


title: NO_962


title: NO_972


title: NO_967


title: NO_965


title: NO_959


title: NO_961


title: NO_960


title: NO_957


title: NO_958


title: NO_964


title: NO_963


title: NO_952


title: NO_944


title: NO_950


title: NO_956


title: NO_948


title: NO_953


title: NO_955


title: NO_951


title: NO_946


title: NO_947


title: NO_954


title: NO_949


title: NO_945


title: NO_942


title: NO_939


title: NO_928


title: NO_935


title: NO_938


title: NO_943


title: NO_941


title: NO_937


title: NO_940


title: NO_932


title: NO_934


title: NO_929


title: NO_936


title: NO_933


title: NO_930


title: NO_927


title: NO_931


title: NO_921


title: NO_924


title: NO_926


title: NO_920


title: NO_923


title: NO_908


title: NO_918


title: NO_919


title: NO_913

value: mutant


title: NO_917


title: NO_912


title: NO_925


title: NO_914


title: NO_911


title: NO_916


title: NO_909


title: NO_906


title: NO_922


title: NO_900


title: NO_915


title: NO_910


title: NO_903


title: NO_905


title: NO_907


title: NO_901


title: NO_898


title: NO_902


title: NO_896


title: NO_899


title: NO_892


title: NO_897


title: NO_891


title: NO_889


title: NO_893


title: NO_894


title: NO_904


title: NO_888


title: NO_886


title: NO_884


title: NO_887


title: NO_882


title: NO_890


title: Thp, 0h, S2 siRNA, repl. 3

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

hyb_protocol: Following fragmentation, cRNA were hybridizedAffymetrix GeneChip Human Genome U219 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Gene TitanTM MC Instrument.

data_processing: Possible batch effects caused by the different hybridizations were corrected for with ComBat tool with default parameters. The data were processed using the robust multi-array average (RMA) algorithm, quantile-normalized (Bioconductor affy package) and log2-transformed. Th17-specific genes were identified between the matched Th17- and Th0-measurements (same time point and culture) in the control-siRNA data using paired and moderated t-statistic (Bioconductor limma package). Genes with false discovery rate (FDR) < 0.1 were defined as changed for each time point. The effect of STAT3 knockdown on the gene expression was assessed using the Th17 measurements from the matched siRNA and scramble samples using the same analysis methods as above.

label: Biotin

source_name: human cord blood derived T cells

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

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturers instructions.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit from QIAGEN  according to the manufacturer's instructions.

treatment_protocol: Isolated CD4+ T cells were activated with plate-bound anti-CD3 (750 ng/24well culture plate and 3.75ug/ 6 well culture plate, Immunotech, Marseille, France) and soluble anti-CD28 (1 μg/ml, Immunotech) in X-vivo 20 serum free medium (Lonza, Basel, Switzerland) supplemented with 2 mM L-Glutamine (#G7513, Sigma, St. Louis, MO, USA), and 50 U/ml Penicillin and cultured at 37°C in 5 % CO2. IL-6 (20 ng/ml, Roche, Basel, Switzerland), IL-1β (10 ng/ml) and TGFβ (10 ng/ml) in the presence of neutralizing anti-IFNγ (1 μg/ml) and anti-IL4 (1 μg/ml) were used to initiate Th17 polarization. Control Th0 cells were cultured in a medium containing only the neutralizing antibodies. All cytokines and neutralizing antibodies were purchased from R&D Systems (Minneapolis, MN, USA) unless otherwise stated. For STAT3 target gene identification, cells were harvested at 2, 12, 24, and 72 h time points. Three biological replicates were prepared, each time including all three different individual STAT3 siRNAs and non-targeting control siRNA.

tag: cell type

value: Thp

value: siRNA


title: NO_883


title: NO_885


title: NO_895


title: NO_881


title: NO_880


title: Thp, 0h, scramble, repl. 3

value: scramble


title: NO_802


title: NO_807


title: Thp, 0h, D2 siRNA, repl. 3


title: Th17, 72h, S2 siRNA, repl. 3


title: NO_879


title: Th17, 72h, scramble, repl. 3


title: Th17, 72h, D1 siRNA, repl. 3


title: Th17, 72h, D2 siRNA, repl. 3


title: NO_776


title: NO_761


title: NO_780


title: Th17, 2h, D2 siRNA, repl. 3


title: Th17, 2h, scramble, repl. 3


title: NO_749


title: Thp, 0h, D1 siRNA, repl. 3


title: Th17, 2h, D1 siRNA, repl. 3


title: Th17, 24h, S2 siRNA, repl. 3


title: Th17, 2h, S2 siRNA, repl. 3


title: Th17, 12h, scramble, repl. 3


title: Th0, 72h, D1 siRNA, repl. 3


title: Th0, 24h, D1 siRNA, repl. 3


title: Th17, 12h, D1 siRNA, repl. 3


title: Th17, 24h, D2 siRNA, repl. 3


title: Th0, 2h, D1 siRNA, repl. 3


title: Th0, 72h, S2 siRNA, repl. 3


title: Th17, 12h, S2 siRNA, repl. 3


title: Th0, 12h, S2 siRNA, repl. 3


title: Th17, 24h, scramble, repl. 3


title: Th17, 24h, D1 siRNA, repl. 3


title: Th0, 24h, D2 siRNA, repl. 3


title: Th0, 72h, scramble, repl. 3


title: Th0, 12h, scramble, repl. 3


title: Th17, 12h, D2 siRNA, repl. 3


title: Th0, 2h, S2 siRNA, repl. 3


title: Thp, 0h, D2 siRNA, repl. 2


title: Th17, 72h, scramble, repl. 2


title: Th0, 24h, S2 siRNA, repl. 3


title: Th0, 2h, scramble, repl. 3


title: Th0, 2h, D2 siRNA, repl. 3


title: Th0, 12h, D1 siRNA, repl. 3


title: Th17, 72h, D2 siRNA, repl. 2


title: Th0, 72h, D2 siRNA, repl. 3


title: Th0, 24h, scramble, repl. 3


title: Thp, 0h, scramble, repl. 2


title: Th0, 12h, D2 siRNA, repl. 3


title: Th17, 2h, scramble, repl. 2


title: Th17, 72h, S2 siRNA, repl. 2


title: Thp, 0h, S2 siRNA, repl. 2


title: Thp, 0h, D1 siRNA, repl. 2


title: Th17, 24h, D2 siRNA, repl. 2


title: Th17, 72h, D1 siRNA, repl. 2


title: Th17, 24h, scramble, repl. 2


title: Th17, 2h, S2 siRNA, repl. 2


title: Th17, 12h, D2 siRNA, repl. 2


title: Th17, 24h, S2 siRNA, repl. 2


title: Th17, 2h, D1 siRNA, repl. 2


title: Th17, 12h, scramble, repl. 2


title: Th0, 72h, scramble, repl. 2


title: Th17, 12h, S2 siRNA, repl. 2


title: Th0, 2h, scramble, repl. 2


title: Th0, 72h, S2 siRNA, repl. 2


title: Th0, 72h, D1 siRNA, repl. 2


title: Th0, 12h, S2 siRNA, repl. 2


title: Th17, 24h, D1 siRNA, repl. 2


title: Th0, 24h, scramble, repl. 2


title: Th17, 12h, D1 siRNA, repl. 2


title: Th0, 12h, scramble, repl. 2


title: Th0, 24h, S2 siRNA, repl. 2


title: Th0, 2h, D1 siRNA, repl. 2


title: Th0, 2h, D2 siRNA, repl. 2


title: Th0, 24h, D1 siRNA, repl. 2


title: Thp, 0h, scramble, repl. 1


title: Thp, 0h, D1 siRNA, repl. 1


title: Th0, 72h, D2 siRNA, repl. 2


title: Thp, 0h, D2 siRNA, repl. 1


title: Th17, 72h, scramble, repl. 1


title: Th17, 2h, D2 siRNA, repl. 2


title: Th0, 12h, D2 siRNA, repl. 2


title: Th17, 24h, scramble, repl. 1


title: Th17, 24h, S2 siRNA, repl. 1


title: Th17, 12h, scramble, repl. 1


title: Th0, 12h, D1 siRNA, repl. 2


title: Th17, 72h, D2 siRNA, repl. 1


title: Th0, 2h, S2 siRNA, repl. 2


title: Th0, 2h, scramble, repl. 1


title: Th0, 72h, D1 siRNA, repl. 1


title: Th0, 24h, D2 siRNA, repl. 2


title: Thp, 0h, S2 siRNA, repl. 1


title: Th17, 72h, S2 siRNA, repl. 1


title: Th17, 2h, S2 siRNA, repl. 1


title: Th17, 24h, D2 siRNA, repl. 1


title: Th17, 2h, D2 siRNA, repl. 1


title: Th0, 2h, D2 siRNA, repl. 1


title: Th0, 2h, D1 siRNA, repl. 1


title: Th17, 2h, D1 siRNA, repl. 1


title: Th17, 12h, D2 siRNA, repl. 1


title: Th17, 24h, D1 siRNA, repl. 1


title: Th17, 72h, D1 siRNA, repl. 1


title: Th17, 2h, scramble, repl. 1


title: Th17, 12h, S2 siRNA, repl. 1


title: Th17, 12h, D1 siRNA, repl. 1