title: Control-MDA-PCa2b

city: Minneapolis

first: Mohammad

last: Saleem

state: Mn

address: 2231 6th St SE

department: Urology

institute: University of Minnesota

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_PTC-209 − Ct_Cntrl)
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports Treated/control (i.e., MDA-Pca2b-treated with PTC-209/DMSO treated MDA-PCa2b) ratios.

label: SYBR Green

source_name: African American Metaststic prostate cancer cell line

label_protocol: PCR assays were performed using the RT² Profiler™ PCR Array Human Prostate Cancer (Qiagen, Germantown, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Pittsburgh). Quantitative real-time PCR were performed (Applied Biosystems 7500)  at 95 0C for  10 mins [95 0C  for  15 seconds, and 60 0C for 60 seconds] for 45 cycles.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell line

value: Metaststic Prostate cancer cell line

tag: activation agent

value: control

tag: time


title: WT -LPS 4

status: Public on Apr 19 2018

type: RNA

city: Pittsburgh

first: Christine

last: Milcarek

state: PA

address: 200 Lothrop Street

department: Immunology

country: USA

institute: University of Pittsburgh

description: SST RMA expression value from Affymetrix Expression Console

hyb_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.

data_processing: CHP files were generated from CEL files using Expression Console from Affymetrix, using SST-RMA analysis algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: wild type

growth_protocol: Primary splenic B cells were isolated from each mouse using MACS columns.

extract_protocol: RNA was isolated from B cells at noted timepoints via Macherey Nagel Nucleospin RNA kits.

treatment_protocol: Unstimulated cells were processed immediately.  Stimulated cells were cultured in media + LPS for 72 hours before processing.

tag: strain

tag: cell type

value: B cell

tag: agent

tag: genotype/variation

value: wild type


title: WT -LPS 1

scan_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.


title: PTC-209 treated MDA-Pca2b

description: Treated

organism: Homo sapiens

value: PTC-209 treated


title: CR Pt AD2

status: Public on Apr 18 2018

city: Houston

first: Jing

last: Yang

state: Texas

address: 7455 Fannin

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction.

source_name: Complete remission myeloma patient bone marrow adipocytes

label_protocol: 200 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: All isolated adipocytes were cultured in DMEM medium supplemented with 10% FBS (Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted using the TRIzol reagent according to the manufactory's guideline. Then the RNA was purified by the Qiagen RNeasy Mini Kit column.

treatment_protocol: nADs were isolated from normal human bone marrow, CR Pt ADs were isolated from complete remission myeloma patient bone marrow

tag: disease state

value: Complete remission myeloma

tag: tissue

value: BM

value: adipocytes


title: nAD6

source_name: Human bone marrow adipocytes

value: control (normal)


title: CR Pt AD9


title: CR Pt AD8


title: CR Pt AD3


title: CR Pt AD5


title: nAD4


title: CR Pt AD12


title: CR Pt AD10


title: CR Pt AD11


title: CR Pt AD1


title: CR Pt AD6


title: nAD5


title: nAD3


title: nAD2


title: CR Pt AD7


title: CR Pt AD4


title: CTRL_Pen_1

city: Granada

first: Jose

middle: Antonio

last: Lopez-Escamez

state: Granada

address: Av. Ilustracion 114

department: Genomics of vestibular disorders

country: Spain

institute: Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: Biotin

source_name: PBMC Penicillium stimulation

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

extract_protocol: RNA was extracted using the RNA isolatin Kit from Roche in accordance to the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 5ug/mL Mix Aspergillus or Mix Penicillium for 16h

value: PBMC

tag: diagnosis

value: Healthy control


title: CTRL_Asp_3

source_name: PBMC Aspergillus stimulation


title: CTRL_Asp_1


title: nAD1


title: CTRL_Pen_2


title: CTRL_3

source_name: PBMC non-stimulated


title: CTRL_Pen_3


title: CTRL_Asp_2


title: CTRL_2


title: VM_Pen_5

value: Vestibular migarine


title: CTRL_4


title: VM_Pen_3


title: VM_Pen_4


title: VM_Pen_2


title: VM_Pen_1


title: VM_Asp_2


title: VM_Asp_4


title: MD_Pen_4

value: Meniere disease


title: CTRL_1


title: MD_Pen_3


title: MD_Asp_3


title: MD_Pen_2


title: MD_Asp_2


title: MD_Asp_4


title: VM_Asp_1


title: input pre-B ChIP-seq

type: SRA

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

description: pre-B input control

library_source: genomic

data_processing:
Duplicated reads were removed before mapping.
Experimental and input control fastaq tags were aligned to the mouse reference genome (mm9) using Bowtie 0.12.9. Alignment parameters used:-a -v 2 -m 3 --best --strata
All reads mapping with their best alignment score at more than 3 sites in the genome were discarded.
Confident peaks were called using MACS (version 1.4.2), with FDR<= 1% and the default p value (1E-5).
Genome_build: mm9
Supplementary_files_format_and_content: file format: bed; content: confident peaks (as called by MACS).

molecule: genomic DNA

source_name: RAG-/-µ+ pre-B cells

growth_protocol: Bone marrow and spleen cells were isolated from 6 to 14 wk old C57BL/6 mice, including both males and females. DN Thymocytes were obtained from 4- to 8-wk-old Rag1-/- mice. DP Thymocytes were obtained from 4- to 8-wk-old Rag1-/- mice carrying a rearranged TCRb transgene.

extract_protocol:
For bone marrow subset purification we used B6.RAG1-/-mice to obtain pro-B cells.  B6.RAG-/-+ mice bearing a rearranged IgM transgene were used to obtain pre-B cells. For pro-B IL7, RAG1-/- pro-B cells were cultured with IL7 for 7 days.
For each sample 1 - 10 ng of IP material or input control sample was prepared into sequencing libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturers protocol. Samples were amplified using 18 cycles of PCR and then size selected on 2% EX agarose gels (Thermo Fisher) and bands cut at 300bps (+ 25 bps) and cleaned up using DNA Clean & Concentrator-25  (Zymo Research). The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.

value: Pre-B cells


title: MD_Pen_1


title: VM_Asp_3


title: input DN ChIP-seq

description: DN input control

source_name: Rag1 -/- thymocytes

value: CD4-CD8- (DN) thymocytes


title: MD_Asp_1


title: VM_6


title: VM_5


title: VM_3


title: VM_2


title: VM_4


title: CTRL_5


title: the infected cell H2

city: Wuhan

first: shulin

last: fu

address: No. 68 Changqing Gardern

country: China

institute: Wuhan Polytechnic University

library_source: transcriptomic

data_processing:
The raw data of RNA-seq analysis were filtered by utilizing FASTQC software.
The filtered reads were aligned and mapped to the reference genome (Sus-scrofa.Sscrofa10.2.dna.toplevel.fa) by using Tophat2
The unique mapped gene reads were standardized by reads per kilobases per million reads.
DEGs were screened using DESeq version 1.18.0 with a fold change of >2 and p < 0.05
Genome_build: the reference genome (Sus-scrofa.Sscrofa10.2.dna.toplevel.fa)
Supplementary_files_format_and_content: read counts, RPKM values for each Sample

organism: Sus scrofa

source_name: porcine aortic vascular endothelial cells

growth_protocol: PAVECs were resuspended in 5 mL M-199 medium containing 10% fetal bovine serum , and cultured in a T-25 tissue-culture plate

extract_protocol:
The total RNA of PAVECs was extracted using TRIzol Reagentfrom infected and uninfected cells. Total RNA was purified using the Dynabeads mRNA Purification Kit.
The cDNA libraries were constructed with RNA isolated from PAVECs using the TruSeq Stranded mRNA library preparation kit . cDNA was carried out using deoxynucleoside triphosphates containing DNA polymerase, dUTP, and RNase. End repair was achieved by adding dATP to all free 3’ ends, and unique index sequences of the fragments were added with adaptor ligation. The quantity and quality of the cDNA libraries were evaluated using an Agilent 2100 bioanalyzer and ABI StepOnePlus Real-Time PCR system. The obtained libraries were sequenced using the Illumina HiSeq 4000 platform.

treatment_protocol: PAVECs (1 × 106) were seeded into 24-well plates and infected with H. parasuis SH0165 strain with a multiplicity of infection of 1. After co-culture for 12 h at 37 °C with 5% CO2, the supernatant was removed. The cells were collected and washed three times with 1% sterile phosphate-buffered saline for transcriptomic analysis.

value: H. parasuis SH0165 strain


title: the infected cell H3


title: MD_lowbasal_4


title: VM_1


title: MD_lowbasal_3


title: the infected cell H

description: H


title: the control cell K2


title: MD_highbasal_3


title: MD_lowbasal_2


title: MD_highbasal_2


title: MD_highbasal_1


title: MD_lowbasal_1


title: the control cell K

description: K


title: HuccT1 control 3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Total RNA was isolated from HuccT1 cells and analyzed miRNA expression by microarray.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: cholangiocarcinoma

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: HuccT1 cells were obtained and cultured as recommended by the supplier.

extract_protocol: RNA samples were extracted from cells using miRNeasy mini kit (Qiagen).

treatment_protocol: HuccT1 cells were treated with 0 or 10 ng/ml of TGF-β for 72 hours.

tag: treatment


title: the control cell K3


title: H1K85ac_ChIPSeq

city: Beijing

first: Zhiming

last: Li

state: Beijing

address: Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences

institute: Peking University Health Science Center

data_processing:
Analysis of base composition and quality control
Data were filtered using the following specifications: SOAPnuke filter -l 5 -q 0.5 -n 0.1 -Q 2 -c 18 -5 1
ChIP-seq reads were aligned to the hg19 genome assembly using SOAPaligner/SOAP2 with the following configurations: soap_mm_gz -p 4 -v 2 -s 35
Peaks were called using SICER with the following parameters: SICER hg19 1 200 0.8 600 0.01
Genome_build: hg19
Supplementary_files_format_and_content: wig file

source_name: HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy’s 5A medium supplemented with 10% FBS and 1% penicillin/streptomycin in a 37°C incubator with a 5% CO2 and humidified atmosphere

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Colorectal Carcinoma

value: colon

value: Epithelial

tag: chip antibody

value: H1K85ac (PTM Biolabs, catalog# PTM-180)


title: input DNA


title: HuccT1 TGF-b 3

value: TGF-beta


title: HuccT1 TGF-b 1


title: ChIP_NPC_SrfOE_Srf_rep1

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

institute: Kyoto Univ.

description: Srf overexpression

data_processing:
The low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1.
Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm9) with BWA 0.7.12 using the default parameters.
The reads with high mapping quality (MAPQ>=20) were used for further analysis. The duplicate reads were removed with the Picard tool. The reads mapping to the mitochondrial DNA (chrM) were excluded for further analysis.
Peak detection was performed using MACS ver. 1.3.7.1, with parameters --mfold=8 --gsize=2.43e+09 --pvalue 1e-5.
Peaks falling within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were excluded from further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bw (bigwig) *The data were normalized as RPM (reads per million)

source_name: Neural progenitor cells overexpressing Srf

growth_protocol: Neural progenitor cells were maintained on a gelatin-coated culture plate in a NPC medium consisting of RHB basal (StemCells) containing epidermal growth factor (EGF) (Peprotech) at 10 ng/ml and human basic fibroblast growth factor (bFGF) (Peprotech) at 10 ng/ml. NPC culture also used another NPC medium, N2B27 medium, which was purchased (Takara) or prepared as a 1:1 mixture of Neurobasal (Thermo Fisher Scientific) and DMEM/F12 (1:1) with L-glutamine and sodium bicarbonate (Thermo Fisher Scientific) supplemented with 1× N2 supplement (Thermo Fisher Scientific), 1× B-27 supplement (Thermo Fisher Scientific), an additional 500 µM L-glutamine (Thermo Fisher Scientific), 10 µg/ml insulin (Wako) and 37.5 µg/ml bovine serum albumin (BSA) fraction V (Sigma-Aldrich) supplemented with 10 ng/ml epidermal growth factor (EGF) (Peprotech) and 10 ng/ml human basic fibroblast growth factor (bFGF) (Peprotech).

extract_protocol:
Cells were fixed in 1% paraformaldehyde at room temperature for 10 min followed by quenching with 125 mM glycine at room temperature for 5 min. Fixed cells were washed with cold PBS twice. Cells were harvested by scraper and centrifuged at 700 × g for 3 min and then resuspended in nucleic lysis buffer (10 mM Tris-HCl, 10mM EDTA, 1% SDS, 200 mM NaCl, pH 7.5). The genomic DNA was fragmented with Bioruptor (Cosmo Bio) at 4 °C to a size range between 300 and 600 bp. Cell contaminants were removed by centrifugation. A part of cleared solution was used as the input sample. An anti-SRF antibody (clone D71A9; Cell Signaling Technology) or anti- Histone H3 acetyl Lys27 antibody (Active Motif, #39133) were prebound by incubating with Protein-G Dynabeads (Thermo Fisher Scientific) in IP dilution buffer (16.7 mM Tris-HCl, 1.2 mM EDTA, 1.1% (vol/vol) Triton X-100, 167 mM NaCl, 0.01% SDS, pH 8.0) and then incubated at 4 °C overnight with constant rotation. Samples were washed twice with IP dilution buffer, twice with low NaCl buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, 0.1% SDS, pH 8.0), twice with high NaCl buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, 0.1% SDS, pH 8.0), twice with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, pH 8.0) and twice with TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). The DNA-protein complex was finally eluted with elution buffer (25 mM Tris-HCl, 5 mM EDTA, 0.5% SDS, pH 7.5). Eluates and input samples were treated with Pronase (Roche) at 42 °C for 2 h followed by 65 °C overnight with constant shaking. DNA was purified with MinElute Reaction Cleanup Kit (Qiagen).
Immunoprecipitated DNA was ligated with adaptors of Illumina TruSeq using TruSeq ChIP Sample Prep Kit (Illumina). Libraries were assessed for quality and quantity using Agilent Bioanalyzer 2000 and the KAPA Library Quantification Kit for Illumina (KAPA Biosystems).

treatment_protocol: For establishing OE cells, the transgene of Srf was introduced retrovirally.

value: In vitro differentiated neural progenitor cells

tag: antibody


title: ChIP_Hep_Srf_rep2

source_name: Hepatoblasts (expressing no ectopic gene)

growth_protocol: Hepatoblasts were maintained on a type IV collagen-coated culture plate in a medium consisting of a 1:1 mixture of DMEM/Ham’s F-12 with L-glutamine, HEPES and sodium pyruvate (Wako) supplemented with 10% fetal bovine serum (FBS) (vol/vol) (Nichirei Bioscience), 1 µg/ml insulin (Wako), 100 nM dexamethasone (Sigma-Aldrich), 10 mM nicotinamide (Sigma-Aldrich), 50 µM β-mercaptoethanol (Nacalai Tesque), 50 ng/ml human recombinant hepatocyte growth factor (HGF; Peprotech) and 20 ng/ml EGF.

value: Primary culture isolated from fetal liver

value: anti-SRF antibody (clone D71A9; Cell Signaling Technology)


title: ChIP_NPC_SrfOE_Srf_rep2

description: Srf overexpression


title: ChIP_Hep_Srf_rep1


title: ChIP_NPC_SrfOE_input

description: Srf overexpression


title: HuccT1 control 1

value: control


title: ChIP_NPC_control_Srf_rep2

source_name: Neural progenitor cells expressing no ectopic gene


title: ChIP_NPC_control_Srf_rep1


title: ChIP_NPC_control_input


title: ob BAT3

first: Linkang

last: Zhou

address: Haidian District

institute: Tsinghua Unversity

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Array (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) using the Genechip2 Scanner 3000 7G.

data_processing: Quality control and statistical analyses of all Mouse Gene 1.0 ST microarray data was conducted using R/Bioconductor. Methods like scatterplot, distribution histograms, boxplots, and unsupervised Principle Component Analysis (PCA) were employed to visualize the data before and after preprocessing procedures. All arrays were consistent and comparable for further analyses, and we performed background adjustment, quantile normalisation and summarisation of transcript-level intensity for all arrays using the Robust Multi-array Average (RMA) algorithm, followed by two rounds of probeset filtering. First, control probesets were removed, and 28,858 main probesets out of all 35,556 were retained. Then, the Detection Above Background (DABG) p-values for probesets were calculated using the xps package, and only the significant ones (p < 0.05) were considered as 'present'? We only retained probesets flagged as present in at least one sample for each type of tissue, and used the package LIMMA to identify probesets that were differentially expressed between the ob/ob/Cidea-/-/Cidec-/- and ob/ob mice . The Benjamini and Hochberg method was used to estimate the false discovery rate (FDR) and correct for multiple hypotheses testing. Annotation was taken, and genes that changed by log fold of at least 0.5 between ob/ob/Cidea-/-/Cidec-/- and ob/ob mice and with a FDR < 0.05 were considered significant. The up- and down-regulated genes were further mapped to biological pathways using DAVID Bioinformatics Resources 6.8, NIAID/NIH.

source_name: Brown fat from ob/ob/ mice

label_protocol: Single-stranded cDNA was  fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: 4 months old mice were used.

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

treatment_protocol: Mice were maintained at chow diet.

tag: Sex

value: Male

tag: age

value: 4 months

tag: genotype

value: ob/ob mice

value: brown fat


title: ob/Cidea/Cidec BAT2

source_name: Brown fat from ob/ob/Cidea-/-/Cidec-/- mice

value: ob/ob/Cidea-/-/Cidec-/- mice


title: ChIP_Hep_input

source_name: Hepatoblasts (expressing no ectopic gene_


title: ob BAT1


title: CTR T48 MYCy69

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description:
DNA (ChIP-enriched)
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C.  The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use).  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Chromatin states were learned using ChromeHMM version 1.10
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

source_name: RMS cell line, mutant HRAS

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.  DNase DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Cells were treated with either DMSO or Trametinib (100 nM) for 48 hours in complete media.

value: Anti-c-Myc antibody [Y69] Recombinant (Abcam, ab32072)

tag: enrichment target

value: MYC

tag: target function

value: General Amplification Transcription Factor

value: 48 hr

value: Trametinib 100nM


title: CTR D48 Pol2S2pAMR

value: Pol2-Ser2p (Active motif, 91115)

value: Transcription

value: DMSO


title: CTR T48  Pol2S2pAMR


title: CTR D48 MYCy69


title: LN_stroma_nomal

city: Shanghai

first: Yan

last: Gu

address: 800 Xiangyin Road

institute: Second Miilitary Medical University

description: Gene expression in stromal cells from nomal lymph nodes

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: lymph node stromal cells, without tumor inoculation

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: The 4T1 mammary carcinoma was subcutaneously inoculated in the mammary gland of C57BL/6 mice. Two weeks later, tumor-draining lymph nodes were dissociated and stromal cells (CD45-) were sorted using a MoFlo XDP flow cytometer. Lymph nodes stromal cells from normal mice without tumor bearing were set as controls.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: lymph node

tag: gender

value: female

value: stromal cells


title: ob/Cidea/Cidec BAT3


title: ob/Cidea/Cidec WAT2

source_name: White fat from ob/ob/Cidea-/-/Cidec-/- mice

value: white fat


title: ob BAT2

value: Male


title: LN_stroma_tumor

description: Gene expression in stromal cells from tumor-draining lymph nodes

source_name: lymph node stromal cells, tumor inoculation


title: LN_B cell_tumor

description: Gene expression in B cells from tumor-draining lymph nodes

source_name: lymph node B cells, tumor inoculation

growth_protocol: The 4T1 mammary carcinoma was subcutaneously inoculated in the mammary gland of C57BL/6 mice. Two weeks later, tumor-draining lymph nodes were dissociated and B cells (CD19+) were sorted using a MoFlo XDP flow cytometer. Lymph nodes B cells from normal mice without tumor bearing were set as controls.

value: B cells


title: ob/Cidea/Cidec WAT1

value: 4 months


title: ob/Cidea/Cidec BAT1

value: brown fat


title: S-5-2

city: Goyang

first: Hee-sung

last: Chae

state: Gyeonggi-do

address: Dongguk-ro 32

department: Department of pharmacy

country: South Korea

institute: Dongguk university

description: sauchinone 5 μM

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human hepatoma cells

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

tag: cell line

value: sauchinone 5 microM


title: ob/Cidea/Cidec WAT3

tag: strain

value: ob/ob/Cidea-/-/Cidec-/- mice


title: ob WAT1

source_name: White fat from ob/ob mice

value: ob/ob mice


title: ob WAT3


title: S-50-1

description: sauchinone 50 μM

value: sauchinone 50 microM


title: S-50-2

description: sauchinone 50 μM


title: ob WAT2


title: S-0-5-2

description: sauchinone 0.5 μM

value: sauchinone 0.5 microM


title: S-5-1

description: sauchinone 5 μM


title: N-3

description: Non-treated

value: Non-treated


title: N-2

description: Non-treated


title: WT_3

city: New York

first: Susan

middle: K.

last: Logan

state: NY

address: 450 E 29 Street

institute: New York University School of Medicine

description: Pair 3

data_processing:
Sequence files were generated in FASTQ format by Bcl2fastq version 1.8.4.
Alignments to mouse genome version mm9 were done by TopHat version 2.0.9 with --segment-length 25 -g 1 --library-type fr-unstranded -x 1 --fusion-parameter settings.
Gene count was done by HTSeq version 0.6.1 with --minaqual=10 --mode=union settings.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files incudes gene and gene count.

source_name: testes

extract_protocol:
Testes were dissected by removing the tunica and snap frozen in dry ice-ethanol. RNA was extracted using RNeasy Plus Micro kit and was further treated with TURBO DNase.
RNA libraries were prepared from 500ng total RNA using the Illumina TruSeq polyA v2 kit following the manufacturer’s protocol, with the exception that 13 cycles of PCR were performed. The libraries were normalized to 4nM, pooled in an equimolar fashion, distributed uniformly across 2 lanes on high output HiSeq 2500 flow cells using v4 reagents.

tag: strain/background

value: mixed

value: WT Uxt F/Y

value: male

value: testes

value: 6 days post partum


title: KO_3

description: Pair 3

value: KO Uxt F/Y;Vasa-Cre


title: S-0-5-1

description: sauchinone 0.5 μM


title: KO_2

description: Pair 2


title: 2308 WT, biological rep 2

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from stationary phase wildtype 2308 cells

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on a B. abortus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

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

organism: Brucella abortus

source_name: Brucella abortus stationary phase

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to late exponential phase in brucella broth at 37C with aeration

extract_protocol: Total bacterial RNA was isolated using Trizol according to the manufacturer's recommendations (Invitrogen)

treatment_protocol: Once reaching stationary phase (measured by colony forming unit counts) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: sample

value: Whole cell

value: Wildtype

tag: growth phase

value: Stationary


title: 2308 WT, biological rep 1


title: CC093 (ybeY), biological rep 1

description: Gene expression data from stationary phase 2308 cells containing ybeY mutation

value: ybeY


title: CC093 (ybeY), biological rep 2


title: WT_2

description: Pair 2

tag: genotype/variation


title: KO_1

description: Pair 1

tag: tissue


title: WT_1

description: Pair 1


title: ChIP_NPC_SrfOE_H3K27ac

description: Srf overexpression

tag: cell type

value: In vitro differentiated neural progenitor cells

value: nti- Histone H3 acetyl Lys27 antibody (Active Motif, #39133)


title: ChIP_NPC_control_H3K27ac


title: ChIP_Hep_H3K27ac_rep1

value: Primary culture isolated from fetal liver


title: ChIP_Hep_H3K27ac_rep2


title: 48hr BFT2 rep 1 [RNA-seq]

city: Baltimore

first: Winston

last: Timp

address: 3400 N. Charles St. Clark 102A

department: Biomedical Engineering

institute: Johns Hopkins University

data_processing:
Kallisto was used to perform pseudoalignment of the raw RNA-seq data. The following parameters were used: kallisto quant -b 100 --single -l 200 -s 20
Sleuth was used to quantify gene expression and perform differential expression analyses.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.kallisto.abundance.tsv: Tab-delimited text files include TPM values for each Sample.

source_name: HT29/C1 cells

growth_protocol: HT29/C1 cells were grown in DMEM (+ 10% FBS and 1% P/S) for 4 days before treatment.

extract_protocol:
Cells were washed once with PBS, collected using a cell scraper, and RNA was extracted from cells using the Qiagen RNeasy mini kit. After RNA extraction, the RNA pellet was flash frozen using 100% ethanol and dry ice. Samples were then stored at -80ºC.
For library preparation, samples were removed from storage, and mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Afterwards, a non-directional RNA-seq library was constructed using the NEBnext Ultra RNA Library Prep kit from Illumina. The 2nM pooled RNA-seq library was sequenced using the Illumina HiSeq.

treatment_protocol: Cells were treated with 100ng.mL BFT2 in DMEM (without FBS and P/S) for 24 or 48 hours.

value: colon epithelial cell line

tag: disease

value: Colorectal adenocarcinoma

tag: treatment

value: 100ng/mL BFT2

tag: time point


title: 48hr Baseline rep 2 [RNA-seq]


title: 24hr BFT2 rep 2 [RNA-seq]


title: 48hr BFT2 rep 2 [RNA-seq]


title: 48hr Baseline rep 1 [RNA-seq]


title: 24hr BFT2 rep 1 [RNA-seq]


title: D18C_Ovid_2

city: Wanju

first: Jun-Mo

last: Kim

state: Jeollabuk-do

address: 1500, Kongjwipatjwi-ro

department: Animal Genomics and Bioinformatics

institute: National Institute of Animal Science

data_processing:
Quality of RNA-seq reads from all of sample tissues were checked using FastQC.
Reads passed the quality control were mapped to sus scrofa genome (10.2).
The reads were counted using featurecount tool
The reads were nomalized using FPKM by Cufflinks
DEGs were detacted by both tools such as Cuffdiff(Cufflinks) and GLM(edgeR)
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include raw counts of genes for each sample.

source_name: Oviduct tissue

extract_protocol:
RNA extraction using Trisol
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide

tag: oestrous peroid

value: 18 day


title: 24hr BFT2 rep 3 [RNA-seq]


title: 24hr Baseline rep 3 [RNA-seq]


title: NPC_shActb_2_rep2

description: Actb-knockdown NPCs

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K G4122F for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8×60 K array slides.

data_processing: The array data were analyzed using GeneSpring software (Agilent). Gene expression values were normalized by excluding low-signal intensity data and percentile shifts.

source_name: Actb-knockdown NPCs

label_protocol: Microarray experiments were performed according to the manufacturer’s instruction. Twenty hundred nanograms of total RNA was labelled with cyanine 3-CTP and hybridized in Whole Mouse Genome Microarray 4x44K G4122F (Agilent Technologies).

growth_protocol: Neural progenitor cells were maintained on a gelatin-coated culture plate in a NPC medium consisting of RHB basal (StemCells) containing epidermal growth factor (EGF) (Peprotech) at 10 ng/ml and human basic fibroblast growth factor (bFGF) (Peprotech) at 10 ng/ml.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and assessed by Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent Technologies).

treatment_protocol: The transgene for shActb exprssion was introduced retrovirally.


title: 24hr Baseline rep 2 [RNA-seq]


title: 24hr Baseline rep 1 [RNA-seq]


title: NPC_shEGFP_rep1

description: Control NPCs for knockdown

source_name: Control NPCs for knockdown

treatment_protocol: The transgene for shEGFP exprssion was introduced retrovirally.


title: NPC_shEGFP_rep2

description: Control NPCs for knockdown


title: D18C_Ovid_1


title: NPC_EGFP_rep2

description: Control NPCs for overexpression

source_name: Control NPCs for overexpression

treatment_protocol: The transgene of EGFP was introduced retrovirally.


title: NPC_Srf_rep2

description: Srf-overexpressing NPCs

source_name: Srf-overexpressing NPCs

treatment_protocol: The transgene of Srf was introduced retrovirally.


title: NPC_shActb_2_rep1

description: Actb-knockdown NPCs


title: NPC_Srf_rep1

description: Srf-overexpressing NPCs


title: D18C_Ovid_0


title: 48hr Baseline rep 3 [RNA-seq]


title: NPC_Mkl1_rep2

description: Mkl1-overexpressing NPCs

source_name: Mkl1-overexpressing NPCs

treatment_protocol: The transgene of Mkl1 was introduced retrovirally.


title: NPC_shActb_1_rep1

description: Actb-knockdown NPCs


title: NPC_shActb_1_rep2

description: Actb-knockdown NPCs


title: NPC_EGFP_rep1

description: Control NPCs for overexpression


title: D18C_Ovary_2

source_name: Ovary tissue


title: D18C_Ovary_0


title: NPC_Mkl1_rep1

description: Mkl1-overexpressing NPCs


title: D18C_Ovary_1


title: D18C_Endo_2

source_name: Endometrium tissue


title: HuccT1 TGF-b 2

source_name: cholangiocarcinoma

value: TGF-beta


title: D15C_Ovid_3

value: 15 day


title: 24hr BFT2 rep 1 [ChIP-seq]

description:
Replicates were combined into 1 processed data file:
out.24hrbft2_ppr.IDR0.1.filt.narrowPeak

data_processing:
After sequencing, the data was analyzed using the pipeline developed by the Kundaje lab, as outlined on ENCODE. Briefly, reads were trimmed, aligned and filtered using Bowtie2 and peaks were called using MACS2. The three replicate peak files were combined in order to create one consensus file for each treatment condition using an irreproducible discovery rate (IDR) threshold of 0.1. For all analyses, the “optimal set” consensus file was used.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_ppr.IDR0.1.filt.narrowPeak: narrowPeak files are a bed format file that contain chromosome, chromosome start, chromosome end, name, score, strand, signal value, P-value, q-value and peak status.

extract_protocol: ATAC-seq was performed using the protocol outlined by Buenrostro et al. (2015). Briefly, cells were washed with 50uL cold 1x PBS buffer, then centrifuged at 500g for 5 minutes at 4°C. Cells were then resuspended in 50uL cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) , gently lysed to preserve cell nuclei, and centrifuged again at 500g for 10 minutes at 4°C. Cells were then washed 3x with wash buffer (lysis buffer without igepal). After each wash, cells were centrifuged at 500g for 5 minutes at 4°C. After washing, cell nuclei were resuspended in the transposition reaction mix and incubated for 30 minutes at 37°C. After transposition, DNA was purified using a Qiagen MinElute PCR Purification Kit and eluted in 10uL elution buffer. DNA was stored at -20°C until fragments were amplified via PCR. All of the DNA purified following transposition was PCR amplified. To do so, the following were combined in a 0.2mL PCR tube: 10uL transposed DNA, 10uL nuclease-free H2O, 2.5uL 25uM custom Nextera PCR primer 1, 2.5uL 25uM custom Nextera barcoded PCR primer 2, 25uL NEBNext high-fidelity 2x PCR master mix. The components were amplified as follows: 1 cycle of 72C for 5 min, 98C for 30 sec; 5 cycles of 98C for 10 sec, 63C for 30 sec, 72C for 1 min. After initial amplification, the number of additional cycles to run was determined using qPCR. For this, the following were combined in a 0.2mL PCR tube: 5uL of previously PCR-amplified DNA, 4.5uL of nuclease-free H2O, 0.25uL of 25uM custom Nextera PCR primer 1, 0.25uL of 25uM custom Nextera PCR primer 2, 5uL KAPA SYBR FAST qPCR master mix (2x) (total reaction 15 ul). The components were amplified as follows: 1 cycle of 98C for 30 sec; 20 cycles of 98C for 10 sec, 63C for 30 sec, 72C for 1 min. To calculate the number of additional cycles of PCR needed, linear Rn versus cycle was plotted and the cycle number that corresponds with 1/3 of the maximum fluorescent intensity was determined. After the number of additional PCR cycles was determined, the remaining 45uL of PCR product was run as follows: 1 cycle of 98C for 30 sec; N cycles (as determined via qPCR) of 98C for 10 sec 63C for 30 sec, 72C for 1 min. Finally, the amplified library was purified using 0.9x Ampure beads at room temperature, and eluted in 20uL RNase-free H2O.


title: 48hr Baseline rep 3 [ChIP-seq]

description:
Replicates were combined into 1 processed data file:
out.48hrblank_ppr.IDR0.1.filt.narrowPeak


title: D18C_Endo_1


title: 24hr BFT2 rep 2 [ChIP-seq]


title: 48hr Baseline rep 2 [ChIP-seq]


title: 48hr BFT2 rep 2 [ChIP-seq]

description:
Replicates were combined into 1 processed data file:
out.48hrbft2_ppr.IDR0.1.filt.narrowPeak


title: 48hr BFT2 rep 3 [ChIP-seq]


title: 24hr Baseline rep 2 [ChIP-seq]

description:
Replicates were combined into 1 processed data file:
out.24hrblank_ppr.IDR0.1.filt.narrowPeak


title: 48hr BFT2 rep 1 [ChIP-seq]


title: 24hr Baseline rep 3 [ChIP-seq]


title: D18C_Endo_0


title: 24hr BFT2 rep 3 [ChIP-seq]


title: 24hr Baseline rep 1 [ChIP-seq]


title: D15C_Ovid_1


title: PolysomeProfiling1

city: Lubbock

first: Degeng Wang

last: Wang

state: TX

address: 1207 Gilbert Drive

department: Environmental Toxicology

institute: Texas Tech University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  and then mapped to hg19 whole genome using tophat
Read counts was calculated with htseq-count for each gene. RPKM were then calculated based on gene total exon length and total read counts for each sample
Genome_build: HG19
Supplementary_files_format_and_content: Tab-delimitted text file including RPKM values for each Sample

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols


title: PolysomeProfiling2


title: RNA-Seq3


title: HuccT1 control 2

value: control


title: LN_B cell_nomal

description: Gene expression in B cells from nomal lymph nodes

source_name: lymph node B cells, without tumor inoculation

value: lymph node

value: female

value: B cells


title: D15C_Ovid_0


title: 48hr Baseline rep 1 [ChIP-seq]


title: RNA-Seq1


title: GRO-seq2


title: D15C_Ovary_3


title: D15C_Ovid_2


title: GRO-seq1


title: D15C_Ovary_2


title: D15C_Ovary_1


title: D15C_Ovary_0


title: D15C_Endo_2


title: RNA-Seq2


title: D12C_Ovid_3

value: 12 day


title: D12C_Ovary_0


title: D15C_Endo_1


title: D12C_Ovid_1


title: D15C_Endo_0


title: D12C_Endo_2


title: D12C_Ovary_1


title: D12C_Endo_3


title: D12C_Ovid_2


title: D15C_Endo_3


title: D12C_Endo_0


title: D12C_Ovary_3


title: D12C_Ovary_2


title: D12C_Endo_1


title: D9C_Ovid_1

value: 9 day


title: D12C_Ovid_0


title: D9C_Ovary_0


title: D9C_Ovid_0


title: D9C_Ovary_1


title: D9C_Ovary_2


title: D9C_Ovid_2


title: D9C_Endo_1


title: 48hr BFT2 rep 3 [RNA-seq]


title: D9C_Endo_0


title: D6C_Ovid_1

value: 6 day


title: D6C_Ovid_0


title: D6C_Ovary_1


title: D6C_Ovary_2


title: D6C_Endo_2


title: D3C_Ovid_1

value: 3 day


title: D6C_Endo_1


title: D6C_Endo_0


title: D3C_Ovid_0


title: D6C_Ovary_0


title: D9C_Endo_2


title: D3C_Ovid_2


title: KDM5C H514A

city: Ann Arbor

first: Christina

middle: N

last: Vallianatos

state: MI

address: 1241 East Catherine

department: Human Genetics

institute: University of Michigan

data_processing:
Reads were trimmed to 60bp using BBDuk (version 35.51) and mapped to mm9 using STAR (2.5.3a) allowing no mismatches. Only uniquely mapping reads were analyzed further. Due to low mapability of read2, only read1 was used for further analysis.
BAM files were converted to BigWig files in a strand specific manner. Bigwigs were normalized to 10 million non-rRNA and non-mitochondrial reads.
DESeq2 was used to call differential gene expression between genotypes. Cuffdiff was used to calculate FPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to 10 million non-rRNA non-mtRNA reads. DESeq2 files represent differential gene expression between genotypes.

source_name: mouse forebrain neuronal culture

growth_protocol: Mouse forebrain tissue was dissected from E16 embryos, and cells were dissociated, plated, and cultured as described in PMID: 26804915.

extract_protocol:
Cells were homogenized in TRI Reagent (Sigma) and subjected to total RNA isolation using RNEasy Mini Kit (Qiagen). Ribosomal RNA was depleted using RiboMinus Eukaryotic Kit v2 (Life Technologies).
Libraries were prepared using Direct Ligation of Adapters to First-strand cDNA as described in PMID: 25607527

treatment_protocol: Cells were infected on day in vitro (DIV) 1 with lentivirus containing human KDM5C cDNA (wildtype, WT; patient mutation, RH; or catalytically inactive, HA) or vector (E). Puromycin selection occured at DIV 4, and cells were harvest at 10 DIV.

value: mouse forebrain neuronal culture

value: HA


title: KDM5C WT

value: WT


title: KDM5C R1115H

value: RH


title: D3C_Ovary_0


title: D3C_Endo_2


title: Vector

value: V


title: D3C_Ovary_1


title: D0C_Ovid_2

value: 0 day


title: D3C_Endo_0


title: D0C_Ovid_0


title: D0C_Ovid_1


title: D0C_Ovary_2


title: D3C_Endo_1


title: D0C_Ovary_1


title: D0C_Ovary_0


title: cumulus_oocyte_complex-sample49

city: İstanbul

first: Hüseyin Okan

last: Soykam

address: Teknopark İstanbul, Sanayi Mh. Teknopark Blv. No: 1/4A, Kuluçka Merkezi, Pendik, 34906, İstanbul

department: Bioinformatics

country: Turkey

institute: Epigenetiks Genetik Biyoinformatik Yazılım A.Ş.

description:
homo_sapiens_cumulus_oocyte_complex-sample49-high_oocyte_quality-moderate_embryo_quality-negative_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

hyb_protocol: cDNA was hybridized using the NimbleGen Hybridization System.

scan_protocol: Washing and drying of the array were carried out with a NimbleGen MS 2000 Microarray Scanner, and raw probe expression data was collected from microarray images using DEVA software.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package.
Roche's DEVA software computed signal intensities from image files. Those values are background corrected and RMA normalized using NimbleScan software.

source_name: Woman10, high oocyte quality, moderate embryo quality

label_protocol: cDNA was marked using a Single Color DNA Labeling Kit (NimbleGen, Roche, Germany).

growth_protocol:
Ovarian stimulation therapy was applied to women prior to ICSI.  Recombinant FSH (Gonal F, Serono International SA, Geneva 75–225 IU) was administered according to the patient’s ovarian response. 0.1 mg GnRH analog (Decapeptyl, Ferring GmbhH Kiel, Germany) was started on the 21st day of the previous menstrual cycle.
Transvaginal ultrasonography was performed at regular intervals during the induction, and blood estradiol and progesterone levels were measured in order to assess follicular development. Human chorionic gonadotropin (hCG, Ovitrelle, Merck-Serono S.p.A. Rome, Italy, 5000–10000 IU) was administered when the diameters of follicles achieved a sufficient size. After 34–36 h, the follicles were aspirated transvaginally into sterile tubes under anesthesia

extract_protocol: Total RNA was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. cDNA synthesis from total RNA was carried out using a Superscript Double Chain cDNA Synthesis Kit (Invitrogen Life Technologies, Carlsbad, CA, USA).

value: cumulus cells

value: Negative

tag: cumulus cells_quality

value: High

value: Moderate


title: cumulus_oocyte_complex-sample33

description:
homo_sapiens_cumulus_oocyte_complex-sample33-low_oocyte_quality-moderate_embryo_quality-negative_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman7, low oocyte quality, moderate embryo quality

value: Low


title: HepaRG_BAP_1µM_fatty_acids_ethanol_25mM_replicate3

city: Rennes

first: Simon

last: Bucher

address: 2 Avenue du Pr. L. Bernard

country: France

institute: INSERM U1241

hyb_protocol: The same amount of Cy3-labeled cRNA (600 ng) was fragmented at 60°C for 30 min in a reaction volume of 25 μl containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturer's instructions. Following the fragmentation reaction, 25 μ of 2× Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture. 40 μL of the mixture were hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 h at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with GE Wash buffer 2 at 37 °C (Agilent).

scan_protocol: Microarray were scanned immediately after washing with the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides. The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 072363_D_F_20150612).

data_processing: All 36 microarrays (3 replicates per condition) were qualified (QC from feature extraction) and further analyzed using GeneSpring software (Agilent Technologies). Microarray data were first normalized based on the 75th percentile shift. Then, a filtration by “flag” and “signal intensity” was applied. Were retained only the entities in which at least 100% of the values in any of the twelve conditions had a “detected flag” (i.e. a positive and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which at least 100% of the values in any one of the twelve conditions were within the range of interest (i.e. 20–100th percentile).

source_name: HepaRG cells, BAP 1 µM, oleic and stearic acids 150 µM, ethanol 25 mM

label_protocol: Total RNA, in presence of an external spike-in RNA mixture, were amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following the manufacturer's instructions. Starting from 50 ng total RNA purified from cell culture sample, amplification yield was 6.4 ± 0.9 μg cRNA and specific activity was 14.4 ± 1.0 pmol Cy3 per μg cRNA.

growth_protocol: HepaRG cells were cultured according to the standard protocol described by Aninat et al., (Drug Metab Dispos 2006).  Briefly, HepaRG cells were seeded at a density of 2.6 10^4 cells/cm2 and were first incubated in a William’s E medium supplemented with 10% FBS, 100 units/ml penicillin, 100 µg/ml streptomycin, 2 mM glutamine, 5 µg/ml insulin and 50 µM hydrocortisone hemisuccinate. After 2 weeks, cell differentiation was induced by the same culture medium supplemented with 2% DMSO (differentiation medium) for 2 additional weeks.

extract_protocol: Total RNA were extracted from around 6.10^5 heparg cells using the quiagen miRNeasy mini kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Differentiated HepaRG cells (Aninat et al., Drug Metab Dispos 2006) were treated during 16 days with or without a mixture of fatty acids (150 µM stearic acid and 150 µM oleic acid). After 2 days from the start of the experiments, steatotic and non-steatotic cells were also treated with 1 or 2.5 µM B[a]P, associated or not with 25 mM ethanol. Independent cultures were performed in triplicate. In total, 36 samples were analyzed in this study.

tag: oleic and stearic acids 150 µm

value: yes

tag: bap

value: 1 µM

tag: ethanol 25 mm


title: D0C_Endo_2


title: cumulus_oocyte_complex-sample44

description:
homo_sapiens_cumulus_oocyte_complex-sample44-low_oocyte_quality-moderate_embryo_quality-negative_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman9, low oocyte quality, moderate embryo quality

tag: gender

value: female


title: cumulus_oocyte_complex-sample18

description:
homo_sapiens_cumulus_oocyte_complex-sample18-low_oocyte_quality-high_embryo_quality-positive_clinical_pregnancy-positive_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman4, low oocyte quality, low embryo quality

value: Positive


title: cumulus_oocyte_complex-sample12

description:
homo_sapiens_cumulus_oocyte_complex-sample12-low_oocyte_quality-low_embryo_quality-negative_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman3, low oocyte quality, low embryo quality


title: cumulus_oocyte_complex-sample23

description:
homo_sapiens_cumulus_oocyte_complex-sample23-high_oocyte_quality-moderate_embryo_quality-positive_clinical_pregnancy-positive_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman5, high oocyte quality, moderate embryo quality


title: cumulus_oocyte_complex-sample39

description:
homo_sapiens_cumulus_oocyte_complex-sample39-high_oocyte_quality-high_embryo_quality-negative_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman8, high oocyte quality, high embryo quality


title: kidney_Glucans_SVCV_rep4

city: Vigo

first: Patricia

last: Pereiro

state: Pontevedra

address: C/Eduardo Cabello, 6

department: Immunology and Genomics

institute: IIM-CSIC

description: SAMPLE 32

hyb_protocol: Each amplified and labelled sample was briefly hybridized at 65°C for 17 hours

scan_protocol: The signal was captured, processed, and segmented using an Agilent G2565B scanner (Agilent Technologies, Madrid, Spain) with the Agilent Feature Extraction Software (v9.5) protocol GE1-v5_95 using an extended dynamic range and preprocessing by the Agilent Feature Extraction v9.5.5.1

data_processing: The results for the fluorescence intensity data and quality annotations were imported into GeneSpring GX version 14.9 (Agilent Technologies). All of the control features were excluded from the subsequent analyses. After grouping the biological replicates (4 replicates per treatment), entities with an expression between the 20th and 95th percentile in the raw data were retained and used in the subsequent analyses. The gene-level experiment was carried out by normalizing the data by a percentile shift at the 75th percentile and using as baseline transformation the median of all samples. Differentially expressed genes were identified through Volcano Plot filtering. An unpaired t-test was conducted without correction and data were considered significant at p ≤ 0.01. The fold-change cut-off was set at 1.5.

organism: Danio rerio

source_name: kidney, Glucans-SVCV

label_protocol: Total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One Color Microarray- Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit.

growth_protocol: Zebrafish were obtained from our experimental facility, where the fish were cultured using established protocols (Westerfield, 2000; Nüsslein-Volhard & Dahm, 2002) (see http://zfin.org/zf_info/zfbook/zfbk.html).

extract_protocol: Total RNA was isolated using the Maxwell 16 LEV Simply RNA Tissue Kit (Promega, Madison, WI, USA) according to the manufacturer’s instructions

tag: age

value: adults

value: wild type

value: Kidney


title: HepaRG_BAP_2.5µM_ethanol_25mM_replicate3

source_name: HepaRG cells, BAP 2.5 µM, ethanol 25 mM

value: no


title: cumulus_oocyte_complex-sample28

description:
homo_sapiens_cumulus_oocyte_complex-sample28-high_oocyte_quality-high_embryo_quality-positive_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman6, high oocyte quality, high embryo quality


title: HepaRG_BAP_1µM_replicate3

source_name: HepaRG cells, BAP 1 µM


title: HepaRG_BAP_2.5µM_fatty_acids_ethanol_25mM_replicate3

source_name: HepaRG cells, BAP 2.5 µM, oleic and stearic acids 150 µM, ethanol 25 mM


title: D0C_Endo_1

source_name: Endometrium tissue


title: HepaRG_ctrl_ethanol_25mM_replicate3

source_name: HepaRG cells, ctrl

value: 0 µM


title: cumulus_oocyte_complex-sample2

description:
homo_sapiens_cumulus_oocyte_complex-sample2-high_oocyte_quality-moderate_embryo_quality-negative_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman1, high oocyte quality, moderate embryo quality


title: HepaRG_BAP_1µM_fatty_acids_replicate3

source_name: HepaRG cells, BAP 1 µM, oleic and stearic acids 150 µM


title: cumulus_oocyte_complex-sample9

description:
homo_sapiens_cumulus_oocyte_complex-sample9-high_oocyte_quality-high_embryo_quality-negative_clinical_pregnancy-negative_live_birth
Amongst multiple oocyte-cumulus complex samples acquired from patient, only cumulus cells from each oocyte that developed an embryo were transfered to patient and thereby analysed.

source_name: Woman2, high oocyte quality, high embryo quality


title: HepaRG_ctrl_fatty_acids_ethanol_25mM_replicate3

source_name: HepaRG cells, ctrl, oleic and stearic acids 150 µM, ethanol 25mM


title: HepaRG_BAP_2.5µM_replicate3

source_name: HepaRG cells, BAP 2.5 µM


title: HepaRG_BAP_1µM_ethanol_25mM_replicate3

source_name: HepaRG cells, BAP 1 µM, ethanol 25 mM


title: HepaRG_ctrl_replicate3


title: HepaRG_BAP_1µM_fatty_acids_ethanol_25mM_replicate2

source_name: HepaRG cells, BAP 1 µM, oleic and stearic acids 150 µM, ethanol 25 mM


title: kidney_Glucans_SVCV_rep3

description: SAMPLE 31

tag: strain


title: HepaRG_BAP_2.5µM_fatty_acids_replicate3

source_name: HepaRG cells, BAP 2.5 µM, oleic and stearic acids 150 µM


title: HepaRG_ctrl_fatty_acids_replicate3

source_name: HepaRG cells, ctrl, oleic and stearic acids 150 µM


title: HepaRG_BAP_2.5µM_fatty_acids_ethanol_25mM_replicate2


title: D0C_Endo_0


title: kidney_Glucans_SVCV_rep2

description: SAMPLE 30


title: AsPC-1_EGF_24hr

city: Houston

first: Mien-chie

last: Hung

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

data_processing:
Use Life Technologies software Life Scope 1.3.1 to process raw SOLiD xsq files, map to human transcriptome (hg19), and generate whole transcriptome read counts and normalized RPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each sample

growth_protocol: cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM)/F12 or RPMI 1640 medium (for pancreatic cancer cell lines) supplemented with 10% fetal bovine serum and antibiotics

extract_protocol: Total RNA were extracted using TRIzol Reagent, following the user guide from the manufacturer (Life Technologies #15596018).

treatment_protocol: cells were treated with EGF or ANG/hRNase5 at a concentration of 50 ng/ml and 1 ug/ml respectively in serum-starved conditions for 1hr, 5hr and 24hr

tag: cell line

value: pancreatic cancer cell line

tag: treated with

value: EGF 24hr


title: kidney_Glucans_SVCV_rep1

description: SAMPLE 29


title: AsPC-1_EGF_1hr

value: EGF 1hr


title: AsPC-1_EGF_5hr

value: EGF 5hr


title: kidney_PolyI:C_SVCV_rep2

description: SAMPLE 26

source_name: kidney, PolyI:C-SVCV


title: kidney_PolyI:C_SVCV_rep1

description: SAMPLE 25


title: AsPC-1_ANG/hRNase5_24hr

value: ANG/hRNase5 24hr


title: kidney_LPS_SVCV_rep4

description: SAMPLE 24

source_name: kidney, LPS-SVCV


title: AsPC-1_ANG/hRNase5_5hr

value: ANG/hRNase5 5hr


title: kidney_PolyI:C_SVCV_rep4

description: SAMPLE 28


title: 9985131140_R06C02: genomic DNA from saliva sample

type: genomic

city: Madison

first: Andy

last: Madrid

state: Wisconsin

address: 600 Highland Ave

department: Neurological Surgery

institute: University of Wiconsin - Madison

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

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

data_processing:
minfi v1.20
csv files for each sample contain the CpG ID and the beta value for all of the CpGs tested in the study

label: Cy3, Cy5

source_name: saliva sample from sample with LSI 2

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and gel-purified from samples using the Oragene kit according to manufacturer's instructions

value: Female

value: saliva

tag: lsi score

value: prepubescent


title: 9985131140_R05C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 1.5


title: 9985131140_R06C01: genomic DNA from saliva sample


title: 9985131140_R03C02: genomic DNA from saliva sample


title: 9985131140_R05C02: genomic DNA from saliva sample


title: 9985131140_R04C02: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 2.5


title: kidney_LPS_SVCV_rep3

description: SAMPLE 23


title: kidney_PolyI:C_SVCV_rep3

description: SAMPLE 27


title: 9985131140_R02C02: genomic DNA from saliva sample


title: HepaRG_BAP_2.5µM_ethanol_25mM_replicate2

source_name: HepaRG cells, BAP 2.5 µM, ethanol 25 mM

value: yes


title: 9985131140_R04C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 4


title: HepaRG_ctrl_ethanol_25mM_replicate2

source_name: HepaRG cells, ctrl


title: AsPC-1_mock

value: none (untreated)


title: HepaRG_BAP_1µM_fatty_acids_replicate2

value: 1 µM


title: HepaRG_BAP_1µM_ethanol_25mM_replicate2


title: 9985131140_R03C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 6.5


title: Panc-1_EGF_24hr


title: HepaRG_BAP_2.5µM_replicate2


title: 9985131140_R02C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 5


title: kidney_LPS_SVCV_rep1

description: SAMPLE 21

value: adults


title: kidney_PBS_SVCV_rep3

description: SAMPLE 19

source_name: kidney, PBS-SVCV

value: wild type


title: kidney_PBS_SVCV_rep4

description: SAMPLE 20

value: Kidney


title: HepaRG_ctrl_replicate2

value: no


title: Panc-1_EGF_5hr


title: HepaRG_BAP_2.5µM_fatty_acids_replicate2


title: 9985131164_R06C02: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 9.5


title: kidney_LPS_SVCV_rep2

description: SAMPLE 22


title: Panc-1_ANG/hRNase5_24hr


title: 9985131164_R05C02: genomic DNA from saliva sample


title: Panc-1_EGF_1hr


title: kidney_PBS_SVCV_rep2

description: SAMPLE 18


title: Panc-1_ANG/hRNase5_5hr


title: kidney_PBS_SVCV_rep1

description: SAMPLE 17


title: 9985131164_R04C02: genomic DNA from saliva sample


title: kidney_Glucans_MEM_rep4

description: SAMPLE 16

source_name: kidney, Glucans-MEM


title: Panc-1_ANG/hRNase5_1hr

value: ANG/hRNase5 1hr


title: HepaRG_BAP_1µM_replicate2

source_name: HepaRG cells, BAP 1 µM


title: 9985131140_R01C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 1


title: HepaRG_BAP_2.5µM_fatty_acids_ethanol_25mM_replicate1

source_name: HepaRG cells, BAP 2.5 µM, oleic and stearic acids 150 µM, ethanol 25 mM


title: 9985131164_R03C02: genomic DNA from saliva sample


title: HepaRG_ctrl_fatty_acids_ethanol_25mM_replicate1

source_name: HepaRG cells, ctrl, oleic and stearic acids 150 µM, ethanol 25mM

value: 0 µM


title: 9985131164_R02C02: genomic DNA from saliva sample


title: HepaRG_BAP_1µM_fatty_acids_ethanol_25mM_replicate1

source_name: HepaRG cells, BAP 1 µM, oleic and stearic acids 150 µM, ethanol 25 mM


title: HepaRG_BAP_2.5µM_ethanol_25mM_replicate1


title: Panc-1_mock

value: pancreatic cancer cell line


title: HepaRG_ctrl_fatty_acids_replicate2

source_name: HepaRG cells, ctrl, oleic and stearic acids 150 µM


title: HepaRG_ctrl_ethanol_25mM_replicate1


title: kidney_Glucans_MEM_rep3

description: SAMPLE 15


title: kidney_Glucans_MEM_rep2

description: SAMPLE 14


title: HepaRG_BAP_1µM_ethanol_25mM_replicate1

source_name: HepaRG cells, BAP 1 µM, ethanol 25 mM


title: 9985131164_R05C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 2


title: 9985131164_R01C02: genomic DNA from saliva sample


title: kidney_Glucans_MEM_rep1

description: SAMPLE 13


title: 9985131164_R06C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 1.5


title: tSH2Δ mutant Rep2 ATAC

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-seq: Raw reads that contain Illumina adapter sequence were filtered by TagDust (v1.12) at an FDR threshold of 0.001. Reads were then aligned to the sacCer3 genome using Bowtie (v1.1.2) using options: -m 1, --seed=123, and --nomaqround. Samtools (v0.1.9) and bedtools (v2.25.0) were used for post-alignment data conversions. Gene counts were calculated using HTSeq (v0.6.1) and the sacCer3 sgdGene table from UCSC Genome Browser. GO terms were generated using DAVID (v6.8).
ATAC-seq alignments and initial analysis: Fastq sequence files were first filtered for high quality reads using trimgalore (v0.4.1), "trim_galore -q 20 --nextera --length 20", then aligned to the sacCer3 genome using bowtie2, "bowtie2 --threads 6 --very-sensitive --maxins 2000". After converting bowtie2 output files to bam files using samtools (v1.3.1). Next bedtools (v2.25.0) "bamtobed" was used to convert bam output files to bed file format to do the subsequent steps.  Using simple custom awk scripts, exact Tn5 transposase bp insertion sites were created from the bed files by adjusting the insertion sites +4bp for positive strand sequences while adjusting -5bp for negative stranded sequences and adjusting the bed file region to just the 1bp region at the insertion sites.  This bed file was then converted back to bam format using bedtools "bedtobam" before normalizing the sequence counts using Deeptools' bamCoverage (v2.2.4), " --binSize 1 --fragmentLength 1 --normalizeTo1x 12100000 --minMappingQuality 20",  to create a bigWig output file for each replicate.
ATAC-seq signal meta-analysis: Differential genes determined using DESeq2 were used to create a list of upregulated (567) and downregulated (598) genes in the mutant yeast strain compared to the wildtype.  A similar number of genes where the expression level had little to no change (DESeq2 padj>0.5) but also reflecting a range of baseline level of transcription was selected (601 genes).  Cell cycle (800 genes, Spellman 1998) and histone (8 genes) gene lists were compiled.   Each set of genes were sorted in decreasing order from highest transcribed to lowest transcribed. Using computematrix.py and plotheatmapper.py programs from Deeptools (v2.2.4), the normalized ATAC-seq signal for a scaled region representing each of the genes in our gene subsets plus/minus 1kb were compiled and plotted.
Genome_build: sacCer3
Supplementary_files_format_and_content: BAM files contain RNA aligned reads to the sacCer3 genome after filtering out reads that contained adapter sequence. Tab-delimited text files include calculated RPKM values for all genes, as well as differentially abundant gene data (including calculated RPKMs, DESeq p-values, and RPKM fold changes).

organism: Saccharomyces cerevisiae

source_name: tSH2Δ mutant Rep2 ATAC

growth_protocol: WT and tSH2Δ cells were grown in YPD. Overnight saturated cultures were diluted back to an optical density of 0.2 and were allowed to grow until  they reached an OD of 1.  For ATAC seq, we used 5 million cells of WT and tSH2Δ.

extract_protocol:
For ATAC seq: Five million wild-type (S288C) and spt6-tSH2Δ cell were collected during their linear phase of growth. Three replicates each were collected for the wild type and mutant (total of 6 samples). ATAC-seq libraries were made as described (Buenrostro et al., 2015; Schep et al., 2017), with the exception of a double-sided SPRI bead size selection step of each library, using 0.5x and 1x ratio of SPRI beads to obtain a library size range of ~150 bp to ~2 kb.For RNAseq:  RNA was extracted from 10 million cells using acid phenol extraction method followed by DNAse treatment before subjecting it to library preparation.
For RNA-seq:  RNA was extracted from 10 million cells using acid-phenol extraction method followed by DNAse treatment before subjecting it to library preparation.
For ATAC-seq: WT replicates were index labelled using Ad2.1_TAAGGCGA, Ad2.2_CGTACTAG, and Ad2.3_AGGCAGAA Illumina indexes, while the mutant libraries were indexed using Ad2.6_TAGGCATG, Ad2.7_CTCTCTAC, and Ad2.8_CAGAGAGG (Buenrostro 2013). All 6 libraries were combined and sequenced on a single lane of Illumina Hiseq 2500 using v4 chemistry for 50bp paired-end output.
For RNA-seq: WT and spt6-tSH2Δ strains were cultured in YPD for 4 hours after diluting overnight saturated cultures to an OD600 of 0.2. RNA was extracted from the cells using acid-phenol method as described. Residual DNA was eliminated using DNase treatments (DNAse I, Ambion Cat #AM2222). Library preparation and sequencing were performed at the High-Throughput Sequencing Facility (HTSF) at UNC-Chapel Hill. Libraries were prepared using TruSeq Stranded Total RNA with RiboZero Gold Library Prep Kit (Illumina) and were sequenced using Illumina HiSeq 2500 (50 bp, single-end reads).

treatment_protocol: No treatment were performed prior to library preps

tag: genotype


title: tSH2Δ mutant Rep3 ATAC

source_name: tSH2Δ mutant Rep3 ATAC


title: kidney_PolyI:C_MEM_rep4

description: SAMPLE 12

source_name: kidney, PolyI:C-MEM

tag: tissue


title: tSH2Δ mutant Rep1 ATAC

source_name: tSH2Δ mutant Rep1 ATAC


title: kidney_PolyI:C_MEM_rep3

description: SAMPLE 11


title: HepaRG_BAP_2.5µM_fatty_acids_replicate1

source_name: HepaRG cells, BAP 2.5 µM, oleic and stearic acids 150 µM


title: HepaRG_ctrl_fatty_acids_replicate1


title: HepaRG_BAP_1µM_fatty_acids_replicate1

source_name: HepaRG cells, BAP 1 µM, oleic and stearic acids 150 µM


title: 9985131164_R04C01: genomic DNA from saliva sample


title: kidney_PolyI:C_MEM_rep2

description: SAMPLE 10


title: 9985131164_R03C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 5.5


title: WT Rep1 ATAC

source_name: WT Rep1 ATAC

value: WT


title: WT Rep2 ATAC

source_name: WT Rep2 ATAC


title: tSH2Δ mutant Rep3 RNA

source_name: tSH2Δ mutant Rep3 RNA


title: kidney_PolyI:C_MEM_rep1

description: SAMPLE 9


title: kidney_LPS_MEM_rep4

description: SAMPLE 8

source_name: kidney, LPS-MEM


title: OreR_ATAC-seq rep2

city: Oxford

first: Sebastian

last: Kittelmann

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
OreR.NARROWPEAK
OreR_peaks.txt
OreR_summits.bed

data_processing:
RNAseq: Reads were aligned to FlyBase D. melanogaster genome version 6.12 using TopHat 2.1.1.
Transcripts were quantified using Cufflinks 2.2.1.
Differential expression analysis was done using Cuffdiff.
ATAC-seq: Reads were end-to-end aligned to D. melanogaster genome version 6.12 (FlyBase) using bowtie2.
Low quality reads were filtered and duplicates were removed using SAMtools.
Reads were re-centered according to Buenrostro et al. (2013) DOI:10.1038/NMETH.2688.
Peaks were called with MACS2.
Genome_build: FlyBase D. melanogaster genome version 6.12
Supplementary_files_format_and_content: Cufflinks files contain output from Cufflinks for each RNAseq replicate
Supplementary_files_format_and_content: narrowPeak files contain peak locations together with peak summit, pvalue and qvalue
Supplementary_files_format_and_content: peaks.txt files are tabular files which contains information about called peaks
Supplementary_files_format_and_content: summits files contain peak summit locations for every peak. Column1: chromosome; Column2: start position of summit; Column3: end position of summit; Colun4: label; Column5: -log10pvalue

organism: Drosophila melanogaster

source_name: second (T2) pupal legs

growth_protocol: Flies were kept at 25 °C on standard food. Pupae were collected within 1 h after puparium formation and were allowed to develop for another 20-28 h at 25 °C.

extract_protocol:
Leg cells were lysed in 50 µl Lysis Buffer (10 mM Tris-HCl, pH = 7.5; 10 mM NaCl; 3 mM MgCl2; 0.1 % IGEPAL). Nuclei were collected by centrifugation at 500 g for 5 min. Approximately 60,000 nuclei were suspended in 50 µl Tagmentation Mix [25 µl Buffer (20 mM Tris-CH3COO-, pH = 7.6; 10 mM MgCl2; 20 % Dimethylformamide); 2.5 µl Tn5 Transposase; 22.5 µl H2O] and incubated at 37 °C for 30 min. After addition of 3 µl 2 M NaAC, pH = 5.2 DNA was purified using a QIAGEN MinElute Kit.
PCR amplification for library preparation was done for 15 cycles with NEBNext High Fidelity Kit; primers were used according to Buenrostro et al. (2013) DOI:10.1038/NMETH.2688

treatment_protocol:
Tissue was kept in ice cold PBS until chromatin extraction.
Pupae were dissected under PBS.

value: Oregon R

value: 20-28 h after puparium formation

value: second (T2) pupal legs


title: 9985131164_R02C01: genomic DNA from saliva sample

source_name: saliva sample from sample with LSI 2.5

value: Female


title: OreR_ATAC-seq rep1


title: WT Rep3 ATAC

source_name: WT Rep3 ATAC


title: kidney_LPS_MEM_rep3

description: SAMPLE 7


title: kidney_LPS_MEM_rep2

description: SAMPLE 6


title: eworo_ATAC-seq rep2

description:
eworo.NARROWPEAK
eworo_peaks.txt
eworo_summits.bed

value: ebony[4],white ocelli[1], rough[1]


title: tSH2Δ mutant Rep2 RNA

source_name: tSH2Δ mutant Rep2 RNA


title: eworo_ATAC-seq rep1


title: OreR_ATAC-seq rep3


title: WT Rep3 RNA

source_name: WT Rep3 RNA


title: tSH2Δ mutant Rep1 RNA

source_name: tSH2Δ mutant Rep1 RNA


title: kidney_LPS_MEM_rep1

description: SAMPLE 5


title: WT Rep2 RNA

source_name: WT Rep2 RNA


title: kidney_PBS_MEM_rep3

description: SAMPLE 3

source_name: kidney, PBS-MEM


title: HepaRG_BAP_2.5µM_replicate1

source_name: HepaRG cells, BAP 2.5 µM


title: HepaRG_ctrl_replicate1

source_name: HepaRG cells, ctrl


title: WT Rep1 RNA

source_name: WT Rep1 RNA


title: kidney_PBS_MEM_rep2

description: SAMPLE 2


title: 7106.Gtype

city: Kongens Lyngby

first: Haja

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

description: 7106: H2

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Genomic DNA extracted from ham muscle was genotyped using Illumina Porcine SNP60v2 BeadChip.

source_name: Ham muscle

label_protocol: Not provided

growth_protocol: Danish Landrace male pigs were slaughtered at 100 kg. Ham muscle samples were collected by punch biopsies, genomic DNA was extracted by Qiagen DNA Minikit and subjected to Illumina Porcine 60K v2 chip

extract_protocol: Punch biopsy at slaughterhouse and Qiagen DNA Minikit

treatment_protocol: Danish Landrace males pigs were categorised into low, medium and high summarised EBVs of skatole and human nose scores, derived from the sires of each pig.

value: male

tag: group

value: high boar taint

value: Ham muscle


title: 7325.Gtype

description: 7325: H10


title: eworo_ATAC-seq rep3


title: 7131.Gtype

description: 7131: H7


title: Female 5 cervico-vaginal lavage

city: Boston

first: Caroline

middle: Attardo

last: Genco

state: MA

address: 136 Harrison Ave

institute: Tufts University

data_processing:
fastq files were examined with the Rockhopper program.  This program performs alignment, gene counts, normalization and outputs expression levels for each gene in each samples.  Adjusted q values are also assigned to each pair-wise comparison between all samples.  Fastq files were aligned to the genome of Neisseria gonorrheoae FA1090
Supplementary_files_format_and_content: Text files with normalized expression values for each gene

organism: Neisseria gonorrhoeae

source_name: female cervico-vaginal lavage

extract_protocol:
TRIzol,  both prokaryotic and eukaryotic rRNA was depleted from all samples
TruSeq RNA Preparation Kit

tag: source

value: female cervico-vaginal lavage


title: 8332.Gtype

description: 8332: H11


title: Female 7 cervico-vaginal lavage


title: 7306.Gtype

description: 7306: H9


title: Male 5 isolate grown in CDM

source_name: Planktonic cells

value: strain isolated from subject


title: 9313.Gtype

description: 9313: H15


title: Male 6 isolate grown in CDM


title: kidney_PBS_MEM_rep4

description: SAMPLE 4

value: adults

value: wild type


title: U87

city: Guangzhou

first: Diling

last: Chen

state: Guangdong

address: No.100, Xianliezhong Road

institute: Guangdong Institute of Microbiology, Guangzhou China 510070

description:
TMM_normalized_reads_count_per_million.txt
N

data_processing:
For circRNA expression analysis, the reads were to mapped genome using the STAR (58) and DCC (59) was used to identify the cirRNA and to estimate the circRNA expression
TMM (trimmed mean of M-values) was used to normalize the gene expression
Genome_build: hg19
Supplementary_files_format_and_content: txt TMM normalized junction read counts

source_name: glioma cells

growth_protocol: U87 glioma cells were cultured in high-glucose DMEM (C11995500BT, Gibco, USA) supplemented with 10% fetal calf serum (10099–141, Gibco, Australia) and 1× penicillin–streptomycin solution. L3-treated U87 cells were U87 cells treated with 12.5 μg/ml L3 for 24 h.

extract_protocol:
total RNA  was extracted with TRIzol® Reagent (Life technologies)
RNA sequencing libraries were prepared from 2μg of total RNA using the TruSeq Kit (Illumina, Inc.) with modifications. Instead of purifying poly-A RNA using poly-dT primer beads, we removed ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Illumina, Inc.). Linear RNA was removed using RNase R (Epicentre, Inc). Poly-T oligo-attached magnetic beads (Illumina, Inc.) were used to remove residual poly-A RNA. All other steps were performed according to the manufacturer's protocols.

value: U87 glioma cell line

value: brain

tag: treatment


title: Male 4 isolate grown in CDM


title: L3-treated_U87

description:
TMM_normalized_reads_count_per_million.txt
LZ

value: L3-treated U87 cells


title: Female 6 cervico-vaginal lavage


title: 7107.Gtype

description: 7107: H6


title: patient C post-Vorinostat

city: Amsterdam

first: Liqin

address: Plesmanlaan 121

country: Netherlands

institute: NKI-AVL

description: Custom Target Enrichment Agilent SureSelect DNA XT2 - 16 per pool

data_processing:
Library strategy: exome-seq
The reads were sequenced using a stranded protocol and aligned against the human genome, build 38
Readcounts were generated using a custom script based on the same strategy as HTSeq-count
Mapped BAM files were used to analyse BRAF and MEK inhibitor resistance related the hot spot mutations. Integrative Genomics Viewer (IGV) was used to visualize mutation allele frequencies
Using IGV, we found KRAS and NRAS mutations in the samples. In our study, we claimed as the BRAF and MEK inhibitor resistant mechanisms
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: KRAS and NRAS mutation allele frequency pre- and post HDACi treatment

source_name: BRAF mutant melanoma patient biopsy

extract_protocol:
NKI 178 Cancer Gene Panel (SeqCapEZ Choice) - GCF.   DNA Library preparation:
dsDNA input: 240 - 428 ng
Fragmented by covaris shearing to a length of 240 bp
Kit used for DNA library prep: KAPA HTP Library Preparation Kit (Cat no. KK8234 07961901001) (According to protocol: KAPA HTP Library Preparation Kit for Illumina platforms (KR0426 v5.16)
Amount of PCR cycles: 6
NKI 178 DNA seq Cancer Gene Panel, Custom Target Enrichment with Agilent SureSelect DNA XT2. Enrichment:
178 gene custom bait library used: SeqCap EZ Choice (cat.no. 06266282001)
Protocol: Nimblegen SeqCap EZ library SR User's Guide Version 4.1 (chapter 5 / 6 / 7)
Adjustment: we used the Kapa HiFi PCR kit (KK2601), 12 cycles PCR (post enrichment)

treatment_protocol: Patients were treated with Vorinostat (a safe single oral daily dose of 360 mg)

tag: disease state

value: skin cancer

value: BRAF mutant melanoma patient biopsy

tag: sample type

value: patient C post-Vorinostat


title: Male 3 isolate grown in CDM


title: 1326.Gtype

description: 1326: H1


title: kidney_PBS_MEM_rep1

description: SAMPLE 1

value: Kidney


title: Male 2 isolate grown in CDM


title: 1334.Gtype

description: 1334: H4


title: Male 1 isolate grown in CDM


title: patient B post-Vorinostat

value: patient B post-Vorinostat


title: patient B pre-Vorinostat

value: patient B pre-Vorinostat


title: 1306.Gtype

description: 1306: H16


title: 1331.Gtype

description: 1331: H3


title: E13-14D

city: Marseille

first: Thom

middle: Thi

last: Tran

address: 163, avenue de Luminy

department: Marseille

institute: INSERM

description: Gene expression from left ventricle of 6 month- old Nkx2-5Δcompaction mice

hyb_protocol: 0,6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent for 8-pack microarray format following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Hi-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Genome Oligo Microarrays (Feature Number version) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed  at room temperature with GE Wash Buffer 1 (Agilent), then 1 minute at room temperature with GE Wash Buffer 1 (Agilent), and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using AgilentG3_GX_1color setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 028005_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities. Data  was first log2 transformed then quantile normalization was applied to sample data to correct for global intensity and dispersion . Then, a filtering at 75% was used to keep only genes expressed over the background noise, so 22 114 probes

source_name: Left ventricle, Nkx2-5Δcomp, 6 months old, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification, Rneasy mini kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from left ventricle of 6 month-old control, Nkx2-5∆trab and Nkx2-5∆comp mice (n=4 for each group) using TRIzol Reagent according to the manufacturer’s procedure (Invitrogen, Life Technologies). The concentration of RNA was determined by reading absorbance at 260 nm on NanoDrop (ND-1000, ThermoScientific). The quality of RNA was confirmed on the Agilent 2100 Bioanalyzer (Agilent technologies, Germany) with the Agilent RNA 6000 Nano chips. The samples with the RIN (RNA Integrity Number) closed to 10 were used for microarray

value: left ventricle

tag: embryonic stages of tamoxifen injection in the deletion of nkx2-5


title: Male 6 swab

description:
Expression_male_vivo_vs_vitro
Expression_male_vs_female_invivo

source_name: male urethral swab

value: male urethral swab


title: E10-11A

description: Gene expression from left ventricle of 6 month- old Nkx2-5Δtrabelculation mice

source_name: Left ventricle, Nkx2-5Δtrab, 6 months old, replicate 1


title: Male 5 swab


title: E10-11D

source_name: Left ventricle, Nkx2-5Δtrab, 6 months old, replicate 4


title: HepaRG_ctrl_fatty_acids_ethanol_25mM_replicate2

source_name: HepaRG cells, ctrl, oleic and stearic acids 150 µM, ethanol 25mM

tag: oleic and stearic acids 150 µm

value: yes

value: 0 µM


title: patient C pre-Vorinostat

value: patient C pre-Vorinostat


title: 1338.Gtype

description: 1338: H5

value: male

value: high boar taint

value: Ham muscle


title: patient A Post-Vorinostat cycle1

value: patient A Post-Vorinostat cycle1


title: Male 4 swab


title: E10-11C

source_name: Left ventricle, Nkx2-5Δtrab, 6 months old, replicate3


title: E13-14A

source_name: Left ventricle, Nkx2-5Δcomp, 6 months old, replicate 1


title: E10-11B

source_name: Left ventricle, Nkx2-5Δtrab, 6 months old, replicate 2


title: CT3

description: Gene expression from left ventricle of 6 month- old control mice

source_name: Left ventricle, Control, 6 months old, replicate 3

value: control, non injection


title: CT4

source_name: Left ventricle, Control, 6 months old, replicate 4


title: 9138.Gtype

description: 9138: H14


title: Male 3 swab


title: E13-14B

source_name: Left ventricle, Nkx2-5Δcomp, 6 months old, replicate 2


title: E13-14C

source_name: Left ventricle, Nkx2-5Δcomp, 6 months old, replicate 3


title: patient A pre-Vorinostat

value: patient A pre-Vorinostat


title: 9129.Gtype

description: 9129: H13

source_name: Ham muscle


title: Male 2 swab


title: 8338.Gtype

description: 8338: M16

value: medium boar taint


title: 7305.Gtype

description: 7305: H8


title: patient A post-Vorinostat cycle 2

value: skin cancer

value: BRAF mutant melanoma patient biopsy

value: patient A post-Vorinostat cycle 2


title: Male 1 swab


title: 9128.Gtype

description: 9128: H12


title: 4366_8_CF11887 patient B post-Vorinostat

description: polyA+ stranded RNA Library prep from total-RNA

data_processing:
The reads were sequenced using a stranded protocol and aligned against the human genome, build 38, using Tophat 2.1 with bowtie 1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
To aviod noise fold change caused by low reads. The reads counts from In vitro A375 A375R and A375DR were filtered greater than 50
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

molecule: polyA RNA

source_name: patient B post-Vorinostat

growth_protocol: A375 parental,  cells grow in DMEM-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine. A549 cell grow in RPMI-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine. A375R were cultured in the same culture condition plus 2µM vemurafenib. A375DR cells were cultured in the same culture condition plus 0.5µM Dabrafenib and 10nM Trametinib

extract_protocol:
A375, A375R and A375DR RNA was isolated using TRIZOL, patient biopisy RNA isolation kit from qiagen
Stranded RNA libraries were prepared for sequencing according to Illumina instructions

treatment_protocol: In vitro: A375, A375R, A375DR cells were treated with 1µM Vorinostat. Patient samples, Patients were treated with Vorinostat (a safe single oral daily dose of 360 mg)

tag: individual

value: patient B

value: post-Vorinostat


title: 7112.Gtype

description: 7112: M7


title: 4366_7_CF11942 patient B pre-Vorinostat

source_name: patient B pre-Vorinostat

value: pre-Vorinostat


title: 4366_9_CF11888 patient C pre-Vorinostat

source_name: patient C pre-Vorinostat

value: patient C


title: 4366_10_CF11889 patient C post-Vorinostat

source_name: patient C post-Vorinostat


title: 4366_3_CF11886 patient A post-Vorinostat cycle 2

source_name: patient A post-Vorinostat cycle 2

value: patient A

value: post-Vorinostat cycle 2


title: CT2

source_name: Left ventricle, Control, 6 months old, replicate 2

value: left ventricle


title: CT1

source_name: Left ventricle, Control, 6 months old, replicate 1


title: 7110.Gtype

description: 7110: M6

value: male


title: 8325.Gtype

description: 8325: M12


title: 4366_2_CF11882 patient A Post-Vorinostat cycle1

source_name: patient A Post-Vorinostat cycle1

value: post-Vorinostat cycle1


title: 8106.Gtype

description: 8106: M9

value: Ham muscle


title: 4366_1_CF11880 patient A pre-Vorinostat

source_name: patient A pre-Vorinostat


title: 3842_7_A375DR_drug_withdrawal

description: polyA+ stranded RNA Library prep from cells

source_name: A375DR cells

value: BRAF mutant melanoma cell line A375DR

value: drug withdrawal


title: 3842_8_A375DR_Vorinostat

source_name: A375DR cells treated with Vorinostat

value: treated with Vorinostat


title: 9328.Gtype

description: 9328: M15

value: medium boar taint


title: 9304.Gtype

description: 9304: M14


title: 3842_5_A375R_Vorinostat

source_name: A375R cells treated with Vorinostat

value: skin cancer

value: BRAF mutant melanoma cell line A375R


title: 9135.Gtype

description: 9135: M13


title: 3842_4_A375R_drug_withdrawal

source_name: A375R cells


title: 2687_3_A375_SA_vorinostat_treated

source_name: A375 Parental cells treated with Vorinostat

value: BRAF mutant melanoma cell line A375 (parental)


title: 2687_1_A375__-3213-__UT_untreated

source_name: A375 Parental cells

value: untreated


title: ST2734-3

city: Albany

first: Guangchun

last: Bai

address: New Scotland Ave

department: DIMD

institute: Albany Medical College

data_processing:
trimmed using IDLE
Expression analysis conducted using RNA-Rocket
Align and assemble transcript to Streptococcus pneumoniae D39
Differential expression analysis

organism: Streptococcus pneumoniae

source_name: Δpde1Δpde2 (ST2734)

growth_protocol: Bacteria were grown in Todd-Hewitt broth supplemented with 0.5% yeast extract (THY)

extract_protocol:
Bacteria were harvested by centrifugation and were disrupted using a beadbeater (BIoSpec). RNA was prepared using a trizol-based protocol and treated with DNase using Rnase-free Dnase Set (Qiagen).
Libraries were constructed using ScriptSeq complete kit (Bacteria)(Epicentre) following the manufacturer's mannual.
rRNA was removed using Ribo-Zero magnetic kit (Epicentre). Library was generated using ScriptSeq Complet Kit (Bacteria) (Epicentre) following the manufacturer's mannuals. Samples 1 to 6 were amplified with index PCR primers 1 to 6, respectively, from Script Seq Index PCR primers (Epicentre).

value: Pde1/Pde2 mutant


title: 2111.Gtype

description: 2111: M3

source_name: Ham muscle


title: DMF 12hour biological rep1

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation and labeling, 3.5 ug of  ss-cDNA was hybridized for 16 hours at 45C  on each array.  The human gene 2.0st arrays were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: The human gene 2.0st arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were background adjusted, normalized and summarized by the RMA method.

source_name: Cells treated with DMF for 12h

label_protocol: Biotinylated ss-cDNA was prepared using the Ambion Whole Transcript Assay (4411972, Affymetrix Terminal Labeling Kit (901524) with 100 ng of total RNA as input.

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FCS, 1% L-glutamine, 1% penicillin–streptomycin.

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: Cells were  treated with 100 uM of DMF for 6 and 12 hours.

tag: cell type

value: neuroblastoma

tag: myc status

value: N-Myc


title: WT-3

source_name: wild-type

value: wild-type


title: DMF 12hour biological rep2


title: CY5-FGF23

city: Wakayama

first: Mitsuru

last: Yashiro

state: Wakayama Prefecture

address: 811-1, Kimiidera

department: Nephrology

institute: Wakayama Medical University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: Agilent software was used to obtain LOWESS normalized, background subtracted data.

source_name: mIMCD3 without FGF23 stimulation

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Mouse renal epithelial cell line, mIMCD3, was used for this study and purchased from Riken cell bank (Tsukuba, Japan). The cells were cultured with DMEM/F12 with 10% FBS (SH30079.03, Hyclone, Logan, UT, USA) under CO2 incubator at 37°C and 5%CO2

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

treatment_protocol: The mIMCD3 cell line was cultured with or without 10ng/mL of FGF23 (2629FG, R&D systems) for 4 hours.

value: tubule epithelial cells

source_name: mIMCD3 with FGF23 stimulation


title: CY3-FGF23


title: 3128.Gtype

description: 3128: M4

tag: gender


title: 1111.Gtype

description: 1111: M1


title: WT-2


title: WT-1


title: ST2734-2


title: 1113.Gtype

description: 1113: M2


title: DMF 6hour biological rep1

source_name: Cells treated with DMF for 6h


title: 8102.Gtype

description: 8102: M8


title: 8308.Gtype

description: 8308: M11


title: DMF 6hour biological rep2


title: Hep_EGFP

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

institute: Kyoto Univ.

description: Control

hyb_protocol: The fragmented and biotin-labeled cDNA targets were hybridized to mouse Gene 2.0 ST arrays (Affymetrix) according to Affymetrix protocols.

scan_protocol: Hybridized arrays were scanned using an Affymetrix GeneChip Scanner.

data_processing: The array data were analyzed using GeneSpring software. Gene expression values were normalized by excluding low-signal intensity data and percentile shifts.

source_name: Hepatoblasts, Control

label_protocol: Transcriptional amplification were performed using 200 ng of total RNA following the Whole Transcript (WT) Expression kit  Ambion/Affymetrix).

growth_protocol: Hepatoblasts were maintained on a type IV collagen-coated culture plate in a medium consisting of a 1:1 mixture of DMEM/Ham’s F-12 with L-glutamine, HEPES and sodium pyruvate (Wako) supplemented with 10% fetal bovine serum (vol/vol) (Nichirei Bioscience), 1 µg/ml insulin (Wako), 100 nM dexamethasone (Sigma-Aldrich), 10 mM nicotinamide (Sigma-Aldrich), 50 µM β-mercaptoethanol (Nacalai Tesque), 50 ng/ml human recombinant hepatocyte growth factor (HGF) (Peprotech) and 20 ng/ml epidermal growth factor (EGF) (Peprotech).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and was assessed by Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent Technologies).

value: Primary culture isolated from fetal liver

value: Hepatoblasts


title: 1314.Gtype

description: 1314: L6

value: male

value: low boar taint


title: 1325.Gtype

description: 1325: L7

value: Ham muscle


title: 3114.Gtype

description: 3114: L9


title: Hep_Srf

description: Srf overexpression

source_name: Hepatoblasts, Srf overexpression


title: 9137.Gtype

description: 9137: L14


title: 1101.Gtype

description: 1101: L1


title: DMSO biological rep2

source_name: Cells treated with DMSO for 12h


title: 8101.Gtype

description: 8101: L12


title: 8117.Gtype

description: 8117: M10


title: 3130.Gtype

description: 3130: M5


title: HepaRG_BAP_1µM_replicate1

source_name: HepaRG cells, BAP 1 µM

value: no

tag: bap

value: 1 µM

tag: ethanol 25 mm


title: ST2734-1


title: DMSO biological rep1


title: 7312.Gtype

description: 7312: L11


title: 1112.Gtype

description: 1112: L3