title: D6_464

status: Public on Jun 22 2018

first: Jamal

last: Tazi

description: blood

data_processing:
Sequencing quality control: Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software. The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
The reads were subjected to standard quality control (QC) and filter criteria according to the following parameters: (1) trimming and cleaning reads that aligned to primers and/or adaptors,(2) reads with over 50% of low-quality bases (quality value ≤15) in one read, and (3) reads with over 10% unknown bases (N bases). We have used a software called Trimmomatic to remove primers and also to remove bad quality reads. After filtering, we removed short reads (<36bp), the remaining reads are called "clean reads" and stored as FASTQ format.
Once we did confident in the quality of our sequencing data, we proceeded to align the clean reads within FASTQ files to a reference sequence. Alignments have been performed using TopHat2 v2.0.8b tool against human GRCh38 reference genome. Tophat2 is a splice-aware aligner that use bowtie2 aligner to align the data before counting the reads that have mapped to all the genes. Bowtie2 behavior was adjusted to support local alignment by set to sensitive. TopHat2 ouputs were stored in BAM files (accepted_hits.bam typically) which contain all the alignments. TopHat2 output also report statistics on alignments.  As SAM file format were then required to count reads, BAM files have been sorted by name and converted to SAM format using samtools-1.3.1 software. To compute gene level raw counts from mapped reads in each library we used the tool htseq-count v0.6.1p1 of the Python package HTSeq, using the default union-counting mode. HTSeq package produced raw counts table per library, raw counts were needed to operate gene’s expression level. DEGs (Differentially Expressed Genes) screening is aimed to find differential expressed genes between samples and perform further function analysis on them.
Genome_build: GRCh38
Supplementary_files_format_and_content: One text file by sample (tab delimited) with a first column for gene identification. The next column corresponds to the raw read counts (non-normalized).

source_name: PBMCs

extract_protocol:
Total RNA extraction was performed according to the Qiagen miRNeasy kit. RNA concentrations were determined using Qubit fluorometric quantification and purity by the RNA 6000 Bioanalyzer kit (Agilent)
RNA-Seq libraries were constructed with the Truseq stranded mRNA sample preparation (Low throughput protocol) kit from Illumina.    Poly-A based mRNA enrichment: 1.2µg of total RNA was used for the construction of the libraries.
 Using poly-T oligo attached magnetic beads, 1,2µg of total RNA was purified in order to obtain only poly-A mRNA.    Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.  The cleaved RNA fragments are copied into first strand cDNA using SuperScript IV reverse transcriptase, Actinomycin D and random hexamer primers. The Second strand cDNA was synthesized by replacing dTTP with dUTP. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with 15 cycles of PCR. The final cDNA libraries were validated with a Fragment Analyzer (Advanced Analytical, Ankeny, IA) and quantified with a KAPA qPCR kit (Kapa Biosystems, Wilmington, MA).    Library sequencing: On 8 sequencing lane of a flowcell V4, the 32 libraries were pooled in equal proportions by sets of 4 libraries per lane, denatured with NaOH and diluted to 16 pM before clustering. Cluster formation, primer hybridization and single-end read, 50 cycles sequencing were performed on cBot and HiSeq2500 (Illumina, San Diego, CA) respectively.

treatment_protocol: The CD4 T cells were uninfected or infected with the YU2 strain and were untreated or treated for 6 days

tag: yu2 strain infection

value: Not Infected

tag: cell type

value: purified CD4+ T cells

value: PBMCs


title: D6_GLU

type: SRA

city: Montpellier

address: 1919 Route de Mende

country: France

institute: CNRS

description: blood

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: treatment

value: GLUCURONIDE


title: D6I_DARU

description: blood

value: Infected

value: DARUNAVIR


title: Embryo at early gastrula, injected with 0.5ng Gam1 mRNA, biological replicate 2

status: Public on Jun 23 2018

type: RNA

city: Notre Dame

first: Paul

last: Huber

state: IN

address: University of Notre Dame

country: USA

institute: University of Notre Dame

description:
EG_Gam1.02
Gene expression data from Xenopus laevis embryos at the early gastrula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation, per manufacturer's recommendations (http://www.affymetrix.com/support/technical/byproduct.affx?product=X_laevis_2).

scan_protocol: The hybridized probe array is scanned by the GeneChipTM Scanner 3000.

data_processing: The Affymetrix data files were processed using Bioconductor software package (http://www.bioconductor.org/). The mean fluorescence intensity was derived from a log2 transformation of the normalized data.

label: biotin

organism: Xenopus laevis

source_name: Xenopus embryos 9 hours post fertilization, injected with 0.5ng Gam1 mRNA

label_protocol: Total RNA (50-500 ng) was used for cDNA synthesis according to the GeneChip 3’ IVT Express Kit for Affymetrix microarray chips. The cDNA was then converted to double-stranded DNA and used as a template for transcription of amplified RNA (aRNA) which was labeled with a biotin-conjugated nucleotide. aRNA samples (15 ug) were subsequently purified and fragmented to produce probes for hybridization onto Xenopus laevis 2.0 GeneChip 3’expression arrays.

growth_protocol: Female X. laevis were injected with 500 units of human chorionic gonadotropin (HCG) at least 12 hours prior to spawning. Testes were isolated and stored at 4oC in high salt MBS (0.7 mM CaCl2, 108 mM NaCl, 1 mM KCl, 1 mM MgSO4, 5 mM HEPES, pH 7.8, 2.5 mM NaHCO3 ) for up to a week. Minced testis and eggs were mixed together with 3 mL 1/3 MMR (0.1 M NaCl, 2.0 mM KCl, 1 mM MgSO4, 2 mM CaCl2, 5 mM HEPES, pH7.8) and left to fertilize at room temperature. After 10 minutes, eggs were flooded with additional 1/3 MMR and after an additional 30 minutes eggs were washed with 2% cysteine (< 5 minutes) in order to remove the jelly coating, upon which eggs were washed 8 times with 1/3 MMR.

extract_protocol: Twenty embryos from each time point were homogenized in 500 uL proteinase K buffer (100 mM Tris pH 8, 150 mM NaCl, 12.5 mM EDTA pH 8.0, 1% SDS, 200 ug proteinase K) and incubated at 37oC for one hour. Samples were then extracted twice with an equal volume of phenol, pH 4.5, and twice with 24:1 chloroform:isoamylalcohol. RNA was purified using an RNeasy spin column (Qiagen, #74104) and precipitated with 2.5 volumes of ice-cold ethanol.

treatment_protocol: Embryos were injected in the animal hemisphere (volumes ranged between 5 to 30 nl) and allowed to develop at room temperature in 1/3 MMR.

value: Whole embryo

tag: developmental stage

value: Early gastrula

tag: age

value: 9 hours post fertilization

value: Gam1 mRNA


title: D5I_GLU

description: blood


title: D5I_464

description: blood


title: D6I_GLU

description: blood


title: D3_GLU

description: blood


title: D6_DARU

description: blood


title: D3_464

description: blood


title: D6I_DMSO

description: blood

value: DMSO


title: D3_DMSO

description: blood


title: D3_DARU

description: blood


title: A549_CPP_AGO1_SCRAMBLE_48hr_rep2

city: Bangkok

first: Piyapat

last: Pin-on

address: ChalongKrung

country: Thailand

institute: KMITL

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: All microarray experiment were classified as down-regulated (Dn), neutral (Nu), or up-regulated (Up) genes using our software, namely CU-DREAM.

source_name: Epithelial cell, A549, CPP-AGO1-SCRAMBLE, 48hr, replicate 2

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop, Wilmington, USA).

growth_protocol: A549 cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Scientific) with 2mM L-glutamine (Sigma-Aldrich), 10% (v/v) heat-inactivated fetal bovine serum (Thermo Scientific), 10 mg/ml antibiotic/antimycotic (Thermo Scientific), at 37oC and 5% (v/v) CO2.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA). Purity and integrity were evaluated by the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: The purified CPP-AGOs were conjugated to U21. Briefly, desired amount 600 ng of each CPP-AGOs protein were mixed with 200 nM of each PolyUs in conjugation buffer [1.5 mM MgCl2, 5% glycerol, 50 mM KCl and 20 mM Tris HCl pH 7.0] and incubated at 37 oC water-bath for 30 minutes. The conjugated complexes of CPP-AGOs-PolyUs and scramble were added to 500 µl DMEM cultured of A549 cell lines. 7.5x104 cells in 24 well-plate to let the complexes penetrate into cells. After transfection for 2 days, cells were collected to observe  gene expression changes.

tag: cell line

tag: transfection

value: scramble

tag: gender

value: male


title: Embryo at late gastrula, injected with 0.5ng Gam1 mRNA, biological replicate 1

description:
LG_Gam1.01
Gene expression data from Xenopus laevis embryos at the late gastrula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.

source_name: Xenopus embryos 13.5 hours post fertilization, injected with 0.5ng Gam1 mRNA

value: Late gastrula

value: 13.5 hours post fertilization


title: Embryo at early gastrula, injected with 0.5ng Gam1 mRNA, biological replicate 1

description:
EG_Gam1.01
Gene expression data from Xenopus laevis embryos at the early gastrula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.


title: Embryo at early gastrula, injected with 0.5ng Gam1 mRNA, biological replicate 3

description:
EG_Gam1.03
Gene expression data from Xenopus laevis embryos at the early gastrula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.


title: D5I_DMSO

description: blood


title: Embryo at early gastrula, injected with 9.2nL water, biological replicate 1

description:
EG_ddH2O.01
Gene expression data from Xenopus laevis embryos at the early gastrula developmental stage which were injected at one cell with 9.2nL water.

source_name: Xenopus embryos 9 hours post fertilization, injected with 9.2nL water

value: water


title: D5_DARU

description: blood


title: D5_464

description: blood


title: D5_GLU

description: blood


title: D4I_GLU

description: blood


title: D5I_DARU

description: blood


title: D5_DMSO

description: blood


title: D4I_DARU

description: blood


title: D4I_464

description: blood


title: D4_GLU

description: blood


title: D4_DMSO

description: blood


title: WCM1262 PDOX

city: New York

first: Himisha

last: Beltran

state: New York

address: 413 East 69th Street

institute: Weill Cornell Medicine

data_processing:
All reads were independently aligned with STAR_2.4.0f1 for sequence alignment against the human genome build hg19, downloaded via the UCSCgenomebrowser[http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/], and SAMTOOLS v0.1.19 8 for sorting and indexing reads
Cufflinks (2.0.2) was used to get the expression values (FPKMS), and Gencode v19 10 GTF file for annotation
Since the sequenced samples from the published data were processed using different library preps, batch normalization was done using ComBat from sva bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: First column represents the gene name, and second represents the expression level (FPKM) for each gene.

source_name: WCM1262 PDOX

growth_protocol: Organoids are cultured in prostate specific culture media composed of Advanced DMEM (Invitrogen) with GlutaMAX (1x, Invitrogen), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco), Primocin 100ug/mL (InvitroGen), B27 (Gibco), N-Acetylcysteine 1.25mM (Sigma-Aldrich), Mouse Recombinant EGF 50ng/mL (Invitrogen), Human Recombinant FGF-10 20ng/mL (Peprotech), Recombinant Human FGF-basic 1ng/mL (Peprotech), A-83-01 500nM (Tocris), SB202190 10uM (Sigma-Aldrich), Nicotinaminde 10mM (Sigma-Aldrich, (DiHydro) Testosterone 1nM (Sigma-Aldrich) PGE2 1uM (R&D Systems), Noggin conditioned media (5%) and R-spondin conditioned media (5%) and combined with growth factor-reduced Matrigel (Corning) in a 1:2 volume ratio.

extract_protocol:
mRNA was extracted from organoids and PDOXs using RNAsy Mini Kit (QUiAGEN) and Maxwell 16 LEV simplyRNA Tissue Kit.
Specimens were prepared for RNA sequencing using TruSeq RNA Library Preparation Kit v2 as previously described (Beltran et al., 2016). RNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies). cDNA was synthesized from total RNA using Superscript III (Invitrogen). Each sample was then sequenced with the HiSeq 2500 to generate 2 × 75-bp paired-end reads.

value: prostate organoid


title: D4_464

description: blood

value: Not Infected


title: D4_DARU

description: blood

value: purified CD4+ T cells


title: D3I_464

description: blood

value: PBMCs


title: D3I_GLU

description: blood

value: GLUCURONIDE


title: D3I_DMSO

description: blood

value: Infected


title: D4I_DMSO

description: blood


title: D3I_DARU

description: blood

value: DARUNAVIR


title: WCM154 PDOX

source_name: WCM154 PDOX


title: WCM155 organoid 2D

source_name: WCM155 organoid 2D


title: WCM1078 organoid

source_name: WCM1078 organoid


title: WCM154 organoid 2D

source_name: WCM154 organoid 2D


title: WCM1262 organoid

source_name: WCM1262 organoid


title: WCM155 organoid

source_name: WCM155 organoid


title: WCM154 organoid

source_name: WCM154 organoid


title: WCM1078 PDOX

source_name: WCM1078 PDOX


title: D2214P, biological rep3

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

description: Nonmucoid clinical isolate, small colonies

hyb_protocol: Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed with Affymetrix Expression Console software. Subsequent analysis was carried out with DNA-Chip Analyzer 2008. The 12 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.

organism: Burkholderia multivorans

source_name: D2214P isolate with 17h growth in SM medium

label_protocol: RNA was processed for use on Affymetrix custom dual species Burkholderia arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix, Santa Clara, CA) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 2 ug of cDNA were fragmented with DNase and end-labeled with biotin using terminal polynucleotidyl transferase (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, was assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: D2095, D2095R, D2214G and D2214P bacterial isolates were grown in 100 ml SM medium contained into 250 ml Erlenmyer flasks at 37ºC, 250 r.p.m. for 17 h

extract_protocol: Total RNA extraction was carried out using the RNeasy MiniKit (Qiagen) by following manufacturer’s recommendation

treatment_protocol: Bacterial cells were resuspended in RNAprotect bacteria reagent (Qiagen).

tag: isolate


title: D2095R, biological rep2

description: Nonmucoid laboratory isolate

source_name: D2095R isolate with 17h growth in SM medium


title: D2095, biological rep2

description: Mucoid isolate

source_name: D2095 isolate with 17h growth in SM medium


title: D2095, biological rep3

description: Mucoid isolate


title: D2214P, biological rep2


title: D2095R, biological rep3

description: Nonmucoid laboratory isolate


title: D2095R, biological rep1

description: Nonmucoid laboratory isolate


title: D2214P, biological rep1


title: D2095, biological rep1

description: Mucoid isolate


title: heterozygous_shield_pool1

city: Bad Nauheim

first: Michelle

middle: M

last: Collins

state: Hessen

address: Ludwigstrasse 42

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

hyb_protocol: Agilent Gene Expression Hybridisation Kit (Agilent Technologies); performed by OakLabs according to manufacturer's protocol

scan_protocol: Fluorescence signals detected by SureScan Microarray Scanner (Agilent Technologies); performed by OakLabs

data_processing:
Performed by OakLabs as follows: Data of all samples are quantile normalised using the ranked median quantiles according to Bolstad et al. “A comparison of normalisation methods for high density oligonucleotide array data based on variance and bias”, Bioinformatics (19), 2003, Oxford Univ Press. Briefly, the mean signal of each target is ranked relative to all other targets. The ranked signal value is replaced with the median quantile value of the same rank.
Raw data output columns, from OakLabs:  ProbeName (An Agilent-assigned identifier for the probe synthesized on the microarray), GeneName (This is an identifier for the gene for which the probe provides expression information), SystematicName (This is an identifier for the target sequence that the probe was designed to hybridize with),  gProcessedSignal (The signal left after all the FE processing steps have been completed. In the case of one colour, ProcesssedSignal contains the Multiplicatively Detrended BackgroundSubtracted Signal if the detrending is selected and helps. If the detrending does not help, this column will contain the BackgroundSubtractedSignal.), gMedianSignal (Raw median signal of feature in green channel), gBGMeanSignal (Mean local background signal computed per channel), gBHSubSignal (equals background-subtracted signal), glsPosAndSignif (Boolean flag, established via a 2-sided t-test, indicates if the mean sig- nal of a feature is greater than the corresponding background and if this difference is significant. 1 indicates feature is positive and significant above background), glsWellAboveBG (Boolean flag indicating if a feature is WellAbove Background or not, feature passes gIsPosAndSignif and additionally the gBGSubSignal is greater than 2.6*gBGSDUsed).

organism: Danio rerio

source_name: whole embryo pools, shield stage, heterozygous

label_protocol: Low Input QuickAmp Labeling Kit (Agilent Technologies); performed by OakLabs according to manufacturer's protocol

growth_protocol: Embryos were grown at 28C until the relevant stages were reached.

extract_protocol: RNA was isolated using Trizol and standard purification methods.  RNA quality control was performed using 2100 Bioanalyser (Agilent Technologies).

value: shield

tag: genotype/variation

value: heterozygous


title: MZpitx2c_shield_pool1

source_name: whole embryo pools, shield stage, MZpitx2c


title: pitx2cGOF_dome_pool1

source_name: whole embryos pools, dome stage, injected with pitx2c mRNA at 1-cell stage

value: dome


title: control_dome_pool1

source_name: whole embryos pools, dome stage, uninjected

value: uninjected


title: D2214G, biological rep1

description: Nonmucoid clinical isolate, large colonies

source_name: D2214G isolate with 17h growth in SM medium


title: D2214G, biological rep2


title: D2214G, biological rep3


title: MiRNA mimic mix transfection  PC10, triplicate 2

city: Chiba-shi, Chyuou-ku

first: Sotaro

last: Kanematsu

state: Chiba

address: Nitona-chyo 666-2

department: Division of Genetic Diagnostics

country: Japan

institute: Chiba Cancer Center

description: Gene expression after 48hr in miRNA mimic mix transfected cells

hyb_protocol: For hybridization, 600 ng of Cy-3 cRNA was hybridized to an Agilent SurePrint G3 Gex Human V3 microarray.

scan_protocol: Microarrays were scanned and the intensity values were quantified using a Surescan Microarray Scanner (Agilent Technologies, Tokyo, Japan).

data_processing: After background subtractions, the raw intensity data was analyzed using the Bioconductor package “Agilp”.

source_name: MiRNA mimic mix transfection

label_protocol: A total of 200 ng of RNA was amplified and labeled with Cyanine 3 (Cy-3).

growth_protocol: PC10 and ACC-LC-73 were grown to 40-60% confluency in 12-well cell culture plates (Falcon, Tokyo, Japan), and then the medium was changed to Opti-MEM (Thermo fisher Scientific, Tokyo, Japan) before transfection.

extract_protocol: Total RNA was isolated from cells using TRIzol reagent (Thermo fisher Scientific, Tokyo, Japan).

treatment_protocol: A total of 40 pmol of miRNA mimic (Thermo fisher Scientific, Tokyo, Japan), or mock was transfected into cells using Lipofectamine 2000 (Thermo fisher Scientific, Tokyo, Japan) according to manufacturer’s instructions. Transfection was performed in triplicate. After incubating for 24 hours, the cell medium was changed to RPMI1640 supplemented with 10% FBS. Transfected cells were collected at 48 hours after transfection.

value: mix


title: MiRNA mimic mix transfection  ACC-LC-73, triplicate 2


title: MiRNA mimic mix transfection  ACC-LC-73, triplicate 3


title: MiRNA mimic mix transfection  PC10, triplicate 1


title: Mock transfection PC10

description: Gene expression after 48hr in mock transfected cells

source_name: Mock transfection

value: mock


title: MiRNA mimic mix transfection  ACC-LC-73, triplicate 1


title: Mock transfection ACC-LC-73


title: MiRNA mimic mix transfection  PC10, triplicate 3


title: Frontal cortex- Hyperglycemic- 5

city: Uppsala

first: Rickard

last: Lindblom

address: House 50, 4th floor, Uppsala University Hospital

department: Cardiothoracic Surgery and Anesthesiology

country: Sweden

institute: Uppsala University Hospital

description: Gene expression in frontal cortex of young adult pigs following hyperglycemic cardiac arrest

hyb_protocol: GeneChip® ST Arrays (GeneChip® Porcine Gene 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (P/N 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G GeneChip® accoding to the Expression Wash, Stain and Scan Manual (P/N 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA).

data_processing:
The raw data was normalized in the free software Expression Console, provided by Affymetrix (http://www.affymetrix.com), using the robust multi-array average (RMA) method (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. 2003; Li C, Wong WH, 2001). Principal component analysis (PCA) was applied in order to visualize the data, more specifically, the “princomp” function in R (http://www.r-project.org) was used.  It revealed that one sample (PA231_djur12_140627) was highly aberrant, probably from technical reasons of tissue handling, and was therefore excluded from the analysis. After excluding the outlier sample, normalization was performed again as described above. Subsequent analysis of the gene expression data from the remaining 11 samples was carried out in the freely available statistical computing language R (http://www.r-project.org), using packages available from the Bioconductor project (www.bioconductor.org). In order to search for the differentially expressed genes, between the HG and the NG groups, an empirical Bayes moderated t-test was applied (Smyth, G. K. 2004), employing the ‘limma’ package with the robust method (Gentleman, R., Carey, V., Huber, W., Irizarry, R., Dudoit, S., ed. 2005). To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg (Benjamini Y, H. Y. 1995). The adjusted p-values correspond to the false discovery rate (FDR). Heat maps were generated in Genesis 1.0 using the normalized data for each sample. The data was adjusted by using the command “mean center genes” and hierarchical clustering was performed according to Genesis 1.0 Operation Manual (Austria, 2001, version 1.0).
No regard to fold-change was taken. An empirical Bayes moderated t-test was applied (Smyth, G. K. 2004), employing the ‘limma’ package with the robust method (Gentleman, R., Carey, V., Huber, W., Irizarry, R., Dudoit, S., ed. 2005). To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg (Benjamini Y, H. Y. 1995). The adjusted p-values correspond to the false discovery rate (FDR).

organism: Sus scrofa

source_name: Homogenized frontal cortex- post hyperglycemic cardiac arrest

label_protocol: RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA). 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 1, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Isolation of total RNA from the pigs was performed by quickly dissecting approximately 100 mg of the frontoparietal cortex, and instantly putting the brain tissue in homogenizing buffer containing β-mercaptoethanol according to manufacturer’s protocol (Qiagen Inc., Valencia, California, USA). The tissue was then immediately homogenized using a Polytron homogenizer and total RNA isolated by RNeasy Mini kit (Qiagen) with absorbance determined at 260 and 280 nm.

treatment_protocol: Piglets were randomized to high or normal glucose levels, as regulated by glucose and insulin infusions with target levels of 8.5–10 mM (hyperglycemic group) and 4–5.5 mM (normoglycemic group), respectively. Under anesthesia cardiac arrest was induced by applying alternating current resulting in ventricular fibrillation allowing to continue for 5 min followed by 8 min of cardiopulmonary resuscitation, than direct-current defibrillation was applied to restore spontaneous circulation. After 180 min observation period the study was finished by terminating the piglets in deep anesthesia and the brain was removed and stored in – 70 ˚C until usage.

value: frontal cortex

value: piglet, around 25kg

value: glucose and insulin infusions with target levels of 8.5-10 mM


title: Frontal cortex- Hyperglycemic- 4


title: Frontal cortex- Normoglycemic- 5

description: Gene expression in frontal cortex of young adult pigs following normoglycemic cardiac arrest

source_name: Homogenized frontal cortex- post normoglycemic cardiac arrest

value: glucose and insulin infusions with target levels of 4-5.5 mM


title: Frontal cortex- Normoglycemic- 6


title: Frontal cortex- Normoglycemic- 2


title: Frontal cortex- Normoglycemic- 3


title: Frontal cortex- Normoglycemic- 4


title: Frontal cortex- Hyperglycemic- 3


title: Frontal cortex- Hyperglycemic- 1


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 5

city: Los Angeles

first: Kam

middle: D.

last: Dahlquist

state: CA

address: 1 LMU Drive, MS8220

department: Biology

institute: Loyola Marymount University

description: Ontario chip; post-washing slide coating of 2% PEG (MW cut-off 2000) in 1:1 solution of acetone and toluene

hyb_protocol: 85 μL of hybridization master mix was added to each labeled, paired, and dried aRNA sample. The hybridization master mix contained 100 μL DIG Easy Hyb solution (Roche Applied Science, catalog #11796895001), 0.38 μL of 1 μg/μL oligo dA (10-20mer) solution (Invitrogen, catalog #POLYA.GF) , and 5 μL of 10 mg/mL DNA, MB-grade from fish sperm (Roche Applied Science, catalog #11467140001) and was heated to 65-70°C for two minutes and cooled to room temperature before adding 85 μL of it to the labeled aRNA. After the hybridization master mix was added to the aRNA, it was heated to 65-70°C for two minutes and cooled to room temperature for two minutes before being applied to the microarray chip. Hybri-slips (Sigma-Aldrich, catalog #H0784) cover slips were used and the chip hybridized in a Corning Hybridization Chamber (catalog #2551) with 2 X 11 μL nuclease-free water inside the wells of the chamber. Microarrays were incubated in a 37°C water bath for 15-16 hours. Cover slips were removed from the microarray by dunking in 1X SSC buffer at room temperature. Slides were immediately transferred to a 50 mL conical tube containing 1X SSC/1% SDS buffer and incubated in a 50°C water bath for 15 minutes; slides were transferred and incubated twice more in 1X SSC/1% SDS at 50°C for 15 minutes each time. Slides were then washed by plunging up and down 4-6 times in 1X SSC at room temperature and plunging up and down 4-6 times in 0.1X SSC at room temperature. Slides were pulled out slowly from this final wash and any remaining water droplets were chased off with a compressed air duster. Slides were optionally dipped in a slide coating solution of 2% PEG (MW cut-off 2000) in 1:1 solution of acetone and toluene (see description column of SAMPLES table) before scanning. A complete protocol is found here: http://www.openwetware.org/wiki/Dahlquist:DNA_Microarray_Protocol

scan_protocol: Slides were scanned with an Axon GenePix 4000B Scanner (Molecular Devices). Preview scans were performed to manually or automatically set the PMT gain for the 635 wavelength channel and for the 532 wavelength channel; power was at 100% for both channels. For auto-PMT scans, the saturation tolerance was set to the default value of 0.05%. For the data scan, pixel size was set to 10 μm, lines to average was set to 2, and focus position was set to 0 μm. The GenePix Pro 6.1 software (v6.1.0.2) was used with the AxGenePixDemo.dll (v2.1.1.39) driver. When detecting features, the following settings were used: Find irregular features, Resize features during alignment to minimum diameter of 33% and maximum diameter of 200%, Flag features that fail background threshold criteria as Not Found, Estimate warping and rotation when finding blocks, and Automatic Image Registration: Max translation of 10 pixels. Note that two chip types were used in this study: GCAT and Ontario (see SAMPLES table). The GCAT chips had two sets of blocks representing the full genome of S. cerevisiae at the top and bottom of the chip. The .gal file provided for this chip only had information for one set of blocks, so each of the GCAT chips had its features found twice, once for the top and once for the bottom, generating two .gpr results files (see SAMPLES table). The GCAT .gal file can be found here: https://github.com/kdahlquist/DahlquistLab/raw/master/GEO_submission/yeast_GCAT_gal.gal. The Ontario chip had a single .gal file for the entire chip; duplicate spots for genes were placed side-by-side. The Ontario .gal file can be found here: https://github.com/kdahlquist/DahlquistLab/raw/master/GEO_submission/Ontario_Y6.4Kv7.GAL. Complete details are found here: http://www.openwetware.org/wiki/Dahlquist:GenePix_Pro_Software_Protocol.

data_processing: A full description of the data processing is found here: http://www.openwetware.org/wiki/Dahlquist:Microarray_Data_Analysis_Workflow. Briefly, an R script was written to perform the data processing steps. Follow the links to download the script (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/GCAT-and-Ontario_normalization_script.R) and required GCAT (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/GCAT_Targets_20160616.csv) and Ontario (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/Ontario_Targets_wt-dCIN5-dGLN3-dHAP4-dHMO1-dSWI4-dZAP1_20160616.csv) Targets files to run it. Put the script, Targets files, and all .gpr files in the same folder to run. A script to automatically generate MA and box plots showing the results of the normalization can be downloaded from here (https://github.com/kdahlquist/DahlquistLab/raw/master/normalization/generate_MA_and_box_plots.R) . The results reported here were produced with Version x64 3.1.0 of R. Version 3.20.1 of the limma package (Smyth, G. K., 2005, Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor, pp. 397-420, Springer New York.) was used to perform within-chip normalization. Briefly the script extracts the Log Ratio (635/532) values (column AS in Excel) of the .gpr file for each spot and removes bad spots (flagged as -50 in the .gpr file), and the control spots labeled Arabidopsis and 3XSSC. It performs the loess normalization using the normexp method. It performs between-chip normalization using the median absolute deviation (MAD). Ratios of the dye-swapped samples were corrected so that the ratio reported is experimental timepoint/t0 control. Then duplicate spots corresponding to the same gene are averaged and the data from the two chips are merged. The log2 ratios (experimental/control) are rounded to four decimal places. The processed data file only reports genes that were present on the Ontario chip type. Genes that were only found on the GCAT chip type and not the Ontario chip type were discarded because there was not enough replicate data for those genes to make downstream analysis meaningful.

organism: Saccharomyces cerevisiae

source_name: t120 60 min cold shock followed by 60 min recovery replicate 5

label_protocol: 1 μg aliquots of total RNA were converted to aRNA using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion/LifeTechnologies catalog #AM1753), according to the manufacturer's instructions. Five aliquots of each t0 sample were amplified and then mixed together and one aliquot of each of the other timepoints was amplified. 20 μg aliquots of aRNA (5 aliquots of the mixed t0, one aliquot each for the other timepoints) were then labeled with either Cy3 or Cy5 (CyDye Post-Labeling Reactive Dye Packs, GE Healthcare Life Sciences catalog #RPN5661), using the Amino Allyl MessageAmp II aRNA Amplification Kit, according to the dye orientation chosen for the particular replicate experiment (see SAMPLES table). Labeling efficiency was checked by spectroscopy using Bio-Rad trUView Cuvettes and SmartSpec 3000 or on an Implen Nanophotometer. The t0 labeled samples were mixed together and 5 μg aliquots of the labeled, mixed t0 sample were then combined with 5 μg aliquots of labeled aRNA from each of the other timepoints for that replicate flask. The combined aRNA samples were then fragmented using Ambion (now LifeTechnologies) RNA Fragmentation Reagents (catalog #AM8740) according to the manufacturer's instructions and dried in a speedvac to <= 5 μL. A complete protocol is found here: http://www.openwetware.org/wiki/Dahlquist:DNA_Microarray_Protocol.

growth_protocol: 5 mL liquid overnight cultures of the appropriate strain of S. cerevisiae were inoculated with a single colony into YEPD (wild type strain) or YEPD + 200 μg/mL G418 (gene deletion strains) medium and incubated overnight at 30°C, shaking at 250 rpm. The next morning, these cultures were used to inoculate larger 750 mL cultures by adding a 1/500th volume of the overnight culture to a 2800 mL Fernbach flask containing YEPD (wild type strain) or YEPD 200 μg/mL G418 (gene deletion strains) medium. Two independent biological replicate experiments (flasks) of the same strain were carried out on the same day. Growth was monitored by reading the OD600 of the cultures at appropriate time intervals.

extract_protocol: Total RNA was extracted from a single cell pellet from each timepoint using the Ambion (now LifeTechnologies) RiboPure Yeast Kit, catalog #AM1926, according to the manufacturer's instructions. The DNase treatment from the kit was substituted with the Turbo DNA-free Kit (Ambion/LifeTechnologies catalog #AM1907), using the rigorous DNAase treatment option of the manufacturer's protocol. Quality of the total RNA was checked by UV spectroscopy using Bio-Rad trUView Cuvettes and SmartSpec 3000 or on an Implen Nanophotometer and by non-denaturing agarose gel electrophoresis (Lonza Reliant Precast RNA Gel, catalog #54948). Total RNA was stored at -80°C.

treatment_protocol: Once the culture reached an OD600 of >= 0.2 at 30°C, the cold shock and recovery experiment was begun. Three 40 mL samples were collected at time zero (t0) before cold shock, and the flask was shifted to a 13°C water bath incubator/shaker, shaking at 250 rpm. Three 40 mL samples each were collected after 15 minutes (t15), 30 minutes (t30), and 60 minutes (t60) of cold shock at 13°C. The flask was then shifted to a 30°C water bath and manually swirled for 5 minutes, before being dried off and returned to the 30°C incubator/shaker at 250 rpm. Three 40 mL samples were collected after a total of 30 minutes at 30°C (t90) and 60 minutes at 30°C (t120). Immediately after collection, the samples were spun at 4000 rpm in a table-top centrifuge for 3 minutes at room temperature. The supernatant was discarded and the pellets were immediately frozen in a dry ice/ethanol bath and stored at -80°C.

tag: strain

tag: gene deleted

value: ZAP1 (YJL056C)

value: t120 60 min cold shock 13 degrees followed by 60 min recovery 30 degrees

source_name: t0 before cold shock control replicate 5

value: t0 before cold shock control 30 degrees


title: H1048_POU2F3_CHIP_input

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Sequencing reads were mapped into reference human genome hg19 using Bowtie2
Peakcalling was done using MACS2 FDR cut off 5% with broad peak and narrow peak option for H3K27ac and POU2F3, respectively
The H3K27ac peaks in knockout experiment were merged with corresponding control ChIP-seq using BEDtools
Normalized tag count was calculated using MACS2.0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contain normalized tag count

molecule: genomic DNA

source_name: Small cell lung cancer

growth_protocol: NCI-H1048 cells were cultured in HITES, NCI-H128 cells were cultured in RPMI with 20% FBS and penicillin/streptomycin. All other cells were cultured in RPMI with 10% FBS and penicillin/streptomycin or HITES, .

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, ChIP DNA was end-repaired, 3’-adenylated, and then ligated with indexed adaptor. These DNA was size selected (200-400 bp) via agarose gel electrophoresis, and PCR amplified. Final products were purified using AMPure XP beads.

treatment_protocol: All parental cell lines were gowring exponentially upon harvest. Cells were lentivirally infected with sgRNA for knockout.

value: Small cell lung cancer

value: exponentially growing cells with no infection

tag: chip antibody


title: H1048_sgPOU2F3_H3K27ac_CHIP

value: infected with sgPOU2F3_2, collected cells at day 2 post infection

value: H3K27ac (abcam ab4729)


title: H1048_sgPOU2F3_H3K27ac_CHIP_input


title: H1048_POU2F3_CHIP

value: POU2F3 (Santa Cruz SC330)


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 5

source_name: t90 60 min cold shock followed by 30 min recovery replicate 5

value: t90 60 min cold shock 13 degrees followed by 30 min recovery 30 degrees


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 4

source_name: t0 before cold shock control replicate 4

source_name: t120 60 min cold shock followed by 60 min recovery replicate 4


title: Frontal cortex- Hyperglycemic- 2


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 4

source_name: t90 60 min cold shock followed by 30 min recovery replicate 4


title: Frontal cortex- Normoglycemic- 1


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 3

source_name: t90 60 min cold shock followed by 30 min recovery replicate 3

source_name: t0 before cold shock control replicate 3


title: H1048_sgHROSA_H3K27ac_CHIP_input

value: infected with sgNeg, collected cells at day 2 post infection


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

source_name: t90 60 min cold shock followed by 30 min recovery replicate 2


title: H1048_sgHROSA_H3K27ac_CHIP


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 3

source_name: t120 60 min cold shock followed by 60 min recovery replicate 3


title: H889_1_input


title: H889_2_input


title: H889_2_H3K27ac


title: L311_1_H3K27ac


title: H82_2_H3K27ac


title: H889_1_H3K27ac


title: L311_2_H3K27ac


title: S. cerevisiae BY4741 delZAP1 60 min cold shock vs before cold shock replicate 5

source_name: t60 60 min cold shock replicate 5

value: t60 60 min cold shock 13 degrees


title: L311_1_input


title: L311_2_input


title: S. cerevisiae BY4741 delZAP1 30 min cold shock vs before cold shock replicate 5

source_name: t30 30 min cold shock replicate 5

value: t30 30 min cold shock 13 degrees


title: S. cerevisiae BY4741 delZAP1 60 min cold shock vs before cold shock replicate 3

source_name: t60 60 min cold shock replicate 3


title: H82_2_input


title: S. cerevisiae BY4741 delZAP1 60 min cold shock vs before cold shock replicate 4

source_name: t60 60 min cold shock replicate 4


title: S. cerevisiae BY4741 delZAP1 60 min cold shock vs before cold shock replicate 2

source_name: t60 60 min cold shock replicate 2


title: S. cerevisiae BY4741 delZAP1 15 min cold shock vs before cold shock replicate 4

source_name: t15 15 min cold shock replicate 4

value: t15 15 min cold shock 13 degrees


title: S. cerevisiae BY4741 delZAP1 30 min cold shock vs before cold shock replicate 3

source_name: t30 30 min cold shock replicate 3


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 60 min recovery vs before cold shock replicate 2

description: Ontario chip; no post-washing slide coating

source_name: t120 60 min cold shock followed by 60 min recovery replicate 2

value: SWI4 (YER111C)


title: S. cerevisiae BY4741 delZAP1 15 min cold shock vs before cold shock replicate 5

source_name: t15 15 min cold shock replicate 5

source_name: t0 before cold shock control replicate 5


title: S. cerevisiae BY4741 delZAP1 15 min cold shock vs before cold shock replicate 3

source_name: t15 15 min cold shock replicate 3


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 60 min recovery vs before cold shock replicate 4

source_name: t120 60 min cold shock followed by 60 min recovery replicate 4

source_name: t0 before cold shock control replicate 4


title: S. cerevisiae BY4741 delZAP1 30 min cold shock vs before cold shock replicate 4

source_name: t30 30 min cold shock replicate 4


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 60 min recovery vs before cold shock replicate 3

source_name: t0 before cold shock control replicate 3


title: S. cerevisiae BY4741 delZAP1 15 min cold shock vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

source_name: t15 15 min cold shock replicate 2


title: S. cerevisiae BY4741 delZAP1 30 min cold shock vs before cold shock replicate 2

source_name: t30 30 min cold shock replicate 2


title: H69_2_input

source_name: Small cell lung cancer


title: H69_1_input


title: H69_2_H3K27ac


title: H82_1_input


title: H69_1_H3K27ac


title: H526_2_input


title: H526_2_H3K27ac


title: H526_1_H3K27ac


title: H524_2_input


title: H526_1_input


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 30 min recovery vs before cold shock replicate 2

source_name: t90 60 min cold shock followed by 30 min recovery replicate 2


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 30 min recovery vs before cold shock replicate 4

source_name: t90 60 min cold shock followed by 30 min recovery replicate 4


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 30 min recovery vs before cold shock replicate 3

source_name: t90 60 min cold shock followed by 30 min recovery replicate 3


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 30 min recovery vs before cold shock replicate 1

source_name: t0 before cold shock control replicate 1

source_name: t90 60 min cold shock followed by 30 min recovery replicate 1


title: H524_2_H3K27ac


title: H524_1_input


title: H524_1_H3K27ac


title: S. cerevisiae BY4741 delSWI4 60 min cold shock followed by 60 min recovery vs before cold shock replicate 1

source_name: t120 60 min cold shock followed by 60 min recovery replicate 1


title: H510_2_input


title: H82_1_H3K27ac


title: H510_2_H3K27ac


title: S. cerevisiae BY4741 delSWI4 30 min cold shock vs before cold shock replicate 2


title: S. cerevisiae BY4741 delSWI4 60 min cold shock vs before cold shock replicate 1

source_name: t60 60 min cold shock replicate 1


title: H510_1_input


title: H510_1_H3K27ac


title: S. cerevisiae BY4741 delSWI4 30 min cold shock vs before cold shock replicate 4


title: H446_2_input


title: S. cerevisiae BY4741 delSWI4 30 min cold shock vs before cold shock replicate 3

source_name: t30 30 min cold shock replicate 3


title: S. cerevisiae BY4741 delSWI4 60 min cold shock vs before cold shock replicate 2

source_name: t60 60 min cold shock replicate 2


title: H446_2_H3k27ac


title: H446_1_input


title: S. cerevisiae BY4741 delSWI4 60 min cold shock vs before cold shock replicate 3

source_name: t60 60 min cold shock replicate 3


title: S. cerevisiae BY4741 delSWI4 60 min cold shock vs before cold shock replicate 4

source_name: t60 60 min cold shock replicate 4

source_name: t0 before cold shock control replicate 4


title: TSA_expression_rep1 [2014]

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

description: Jurkat cell line treated 8h with TSA, biological replicate 1

hyb_protocol: Hybridization mix was laid onto each sector of subarray gasket slide and sandwiched against a 8 x 65K format oligonucleotide microarray (Human v1 Sureprint G3 Human GE 8x60k Microarray, Agilent design ID 028004) inside a hybridization chamber which wqs hybridized overnight at 65ºC in a rotisserie oven rotating at 10 rpm for a total of 17 hours. Subsequently array chambers were disassembled submerged in Agilent Gene Expression Buffer 1 and washed 1 minute in another dish with the same solution with a magnetic stirrer at 200 rpm at room temperature, followed by 1 minute in gilent Gene Expression Buffer 2 with a magnetic stirrer at 200 rpm at 37ºC and immediate withdrawal from the solution and air drying.

scan_protocol: Fluorescent signal was captured into TIF images with an Agilent scanner using recommended settings (20 bit, 5 um resolution, 100% PMT and 100% laser power) with Scan Control software (Agilent).

data_processing: Signal intensities were extracted into a tabulated text file using Feature Extraction software (Agilent) using the appropriate array configuration and annotation files. The normalized log2intensities were obtained using quantile method with normexp background correction the Bioconductor Limma package in R.

label_protocol: For each sample 100 ng of total RNA mixed with 2 ul of 1:10000 Agilent One Color Spike Mix were reversed transcribed into cDNA with a T7 promoter and the cDNA was in vitro transcribed into cRNA in the presence of Cy3-CTP using the Low input quick Amp kit (Agilent). Labelled samples were purified using RNeasy mini spin columns (Qagen) and yield and specific activity wwere assessed by spectrophotometry (Nanodrop) and confirmed to be within specifications (>825 ng and >6 pmol Cy3/ug cRNA). 600 ng of cRNA were preblocked and fragmented in Agilent fragmentation buffer and mixed with  Agilent GEx Hybridization mix.

growth_protocol: RPMI 1640 medium + 10%FBS, 1% glutamine, 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted using High Pure RNA isolation kit (Roche) according to the manufacturer's instructions. cDNA was obtained from 100 ng of total RNA using SuperScript VILO cDNA synthesis (Invitrogen). High RNA integrity was assessed by Bioanalyzer nano 6000 assay with RIN numbers 9.5 fopr T47D_r1 and 9.2 for T47D_r2

treatment_protocol: 160μM of MMQO or 400nM of TSA was added to the cells and incubated for 3h at 37 degrees Celsius

value: male

value: Jurkat

value: lymphoblasts from acute T cell leukemia


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 4

source_name: t120 60 min cold shock followed by 60 min recovery replicate 4

value: HMO1 (YDR174W)


title: TSA_expression_rep2 [2014]

description: Jurkat cell line treated 8h with TSA, biological replicate 2


title: S. cerevisiae BY4741 delSWI4 30 min cold shock vs before cold shock replicate 1

source_name: t30 30 min cold shock replicate 1


title: MMQO_expression_rep3 [2014]

description: Jurkat cell line treated 8h with MMQO, biological replicate 3


title: H211_2_input


title: MMQO_expression_rep2 [2014]

description: Jurkat cell line treated 8h with MMQO, biological replicate 2


title: H446_1_H3K27ac


title: MMQO_expression_rep1 [2014]

description: Jurkat cell line treated 8h with MMQO, biological replicate 1


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 3

source_name: t120 60 min cold shock followed by 60 min recovery replicate 3

value: t120 60 min cold shock 13 degrees followed by 60 min recovery 30 degrees

source_name: t0 before cold shock control replicate 3


title: Jurkat_expression_rep3 [2014]

description: Jurkat cell line under basal growth conditions, biological replicate 3


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

value: t0 before cold shock control 30 degrees

source_name: t120 60 min cold shock followed by 60 min recovery replicate 2


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 4

source_name: t90 60 min cold shock followed by 30 min recovery replicate 4


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 1


title: MMQO_expression_rep1 [2012]

treatment_protocol: 80μM of MMQO was added to the cells and incubated for 8h at 37 degrees Celsius


title: MMQO_expression_rep2 [2012]


title: H211_2_H3K27ac

source_name: Small cell lung cancer

value: Small cell lung cancer


title: S. cerevisiae BY4741 delZAP1 60 min cold shock followed by 60 min recovery vs before cold shock replicate 2

value: ZAP1 (YJL056C)


title: Jurkat_expression_rep2 [2014]

description: Jurkat cell line under basal growth conditions, biological replicate 2


title: Neural precursors WT H3K27me3 ChIP-seq

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
RNA-seq raw data were aligned to the mouse genome mm9 and to gene annotations from Refseq gene using TopHat v2.05. For the ChIP-seq, sequencing reads were aligned to the mouse genome (mm9) using the Bowtie2 software.
The genome-wide read coverage was calculated by BEDTools and in-house Perl programs.
ChIP-seq peaks were identified by MACS2 the p value cutoff is set to 1 x 10-5. Cufflinks v2.0.2 was used to quantify FPKM values
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density.

organism: Mus musculus

source_name: whole cell

growth_protocol: E14 mouse ES cells were cultured in normal ES medium in presence of LIF. Neural precursors were maintained in N2B27 medium supplied with EGF (10 ng/ml, R&D) and FGF-2 (10 ng/ml, R&D)

extract_protocol:
Total mRNA were extracted using the miRNeasy Mini kit (Qiagen). Cells for ChIP-seq were cross-linked with 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. Lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After re-suspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktail (Sigma), the lysates were incubated in the presence of 1,000 units of MNase (NEB, Ipswich, MA, Cat.# M0247S) at 37 °C for 20 min with continuous mixing in thermal mixer (Fisher Scientific, Pittsburgh, PA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 secs on / 30 secs off) using Bioruptor Twin (UCD-400) (Diagenode) and centrifuged at 21,130 x g for 10 min. The supernants were collected and the chromatin content was estimated by the Qubit assay (Invitrogen). The chromatin was then incubated with 5 µg of rabbit monoclonal anti-H3K27me3 antibody (Cell Signaling, Cat.# 9733), 2 µg of rabbit plolyclonal H3K4me3 antibody (Abcam, Ab8580) on a rocker overnight. Protein G beads were added for 3 hours incubation. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl buffer (10 mM Tris-HCl, pH8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after the treatment of RNase A and proteinase K.
RNA-seq libraries and deep sequencing were conducted by Novogene mRNA next-generation sequencing services. Two replicates for each sample were sequenced. ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN). The ChIP-seq libraries were sequenced at single end on an Illumina HiSeq 2000 instrument.

tag: media

tag: cell cycle stage

value: asynchronization

value: Cell Signaling, Cat.# 9733

value: wild type

value: Neural precursors


title: Neural precursors Asf1a KO H3K27me3 ChIP-seq

value: Asfla KO


title: H211_1_input

value: exponentially growing cells with no infection


title: H146_2_input


title: H211_1_H3K27ac

value: H3K27ac (abcam ab4729)


title: S. cerevisiae BY4741 delHMO1 60 min cold shock vs before cold shock replicate 4

value: t60 60 min cold shock 13 degrees


title: Jurkat_expression_rep1 [2014]

description: Jurkat cell line under basal growth conditions, biological replicate 1


title: S. cerevisiae BY4741 delHMO1 60 min cold shock vs before cold shock replicate 3


title: ES cells WT H3K27me3 ChIP-seq

value: DMEM

value: ES cells


title: H146_2_H3K27ac


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 3

source_name: t90 60 min cold shock followed by 30 min recovery replicate 3

value: t90 60 min cold shock 13 degrees followed by 30 min recovery 30 degrees


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 1

source_name: t0 before cold shock control replicate 1

source_name: t90 60 min cold shock followed by 30 min recovery replicate 1


title: S. cerevisiae BY4741 delHMO1 60 min cold shock followed by 30 min recovery vs before cold shock replicate 2

source_name: t90 60 min cold shock followed by 30 min recovery replicate 2


title: H146_1_input


title: Jurkat_expression_rep1 [2012]

value: male

value: Jurkat


title: H146_1_H3K27ac


title: Neural precursors WT H3K4me3 ChIP-seq

value: Abcam, Ab8580


title: Jurkat_expression_rep2 [2012]


title: H128_2_input


title: ES cells WT H3K4me3 ChIP-seq


title: ES cells Asf1a KO H3K27me3 ChIP-seq


title: S. cerevisiae BY4741 delHMO1 60 min cold shock vs before cold shock replicate 1

value: HMO1 (YDR174W)

value: t0 before cold shock control 30 degrees

source_name: t60 60 min cold shock replicate 1


title: S. cerevisiae BY4741 delHMO1 60 min cold shock vs before cold shock replicate 2

source_name: t60 60 min cold shock replicate 2


title: H128_2_H3K27ac

value: Small cell lung cancer


title: ES cells Asf1a KO H3K4me3 ChIP-seq

value: asynchronization


title: H128_1_H3K27ac


title: S. cerevisiae BY4741 delHMO1 30 min cold shock vs before cold shock replicate 3

source_name: t30 30 min cold shock replicate 3

value: t30 30 min cold shock 13 degrees


title: S. cerevisiae BY4741 delHMO1 30 min cold shock vs before cold shock replicate 4

source_name: t30 30 min cold shock replicate 4

source_name: t0 before cold shock control replicate 4


title: H128_1_input


title: Neural precursors WT input

value: no

value: wild type


title: Neural precursors Asf1a KO Input

value: Asfla KO

value: Neural precursors


title: H1048_2_input

value: exponentially growing cells with no infection


title: H1048_2_H3K27ac

value: H3K27ac (abcam ab4729)


title: S. cerevisiae BY4741 delHMO1 15 min cold shock vs before cold shock replicate 4

source_name: t15 15 min cold shock replicate 4

value: t15 15 min cold shock 13 degrees


title: ES cells WT Input

value: DMEM

value: ES cells


title: H1048_1_input


title: Neural precursors WT repeat 2


title: ES cells Asf1a KO Input


title: S. cerevisiae BY4741 delHMO1 30 min cold shock vs before cold shock replicate 2

source_name: t30 30 min cold shock replicate 2


title: Neural precursors WT repeat 1


title: S. cerevisiae BY4741 delHMO1 30 min cold shock vs before cold shock replicate 1

source_name: t30 30 min cold shock replicate 1


title: DMS79_2_input


title: H1048_1_H3K27ac


title: S. cerevisiae BY4741 delHAP4 60 min cold shock followed by 60 min recovery vs before cold shock replicate 4

value: HAP4 (YKL109W)

source_name: t120 60 min cold shock followed by 60 min recovery replicate 4

value: t120 60 min cold shock 13 degrees followed by 60 min recovery 30 degrees


title: Neural precursors Asf1a KO repeat 2


title: Neural precursors Asf1a KO H3K4me3 ChIP-seq

value: Abcam, Ab8580


title: S. cerevisiae BY4741 delHAP4 60 min cold shock followed by 60 min recovery vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

source_name: t120 60 min cold shock followed by 60 min recovery replicate 2


title: S. cerevisiae BY4741 delHMO1 15 min cold shock vs before cold shock replicate 2

value: HMO1 (YDR174W)

source_name: t15 15 min cold shock replicate 2


title: DMS79_2_H3K27ac

source_name: Small cell lung cancer


title: S. cerevisiae BY4741 delHAP4 60 min cold shock followed by 60 min recovery vs before cold shock replicate 3

source_name: t120 60 min cold shock followed by 60 min recovery replicate 3

source_name: t0 before cold shock control replicate 3

value: t0 before cold shock control 30 degrees


title: Neural precursors Asf1a KO repeat 1

source_name: whole cell


title: DMS79_1_input

value: Small cell lung cancer


title: S. cerevisiae BY4741 delHMO1 15 min cold shock vs before cold shock replicate 3

source_name: t15 15 min cold shock replicate 3


title: ES cells WT repeat 2

value: asynchronization


title: ES cells WT repeat 1


title: S. cerevisiae BY4741 delHMO1 15 min cold shock vs before cold shock replicate 1

source_name: t0 before cold shock control replicate 1

source_name: t15 15 min cold shock replicate 1


title: S. cerevisiae BY4741 delHAP4 60 min cold shock followed by 30 min recovery vs before cold shock replicate 3

source_name: t90 60 min cold shock followed by 30 min recovery replicate 3

value: t90 60 min cold shock 13 degrees followed by 30 min recovery 30 degrees


title: S. cerevisiae BY4741 delHAP4 60 min cold shock followed by 30 min recovery vs before cold shock replicate 4

source_name: t90 60 min cold shock followed by 30 min recovery replicate 4


title: DMS114_2_input


title: DMS79_1_H3K27ac


title: ES cells Asf1a KO repeat 2


title: S. cerevisiae BY4741 delHAP4 60 min cold shock followed by 30 min recovery vs before cold shock replicate 2

source_name: t90 60 min cold shock followed by 30 min recovery replicate 2


title: DMS114_2_H3K27ac


title: DMS114_1_input


title: ES cells Asf1a KO repeat 1


title: S. cerevisiae BY4741 delHAP4 60 min cold shock vs before cold shock replicate 3

source_name: t60 60 min cold shock replicate 3

value: t60 60 min cold shock 13 degrees


title: S. cerevisiae BY4741 delHAP4 60 min cold shock vs before cold shock replicate 2

source_name: t60 60 min cold shock replicate 2


title: H889_parental

description:
processed data file:
parental_RPKM.txt

data_processing:
Sequencing reads were mapped into reference human genome hg19 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: txt, normalized RPKM

molecule: polyA RNA

source_name: small cell lung cancer

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

value: exponentially growing cells


title: ENR WT RNA-seq

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

country: United Kingdom

institute: Wellcome Sanger Institute

description: processed data file: geneExpression_KOvsWT_readcounts_normalized.txt

data_processing:
All samples were sequenced using an Illumina Hiseq2000 with single end 50-bp read length. The adapters were trimmed by using the FASTX-Toolkit2.
RNA-seq data: RNA-Seq libraries were quantified with kallisto version 0.43.0 (Bray et al., 2016) by pseudoallignment to the ERCC sequences + RefSeq transcript database downloaded at 28-06-2016, this database was filtered for only the genes that were already identified by deep proteomics. Absolute transcript concentrations per cell were computed by linear-fitting the RNA spike-in TPM values to attomoles. Normalization of readcounts was done in DESeq2 using the rlogTransformation function.
ChIPmentation and ATAC data: Paired-end 50 bp sequencing reads were aligned to mm9 with BWA (Li & Durbin, 2009) allowing one mismatch. Reads were filtered for a quality score of at least 1, PCR duplicates were removed with Picard and reads mapping to the mitochondrial chromosome were discarded. Peaks were identified with MACS 2.0 (Zhang et al, 2008) with a false discovery rate of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq data is in a tab delimited file with per gene: readcounts, transcripts per million, and transcript copynumber per cell. ATAC and ChIPmentation data is in a tab delimited file with all identified peak locations and the DESeq2 normalized readcounts per sample per peak.

source_name: Small intestinal organoids

growth_protocol: Organoids were maintained using ENR medium which contained Dulbecco's Modified Eagle Medium/Ham's F-12 supplemented with Pen/Strep, 10 mM HEPES, 1× Glutamax, 5% R-Spondin-1 (conditioned medium), 10% Noggin (conditioned medium), 1× B27 supplement, 1.25 mM n-Acetyl Cysteine, and recombinant mouse epidermal growth factor (50 ng/mL). Organoids were split every 4-5 days in an 1:4 ratio using mechanical dissociation and plated in fresh BME (Cultrex Reduced Growth Factor Membrane Extract, Type 2, PathClear).

extract_protocol:
Organoids were harvested by using mechanical dissociation followed by multiple ice-cold PBS washes (400 × G, 4°C, 5 min). For RNA-seq, total RNA was extracted with Rneasy RNA extraction kit (Qiagen). For ATAC-seq, organoids were resuspended in Recovery Cell Culture Freezing Medium (Gibco) and snap frozen prior to the ATAC-seq procedure. Once thawed, they were washed with PBS and processed for ATAC-seq. For ChIPmentation, cell pellets were dissolved in PBS and crosslinked in solution by using formaldehyde (1% final volume, shaking 10 minutes at room temperature). Glycine (0.125 M) was added to quench the reaction. Cell pellets were lysed in a volume of 110 μL using lysis buffer (20mM Hepes pH 7.6, 1% SDS, 1x Protease Inhibitor Cocktails. Samples were sonicated using the Biorupter Pico (Diagenode) with 6 cycles (30 sec on / 30 sec off). Afterwards the samples were spun at 16.200×G for 5 min at room temperature and stored at -80°C prior to the ChIPmentation procedure
For RNA-seq experiment,  RNA was purified and ERCC spike-in was added. rRNA was depleted using RiboZero kit. rRNA depleted samples were fragmented for 5 min at 95°C using 5× fragmentation buffer (200mM Tris-acetate, 500mM Potassium Acetate, 150mM Magnesium Acetate, pH8.2) followed by ethanol precipitation. First strand cDNA synthesis was performed using Superscript III (Invitrogen) with the addition of random hexamer primers and Actinomycin D (9ng/mL). Afterwards second strand cDNA synthesis (SuperScript, Invitrogen) was performed with the addition of dUNTPs and random hexamer primers. Samples were cleaned using Qiaquick MinElute Columns (Qiagen) after first and second strand cDNA synthesis. A maximum of 5ng cDNA was used for sample preparation using the KAPA Hyper Prep Kit (KAPA Biosystems). NextFlex DNA barcodes (Bioo Scientific) were used for adapter ligation. Treatment for 15 min at 37°C with USER enzyme was done prior to library amplification. Libraries were amplified using 10 amplification cycles. Post-amplification cleanup was done using Qiaquick MinElute Columns (Qiagen) followed by size selection of 300 base pairs using E-Gel SizeSelect Agarose Gels 2% (Invitrogen). For ChIPmentation the chromatin was incubated overnight at 4°C rotating in dilution buffer (1% Triton X-100, 1.2mM EDTA, 16.7mM Tris pH8, 167mM NaCl), 1x Protease Inhibitor Cocktail (Roche), and 1 μL of antibody (H3K4me3 / H3K27ac / H3K27me3, Diagenode). Per ChIP 10 μL protein A Dynabeads and 10 μL protein G Dynabeads were used. Beads were washed using dilution buffer (+0.15% SDS, +0.1% BSA) and incubated with the chromatin and antibody mix for 60 minutes at 4°C rotating. Afterwards the beads were washed at 4°C once with ChIP wash buffer 1 (2mM EDTA, 20mM Tris pH 8, 1% Triton X-100, 0.1% SDS, 150 mM NaCl), twice with ChIP wash buffer 2 (2mM EDTA, 20mM Tris pH8, 1% Triton X-100, 0.1% SDS, 500 mM NaCl), and twice with TE (1 mM EDTA, 10 mM Tris pH 8). Beads were resuspended in Tagment DNA buffer and 1 μL Tn5 enzyme (produced in-house) and incubated for 10 minutes at 37°C with 550 rpm shaking. Afterwards the beads were washed twice with WBI (20 mM Hepes, 150 mM NaCl, 0.1% SDS, 0.1% DOC, 1% Triton X-100, 1 mM EDTA, 0.5mM EGTA) and twice with WBIV (20mM Hepes, 1mM EDTA, 0.5mM EGTA) with 5 minutes rotating at room temperature in between. Samples were decrosslinked for 1h at 55°C 1000 rpm shaking followed by an overnight incubation at 65°C using elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris pH8) and proteinase K. Samples were incubated one additional hour the next day with elution buffer and proteinase K for 1 hour at 55°C. The samples were purified using 2x SPRI AMPureXP beads. qPCR was used to determine the sufficient amount of PCR cycles needed to amplify the library. The libraries were amplified using the KAPA HiFi Hotstart Ready Mix (KAPA Biosystems) and Nextera Index Kit 1 (i7) and 2 (i5) primers (Illumina). Amplified libraries were purified using an 0.65× SPRI AMPureXP beads incubation followed by an 1.8× SPRI AMPureXP beads incubation. ATAC-seq was performed as described in (Buenrostro et al, 2015) with three modifications. First, the total volume of the tagmentation reaction was halved. Second, the tagmentation reaction was stopped with 44 mM EDTA, 131 mM NaCl, 0.3% SDS and 600 μg/mL proteinase K. Last, a reverse phase 0.65× SPRI beads (Ampure) DNA purification was done after the first PCR.

treatment_protocol: Stem cell enriched organoid cultures (CV) were grown in ENR supplemented with CHIR99021 (3 μM) and valproic acid (1 mM). Stem cell depleted organoid cultures (EN) were grown using ENR medium without R-Spondin-1.

value: Small intestinal organoids

tag: cell type enrichment

value: Normal (ENR medium)

tag: assay

value: RNA-seq


title: DMS114_1_H3K27ac

tag: cell type

value: exponentially growing cells with no infection

value: H3K27ac (abcam ab4729)


title: ENR4 RNA-seq

description: processed data file: geneExpression_readcounts_normalized.txt

tag: tissue


title: ENR Hnf4gKO RNA-seq

source_name: Small intestinal organoids from Hnf4g-KO mouse


title: S. cerevisiae BY4741 delHAP4 60 min cold shock vs before cold shock replicate 4

source_name: t0 before cold shock control replicate 4

tag: treatment

source_name: t60 60 min cold shock replicate 4


title: H82_parental

description:
processed data file:
parental_RPKM.txt


title: H526_parental

description:
processed data file:
parental_RPKM.txt


title: ENR4 H3K4me3

description: processed data file: union_peaks_readcounts_normalized.txt

value: ChIPmentation


title: H510_parental

description:
processed data file:
parental_RPKM.txt


title: ENR4 H3K27me3


title: ENR4 H3K27ac


title: S. cerevisiae BY4741 delHAP4 30 min cold shock vs before cold shock replicate 4

source_name: t30 30 min cold shock replicate 4

value: t30 30 min cold shock 13 degrees


title: S. cerevisiae BY4741 delHAP4 30 min cold shock vs before cold shock replicate 3

source_name: t30 30 min cold shock replicate 3

value: HAP4 (YKL109W)


title: H524_parental

description:
processed data file:
parental_RPKM.txt


title: ENR3 RNA-seq


title: H446_parental

description:
processed data file:
parental_RPKM.txt


title: ENR4 ATAC

value: ATAC-seq


title: S. cerevisiae BY4741 delHAP4 60 min cold shock vs before cold shock replicate 1

source_name: t60 60 min cold shock replicate 1


title: ENR3 H3K4me3


title: S. cerevisiae BY4741 delHAP4 15 min cold shock vs before cold shock replicate 3

value: t15 15 min cold shock 13 degrees

source_name: t0 before cold shock control replicate 3


title: H211_parental

description:
processed data file:
parental_RPKM.txt


title: S. cerevisiae BY4741 delHAP4 15 min cold shock vs before cold shock replicate 4

source_name: t15 15 min cold shock replicate 4


title: S. cerevisiae BY4741 delHAP4 30 min cold shock vs before cold shock replicate 1

source_name: t30 30 min cold shock replicate 1

source_name: t0 before cold shock control replicate 1


title: H69_parental

description:
processed data file:
parental_RPKM.txt


title: ENR3 H3K27me3


title: H128_parental

description:
processed data file:
parental_RPKM.txt


title: H146_parental

description:
processed data file:
parental_RPKM.txt


title: S. cerevisiae BY4741 delHAP4 30 min cold shock vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

source_name: t30 30 min cold shock replicate 2


title: ENR3 H3K27ac


title: ENR3 ATAC


title: S. cerevisiae BY4741 delHAP4 15 min cold shock vs before cold shock replicate 2

source_name: t15 15 min cold shock replicate 2


title: DMS114_parental

description:
processed data file:
parental_RPKM.txt


title: H1048_parental

description:
processed data file:
parental_RPKM.txt


title: S. cerevisiae BY4741 delHAP4 15 min cold shock vs before cold shock replicate 1

source_name: t15 15 min cold shock replicate 1


title: DMS79_parental

description:
processed data file:
parental_RPKM.txt


title: ENR2 RNA-seq


title: CORL311_parental

description:
processed data file:
parental_RPKM.txt


title: NCI-H1048_sgNeg

description:
processed data file:
RNAseq_NCI-H1048_POU2F3.txt

value: day 4 after sgNeg guideRNA infection


title: NCI-H1048_sgPOU2F3e10.1

value: day 4 after sgPOU2F3e10.1 guideRNA infection


title: ENR2 H3K4me3


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 60 min recovery vs before cold shock replicate 5

source_name: t120 60 min cold shock followed by 60 min recovery replicate 5

value: GLN3 (YER040W)

value: t120 60 min cold shock 13 degrees followed by 60 min recovery 30 degrees

source_name: t0 before cold shock control replicate 5

value: t0 before cold shock control 30 degrees


title: ENR2 H3K27ac

source_name: Small intestinal organoids


title: ENR2 H3K27me3


title: NCI-H1048_sgPOU2F3e10.2

source_name: small cell lung cancer

value: day 4 after sgPOU2F3e10.2 guideRNA infection


title: ENR1 Hnf4g

description: processed data file: union_peaks_rawReadcounts_Hnf4g.txt


title: ENR1 ATAC


title: ENR1 H3K4me3


title: EN4 RNA-seq

value: Differentiated (-Rspondin)


title: ENR1 H3K27ac

value: Small intestinal organoids


title: ENR1 H3K27me3

value: Normal (ENR medium)


title: ENR2 ATAC


title: COR-L311_sgNeg

description:
processed data file:
RNAseq_COR-L311_POU2F3.txt

value: day 5 after sgNeg guideRNA infection


title: COR-L311_sgPOU2F3e10.1

value: day 5 after sgPOU2F3e10.1 guideRNA infection


title: COR-L311_sgPOU2F3e10.2

value: day 5 after sgPOU2F3e10.2 guideRNA infection


title: NCI-H526_sgPOU2F3e10.2

description:
processed data file:
RNAseq_NCIH526_POU2F3.txt


title: EN4 H3K4me3

value: ChIPmentation


title: ENR1 RNA-seq

value: RNA-seq


title: NCI-H526_sgPOU2F3e10.1


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 60 min recovery vs before cold shock replicate 2

description: Ontario chip; post-washing slide coating of 2% PEG (MW cut-off 2000) in 1:1 solution of acetone and toluene

source_name: t120 60 min cold shock followed by 60 min recovery replicate 2


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 60 min recovery vs before cold shock replicate 4

source_name: t0 before cold shock control replicate 4

source_name: t120 60 min cold shock followed by 60 min recovery replicate 4


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 60 min recovery vs before cold shock replicate 1

source_name: t120 60 min cold shock followed by 60 min recovery replicate 1


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 30 min recovery vs before cold shock replicate 3

source_name: t90 60 min cold shock followed by 30 min recovery replicate 3

value: t90 60 min cold shock 13 degrees followed by 30 min recovery 30 degrees


title: NCI-H526_sgNeg


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 30 min recovery vs before cold shock replicate 5

source_name: t90 60 min cold shock followed by 30 min recovery replicate 5


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 30 min recovery vs before cold shock replicate 2

source_name: t90 60 min cold shock followed by 30 min recovery replicate 2


title: S. cerevisiae BY4741 delGLN3 60 min cold shock followed by 30 min recovery vs before cold shock replicate 1

source_name: t90 60 min cold shock followed by 30 min recovery replicate 1


title: S. cerevisiae BY4741 delGLN3 60 min cold shock vs before cold shock replicate 2

source_name: t60 60 min cold shock replicate 2

value: t60 60 min cold shock 13 degrees


title: S. cerevisiae BY4741 delGLN3 30 min cold shock vs before cold shock replicate 5

source_name: t30 30 min cold shock replicate 5

value: t30 30 min cold shock 13 degrees


title: S. cerevisiae BY4741 delGLN3 60 min cold shock vs before cold shock replicate 4

source_name: t60 60 min cold shock replicate 4


title: S. cerevisiae BY4741 delGLN3 60 min cold shock vs before cold shock replicate 3

source_name: t60 60 min cold shock replicate 3

source_name: t0 before cold shock control replicate 3


title: S. cerevisiae BY4741 delGLN3 30 min cold shock vs before cold shock replicate 1

source_name: t0 before cold shock control replicate 1

source_name: t30 30 min cold shock replicate 1


title: S. cerevisiae BY4741 delGLN3 30 min cold shock vs before cold shock replicate 2

source_name: t30 30 min cold shock replicate 2

source_name: t0 before cold shock control replicate 2


title: S. cerevisiae BY4741 delGLN3 60 min cold shock vs before cold shock replicate 1

source_name: t60 60 min cold shock replicate 1


title: S. cerevisiae BY4741 delGLN3 30 min cold shock vs before cold shock replicate 4

source_name: t0 before cold shock control replicate 4

source_name: t30 30 min cold shock replicate 4


title: NCI-H211_sgPOU2F3e10.2

description:
processed data file:
RNAseq_NCIH211_POU2F3.txt

source_name: small cell lung cancer


title: EN4 H3K27me3

source_name: Small intestinal organoids


title: EN4 ATAC

value: ATAC-seq


title: EN3 RNA-seq


title: NCI-H211_sgPOU2F3e10.1

value: day 4 after sgPOU2F3e10.1 guideRNA infection


title: S. cerevisiae BY4741 delGLN3 15 min cold shock vs before cold shock replicate 4

value: GLN3 (YER040W)

source_name: t15 15 min cold shock replicate 4

value: t15 15 min cold shock 13 degrees


title: EN3 H3K27me3


title: S. cerevisiae BY4741 delGLN3 15 min cold shock vs before cold shock replicate 5

source_name: t15 15 min cold shock replicate 5

source_name: t0 before cold shock control replicate 5

value: t0 before cold shock control 30 degrees


title: EN3 H3K4me3


title: EN4 H3K27ac


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 60 min recovery vs before cold shock replicate 3

value: CIN5 (YOR028C)

source_name: t120 60 min cold shock followed by 60 min recovery replicate 3

value: t120 60 min cold shock 13 degrees followed by 60 min recovery 30 degrees


title: S. cerevisiae BY4741 delGLN3 15 min cold shock vs before cold shock replicate 2

source_name: t15 15 min cold shock replicate 2


title: EN2 H3K27me3

value: Small intestinal organoids

value: Differentiated (-Rspondin)


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 60 min recovery vs before cold shock replicate 4

source_name: t120 60 min cold shock followed by 60 min recovery replicate 4


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 30 min recovery vs before cold shock replicate 4

source_name: t90 60 min cold shock followed by 30 min recovery replicate 4


title: EN2 H3K4me3


title: EN2 RNA-seq


title: EN3 ATAC


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 30 min recovery vs before cold shock replicate 1

source_name: t90 60 min cold shock followed by 30 min recovery replicate 1


title: EN2 Hnf4g


title: EN2 ATAC


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 30 min recovery vs before cold shock replicate 2

source_name: t90 60 min cold shock followed by 30 min recovery replicate 2


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 30 min recovery vs before cold shock replicate 3

source_name: t0 before cold shock control replicate 3

source_name: t90 60 min cold shock followed by 30 min recovery replicate 3


title: S. cerevisiae BY4741 delCIN5 60 min cold shock vs before cold shock replicate 4

source_name: t60 60 min cold shock replicate 4


title: S. cerevisiae BY4741 delCIN5 60 min cold shock vs before cold shock replicate 3

source_name: t60 60 min cold shock replicate 3


title: S. cerevisiae BY4741 delGLN3 15 min cold shock vs before cold shock replicate 3

source_name: t15 15 min cold shock replicate 3


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 60 min recovery vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

source_name: t120 60 min cold shock followed by 60 min recovery replicate 2


title: S. cerevisiae BY4741 delCIN5 60 min cold shock vs before cold shock replicate 2

source_name: t60 60 min cold shock replicate 2


title: NCI-H211_sgNeg

source_name: small cell lung cancer

value: day 4 after sgNeg guideRNA infection


title: S. cerevisiae BY4741 delCIN5 60 min cold shock followed by 60 min recovery vs before cold shock replicate 1

source_name: t120 60 min cold shock followed by 60 min recovery replicate 1

source_name: t0 before cold shock control replicate 1


title: EN1 H3K27ac

source_name: Small intestinal organoids


title: EN1 H3K27me3


title: EN1 ATAC


title: EN1 H3K4me3


title: EN1 RNA-seq


title: S. cerevisiae BY4741 delCIN5 30 min cold shock vs before cold shock replicate 4

source_name: t30 30 min cold shock replicate 4

source_name: t0 before cold shock control replicate 4


title: S. cerevisiae BY4741 delCIN5 60 min cold shock vs before cold shock replicate 1

source_name: t60 60 min cold shock replicate 1


title: S. cerevisiae BY4741 delCIN5 30 min cold shock vs before cold shock replicate 3

source_name: t30 30 min cold shock replicate 3


title: CV4 H3K27ac

value: Stem cell enriched (+CHIR+VPA)


title: CV4 H3K4me3


title: CV5 H3K27ac


title: CV4 H3K27me3


title: S. cerevisiae BY4741 delCIN5 30 min cold shock vs before cold shock replicate 2

source_name: t30 30 min cold shock replicate 2


title: S. cerevisiae BY4741 delCIN5 15 min cold shock vs before cold shock replicate 4

source_name: t15 15 min cold shock replicate 4


title: S. cerevisiae BY4741 delCIN5 15 min cold shock vs before cold shock replicate 2

source_name: t15 15 min cold shock replicate 2


title: CV4 RNA-seq


title: EN2 H3K27ac


title: S. cerevisiae BY4741 delCIN5 15 min cold shock vs before cold shock replicate 3

source_name: t0 before cold shock control replicate 3


title: S. cerevisiae BY4741 delCIN5 30 min cold shock vs before cold shock replicate 1

source_name: t30 30 min cold shock replicate 1


title: CV3 RNA-seq


title: S. cerevisiae BY4741 delCIN5 15 min cold shock vs before cold shock replicate 1

source_name: t15 15 min cold shock replicate 1


title: CV4 ATAC


title: CV3 H3K4me3


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 60 min recovery vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

value: none (wild type parental strain)


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 60 min recovery vs before cold shock replicate 4

source_name: t120 60 min cold shock followed by 60 min recovery replicate 4


title: CV3 H3K27me3

value: ChIPmentation


title: S. cerevisiae BY4739 wild type 60 min cold shock followed by 60 min recovery vs before cold shock replicate 0

description: GCAT chip; post-washing slide coating of 2% PEG (MW cut-off 2000) in 1:1 solution of acetone and toluene

source_name: t0 before cold shock control replicate 0

source_name: t120 60 min cold shock followed by 60 min recovery replicate 0


title: CV2 RNA-seq

value: RNA-seq


title: CV3 H3K27ac


title: CV2 H3K4me3


title: CV3 ATAC


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 30 min recovery vs before cold shock replicate 4

source_name: t90 60 min cold shock followed by 30 min recovery replicate 4

value: t90 60 min cold shock 13 degrees followed by 30 min recovery 30 degrees


title: CV2 H3K27me3


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 60 min recovery vs before cold shock replicate 3

source_name: t120 60 min cold shock followed by 60 min recovery replicate 3


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 30 min recovery vs before cold shock replicate 3

source_name: t90 60 min cold shock followed by 30 min recovery replicate 3


title: hCOM-ASTRO-2

city: Hospitalet de Llobregat (Barcelona)

first: Meritxell

last: Pons

address: Avinguda Gran Via, 199-203

institute: IDIBELL

data_processing:
The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v4.
Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of fastq.gz sequence files by CASAVA.
Mapping: STAR/2.5.3a
Quantification: RSEM/1.3.0
Genome_build:  GRCh38
Supplementary_files_format_and_content: Processed data refers to a matrix of raw counts for each gene in every sample analyzed.

source_name: Brain - Cerebral Cortex

growth_protocol: Human iPSC were routinely cultured in mTESR medium on matrigel coated plates. Astrocytes were obtained according to Serio et al., 2013 and cultured with CNTF. Human cortical astrocytes were routinely cultured in astrocyte medium (reference: P60101).

extract_protocol:
Total RNA was extracted using Quiazol lysis reagent (Qiagen) and RNAeasy extraction kit (Qiagen) according to manufacturer's instructions.
The RNASeq libraries were prepared from total RNA using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013).  The mRNA was fragmented in the presence of divalent metal cations and at high temperature (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.

value: Astrocytes

tag: disease state

value: healthy


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 30 min recovery vs before cold shock replicate 2

source_name: t90 60 min cold shock followed by 30 min recovery replicate 2


title: S. cerevisiae BY4741 wild type 60 min cold shock vs before cold shock replicate 3

source_name: t60 60 min cold shock replicate 3

value: t60 60 min cold shock 13 degrees


title: CV1 Hnf4g

source_name: Small intestinal organoids


title: CV2 ATAC

value: ATAC-seq


title: CV2 H3K27ac


title: CV1 H3K4me3


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 30 min recovery vs before cold shock replicate 1

source_name: t0 before cold shock control replicate 1

source_name: t90 60 min cold shock followed by 30 min recovery replicate 1


title: S. cerevisiae BY4741 wild type 60 min cold shock followed by 60 min recovery vs before cold shock replicate 1

source_name: t120 60 min cold shock followed by 60 min recovery replicate 1


title: B16-bearing

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

hyb_protocol: 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5

scan_protocol: Scanning was performed in an Affymetrix GeneChip Scanner 3000, according to manifacturer's instruction.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: leukocytes from B16-bearing mice

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets according to standard Affymetrix's procedure.

growth_protocol: Ten millions of B16 melanoma or Lewis Lung Carcinoma (LLC) cells were injected to the back of C57BL6 mice.

extract_protocol: Total RNA was isolated from leukocyte using TRIzol Reagent (Thermo Scientific), according to the manufacturer's instructions.

treatment_protocol: Leukocyte was purified from mice bearing with B16 melanoma or LLC cells

value: leukocyte

value: B16 melanoma-bearing mice


title: hASTRO-control-2

source_name: Skin Fibroblasts

value: iPSC-derived astrocytes

value: control


title: EN3 H3K27ac


title: LLC-bearing

source_name: leukocytes from LLC-bearing mice

value: Lewis Lung Carcinoma-bearing mice


title: CV1 RNA-seq

value: Small intestinal organoids


title: hCOM-ASTRO-1


title: hASTRO-PD-LRRK2-2

value: Parkinson's disease LRRK2 G2019S


title: S. cerevisiae BY4739 wild type 60 min cold shock vs before cold shock replicate 0

value: t0 before cold shock control 30 degrees

source_name: t60 60 min cold shock replicate 0


title: S. cerevisiae BY4739 wild type 60 min cold shock followed by 30 min recovery vs before cold shock replicate 0

source_name: t90 60 min cold shock followed by 30 min recovery replicate 0


title: no-tumor-bearing

source_name: leukocytes from control mice

value: non tumor-bearing mice


title: S. cerevisiae BY4741 wild type 60 min cold shock vs before cold shock replicate 2

source_name: t0 before cold shock control replicate 2

value: none (wild type parental strain)

source_name: t60 60 min cold shock replicate 2


title: hASTRO-PD-LRRK2-1


title: S. cerevisiae BY4741 wild type 60 min cold shock vs before cold shock replicate 1

source_name: t60 60 min cold shock replicate 1


title: S. cerevisiae BY4741 wild type 30 min cold shock vs before cold shock replicate 3

source_name: t30 30 min cold shock replicate 3

value: t30 30 min cold shock 13 degrees

source_name: t0 before cold shock control replicate 3


title: iPSC-PD-LRKK2-1

value: Induced pluripotent stem cells


title: S. cerevisiae BY4741 wild type 30 min cold shock vs before cold shock replicate 4

source_name: t30 30 min cold shock replicate 4

source_name: t0 before cold shock control replicate 4


title: LRL in lung

city: Tokyo

first: Sachie

last: Hiratsuka

address: 8-1 Kawada-cho Shinjyuku-ku

institute: Tokyo Women's Medical University

hyb_protocol: Following fragmentation, 3.6 ug of cRNA were hybridized for 18 hr on Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetreix GeneChip Command Console and Expression Console.

source_name: liver resident cells (LRL) in lung

label_protocol: The cRNA was amplified, labeled using cDNA Biotin Module (Encore) according to the manufacturer's instructions.

growth_protocol: SPF grade normal growth

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: photoconverted LRLs in TCM-stimulating Kaede-transgenic mice

value: liver resident cells


title: LRL in Liver

source_name: liver resident cells (LRL) in liver


title: CV1 ATAC

source_name: Small intestinal organoids

value: Stem cell enriched (+CHIR+VPA)


title: CV1 H3K27ac

value: ChIPmentation


title: S. cerevisiae BY4741 wild type 30 min cold shock vs before cold shock replicate 2

source_name: t30 30 min cold shock replicate 2


title: iPSC-PD-LRKK2-2


title: CV1 H3K27me3


title: NOD1-microinjected Embryos Replicate 2

city: Wuhan

first: M

middle: X

last: Chang

address: Luojiaashan

country: China

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Biological replicate 2 of 3.Zebrafish embryos microinjected with ptGFP1-NOD1.

scan_protocol: just not provided by company

data_processing: Calculate the fold-change as 2-ΔΔCt

label: SYBR Green

source_name: embryos microinjected with ptGFP1-NOD1

label_protocol: SuperArray PCR master mix and diluted first strand cDNA synthesis reaction were added to per-well.

extract_protocol: On average, 150–200 embryos per group were used for RNA extraction using TRIZOL® Reagent (Invitrogen life technologies)

tag: development stage

value: 24 hpf


title: NOD1-microinjected Embryos Replicate 3

description: Biological replicate 3 of 3.Zebrafish embryos microinjected with ptGFP1-NOD1.


title: iPSC-control-1

source_name: Skin Fibroblasts


title: Control Embryos Replicate 3

description: Biological replicate 3 of 3.Control embryos microinjected with empty plasmid ptGFP1

source_name: embryos microinjected with ptGFP1


title: NOD1-microinjected Embryos Replicate 1

description: Biological replicate 1 of 3.Zebrafish embryos microinjected with ptGFP1-NOD1.


title: hASTRO-control-1


title: S. cerevisiae BY4739 wild type 30 min cold shock vs before cold shock replicate 0

source_name: t0 before cold shock control replicate 0

source_name: t30 30 min cold shock replicate 0


title: S. cerevisiae BY4741 wild type 30 min cold shock vs before cold shock replicate 1

source_name: t0 before cold shock control replicate 1

source_name: t30 30 min cold shock replicate 1


title: Control Embryos Replicate 1

description: Biological replicate 1 of 3.Control embryos microinjected with empty plasmid ptGFP1


title: iPSC-control-2


title: WCM154 PDOX

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Briefly, bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark.
Genome_build: hg19
Supplementary_files_format_and_content: methylcall files are in .txt format

source_name: WCM154 PDOX

growth_protocol: In brief, the preparation steps included: 1) MspI enzyme digestion; 2) end repair of digested DNA;3) adenylation; 4) adapter ligation, with pre-annealed 5-methylcytosine–containing Illumina adapters; 5) isolation of library fragments of 150 to 400 bp from a 1.5% agarose gel (using low-range ultra-agarose from Bio-Rad, Des Plaines, IL); 6) bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA) with the following changes: i) CT conversion incubation in a thermocycler (Eppendorf, Hauppauge, NY) with the condition: 30 seconds at 95°C followed by 15 minutes at 50°C for 55 cycles, and ii) elution into nuclease-free water; 7) polymerase chain reaction (PCR) amplification; each library was prepared with FastStart High Fidelity DNA Polymerase (Roche, Indianapolis, IN) and Illumina PCRprimers PE1.0 and 2.0.The thermocycler conditions were given as follows: 5 minutes at 94°C, 18 cycles of 20 seconds at 94°C, 30 seconds at 65°C, 1 minute at 72°C, followed by 3 minutes at 72°C. PCR products were isolated using Agencourt AMPure XP (Beckman Coulter, Brea, CA) beads per manufacturer’s recommended protocol (Agencourt) All amplified libraries were evaluated using a Qubit 1.0 fluorometer and Quant-iT dsDNA HS Assay Kit (Invitrogen, Grand Island, NY) for quantitation and bioanalyzer visualization (Agilent 2100 Bioanalyzer; Agilent, Santa Clara, CA).

extract_protocol:
DNA extractions from organoids and PDOXs were performed using DNeasy Blood and Tissue Kit (QIAGEN) and Maxwell 16 Tissue DNA Purification Kit (Promega). .
errbs

treatment_protocol: No treatments were applied prior to genomic DNA extraction

value: prostate organoid


title: WCM155 organoid

source_name: WCM155 organoid


title: WCM154 organoid

source_name: WCM154 organoid


title: Control Embryos Replicate 2

description: Biological replicate 2 of 3.Control embryos microinjected with empty plasmid ptGFP1


title: S. cerevisiae BY4741 wild type 15 min cold shock vs before cold shock replicate 4

source_name: t15 15 min cold shock replicate 4

value: t15 15 min cold shock 13 degrees