title: A_PTTG3P

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC contentthe clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Qualified reads after filtering low-quality data were analyzed using   TopHat  v2.0.  12. and HTSeq v0.6.1 for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

growth_protocol: A549 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted from A549 cell lines by NucleoSpin RNA XS (Macherey Nagel, Duren, Germany).
A total amount of 3 μg RNA per sample was used as in put material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out. using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H. Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Overexpression of PTTG3P


title: 3_NC180_UNTR: Untreated non-sphere-forming primary glioma cells

status: Public on May 10 2019

type: RNA

city: Planegg-Martinsried

first: Andrea

last: Terrasi

address: Großhaderner Strasse 9

department: Biomedical Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45¬∞C on GeneChip Gene 2.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for gene annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/genecodeg.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Therefore, the expression levels of Ensembl genes specific for 18642 unique mRNAs were obtained.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: untreated primary GBM derived cells

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: Primary patients' derived glioma cells were washed twice with HBSS (Gibco-Invitrogen, Thermo Fisher Scientific, Waltham, MA USA) and coltured with neurocult (NC) media (Stem Cells)

extract_protocol: Total RNA was purified from LO or mock-treated glioma cocultures using Master Pure RNA purification kit (Epicentre Biotechnologies, Illumina; Madison, WI, USA) followed by DNA digestion with DNase I.

treatment_protocol: Total RNA was extracted from cultures and 300ng of DNA-free total RNA were reverse transcribed using the SuperScript II Reverse Transcriptase and random hexamers (both from Thermo Fisher Scientific).

tag: tissue

value: primary human non-sphere-forming glioma cells

tag: cocultured

value: mock


title: Reaggregation comparison, Native (non-reagg) clusters

type: SRA

city: Cambridge

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

country: USA

institute: Harvard University

description:
Veres2019_analysis_data.tar
Misc.Reagg_comparison.processed_counts.tsv.gz
Misc.Reagg_comparison.cell_metadata.tsv
Misc.Reagg_comparison.raw_indrops_counts.tsv.gz

library_source: transcriptomic

data_processing:
All processing steps from raw fastq files to count matrices were performed using the custom pipeline for inDrops data analysis (www.github.com/indrops/indrops) using the the following parameters specified in the YAML file: [trimmomatic arguments]: LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "30". [output_arguments]: filter_alignments_to_softmasked_regions: True. All other parameters were used as in the default_parameters file in the repository github.com/indrops/indrops, commit hash 8a9167.
Genome_build: GRCh38.88
Supplementary_files_format_and_content: '*.raw_indrops_counts.*' files are the raw, unfiltered output from the Indrops processing pipeline. The first column indicates the barcode label using the Indrops pipeline nomenclature, all folllowing columns are UMIFM counts as defined in Klein et al. (2015). The gene corresponding to each column is listed in the header line.
Supplementary_files_format_and_content: '*.processed_counts.*' are filtered counts files, removing undetected genes and filtering cells using the thresholds described in the methods section of Veres et al. 2019. The first column indicates the cell label, all following columns are UMIFM counts for the gene indicated in the header row.
Supplementary_files_format_and_content: '*.cell_metadata.*' files contain metadata associated for all filtered cells in the each dataset. The first row is a header detailing the type of data in each column. These include TSNE coordinates, cluster label annotations and pseudotime values (as appropriate).
Supplementary_files_format_and_content: code_analysis_files.tar is a tarball of all files (primarily loom-formatted) used in generating the analysis, with the accompanying code at https://github.com/meltonlab/scbeta_indrops

molecule: polyA RNA

source_name: in vitro differentiated pluripotent stem cell

growth_protocol: Human embryonic and pluripotent stem cells were maintained and differentiated as described in the methods of (Veres et al. 2018). Differentiation was carried out using step-wise protocols aimed at gradually producing beta cells in vitro.

extract_protocol:
Differentiated clusters were prepared for single cell RNA sequencing as follows: 1-2 mL suspension culture was sampled from the spinner flask, dissociated with TrypLE Express (5-15 minutes at 37 °C), quenched with cold PBS + 1% BSA and gently dispersed with a P1000 pipette. Cells were then centrifuged (300 rpm, 3 min), resuspended in cold PBS+1% BSA and filtered through a 70 µm mesh filter. Centrifugation, resuspension and filtering was repeated a total of 3 times. Cells were then counted and resuspended to the working dilution for inDrops (100,000 cells/mL) in 1X PBS with 13% Optiprep (Sigma; D1556).
Single cell RNA sequencing was carried out using the inDrops platform, as previously described (Klein 2015, Zilionis 2016). Most samples were run using ‘inDrops v2’ barcoded hydrogel beads (1 Cell Bio, Harvard Single Cell Core), and one experiment used ‘inDrops v3’ beads (Harvard Single Cell Core). Following the inDrops protocol, each biological sample was split into several aliquots of 1000-3000 cells after encapsulation. At least two library aliquots were prepared separately from each sample, indexing using recommended index sequences, pooled and sequencing on a NextSeq 500 (Illumina).

tag: cell type

tag: experiment

value: Reaggregation comparison

value: SC-beta protocol v4

tag: Stage

value: Stage 6


title: A_HA

city: Taipei

first: JOU-HO

last: SHIH

state: Please Select

address: 128 Sec. 2, Academia Rd. Nankang, Taipei

country: Taiwan

institute: Institute of Biomedical Sciences, Academia Sinica

tag: cell line

tag: genotype/variation

value: HA control


title: WT_H3K36me3_spike

status: Public on May 09 2019

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were cleaned with trim-galore and aligned to the human genome, hg19, using bowtie2. PCR duplicated reads were removed by SAMtools
ChIP-seq peaks were identified by MACS2 with the parameter of narrow peak for H3K36M peaks, and broad peak calling for H3K36 and H3K27 methylations. For spike-in ChIP-seq results, the sequencing reads were aligned and normalized according to previous published procedures (Orlando et al., 2014). In brief, human (hg19) and drosophila (dm6) genome sequences were combined to produce a reference genome. Cleaned sequencing reads were aligned to the reference genome by bowtie2 with default parameters. The mapped reads were then separated into human and drosophila reads, where the reads mapped to the drosophila genome were used to determine the normalization factor. The number of reads in each sequencing results was counted and normalized by the normalization factor.
For RNA sequencing. Sequence reads were cleaned with trim-galore and then aligned to the human genome hg19 using STAR. The mapped reads were annotated to Refseq genes using TopHat and the FPKM of genes was calculated by Cufflinks. Cuffdiff was used to identify and analyze the differential gene expression using false discovery rate (FDR) < 0.05 as the cutoff.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization Reads Per 10 Million.
Supplementary_files_format_and_content: txt files are tab-delimited text files include reads counts values for each gene

molecule: genomic DNA

source_name: Astrocyte

growth_protocol: T/C28a2 cell, which was the immortalized human juvenile costal chondrocyte, was cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were crosslinked by 1% formaldehyde for 10 mins, and then quenched in 125 mM glycine for 5mins. After washing with cold TBS twice, cells were incubated in lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) for 10 mins on ice. Nuclei were washed and resuspended in MNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) supplemented with 1,000 units of MNase (NEB) and incubated at 37 °C with continuous mixing for 20 mins. The reaction was stopped by adding of 2XSTOP buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), followed by sonication for 10 mins (30 secs on / 30 secs off). For spike-in ChIP-seq, the MNase digested chromatin from drosophila S2 cells was added to 1% to 5% of total chromatin. The chromatin was incubated with antibodies at 4 °C overnight and then subjected to 30 μl of protein G-magnetic beads for additional 2 hours. The beads were extensively washed and bound DNA was eluted with elution buffer (10 mM Tris-HCl, pH8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) and reverse-crosslinked at 65 °C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after treatment of proteinase K and RNase A.
Sequencing libraries were prepared using TruPrep DNA library prep kit (Vazyme) following the manufacturer’s instructions.
The library was sequenced on an Illumina HiSeq Xten platform with pair-end read of 150bp

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

value: WT

tag: chip antibody


title: H3.1K36M#2_H3K4me3

value: hetero K36M mutation at HIST1H3D


title: H3.1K36M#2_H3K36me2_spike


title: H3.1K36M#2_H3K36me3_spike


title: WT_H3K36me2_spike


title: WT_H3K4me1


title: WT_input_spike


title: H3.1K36M#2_input_spike


title: WT_H3K4me3


title: H3.1K36M#2_input


title: H3.1K36M#2_H3K36M


title: WT_input


title: WT1_H3K27ac


title: H3.1K36M#2_H3K27me3


title: H3.1K36M#2_H3K27ac


title: H3.1K36M#1_input_spike


title: H3.1K36M#1_H3K36me3_spike


title: 4_NC180_LO: Non-sphere-forming primary glioma cells cocultured with Large Oncosomes

source_name: LO High cocultured primary GBM derived cells

value: LO High


title: H3.1K36M#1_H3K36me2_spike


title: H3.1K36M#1_H3K4me3


title: H3.1K36M#1_input


title: H3.1K36M#1_H3K4me1


title: H3.3K36M#2_input_spike

value: hetero K36M mutation at H3F3B


title: H3.1K36M#1_H3K27me3


title: H3.3K36M#2_H3K36me3_spike


title: H3.1K36M#1_H3K36M


title: H3.1K36M#1_H3K27ac


title: H3.1K36M#2_H3K4me1


title: WT_H3K27me3


title: H3.3K36M#1_input


title: H3.3K36M#1_H3K36me3_spike


title: H3.3K36M#1_H3K4me1


title: H3.3K36M#1_H3K27me3


title: ECA109 LV-PRMT1A

city: Shanghai

first: Yue

last: Zhao

address: 168 Changhai Road, Shanghai 200433, China

department: Department of Thoracic Surgery

institute: Changhai Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contains counts for each sample

source_name: esophageal squamous cell carcinoma cells

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately, The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: PRMT1 overexpression

tag: cell line source

value: esophageal squamous cell carcinoma (ESCC)


title: H3.3K36M#2_H3K4me1


title: H3.3K36M#2_H3K27ac


title: H3.3K36M#2_H3K27me3


title: H3.3K36M#1_H3K4me3


title: H3.3K36M#2_H3K4me3


title: H3.3K36M#2_input


title: H3.3K36M#1_H3K36me2_spike


title: ECA109 LV-GFP3

value: NC


title: ECA109 LV-PRMT1B


title: H3.3K36M#1_input_spike


title: H3.3K36M#1_H3K27ac


title: H3.3K36M#2_H3K36me2_spike


title: ECA109 LV-PRMT1C


title: ECA109 LV-GFP2


title: ECA109 LV-GFP1


title: Array-X-TBBPA

city: Heidelberg

first: Lisa

middle: Annie

last: Baumann

address: Im Neuenheimer Feld 504

department: COS

institute: University of Heidelberg

hyb_protocol: The cRNA of each sample was labelled once with Cy3-CTP and once with Cy5-CTP. Subsequently, the labelled cRNA samples were purified with the RNeasy mini spin column kit (Qiagen). cRNA yield, quality and dye incorporation efficiency were verified with the Nanodrop spectrophotometer.For final transcriptome analysis, we used Agilent's  Zebrafish Gene Expression Microarray V3 (AMADID 026437) in a 4x44k format, which is a full genome microarray containing 43,803 Danio rerio probes. 825 ng Cy3 and 825 ng Cy5 labelled and purified cRNA was hybridized on the microarrays for 17 h at 65°C in a rotating (10 rpm) hybridization oven (Agilent Technologies). After hybridization, the slides were rinsed in Agilent wash buffers, acetonitrile and in stabilization/drying solution (Agilent Technologies) to wash and protect against ozone-induced dye-degradation.

scan_protocol: Microarray slides were scanned with a Genepix 4100A confocal scanner (Axon Instruments) at a resolution of 5 um and excitation wavelengths of 635 nm and 532 nm in an ozone-free location (NoZone scanner enclosure, SciGene). Images were analyzed for spot identification and for quantification of fluorescent signal intensities with the Genepix Pro software 6.1 (Axon Instruments).

data_processing: Quality control of the microarray data was performed with the R software package 'arrayQualityMetrics' (version 3.34.0), and no outliers were detected. Spots were excluded from the analysis if FG < BG + 2SD (FG: foreground, BG: local background, SD: standard deviation of the local backgrounds of the entire array) for all arrays in the dataset. Background correction was done by applying a normal-exponential convolution model. Within-array adjustment was performed using the Loess normalization, which is an intensity-dependent normalization of the red/green ratio. Responses in eyes of larvae exposed until 5 dpf were contrasted to the corresponding controls at 5 dpf, and responses in eyes of larvae allowed to recover until 8 dpf were contrasted to the corresponding controls at 8 dpf for the two compounds separately, using the R software package 'Limma' (version 3.34.4) as described by Vergauwen et al. (2010). After linear models were fitted to intensity ratios, an empirical Bayes method was used to rank the probes in order of evidence of differential transcription. Differentially expressed transcripts were selected based on the following criteria: logFC (binary logarithm of the fold change) > 0.75 and p< 0.05 where p is the adjusted p value after false discovery rate (FDR) control according to the Benjamini-Hochberg procedure. This resulted in 2 differentially expressed transcript lists: TBBPA 5 dpf and TBBPA 8 dpf.

organism: Danio rerio

source_name: eye tissue

label_protocol: Total RNA was linearly amplified and labelled with the Low Input Quick Amplification Labelling Kit (Agilent Technologies) according to the manufacturer's instructions. In summary, 100 ng RNA was reverse transcribed into cDNA using oligo dT primers. Afterwards, cDNA was transformed into cRNA and amplified.

growth_protocol: Eggs were distributed into pre-incubated 24-well plates containing the exposure solutions latest 2 hours after fertilization (1 egg per well, 2 ml solution per well). Plates were incubated at 28.5°C under a day/night cycle of 14/10 hours. Exposure solutions were renewed daily with freshly prepared solutions.

extract_protocol: Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel), according to the manufacturer's instructions. RNA quality and quantity were determined with a Nanodrop spectrophotometer ND-1000 (Thermo Scientific). RNA integrity (RIN) was verified using a bioanalyzer (Agilent 2100). Only high-quality RNA (average RIN: 8.9 +/- 1.0) was further processed for microarray analysis, which was the case for all samples.

treatment_protocol: For sampling of the eyes of the larvae, they were individually and consecutively transferred into ice-cold water for anesthesia. Single larvae were then placed under a stereomicroscope and the eyeballs were dissected using a small syringe. The eyeballs were quickly transferred to a cooled collection tube on ice to avoid RNA degradation. Larvae were euthanized by decapitation. After collection of eyes from 10 individuals, the tube was frozen in liquid nitrogen and stored at -80°C until further processing.

tag: strain

value: Wild-type AB

tag: exposure

value: control (8 dpf, replicate 1)

value: eye

value: 200 ug/L TBBPA (5 dpf, replicate 1)


title: Array-Z-TBBPA

value: 200 ug/L TBBPA (8 dpf, replicate 3)

value: control (8 pdf, replicate 3)


title: Array-T-TBBPA

value: 200 ug/L TBBPA (5 dpf, replicate 3)

value: control (5 pdf, replicate 1)


title: Array-U-TBBPA

value: control (5 dpf, replicate 1)

value: control (8 pdf, replicate 2)


title: Array-Y2-TBBPA

value: control (8 dpf, replicate 3)

value: 200 ug/L TBBPA (8 dpf, replicate 2)


title: Array-Y-TBBPA


title: Array-Z2-TBBPA


title: Array-W-TBBPA

value: 200 ug/L TBBPA(8 dpf, replicate 1)

value: control (8 pdf, replicate 1)


title: Array-V-TBBPA

value: control (8 dpf, replicate 2)

value: 200 ug/L TBBPA (8 dpf, replicate 1)


title: Array-S-TBBPA

value: control (5 dpf, replicate 3)


title: PBG98 16 h

city: London

first: Michael

middle: A

last: Skinner

address: St Mary's Campus, Norfolk Place

department: Faculty of Medicine, Section of Virology

country: United Kingdom

institute: Imperial College London

data_processing:
Illumina data were processed using RTA with default filter and quality settings then the reads were demultiplexed (allowing no mismatches in the index sequence) with CASAVA
Paired Fastq files were imported into CLC bio’s Genomics Workbench (CLC bio, Qiagen Bioinformatics, Aarhus, Denmark), quality-controlled and thereafter processed using that package (versions 7.5.1)
After quality control, the reads were subjected to quality trimming then mapped and aligned against ENSEMBL galGal4-annotated genes (release 4.82) for quantitative analysis of expression.
RPKM expression levels, Fold change and False Discovery Rates (FDR) were calculated using Kal’s Z test
Genome_build: 4.82
Supplementary_files_format_and_content: TAB-delimited text files, prepared with CLC bio GWB, showing gene expression analysis for each sample; TAB-delimited text files, prepared with CLC bio GWB,  with complete Kal's test output, including RPKM, compared to Mock (not filtered for NaN, INF, -INF)

organism: Gallus gallus

source_name: Chicken embryonic stem cells

growth_protocol: cESC (BP25 clone) were established from blastodermal cells and amplified on irradiated mouse STO feeder cells (Nordion gammacell irradiator) as described previously [Pain et al, Development, 1996]. cESC were proliferated in DMEM/F12 (Gibco, UK) medium containing 10% non-heat inactivated foetal bovine serum (Techgen batch no F 93246, France), 2% chicken serum (Valbiotech, France), 1% sodium pyruvate (100 mM; Gibco, UK), 1% glutamine (200mM; Gibco, UK), 1% non-essential amino acid (Gibco, UK), 0.16 mM β-mercaptoethanol (Sigma, USA), 1% penicillin/streptomycin (Gibco, UK) supplemented with 5 ng/ml human-IGF-1, 1 ng/ml human-SCF, 1 ng/ml human IL6, 1 ng/ml human IL6 Ra and 1000 U/ml mouse-LIF (Peprotech, UK).

extract_protocol:
Total RNA was extracted and processed from mock-, virus infected-, and mock-, IFN- stimulated cESC using the RNeasy kit (Qiagen) according to manufacturers' instrutions. Samples from three independent expereiments were merged and processed as one sample per condition.
RNA libraries were prepared sequenced using the Illumina HiSeq2000 system at the Beijing Genomics Institute (BGI Hong Kong) using standard Illumina protocols.Poly (A) mRNA was purified from total RNA using magnetic beads with oligo (dT) (New England BioLabs, UK). The mRNA was then broken into short fragments using divalent cations at an elevated temperature. Using these cleaved RNA fragments as templates, random hexamer primers (Ivitrogen, Carlsbad, CA) was used for first-strand cDNA synthesis, followed by second-strand cDNA synthesis using DNA polymerase I (New England BioLabs, UK) and RNase H (Invitrogen).

treatment_protocol: Fully confluent cESC  grown in T25 flasks without feeder cells for 2 passages, were washed with phosphate buffer saline (PBS) and infected for 2 h with each one of the viruses (at a multiplicity of infection, MOI, of 5) or mock-infected. The inoculum was then removed and cells were washed and further incubated in maintenance medium for 14h until cell collection/RNA isolation. For chIFN-α stimulation experiments, recombinant chicken chIFN-α was added in culture media to a final concentration of 1000 U/ml. Cells were dissociated with pronase (from Streptomyces griseus, Sigma) and stored at -80°C in RNALater (Sigma) until RNA extraction.

value: Chicken embryonic stem cells

tag: treatment

value: PBG98 16 h


title: Array-L-PTU

hyb_protocol: The cRNA of each sample was labelled once with Cy3-CTP and once with Cy5-CTP. Subsequently, the labelled cRNA samples were purified with the RNeasy mini spin column kit (Qiagen). cRNA yield, quality and dye incorporation efficiency were verified with the Nanodrop spectrophotometer.For final transcriptome analysis, we used Agilent’s Zebrafish Gene Expression Microarray V3 (AMADID 026437) in a 4x44k format, which is a full genome microarray containing 43,803 Danio rerio probes. 825 ng Cy3 and 825 ng Cy5 labelled and purified cRNA was hybridized on the microarrays for 17 h at 65°C in a rotating (10 rpm) hybridization oven (Agilent Technologies). After hybridization, the slides were rinsed in Agilent wash buffers, acetonitrile and in stabilization/drying solution (Agilent Technologies) to wash and protect against ozone-induced dye-degradation.

scan_protocol: Microarray slides were scanned with a Genepix 4100A confocal scanner (Axon Instruments) at a resolution of 5 μm and excitation wavelengths of 635 nm and 532 nm in an ozone-free location (NoZone scanner enclosure, SciGene). Images were analyzed for spot identification and for quantification of fluorescent signal intensities with the Genepix Pro software 6.1 (Axon Instruments).

data_processing: Quality control of the microarray data was performed with the R software package ‘arrayQualityMetrics’ (version 3.34.0), and no outliers were detected. Spots were excluded from the analysis if FG < BG + 2SD (FG: foreground, BG: local background, SD: standard deviation of the local backgrounds of the entire array) for all arrays in the dataset. Background correction was done by applying a normal-exponential convolution model. Within-array adjustment was performed using the Loess normalization, which is an intensity-dependent normalization of the red/green ratio. Responses in eyes of larvae exposed until 5 dpf were contrasted to the corresponding controls at 5 dpf, and responses in eyes of larvae allowed to recover until 8 dpf were contrasted to the corresponding controls at 8 dpf for the two compounds separately, using the R software package ‘Limma’ (version 3.34.4) as described by Vergauwen et al. (2010). After linear models were fitted to intensity ratios, an empirical Bayes method was used to rank the probes in order of evidence of differential transcription. Differentially expressed transcripts were selected based on the following criteria: logFC (binary logarithm of the fold change) > 0.75 and p< 0.05 where p is the adjusted p value after false discovery rate (FDR) control according to the Benjamini-Hochberg procedure. This resulted in 2 differentially expressed transcript lists: PTU 5 dpf and PTU 8 dpf.

label_protocol: Total RNA was linearly amplified and labelled with the Low Input Quick Amplification Labelling Kit (Agilent Technologies) according to the manufacturer’s instructions. In summary, 100 ng RNA was reverse transcribed into cDNA using oligo dT primers. Afterwards, cDNA was transformed into cRNA and amplified.

extract_protocol: Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel), according to the manufacturer’s instructions. RNA quality and quantity were determined with a Nanodrop spectrophotometer ND-1000 (Thermo Scientific). RNA integrity (RIN) was verified using a bioanalyzer (Agilent 2100). Only high-quality RNA (average RIN: 8.9  1.0) was further processed for microarray analysis, which was the case for all samples.

value: Wild-type AB

value: 350 mg/L PTU (8 dpf, replicate 3)

value: eye


title: Array-M-PTU

value: 350 mg/L PTU (8 dpf, replicate 2)


title: CNPV 16 h

value: CNPV 16 h


title: Array-F-PTU

value: 350 mg/L PTU (5 dpf, replicate 3)

value: control (5 pdf, replicate 1)


title: Array-G-PTU

value: control (5 dpf, replicate 1)

value: control (8 pdf, replicate 2)


title: Array-O-TBBPA

value: 200 ug/L TBBPA (5 dpf, replicate 2)


title: Array-E-PTU


title: Array-N-PTU


title: MVA 16 h

value: MVA 16 h


title: Array-R-TBBPA

value: 200 ug/L TBBPA (5 dpf, replicate 1)

value: control (5 pdf, replicate 3)


title: HH29 scRNA-seq

city: Berlin

first: Christian

middle: A.

last: Feregrino

address: Ihnestraße 63

institute: MPI - Molecular Genetics

data_processing:
Base calling, adaptor trimming, joint sequencing runs mapping, de-multiplexing and of the gene / cell count matrices generation using the Cell Ranger software v2 (10X Genomics).
Base calling, adaptor trimming, mapping, de-multiplexing and of the gene / cell count matrices generation using the DropSeq pipeline v1 (https://github.com/broadinstitute/Drop-seq/releases).
Cells with an UMI count of more than 4 times the sample mean or less than 20% of the sample median were filtered out, cells with a mitochondrial or ribosomal contribution to UMI count of more than 10% were also filtered out.
Genome_build: ENSEMBL Gallus gallus 5.0
Supplementary_files_format_and_content: Tab delimited text files. UMI count tables where cells are rows and genes are columns, additional meta-data columns

source_name: Developing hindlimb

extract_protocol:
Cells were dissociated using trypsin 0.25%. Single cells suspensions were fed into Chromium 10x or DropSeq systems
DropSeq
10x v2

tag: dissection

value: Digits 3 and 4

tag: protocol

value: DropSeq

tag: protocol notes

value: Three technical replicates


title: Array-D-PTU

value: 350 mg/L PTU (5 dpf, replicate 1)


title: Array-K-PTU

value: Wild-type AB


title: Array-H-PTU

value: control (8 dpf, replicate 2)

value: 350 mg/L PTU (8 dpf, replicate 1)


title: Array-J-PTU

value: control (8 dpf, replicate 1)

value: eye


title: Array-A-PTU

value: 350 mg/L PTU (5 dpf, replicate 2)


title: Array-P-TBBPA

value: control (5 pdf, replicate 2)


title: Mock 16 h

value: Chicken embryonic stem cells

value: Mock 16 h


title: FP9 16 h

value: FP9 16 h


title: Mock 6 h

value: Mock 6 h


title: Array-Q-TBBPA

value: control (5 dpf, replicate 2)

value: 200 ug/L TBBPA (5 dpf, replicate 1)


title: IFN 6 h

value: IFN 6 h


title: Array-C-PTU


title: Array-B-PTU


title: Array-I-PTU

value: control (8 pdf, replicate 1)


title: Viremic survivors_29

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

hyb_protocol: Following fragmentation, 5,5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips human ST 2.0 microarray (Affimetrix). GeneChips were washed and stained in the Affymetrix  Station.

scan_protocol: Not provided by the company.

data_processing: The normalization of the data was performed with R and the RMA method of the oligo Bioconductor package.

source_name: blood cells

label_protocol: Biotinylated cRNA were prepared with triple amplification from 1 ng total RNA using IVT expressArt Trinucleotide mRNA amplification Pico kit (AmpTec) and GeneChip WT PLUS kit (Affimetrix) mRNAaccording to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: leukocytes

tag: group

value: Viremic survivors


title: Viremic survivors_25

tag: tissue


title: Viremic survivors_32


title: Viremic survivors_31


title: Viremic survivors_27


title: Viremic survivors_33


title: Survivors in recovery phase_41

value: Survivors in recovery phase


title: Viremic survivors_38


title: Viremic survivors_30


title: Viremic survivors_42


title: Survivors in recovery phase_78


title: Viremic survivors_26


title: Viremic survivors_43


title: Survivors in recovery phase_34


title: Survivors in recovery phase_44


title: Viremic survivors_28


title: Survivors in recovery phase_49


title: Survivors in recovery phase_45


title: Survivors in recovery phase_47


title: Viremic survivors_35


title: Viremic survivors_76


title: Survivors in recovery phase_39


title: Survivors in recovery phase_46


title: Survivors in recovery phase_52


title: Survivors in recovery phase_48


title: Survivors in recovery phase_51


title: Survivors in recovery phase_40


title: Fatalities_24

value: Fatalities


title: Fatalities_8


title: Fatalities_23


title: Survivors in recovery phase_36


title: Fatalities_21


title: Fatalities_12


title: Fatalities_11


title: Fatalities_16


title: Fatalities_2


title: Fatalities_5


title: Fatalities_66


title: Fatalities_22


title: Fatalities_13


title: Healthy controls_80

value: Healthy controls


title: Healthy controls_55


title: Healthy controls_82


title: Fatalities_6


title: Fatalities_20


title: Fatalities_17


title: Fatalities_15


title: Fatalities_7


title: Fatalities_9


title: Healthy controls_57


title: Fatalities_19


title: Fatalities_71


title: Fatalities_69


title: Fatalities_70


title: Fatalities_4


title: Healthy controls_60


title: Healthy controls_54


title: patients_43_male_baseline_NASH_T2D

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

institute: Inserm

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Data were RMA-normalized using oligo/Bioconductor and corrected for batch effects using SVA/Bioconductor

source_name: Liver

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

extract_protocol: Extract-All extraction of total RNA follow by RNA clean up (+DNAse digstion) with Rneasy mini kit from Qiagen  were performed according to the manufacturer's instructions.

value: Liver

tag: patient group


title: Healthy controls_81


title: patients_42_male_baseline_NONASH_T2D


title: patients_41_female_baseline_NASH_NOT2D


title: patients_40_male_baseline_NONASH_NOT2D


title: patients_39_female_baseline_NASH_NOT2D


title: patients_37_female_baseline_NASH_T2D


title: Healthy controls_53


title: patients_31_female_baseline_NASH_NOT2D


title: patients_32_male_baseline_NONASH_NOT2D


title: patients_4_male_baseline_NASH_T2D


title: patients_10_female_baseline_NASH_NOT2D


title: patients_30_female_baseline_NONASH_T2D


title: patients_9_female_baseline_NONASH_NOT2D


title: patients_33_female_baseline_NASH_T2D


title: patients_35_male_baseline_NONASH_T2D


title: patients_22_female_baseline_NASH_NOT2D


title: patients_27_female_baseline_NASH_NOT2D


title: patients_36_female_baseline_NASH_T2D


title: patients_24_female_baseline_NONASH_T2D


title: patients_16_male_baseline_NONASH_NOT2D


title: patients_8_male_baseline_NASH_NOT2D


title: patients_28_male_baseline_NONASH_T2D


title: patients_20_male_baseline_NONASH_T2D


title: patients_25_female_baseline_NASH_T2D


title: patients_29_male_baseline_NONASH_NOT2D


title: patients_34_male_baseline_NASH_NOT2D


title: patients_19_male_baseline_NONASH_NOT2D


title: Pair-95-female-followup


title: Pair-65-male-followup


title: patients_2_female_baseline_NASH_NOT2D


title: Pair-10-male-followup


title: Pair-22-female-followup


title: Pair-68-male-followup


title: Pair-68-male-baseline


title: Pair-7-male-followup


title: Pair-37-female-followup


title: Pair-65-male-baseline


title: Pair-40-female-baseline


title: Pair-7-male-baseline


title: Pair-22-female-baseline


title: Pair-27-female-baseline


title: Pair-27-female-followup


title: Pair-95-female-baseline


title: patients_17_female_baseline_NONASH_NOT2D


title: Pair-3-male-baseline


title: Pair-3-male-followup


title: Pair-10-male-baseline


title: Pair-31-female-followup


title: Pair-34-male-followup


title: Pair-13-female-followup


title: Pair-16-female-followup


title: Pair-25-male-followup


title: Pair-48-female-followup


title: Pair-6-male-followup


title: Pair-5-female-followup


title: Pair-26-female-followup


title: Pair-46-female-followup


title: Pair-48-female-baseline


title: Pair-26-female-baseline


title: Pair-37-female-baseline


title: Pair-6-male-baseline


title: Pair-46-female-baseline


title: Pair-5-female-baseline


title: Pair-51-female-followup


title: Pair-32-female-followup


title: Pair-45-female-followup


title: Pair-25-male-baseline


title: Pair-91-female-followup


title: Pair-88-female-followup


title: Pair-16-female-baseline


title: Pair-93-female-followup


title: Pair-31-female-baseline


title: Pair-13-female-baseline


title: Pair-33-male-followup


title: Pair-85-male-followup


title: Pair-86-female-followup


title: Pair-60-male-followup


title: Pair-92-female-followup


title: Pair-34-male-baseline


title: Pair-61-female-followup


title: Pair-55-male-followup


title: Pair-43-female-followup


title: Pair-53-male-followup


title: Pair-41-male-followup


title: Pair-64-female-followup


title: Pair-67-male-followup


title: Pair-61-female-baseline


title: Pair-92-female-baseline


title: Pair-85-male-baseline


title: Pair-55-male-baseline


title: Pair-69-female-followup


title: Pair-88-female-baseline


title: Pair-86-female-baseline


title: Pair-51-female-baseline


title: Pair-45-female-baseline


title: Pair-93-female-baseline


title: Pair-39-female-followup


title: Pair-91-female-baseline


title: Pair-39-female-baseline


title: Pair-43-female-baseline


title: Pair-38-male-followup


title: Pair-64-female-baseline


title: Pair-32-female-baseline


title: Pair-33-male-baseline


title: Pair-60-male-baseline


title: Pair-53-male-baseline


title: Mus musculus genotype wt treatment cdt1 replicate wt_cdt1_25.cel

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: Mus musculus genotype wt treatment cdt1

hyb_protocol: cRNA was hybridized to Affymetric Mouse Gene 2.0 ST oligonucleotide arrays.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner generate raw intensity data.  Affymetrix .CEL files were processed using R/BioConductor packages for RMA-based quantification.

data_processing: Data extraction, QC, and RMA normalization were performed with BioConductor software. Probes were annotated using the Bioconductor GEOQuery package.

organism: Mus musculus

source_name: Caecum

label_protocol: Biotin-labeled cRNA was prepared from total RNA and then fragmented.

growth_protocol: Experiments were carried out using sex matched 8-12 week old C57BL6, ST2-/-, Rag2-/-, and Rag2-/-yc-/- mice.  C57BL/6 were purchased from Jackson Laboratory and ST2-/- mice91 were obtained from Dr. Andrew McKenzie (Laboratory of Molecular Biology, Cambridge University, Cambridge, United Kingdom). Rag2-/- and Rag2-/-yc-/- mice were purchased from Taconic Biosciences with an excluded flora.  All animals were housed under specific pathogen free conditions at the University of Virginia's animal facility and procedures were approved by the Institutional Animal Care and Use Committee at the University of Virginia (IACUC). Bedding exchange every two days between ST2-/- and C57BL6 mice, or Rag2-/- and Rag2-/-yc-/- mice, for a minimum of three weeks was conducted to equilibrate microbiota between strains. Mice were infected using a previously published murine model for CDI19,26,92. 3 days prior to infection, mice were given an antibiotic cocktail in drinking water consisting of 45 mg/L Vancomycin (Mylan), 35 mg/L Colistin (Sigma), 35 mg/L Gentamicin (Sigma), 215 mg/L Metronidazole (Hospira). Mice were then switched to regular drinking water and given a single IP injection (0.032 mg/g) of Clindamycin (Hospira) on Day 1. On Day 0, mice were orally gavaged with 1x108 CFU/ml of C. difficile. Mice were monitored twice daily over the course of infection and evaluated according to clinical scoring parameters. Scores were based on weight loss, coat condition, activity level, diarrhea, posture and eye condition for a cumulative clinical score between 1 and 20.  Mice were euthanized if severe illness developed based on a clinical score 14.

extract_protocol: R20291 and R20291_Cdtb RNA samples were processed by the Affymetrix Gene Chip(R) WT PLUS Reagent Kit and hybridized to the Affymetrix Mouse Gene 2.0 ST GeneChip(R).

treatment_protocol: Isogenic C. difficile strain R20291_CdtB was generated using the ClosTron system of insertional mutagenesis and inactivation CDTb was confirmed by Western blot by us and others19,20.  To prepare the C. difficile inoculum, strains were plated onto BHI agar from frozen stocks and incubated at 37C overnight in an anaerobic work station (Shel Labs). A single colony was inoculated into BHI medium and grown anaerobically overnight at 37C. The next day, cultures were spun for 1 minute at 6,000 X g and washed twice in anaerobic PBS and the optical density was measured.  The culture density was adjusted in anaerobic PBS to 1x108 CFU/mL and loaded into syringes.  Each mouse received 100 ?l (1x107 CFU) of inoculum by oral gavage. C. difficile burden was quantified from caecal contents at Day 2 of infection.  Briefly, caecal contents were resuspended by weight in anaerobic PBS.  Serial dilutions of caecal contents were plated on BHI Agar supplemented with 1% Sodium Taurocholate, 1 mg/mL D-cycloserine and 0.032 mg/mL cefoxitin (Sigma) and anaerobically incubated at 37C overnight followed by colony counts in triplicate.

value: wt

value: C. difficile toxin


title: Pair-67-male-baseline


title: Pair-40-female-followup


title: Pair-38-male-baseline


title: Mus musculus genotype wt treatment cdt1 replicate wt_cdt1_27.cel

description: Mus musculus genotype wt treatment cdt1


title: patients_23_male_baseline_NASH_T2D


title: Mus musculus genotype wt treatment cdt1 replicate wt_cdt1_26.cel

description: Mus musculus genotype wt treatment cdt1


title: 9GATCAGL007SAll.fq

city: Haifa

first: Avi

last: Titievsky

address: Abba Khoushy Ave 199

department: Department of Evolution

country: Israel

institute: University of Haifa

data_processing:
Trimmomatic
Bowtie2
RSEM
Genome_build: GRCM38:mm10
Supplementary_files_format_and_content: Expression table txt format

source_name: Angelman syndrome male

extract_protocol:
Hippocampi were immediately isolated, and the ventral third of the right hippocampus was snap frozen in liquid nitrogen. Tissue was lysed in lysis buffer using a probe sonicator. Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit, Cat No: 74804 (QIAGEN) according to the manufacturer’s instructions. Isolated RNA concentration and quality were determined by Qubit® quantitation assay using Qubit® 2.0 fluorometer (Invitrogen- life technologies, USA) and Agilent 4200 TapeStation System (Agilent Technologies, USA). Samples were prepared for Illumina sequencing using NEB’s Ultra RNA Library Prep Kit for Illumina (NEB#7530) (BioLabs Inc, MA, USA) according to the manufacturer protocol.
Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit, Cat No: 74804 (QIAGEN) according to the manufacturer’s instructions. Isolated RNA concentration and quality were determined by Qubit® quantitation assay using Qubit® 2.0 fluorometer (Invitrogen- life technologies, USA) and Agilent 4200 TapeStation System (Agilent Technologies, USA). Samples were prepared for Illumina sequencing using NEB’s Ultra RNA Library Prep Kit for Illumina (NEB#7530) (BioLabs Inc, MA, USA) according to the manufacturer protocol.  Libraries were loaded at 8 PM and were sequenced with a 2 X 100 bp PE run on Illumina HiSeq 2500 using a V3 flow cell.

value: ventral third of the right hippocampus

tag: age

value: 12-16 weeks old

tag: disease state

value: Angelman syndrome

tag: gender

value: male


title: Pair-41-male-baseline


title: 8ACTTGAL007SAll.fq

source_name: Wild type female

value: Control

value: female


title: Mus musculus genotype wt treatment cdt0 replicate wt_cdt0_32.cel

description: Mus musculus genotype wt treatment cdt0


title: Mus musculus genotype tlr2ko treatment cdt1 replicate tlr2ko_cdt1_44.cel


title: Mus musculus genotype wt treatment cdt1 replicate wt_cdt1_22.cel

description: Mus musculus genotype wt treatment cdt1


title: Mus musculus genotype wt treatment cdt0 replicate wt_cdt0_28.cel

description: Mus musculus genotype wt treatment cdt0


title: Mus musculus genotype tlr2ko treatment cdt1 replicate tlr2ko_cdt1_38.cel


title: Mus musculus genotype wt treatment cdt0 replicate wt_cdt0_33.cel

description: Mus musculus genotype wt treatment cdt0


title: Mus musculus genotype wt treatment cdt1 replicate wt_cdt1_24.cel

description: Mus musculus genotype wt treatment cdt1


title: 6GCCAATL007SAll.fq

source_name: Wild type male


title: 4TGACCAL007SAll.fq

source_name: Angelman syndrome female


title: 5ACAGTGL007SAll.fq


title: 7CAGATCL007SAll.fq


title: 3TTAGGCL007SAll.fq


title: Pair-69-female-baseline


title: Mus musculus genotype tlr2ko treatment cdt1 replicate tlr2ko_cdt1_39.cel


title: 2CGATGTL007SAll.fq


title: Mus musculus genotype tlr2ko treatment cdt0 replicate tlr2ko_cdt0_36.cel


title: Mus musculus genotype wt treatment cdt0 replicate wt_cdt0_31.cel

description: Mus musculus genotype wt treatment cdt0


title: Mus musculus genotype wt treatment cdt0 replicate wt_cdt0_29.cel

description: Mus musculus genotype wt treatment cdt0


title: Mus musculus genotype tlr2ko treatment cdt1 replicate tlr2ko_cdt1_43.cel


title: Mus musculus genotype tlr2ko treatment cdt0 replicate tlr2ko_cdt0_41.cel


title: 11GGCTACL007SAll.fq


title: 12CTTGTAL007SAll.fq


title: Mus musculus genotype tlr2ko treatment cdt1 replicate tlr2ko_cdt1_40.cel


title: 10TAGCTTL007SAll.fq


title: Mus musculus genotype wt treatment cdt0 replicate wt_cdt0_30.cel

description: Mus musculus genotype wt treatment cdt0


title: Mus musculus genotype tlr2ko treatment cdt0 replicate tlr2ko_cdt0_42.cel


title: Mus musculus genotype wt treatment cdt1 replicate wt_cdt1_23.cel

description: Mus musculus genotype wt treatment cdt1


title: Mus musculus genotype tlr2ko treatment cdt0 replicate tlr2ko_cdt0_35.cel


title: 1ATCACGL007SAll.fq


title: Mus musculus genotype tlr2ko treatment cdt0 replicate tlr2ko_cdt0_34.cel


title: Mus musculus genotype tlr2ko treatment cdt1 replicate tlr2ko_cdt1_37.cel


title: 789 Sf1-Cre; Sirt1loxP/loxP

city: irvine

first: Siwei

last: Chen

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

description:
CTTGTA
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls

data_processing:
Genes.FPKM.xls contains FPKM counts for all samples. SKE2_Crick_table.biocycle.xls contains statistical results from software BIO_CYCLE on FPKM counts of samples.
Genome_build: mm10
Supplementary_files_format_and_content: Genes.FPKM.xls ,SKE2_Crick_table.biocycle.xls

source_name: Gastrocnemius skeletal muscle

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Library construction was perfomed according to the Illumina TruSeq mRNA stranded protocol.
Sample were multiplexed into 4 libraries of 8 samples for both genotypes, and sequenced on an Illumina HiSeq 2500 instrument during two single-end 100 cycles sequencing runs. The resulting sequencing data for each library were post-processed and demultiplexed to produce FastQ files using Illumina software CASAVA. Reads failing Illumina's standard
quality tests were not included in the FastQ files. The quality of the remaining sequences was further assessed using the PHRED quality scores produced in real time during the base-calling

value: mixed genetic background

value: 10-week old

tag: time of harvest

value: Sf1-Cre; Sirt1loxP/loxP


title: 823 Control

description:
TGACCA
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls

tag: genotype/variation


title: 827 Sf1-Cre; Sirt1loxP/loxP

description:
CGTACG
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 799 Sf1-Cre; Sirt1loxP/loxP

description:
TAGCTT
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 792 Sf1-Cre; Sirt1loxP/loxP

description:
GATCAG
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 788 Sf1-Cre; Sirt1loxP/loxP

description:
GGCTAC
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 857 Control

description:
ACTTGA
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 852 Control

description:
CAGATC
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 800 Control

description:
ATCACG
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 802 Control

description:
CGATGT
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 826 Sf1-Cre; Sirt1loxP/loxP

description:
CCGTCC
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 856 Control


title: 816 Control


title: 795 Sf1-Cre; Sirt1loxP/loxP


title: 820 Control


title: 817 Sf1-Cre; Sirt1loxP/loxP

description:
GTGAAA
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 815 Sf1-Cre; Sirt1loxP/loxP


title: 854 Control

description:
GCCAAT
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 813 Control

description:
TTAGGC
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 828 Sf1-Cre; Sirt1loxP/loxP

description:
ATTCCT
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 821 Sf1-Cre; Sirt1loxP/loxP


title: 814 Sf1-Cre; Sirt1loxP/loxP


title: 794 Sf1-Cre; Sirt1loxP/loxP


title: 791 Sf1-Cre; Sirt1loxP/loxP


title: 801 Control

description:
ACAGTG
Genes.FPKM.xls
SKE2_Crick_table.biocycle.xls


title: 782 Sf1-Cre; Sirt1loxP/loxP


title: 798 Sf1-Cre; Sirt1loxP/loxP


title: 822 Control


title: 838 Control


title: 832 Control


title: 831 Control


title: wt naïve lung-2

city: Yokohama

first: Shin-ichiro

last: Fujii

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description: lung NKT cells from WT naive mice

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Supplementary_files_format_and_content: cuffdif_out: differential gene detection
Supplementary_files_format_and_content: genes.fpkm: abundance measurements
Genome_build: mm9

source_name: lung NKT cells

extract_protocol:
RNA was extracted using Trizol reagent. NEBNext Ultra RNA Library Prep kit (Cat# E7530L) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NEB protocols

value: lung

tag: cell type


title: EOMES cKO naïve lung-1

description: lung NKT cells from Eomes cKO naive mice


title: wt DCG d7 lung-3

description: lung NKT cells from WT DCG immunized mice


title: EOMES cKO naïve lung-2


title: EOMES cKO DCG d7 lung-3

description: lung NKT cells from EomescKO DCG immunized mice


title: EOMES cKO DCG d7 lung-2


title: wt naïve lung-3

description: lung NKT cells from WT naive mice


title: EOMES cKO thymus-3

description: thymic NKT cells from Eomes cKO naive mouse

source_name: thymic NKT cells

value: thymus


title: wt DCG d7 lung-2


title: EOMES cKO DCG d7 lung-1


title: wt naïve lung-1

description: lung NKT cells from WT naive mice


title: EOMES cKO thymus-2


title: wt DCG d7 lung-1


title: EOMES cKO naïve lung-3


title: EOMES cKO thymus-4


title: 835 Control


title: heatshock_total_input_2

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zurich

description: heatshock_total_2.macs2_peaks.narrowPeak

data_processing:
Basecalls performed using CASAVA version 1.8.2
STAR version 2.6.1 alignment
Peaks identified using MACS2 version 2.1.1 with effective genome size scaled to the transcriptome (1e8)
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak files (bed)

source_name: OCI-Ly1 diffuse B-cell lymphoma cells

growth_protocol: Early passage OCI-Ly1 diffuse large B-cell lymphoma cells were grown in Iscove’s modified Eagle Medium (IMDM) with 10% fetal bovine serum (FBS)

extract_protocol:
TRIzol
Illumina, 1 x 42

tag: cell line

value: diffuse B-cell lymphoma cells

value: 43 C for 1 hr, recovery at 37 C for 1 hr

tag: library strategy

value: RNA-seq

tag: antibody


title: heatshock_total_IP_3

description: heatshock_total_3.macs2_peaks.narrowPeak

data_processing:
Library strategy: MeRIP-seq
Basecalls performed using CASAVA version 1.8.2
STAR version 2.6.1 alignment
Peaks identified using MACS2 version 2.1.1 with effective genome size scaled to the transcriptome (1e8)
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak files (bed)

value: MeRIP-seq

value: SYSY anti-m6A (202 003)


title: untreated_total_input_2

description: untreated_total_2.macs2_peaks.narrowPeak


title: heatshock_total_IP_2


title: untreated_total_IP_1

description: untreated_total_1.macs2_peaks.narrowPeak


title: heatshock_total_IP_1

description: heatshock_total_1.macs2_peaks.narrowPeak


title: untreated_total_IP_2


title: untreated_total_IP_3

description: untreated_total_3.macs2_peaks.narrowPeak


title: heatshock_total_input_3


title: wt thumus-3

description: thymic NKT cells from WT naive mouse

tag: strain


title: untreated_total_input_1

tag: treatment


title: untreated_total_input_3


title: heatshock_total_input_1


title: mockL_16h_3_IP

description:
processed data file:
mockL_16h_3.macs2_peaks.narrowPeak

data_processing:
Library strategy: MeRIP-seq
Basecalls performed using CASAVA version 1.8.2
STAR version 2.5.0 alignment to combined hg38 and viral genome reference (using the appropriate virus genome depending on sample)
Peaks identified using MACS2 version 2.1.1 with effective genome size scaled to the transcriptome (1e8)
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak files (bed)

source_name: Huh7 liver cell line

growth_protocol: Huh7 cells were grown in DMEM (Mediatech) supplemented with 10% fetal bovine serum (HyClone), 25 mM HEPES, and 1X non-essential amino acids (Thermo Fisher Scientific) and seeded in 15 cm plates prior to infection

extract_protocol:
TRIzol
Illumina Tru-seq PolyA RNA,1 x 50

tag: viral strain

tag: time point

value: 16 hours

value: uninfected

value: NEB anti-m6A antibody


title: wt thumus-1

description: thymic NKT cells from WT naive mouse


title: mockL_16h_2_IP

description:
processed data file:
mockL_16h_2.macs2_peaks.narrowPeak


title: mockL_16h_3_Input

data_processing:
Basecalls performed using CASAVA version 1.8.2
STAR version 2.5.0 alignment to combined hg38 and viral genome reference (using the appropriate virus genome depending on sample)
Peaks identified using MACS2 version 2.1.1 with effective genome size scaled to the transcriptome (1e8)
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak files (bed)


title: mockL_16h_1_IP

description:
processed data file:
mockL_16h_1.macs2_peaks.narrowPeak


title: mockL_16h_2_Input


title: P12_BRG1_ATACseq_cKO1

city: Chapel hill

first: Terry

last: Magnuson

state: NC

address: 120 Mason Farm Road, Genetics Medicine Bldg.,

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Alignment to the mm9 genome was performed using bowtie1.
BAM files were generated using samtools
BAM files were converted to bigWig format  using, Deeptools (version 2.5.0) bamCoverage  -bs 1  -bl mm9-blacklist.bed  --normalizeto1x  --scaleFactors  --extend reads =150
Replicates were merged using UCSC tools  bigWigMerge
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of ATAC-seq tracks

source_name: Spermatogenic cells from P12 Brg1 cKO testes

extract_protocol:
Spermatogenic cells were isolated from P12 and P18 testes which were digested with collagnease and trypsin followed by filteration through a 40 micron sieve.  Cells were prepared for ATAC-seq as described (Buenrostro et al 2013)
ATAC-seq libraries were created using protocol from Buenrostro et al 2013, and processed using Nextera adapter sequences for Illumina sequencing

value: Mixed background

value: testes

tag: genotype

value: spermatogenic cells


title: P12_BRG1_ATACseq_WT2

source_name: Spermatogenic cells from P12 Brg1 WT testes


title: P18_BRG1_ATACseq_HET

source_name: Spermatogenic cells from P18 Brg1 HET testes


title: P18_BRG1_ATACseq_WT

source_name: Spermatogenic cells from P18 Brg1 WT testes


title: P12_BRG1_ATACseq_cKO2


title: mockH_24h_3_Input

description:
processed data file:
mockH_24h_3.macs2_peaks.narrowPeak

value: 24 hours


title: mockL_16h_1_Input


title: Spinal motor neuron GFP neg, replicate 6 [SC6_neg]

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

data_processing:
Base-calling using Illumina Cassava 1.7
Alignment to the mouse genome (mm10) performed using HISAT2 version 2.0.3 using the main Galaxy server
Raw read counts were extracted using the GenomicAlignments package in R, with the function SummarizeOverlaps, mode set to "Union"
Differential gene expression analysis was performed on the read counts using DESeq2 version 1.12.4. Only genes with reads in 4 samples or more were considered in the analysis.
Normalized abundance measurements (RPKMs) were generated manually, using transcript lengths from the the Ensembl GRCm38 (version 87) annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: One data file is added providing normalized abundance measurements (RPKM) organized as a matrix for the samples (tab-delimited txt).

source_name: Spinal motor neuron GFP neg

growth_protocol: mESCs were cultured and patterned towards OMN or SC motor neurons with appropriate morphogens as embriod bodies for 5 days. GFP positive and negative fractions were purified using FACS and collected as bulk for RNAseq.

extract_protocol:
Cells were lysed in the presence of RNAse inhibitor and immediately frozen down. Library preparation occurred in the lysis buffer directly, without RNA-extraction.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5-based tagementation.

treatment_protocol: Specification of mESCs into spinal motor neurons was conducted by exposing embryo bodies to the Smoothened Agonist SAG (500 nM) and retinoic acid (RA, 100 nM)  while oculomotor neurons were patterned by SAG (250 nM) and Fgf8 (100 ng/ml) both for 5 days.

tag: source cell type

value: Stem cell-derived motor neuron

tag: disease status

value: Control

tag: cell preparation

value: bulk culture preparation, FACS purified


title: P12_BRG1_ATACseq_WT1

tag: age

tag: tissue


title: mockH_24h_3_IP


title: Spinal motor neuron GFP pos, replicate 6 [SC6]

source_name: Spinal motor neuron GFP pos


title: mockH_24h_2_Input

description:
processed data file:
mockH_24h_2.macs2_peaks.narrowPeak


title: mockH_24h_1_Input

description:
processed data file:
mockH_24h_1.macs2_peaks.narrowPeak


title: Spinal motor neuron GFP neg, replicate 5 [SC5_neg]


title: mockL_48h_3_IP

description:
processed data file:
mockL_48h_3.macs2_peaks.narrowPeak

value: 48 hours


title: mockH_24h_2_IP


title: mockH_24h_1_IP


title: Spinal motor neuron GFP pos, replicate 5 [SC5]


title: Spinal motor neuron GFP neg, replicate 3 [SC3_neg]


title: Spinal motor neuron GFP pos, replicate 4 [SC4]


title: mockL_48h_3_Input


title: wt thumus-2

description: thymic NKT cells from WT naive mouse

value: thymus


title: Spinal motor neuron GFP pos, replicate 3 [SC3]


title: mockL_48h_2_Input

description:
processed data file:
mockL_48h_2.macs2_peaks.narrowPeak


title: mockL_48h_2_IP


title: Oculomotor neuron GFP pos, replicate 6 [OMN6]

source_name: Oculomotor neuron GFP pos


title: Oculomotor neuron GFP neg, replicate 5 [OMN5_neg]

source_name: Oculomotor neuron GFP neg


title: Oculomotor neuron GFP neg, replicate 6 [OMN6_neg]


title: mockL_48h_1_IP

description:
processed data file:
mockL_48h_1.macs2_peaks.narrowPeak


title: Oculomotor neuron GFP pos, replicate 4 [OMN4]


title: mockH_48h_3_IP

description:
processed data file:
mockH_48h_3.macs2_peaks.narrowPeak


title: mockL_48h_1_Input


title: Oculomotor neuron GFP pos, replicate 5 [OMN5]


title: mockH_48h_2_IP

description:
processed data file:
mockH_48h_2.macs2_peaks.narrowPeak


title: Oculomotor neuron GFP neg, replicate 4 [OMN4_neg]


title: mockH_48h_2_Input


title: mockH_48h_1_IP

description:
processed data file:
mockH_48h_1.macs2_peaks.narrowPeak


title: mockH_48h_3_Input


title: zikv_48h_3_Input

description:
processed data file:
zikv_48h_3.macs2_peaks.narrowPeak

value: ZIKV-PR2015 (PRVABC59)

value: infected


title: zikv_48h_2_IP

description:
processed data file:
zikv_48h_2.macs2_peaks.narrowPeak


title: zikv_48h_1_IP

description:
processed data file:
zikv_48h_1.macs2_peaks.narrowPeak


title: mockH_48h_1_Input

value: RNA-seq


title: zikv_48h_3_IP

value: MeRIP-seq


title: wnv_48h_3_IP

description:
processed data file:
wnv_48h_3.macs2_peaks.narrowPeak


title: zikv_48h_1_Input


title: E14_GFP+_RNA-seq

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N. Broadway Avenue

department: Department of Neuroscience

institute: Johns Hopkins University School of Medicine

description:
RNA RPCs
E14_P2_PlusMinus_RNA-Seq.xlsx
H9C83ADXX_2_GCCAAT_1
H9C83ADXX_2_GCCAAT_2
HB7KFADXX_2_ACAGTG_1
HB7KFADXX_2_ACAGTG_2

data_processing:
Bowtie2 alignment ont the mm9 genome assembly
RNA-Seq reads were aligned to the mouse transcriptome (mm9 by UCSC) by Tophat2 , and differentially expressed genes (DEGs) were identified by Cuffdiffs , imposing a cutoff q-val =  0.05 for pairwise comparison.  Bowtie2 was adopted for ChIP-Seq ChIP-Seq and ATAC-Seq reads alignment on the mouse genome (mm9)
Uniquely mappable reads from  ChIP-Seq were retained for peak calling by MACS  (band width = 300, mfold =5, 50, d = 200, max tags per position =1, min FDR q-val cutoff  = 1E-02,  lambda = 1000-10000 bp).    ATAC-Seq regions were called on MACS2 (20) (--broad).
Genome_build: mm9;  liftover to mm10 for  visual display of custom tracks

source_name: retinal cells

growth_protocol: Developmental time course analysis

extract_protocol:
Open chromatin extraction, tagmentation and profiling (ATAC-Seq) performed based on Buenrostro et al. (2013); RNA-Seq extraction performed with Qiagen RNAeasy Mini kit; chromatin extraction, crosslinking, shearing and TF / histone- DNA-complexes were isolated with antibodies (ChIP-Seq) based on (Shang et al. 2000)
ChIP-Seq; RNA-Seq; ATAC-Seq; Libraries prepared  according to the Manufacturer's protocols: TruSeq Nano DNA Library Prep Kit, TruSeq total RNA Sample preparation kit and Nextera DNA sample preparation kit, Illumina® respectively.

treatment_protocol: Lhx2 cKO at E14 (Chx10-Cre-GFP; Lhx2 fl/fl) and  P2 (P0 electroporated pCAG-Cre-GFP construct; Lhx2 fl/fl)

value: retinal progenitor cells (RPCs)

tag: developmental time point

value: post-natal day 2


title: P2_cKO_RNA-seq

description:
RNA Lhx2 cKO
RNA-seq_E14P2_WTKO.xlsx
HCKKMBCXX_1_GCCAAT_1
HCKKMBCXX_1_GCCAAT_2
HCKKMBCXX_1_CTTGTA_1
HCKKMBCXX_1_CTTGTA_2


title: zikv_48h_2_Input


title: E14_cKO_RNA-seq

description:
RNA Lhx2 cKO
RNA-seq_E14P2_WTKO.xlsx
H2GNWBCXX_1_GCCAAT_1
H2GNWBCXX_1_GCCAAT_2
H2GNWBCXX_1_CTTGTA_1
H2GNWBCXX_1_CTTGTA_2

value: embryonic day 14


title: P2_GFP+_RNA-seq

description:
RNA RPCs
E14_P2_PlusMinus_RNA-Seq.xlsx
C14BUACXX_7_ACTTGA_1
C14BUACXX_7_ACTTGA_2
C14BUACXX_8_TAGCTT_1
C14BUACXX_8_TAGCTT_2


title: E14_Wild_Type_RNA-seq

description:
RNA control
RNA-seq_E14P2_WTKO.xlsx
HHL3NBCXX_1_GCCAAT_1
HHL3NBCXX_1_GCCAAT_2
HHL3NBCXX_2_ACAGTG_1
HHL3NBCXX_2_ACAGTG_2


title: P2_cKO_ATAC-seq

description:
open chromatin Lhx2 cKO
H7MJ2BCXX_1_TAAGGCGA_1
H7MJ2BCXX_1_TAAGGCGA_2
H7MJ2BCXX_1_CGTACTAG_1
H7MJ2BCXX_1_CGTACTAG_2


title: P2_Wild_Type_RNA-seq

description:
RNA control
RNA-seq_E14P2_WTKO.xlsx
HCKKMBCXX_2_ACAGTG_1
HCKKMBCXX_2_ACAGTG_2
HCKKMBCXX_2_GTGAAA_1
HCKKMBCXX_2_GTGAAA_2


title: wnv_48h_2_Input

description:
processed data file:
wnv_48h_2.macs2_peaks.narrowPeak


title: wnv_48h_2_IP

value: NEB anti-m6A antibody


title: P2_GFP+_ATAC-seq

description:
open chromatin RPCs
ATAC-Seq_Diff_OCRs.xlsx
HCCGGADXX_1_CGTACTAG_1
HCCGGADXX_1_CGTACTAG_2
HCCGGADXX_1_TAAGGCGA_1
HCCGGADXX_1_TAAGGCGA_2


title: E14_GFP+_ATAC-seq

description:
open chromatin RPCs
ATAC-Seq_Diff_OCRs.xlsx
H2YTFBCXX_2_TAAGGCGA_1
H2YTFBCXX_2_TAAGGCGA_2
H53N5BCXX_2_TAAGGCGA_1
H53N5BCXX_2_TAAGGCGA_2


title: wnv_48h_3_Input


title: P2_Wild_Type_ATAC-seq

description:
open chromatin control
H7MJ2BCXX_2_TAGGCATG_1
H7MJ2BCXX_2_TAGGCATG_2
H7MJ2BCXX_2_AGGCAGAA_1
H7MJ2BCXX_2_AGGCAGAA_2


title: E14_cKO_ATAC-seq

description:
open chromatin Lhx2 cKO
H3TG2BCXX_2_CGTACTAG_1
H3TG2BCXX_2_CGTACTAG_2
H3TG2BCXX_2_TAAGGCGA_1
H3TG2BCXX_2_TAAGGCGA_2


title: wnv_48h_1_IP

description:
processed data file:
wnv_48h_1.macs2_peaks.narrowPeak


title: hcv_48h_3_Input

description:
processed data file:
hcv_48h_3.macs2_peaks.narrowPeak

value: HCV genotype 2A JFH-1 (culture adapted)


title: hcv_48h_2_IP

description:
processed data file:
hcv_48h_2.macs2_peaks.narrowPeak


title: hcv_48h_1_IP

description:
processed data file:
hcv_48h_1.macs2_peaks.narrowPeak


title: hcv_48h_2_Input


title: denv_48h_2_IP

description:
processed data file:
denv_48h_2.macs2_peaks.narrowPeak


title: denv_48h_3_IP

description:
processed data file:
denv_48h_3.macs2_peaks.narrowPeak


title: hcv_48h_3_IP


title: denv_48h_1_IP

description:
processed data file:
denv_48h_1.macs2_peaks.narrowPeak


title: denv_48h_2_Input


title: wnv_48h_1_Input


title: denv_48h_1_Input


title: denv_48h_3_Input


title: E14_Wild_Type_ATAC-seq

description:
open chromatin control
e14wt_703_AGGCAGAA_L002_R1_001
e14wt_703_AGGCAGAA_L002_R2_001
e14wt_705_GGACTCCT_L002_R1_001
e14wt_705_GGACTCCT_L002_R2_001


title: hcv_48h_1_Input


title: disp_rep2

city: Istanbul

first: Tugba

last: Bagci-Onder

state: Sariyer

address: Koc University School of Medicine

department: School of Medicine

country: Turkey

institute: Koc University

data_processing:
a soft adapter trimming was applied to low quality ends of all samples with using cutadapt with - -quality-cutoff=5. The trimmed fastqs were aligned to human genome GRCh37.75 using TopHat2 with default parameters only adding --library-type=fr-unstranded --num-threads=8 –no-mixed –no-coverage-search. Tophat-recondition is used to restore correct and unmapped reads with default parameters. Samtools is used to merge the two BAM files.
Raw read counts are generated using feautureCounts with -s 0 parameter.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: Tab delimeted text files with raw counts for all samples.

source_name: GBM cells

growth_protocol: U373 cells were grown in 10 cm tissue culture plates with DMEM supplemented with 10% FBS and 1% pen/Strep up to 80% confluency. Cells were counted and spheroids were generated using 20.000 cells/20uL droplets for 3 days. Spheroids were collected and washed with 1x dPBS, transferred to 6 well-tissue culture plates as 60 spheroids/well. Spheroids were allowed to disperse for 24 hours. Cells remained in the core and cells dispersed out of the core were seperately collected.

extract_protocol:
High quality total RNA was extracted from samples using Nucleospin RNA kit of Macherey-Nagel and eluted in RNAse free water.
RNA-Seq library preparations were done using established Illumina methods for mRNA-Seq (Part #RS-  122-2001). Briefly, poly A+ RNA was purified from 100 ng of total RNA with oligo-dT beads. Purified  mRNA was fragmented with divalent cations at elevated temperature, to ~200bp. First strand cDNA  synthesis was performed with random hexamer priming and SuperScript II Reverse transcriptase  (Invitrogen, part # 18064-014). Second strand cDNA synthesis was performed using RNAseH and DNA  PolI. Following dscDNA synthesis, the double stranded products are end repaired, followed by addition of  a single ‘A’ base and then ligation of the Illumina TruSeq adaptors. The resulting product was amplified  with 15 cycles of PCR. Each library was made with a unique Index sequence and libraries are pooled at the  desired plexity. The pools were clustered at 6.5pM on a single end read flow cell and sequenced for 50  cycles on an Illumina HiSeq 2500. Primary processing of sequencing images was done using Illumina’s  Real Time Analysis software (RTA) as suggested by the Illumina. CASAVA 1.8.2 software was then used  to demultiplex samples and generate raw reads and respective quality scores. Illumina’s CASAVA 1.8.2  software was used to perform image capture, base calling and demultiplexing.

tag: passages

tag: cell population

value: Dispersive

value: wild type


title: core_rep2


title: disp_rep1

value: Core


title: NOS2ko_7h_rep1

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

institute: Heidelberg University Hospital

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix mouse genome MOE430A Array containing 22,690 gene entries with the GeneChip Fluidics Station 450.

scan_protocol: All microarrays were scanned with the GeneChip® Scanner 3000.

data_processing: Affymetrix GeneChip 5.0 software was used for data analysis according to Affymetrix protocols. Microarray data processing was performed in the R environment. Bioconductor package affy was used for data input, background correction, normalization and calculation of expression values. Data sets were annotated with official gene symbols originating from package moe430a.db using annotate. Resulting gene sets were annotated using in-house scripts and technical information from Affymetrix.

source_name: Pulmonary tissue, 7 hours after LPS treatment

label_protocol: standard Affymetrix protocol

growth_protocol: Male NOS2-/- mice and their wild-type controls (C57BL/6J) were purchased from The Jackson Laboratory (Bar Harbor, Maine). The body weight ranged between 21 and 27 g.

extract_protocol: For microarray analysis, lungs were harvested from wild-type mice after challenge with either saline (N=4, 22h) or LPS (N=3, 7h and 22h respectively) or from NOS2-/- mice after saline (N=1, 22h) or LPS challenge (N=3, 7h and 22h respectively).

treatment_protocol: Mice were challenged with intravenous administration of either normal saline (0.1 ml/10 g body weight) or lipopolysaccharide (LPS, Escherichia coli O111:B4, Sigma, St Louis, MO; 20 mg/kg, dissolved in normal saline 0.1 ml/10 g body weight).

value: LPS, 7h


title: LPS_22h_rep2

source_name: Pulmonary tissue, 22 hours after LPS treatment

value: LPS, 22h


title: LPS_7h_rep3


title: NOS2ko_22h_rep2


title: LPS_22h_rep3


title: NOS2ko_control_22h_rep1

source_name: Pulmonary tissue, 22 hours after saline treatment

value: Saline control, 22h


title: LPS_7h_rep1


title: LPS_22h_rep1


title: LPS_control_22h_rep4


title: NOS2ko_7h_rep3


title: NOS2ko_22h_rep3


title: NOS2ko_22h_rep1


title: LPS_7h_rep2


title: LPS_control_22h_rep2


title: LPS_control_22h_rep3


title: Oculomotor neuron control rep18 [OMN_Ctrl_18]

description: Run00328_L1_1_150917_SN893_0328_BC7Y41ACXX_TAAGGCGA-GTAAGGAG_N701+N505

data_processing:
Base-calling using Illumina Cassava 1.7
Alignment to the human genome (hg38, gencode V29) performed using STAR version 2.5.3 with parameter outSAMstrandField set to intronMotif.
Raw read counts were extracted using rpkmforgenes.py, using gencode V29 gtf file as annotation, with flag -rmnameoverlap
Differential gene expression analysis was performed on the read counts using DESeq version 1.16.1. Only genes with reads in 2 samples or more were considered in the analysis.
Genome_build: hg38, Gencode V29
Supplementary_files_format_and_content: One processed data file is added providing raw read counts organized as a matrix for all samples (excel).

source_name: Oculomotor neuron control

extract_protocol:
Lysis buffer is directly added to the cells after laser capture. No RNA extraction is conducted. The cell lysate is direcly used for library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.

value: Oculomotor neurons

tag: case number (refer to table in paper)


title: Oculomotor neuron control rep19 [OMN_Ctrl_19]

description: Run00328_L1_1_150917_SN893_0328_BC7Y41ACXX_CGTACTAG-TATCCTCT_N702+N503


title: Onuf's nucleus rep6 [Onuf_Ctrl_6]

source_name: Onuf's nucleus

value: motor neurons of Onuf's nucleus in the sacral spinal cord


title: Onuf's nucleus rep4 [Onuf_Ctrl_4]


title: Oculomotor neuron control rep20 [OMN_Ctrl_20]

description: Run00328_L1_1_150917_SN893_0328_BC7Y41ACXX_AGGCAGAA-TATCCTCT_N703+N503


title: Onuf's nucleus rep3 [Onuf_Ctrl_3]


title: Oculomotor neuron control rep17 [OMN_Ctrl_17]

description: Run00322_L4_1_150813_SN893_0322_AC7ELWACXX_GTAGAGGA-GTAAGGAG_N712+N505


title: NOS2ko_7h_rep2


title: Onuf's nucleus rep2 [Onuf_Ctrl_2]


title: Oculomotor neuron control rep16 [OMN_Ctrl_16]

description: Run00322_L4_1_150813_SN893_0322_AC7ELWACXX_AGGCAGAA-ACTGCATA_N703+N506


title: LPS_control_22h_rep1


title: Onuf's nucleus rep7 [Onuf_Ctrl_7]


title: Onuf's nucleus rep1 [Onuf_Ctrl_1]


title: Onuf's nucleus rep5 [Onuf_Ctrl_5]


title: Oculomotor neuron control rep14 [OMN_Ctrl_14]


title: Oculomotor neuron control rep10 [OMN_Ctrl_10]


title: Oculomotor neuron control rep4 [OMN_Ctrl_4]

description: Run00340_L8_1_151113_SN893_0340_AC884PACXX_CGTACTAG-TATCCTCT_N702+N503


title: Oculomotor neuron control rep11 [OMN_Ctrl_11]


title: Oculomotor neuron control rep9 [OMN_Ctrl_9]


title: Oculomotor neuron control rep12 [OMN_Ctrl_12]

description: Run00298_L7_1_150320_SN893_0298_BC724GACXX_TAAGGCGA-ACTGCATA_N701+N506


title: Spinal motor neuron control rep13 [SC_Ctrl_12]

description: Run00329_L2_1_150924_SN893_0329_AC7Y9RACXX_AGGCAGAA-CTCTCTAT_N703+N502

source_name: Spinal motor neuron control

value: lumbar/cervical spinal cord motor neurons


title: Spinal motor neuron control rep12 [SC_Ctrl_11]

description: Run00322_L4_1_150813_SN893_0322_AC7ELWACXX_CGAGGCTG-ACTGCATA_N710+N506


title: Oculomotor neuron control rep5 [OMN_Ctrl_5]

description: Run00340_L8_1_151113_SN893_0340_AC884PACXX_CGTACTAG-AGAGTAGA_N702+N504


title: Oculomotor neuron control rep6 [OMN_Ctrl_6]

description: Run00346_L8_1_151210_SN893_0346_BC880YACXX_CGTACTAG-CTCTCTAT_N702+N502


title: KLF4_KO_CLONE_6_BFP-T2AhKLF4-overexpressing-vector_10ngDOX_1

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description: mRNA

data_processing:
Basecalls performed using CASAVA.
RNA-Seq reads were mapped to hg19 using STAR guided by GTF.
Calculating insert size and standard deviation performed using Picard tools.
RNA-Seq read counting performed using HT-seq.
Normalization and differential expression analyses performed using DEseq2.
BAM to bedgraph performed using bedtools.
bedgraph to bigwig performed using bedGraphToBigWig v4.
Statistics and plotting performed in R v3.3.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_RPM.bw: BigWig (coverage for mapped reads).

source_name: Human prostate cancer cell line (PC3)

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen, CA, USA).
RNA-Seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA, USA).

treatment_protocol: Uninfected PC3 KLF4 wild-type cells and uninfected PC3 KLF4 null cells were grown for 48 hours and collected for RNA extraction. Another cohort of PC3 KLF4 null cells was infected with lentiviruses expressing a DOX inducible KLF4 expression construct (BFP-T2A-hKLF4) or the control empty vector (BFP-T2A). After 48 hours, DOX (10 ng/ml) was added to the culture medium to induce KLF4 expression. Control and KLF4-overexpressing cells were collected for RNA extraction after a 48-hour incubation with DOX.

tag: cell line

tag: cell type

value: prostate cancer cell line

tag: genotype/variation

value: KLF4 null

value: KLF4 overexpression


title: Spinal motor neuron control rep11 [SC_Ctrl_10]

description: Run00322_L4_1_150813_SN893_0322_AC7ELWACXX_CAGAGAGG-CTCTCTAT_N708+N502


title: Oculomotor neuron control rep1 [OMN_Ctrl_1]

description: Run00329_L2_1_150924_SN893_0329_AC7Y9RACXX_GGACTCCT-TATCCTCT_N705+N503


title: Spinal motor neuron control rep10 [SC_Ctrl_9]

description: Run00303_L6_1_150416_SN893_0303_AC725RACXX_CGTACTAG-TATCCTCT_N702+N503


title: Oculomotor neuron control rep13 [OMN_Ctrl_13]


title: Oculomotor neuron control rep7 [OMN_Ctrl_7]


title: Oculomotor neuron control rep3 [OMN_Ctrl_3]

description: Run00332_L1_1_151009_SN893_0332_AC88EVACXX_TAGGCATG-TATCCTCT_N706+N503


title: KLF4_KO_CLONE_6_non-infected_2

description: mRNA


title: Spinal motor neuron control rep9 [SC_Ctrl_8]

description: Run00303_L6_1_150416_SN893_0303_AC725RACXX_CGTACTAG-CTCTCTAT_N702+N502


title: KLF4_KO_CLONE_6_non-infected_1

description: mRNA


title: Oculomotor neuron control rep2 [OMN_Ctrl_2]

description: Run00332_L1_1_151009_SN893_0332_AC88EVACXX_GGACTCCT-ACTGCATA_N705+N506


title: KLF4_KO_CLONE_6_BFP-T2AhKLF4-overexpressing-vector_10ngDOX_2

description: mRNA


title: Oculomotor neuron control rep8 [OMN_Ctrl_8]


title: Oculomotor neuron control rep15 [OMN_Ctrl_15]

description: Run00322_L4_1_150813_SN893_0322_AC7ELWACXX_TAAGGCGA-CTCTCTAT_N701+N502


title: KLF4_WT_CLONE_9_non-infected_2

description: mRNA

value: KLF4 wild-type


title: KLF4_KO_CLONE_6_BFP-T2A-control-vector_10ngDOX_1

description: mRNA

value: vector control expression


title: Spinal motor neuron control rep8 [SC_Ctrl_7]

description: Run00330_L3_1_151001_SN893_0330_BC7Y36ACXX_TAAGGCGA-GTAAGGAG_N701+N505


title: KLF4_KO_CLONE_6_BFP-T2A-control-vector_10ngDOX_2

description: mRNA


title: Spinal motor neuron control rep7 [SC_Ctrl_6]

description: Run00298_L7_1_150320_SN893_0298_BC724GACXX_TAAGGCGA-AGAGTAGA_N701+N504


title: KLF4_WT_CLONE_9_non-infected_1

description: mRNA


title: Spinal motor neuron control rep6 [SC_Ctrl_5]

description: Run00329_L2_1_150924_SN893_0329_AC7Y9RACXX_CGTACTAG-GTAAGGAG_N702+N505


title: Spinal motor neuron control rep5 [SC_Ctrl_4]

description: Run00329_L2_1_150924_SN893_0329_AC7Y9RACXX_TAAGGCGA-ACTGCATA_N701+N506


title: Spinal motor neuron control rep4 [SC_Ctrl_3]

description: Run00330_L3_1_151001_SN893_0330_BC7Y36ACXX_TAAGGCGA-AGAGTAGA_N701+N504


title: Spinal motor neuron control rep1 [SC_Ctrl_1]

description: Run00329_L2_1_150924_SN893_0329_AC7Y9RACXX_TCCTGAGC-AGAGTAGA_N704+N504


title: Spinal motor neuron control rep2 [SC_Ctrl_2]

description: Run00330_L3_1_151001_SN893_0330_BC7Y36ACXX_TAAGGCGA-TATCCTCT_N701+N503


title: S7_LAD_HHST_2329

city: Boston

first: Alice

middle: H

last: Lichtenstein

state: MA

address: 711 Washington St

department: Jean Mayer USDA Human Nutrition Research Center on Aging

institute: Tufts University

data_processing:
Base-calling was performed using bcl2fastq v2.17.1.14
Alignment 1 (*_NR112918.csv files): RNA-seq reads were trimmed for adapter sequence and quality then aligned to reference (see genome build) using CLC Bio's Genomics Workbench v10.1.2 with parameters: quality limit = 0.01, min length = 100, Length fraction = 0.95, Similarity fraction = 0.95.
Alignment 2 (*_Sscrofa10.2.csv files): RNA-seq reads were trimmed for adapter sequence and quality then aligned to the Sus scrofa 10.2 genome assembly using CLC Bio's Genomics Workbench v9.0.1 with parameters: quality limit = 0.01, min length = 100, Length fraction = 0.95, Similarity fraction = 0.95
Reads that mapped uniquely to exons were used as counts (Unique Exon Reads) for differential expression analysis using the Bioconductor package: edge R. Genes were filtered based on a minimum of at least one count per million across three samples in all groups and normalized using the TMM method. Differentially expressed genes were identified using the Cox-Reid profile-adjusted likelihood method and likelihood ratio test. A Benjamini-Hochberg false discovery rate (FDR) method was used to adjust p-values for multiple comparisons
Genes were considered differentially expressed based on an FDR adjusted p <0.1 and absolute fold change ≥1.5. Fold change for genes identified by the edge R two-factor model were interpreted as diet effect: fold change of WD relative to HHD and statin effect: fold change of atorvastatin relative to no atorvastatin. Differentially expressed genes were only attributed to main effects (diet and statin) if there was no significant diet x statin interaction. A significant diet x stain interaction is indicated by a FDR adjusted p <0.1.
Ingenuity Pathway Analysis (IPA; v 9.0, Mountain View, CA, USA) was used to determine relevant biological pathways and functional annotation of differentially expressed genes. Pathways with an absolute Z score ≥ 2 and an FDR adjusted p-value ≤ 0.05 were considered statistically significant.
Genome_build: Alignment 1: "Assembly 11/29/18" from Porcine Translational Research Database (Dawson, Harry D., et al. "The porcine translational research database: a manually curated, genomics and proteomics-based research resource." BMC genomics 18.1 (2017): 643.)
Genome_build: Alignment 2: Sscrofa10.2
Supplementary_files_format_and_content: comma-separated value files with Unique Exon Read values for each sample

organism: Sus scrofa

source_name: left anterior descending coronary artery

extract_protocol:
Coronary artery tissue samples were homogenized, and the RNA was isolated using RNeasy Universal Mini kit (Qiagen, Valencia, CA) per the manufacturer’s instructions. Isolated RNA was treated with Turbo DNase (Ambion, Waltham, MA) to minimize genomic DNA contamination. RNA quality was assessed using the Experion RNA analysis electrophoresis kit (Bio-Rad, Hercules, CA). Samples with an RNA Quality Indicator greater than 7 were sequenced.
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (mRNA purification and fragmentation, cDNA synthesis, end repair, 3’ adenylation, adaptor ligation, and DNA enrichment) per the manufacturer’s instructions. DNA fragment size was determined using Experion DNA 1K chips (Bio-Rad, Hercules, CA) and library quantification was performed using the KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA).

tag: diet

value: Heart Healthy + Statin


title: S4_LAD_HHST_2327

value: left anterior descending coronary artery


title: S8_LAD_HHST_2334


title: S5_LAD_HHST_2339


title: S1_LAD_HH_2336

value: Heart Healthy


title: S15_LAD_ARST_2345

value: Atherogenic + Statin


title: S14_LAD_ARST_2340


title: S6_LAD_HHST_2328


title: S10_LAD_AR_2342

value: Atherogenic


title: S16_LAD_ARST_2362


title: S3_LAD_HH_2343


title: K562 Pair #1 (K1)_Ro 08-2750

last: Kharas

address: 1275 York Avenue

department: Molecular Pharmacology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Trim bases with phred score <10 and remove reads <20bp using TrimGalore!
Alignment using STAR version 2.5.3a with default parameters, sort resulting BAM using samtools v1.5
Count reads per gene using bioconductor package Rsubread against reference TxDb.Hsapiens.UCSC.hg38.knownGene
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values table containing read counts per hg38 UCSC known gene. Columns represent samples, rows represent genes

source_name: CML-BC (erythroid line)

growth_protocol: Cells were grown in RPMI+10%FBS+penicillin/streptomycin and treated at 0.5M/mL

extract_protocol:
Total RNA extracted by columns from frozen cellular dry pellet
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen, Vienna Austria), supplemented with a common set of external RNA controls, according to manufacturer’s recommendations (ERCC RNA Spike-In mix, ThermoFisher Scientific, cat 4456740). An in-house pipeline was used for read mapping and alignment, transcript construction and quantification of data generated by sequencing (HiSeq 2000, NYGC, NY, USA).

treatment_protocol: Ro 08-2750 at 20 uM for 4h (0.1% DMSO final, 1/1000 dilution from a 20 mM DMSO stock) directly in media culture

tag: disease state

value: Chronic Myelogenous Leukemia (CML)

tag: treatment


title: K562 Pair #4 (K4)_Ro 08-2750


title: K562 Pair #3 (K3)_Ro 08-2750


title: K562 Pair #2 (K2)_Ro 08-2750


title: K562 Pair #1 (K1)_DMSO

value: DMSO


title: S2_LAD_HH_2325


title: K562 Pair #2 (K2)_DMSO


title: MOLM13 Pair #4 (M4)_Ro 08-2750

source_name: AML FAB M5a

value: Acute Myeloid Leukemia


title: MOLM13 Pair #4 (M4)_DMSO


title: K562 Pair #4 (K4)_DMSO


title: K562 Pair #3 (K3)_DMSO


title: S9_LAD_AR_2331


title: S11_LAD_AR_2337


title: MOLM13 Pair #3 (M3)_Ro 08-2750


title: S13_LAD_ARST_2326


title: MOLM13 Pair #3 (M3)_DMSO


title: MOLM13 Pair #2 (M2)_Ro 08-2750


title: MOLM13 Pair #1 (M1)_DMSO


title: MOLM13 Pair #1 (M1)_Ro 08-2750


title: P12_SCML2_CnR_cKO2

data_processing:
Library strategy: CUT&RUN
Alignment to the mm9 genome was performed using bowtie2.
BAM files were generated and replicates were merged using samtools.
BAM files were converted to bigWig format, using Deeptools (version 2.5.2) bamCoverage -b input.bam  -o output.bw -of bigwig  -bs 1 -bl  --normalizeUsing RPKM --extendReads=140 --ignoreDuplicates
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files

source_name: Spermatogenic cells from P12 testes

extract_protocol:
Spermatogenic cells were isolated from P12 Brg1WT and Brg1cKO testes by digesting tubules with collagnease and trypsin followed by filteration through a 40 micron sieve.
Libraries were created using Kapa hyperprep DNA library kit for Illumina sequencing with modifications from (Skene et al, 2018; Hanier et al,2018)

tag: strain

tag: antibody


title: P12_SCML2_CnR_cKO1


title: MOLM13 Pair #2 (M2)_DMSO


title: Cb-T2

city: Chicago

first: WEN-CHING

last: CHAN

state: IL

department: Biological Sciences Division

institute: The University of Chicago

data_processing:
Illumina Casava1.7 software used for basecalling.
All RNA-seq reads were used to align to the mm10 genome assembly using STAR v2.5.1b with default configurations.
Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM (Fragments Per Kilobase Million) tables.
Using 1.5 as the fold change cutoff, DEGs (Differentially expressed genes) were detected using both Tuxedo suite (FPKM-based method) and featureCounts-DESeq2 (v2_1.16.1), edgeR (v3.18.1), limma (v3.32.10) (read count-based method) with default configurations.
Genes detected by at least more than one method were collected to create a high-confidence DEG lists.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables were generated using featureCount (v1.26.1) based on GENCODE annotation (vM18).

growth_protocol: The mouse model for cLINCL, in which Tpp1 is disrupted by gene targeting has been previously described (J. Neurosci. 2004, 24(41)9117). The line is being maintained by Tpp1 heterozygous crosses.  In all experiments 4 mo. old Tpp1-/- homozygous males mice were compared to 4 mo. old males wild type siblings.

extract_protocol:
Total RNA was obtained from the cerebellum (Cb) and forebrain/midbrain (F/M) of 4-mo.-old Tpp1-/- and wildtype mice by TRIzol (Thermo Fisher Scientific) extraction followed by a QIAGEN RNeasy Kit®  clean-up procedure which included a DNAse digestion step.
For library making we used the Illumina TruSEQ stranded mRNA Library prep kit in combination with the Illumina provided protocol. Single-end sequencing with 50 base pairs reads

value: 4 mo.-old

tag: Sex

value: male

value: cerebellum

tag: genotype


title: Cb-T1


title: Cb-N2

value: WT


title: P12_SCML2_CnR_WT1

value: P12 Brg1WT


title: P12_SCML2_CnR_WT2


title: Cb-N1


title: F/M-T3

value: forebrain/midbrain


title: Cb-T3


title: Cb-N3


title: F/M-T2


title: F/M-T1


title: Fadu_jq1

city: Nanjing

first: Jie

last: Cheng

state: Jiangsu

address: 136 Hanzhong Road

institute: Nanjing Medical University

description: Gene expression after 24hr 500nM JQ1 treatment in Fadu cell

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

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

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

source_name: Fadu cell, 24hr,  JQ1 500nM

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

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: Head and neck squamous cell carcinoma

value: Fadu


title: F/M-N3


title: Fadu_nc

description: Gene expression after 24hr 0nM JQ1 treatment in Fadu cell

source_name: Fadu cell, 24hr,  JQ1 0nM

value: 24hr, JQ1 0nM


title: Cal27_jq1

description: Gene expression after 24hr 500nM JQ1 treatment in Cal27 cell

source_name: cal27 cell, 24hr,  JQ1 500nM


title: DMSO_vs_SU5416+DAPT

city: Manchester

first: Shane

middle: P

last: Herbert

address: Michael Smith Building, OXford Road

department: Faculty of Biology, Medicine and Health

institute: University of Manchester

hyb_protocol: standard Agilent protocol

scan_protocol: Slides were scanned using Agilent Technologies Scanner G2505C  and protocol GE2_107

data_processing: Normalization and data control using GeneSpring GX software

source_name: Endothelial Cells DMSO treated

label_protocol: standard Agilent protocol

growth_protocol: Tg(kdrl:GFP)s843; Tg(gata1:DsRed)sd2 embryos were obtained by natural mating and raised at 28ºC in E3 media until treatment.

extract_protocol: GFP-positive ECs were isolated by fluorescence-activated cell sorting (FACS) and separated from GFP/dsRed- double-positive erythrocytes directly into lusis buffer of RNAqueous-Micro kit (Thermofisher). Total RNA were extracted following manufacturer's guidelines.

treatment_protocol: Tg(kdrl:GFP)s843; Tg(gata1:DsRed)sd2 embryos were incubated from 22 to 30 hpf with compounds that either promoted (DAPT 100µM), fully repressed (2.5 mM SU5415), or partially repressed (0.63 mM SU5416) angiogenic cell behavior in vivo.

tag: developmental stage

value: 30hrs post fertilization

tag: agent

source_name: Endothelial cells DAPT + SU5416 treated


title: Cal27_nc

description: Gene expression after 24hr 0nM JQ1 treatment in Cal27 cell

source_name: cal27 cell, 24hr,  JQ1 0nM


title: F/M-N2

tag: age

tag: tissue


title: DMSO_vs_DAPT

source_name: Endothelial cells DAPT treated

value: 100 uM DAPT


title: core_rep1

source_name: GBM cells

tag: passages

value: Core

value: wild type


title: F/M-N1


title: HUVECs siMAGI1 rep2

city: Houston

first: Jun-ichi

last: Abe

state: Texas

address: 2121 W Holcombe Blvd. IBT8 803e

institute: University of Texas MD Anderson Cacer Center

hyb_protocol: Following fragmentation and labeling, 5.2 ug of labeled ss-cDNA were hybridized for 16 hrs at 45 degree on GeneChip Mouse Transcriptome arrays. Arrays were washed and stained in Affymetrix Fluidics station 450.

scan_protocol: Arrays were scanned using Affymetrix GCS3000 scanner

data_processing:
The array data were incorporated into the Transcriptome Analysis Console 3.0 software program (Affymetrix), and GeneChip data were normalized using Tukey’s biweight average algorithm and represented as a biweight average on a log2 scale.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: HUVECs siMAGI1 static 24 hrs

label_protocol: Fragmented and biotinylated labeled ss-cDNA were prepared according to standard Affymetrix WT Plus protocol (P/N 703174) from 100 ng total RNA

growth_protocol: HUVECs were either obtained from human collagenase-digested umbilical cord veins and cultured in M200 medium supplemented with LSGS (Cascade Biologics, Portland, OR, USA), 2% fetal bovine serum (Atlanta Biologicals, Flowery Branch, GA, USA), and 1% penicillin/streptomycin. HUVECs were cultured in dishes precoated with 0.2% gelatin type A (#901771; MP Biomedicals, Solon, OH, USA).

extract_protocol: Total RNA was extracted by using an RNeasy Plus Mini Kit (catalog #74134; QIAGEN)  according to the manufacturer's instructions.

treatment_protocol: HUVECs were transfected by control siRNA or MAGI1 siRNA, and after 48 hrs of transfection HUVECs were exposed to disturbed flow (d-flow). After 24 hrs of disturbed flow RNA was extracted for futher microarray processing.

value: HUVECs

tag: transfection

value: MAGI1 siRNA

tag: protocol

value: static


title: HUVECs siMAGI1 rep3


title: HUVECs siMAGI1+DF rep1

source_name: HUVECs siMAGI1 disturbed flow (DF) 24 hrs

value: disturbed flow (d-flow)


title: Input/normal IgG

city: Cambridge

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
ChIP-seq reads aligned to mm10 using bowtie2 (version  2.0.6) with extra parameters (-k 2 -N 1).
bigWig density profiles were created with in-house script incorporating UCSC's wigToBigWig utility.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig – read density profile

source_name: ESCs

extract_protocol:
ChIP-DNA was eluted with Qiagen MinElute PCR purification kit
Ev5-ChIP-Seq libraries were generated   using NEB Next ChIP-Seq Library Prep Master Mix Set for Illumina (NEB. For H3K4me3 ChIP-seq libraries DNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (∼300 bp) and 14 cycles of PCR amplification. Cluster generation and sequencing (36 bp) was performed with the Illumina Genome Analyzer IIx (GAIIx) platform according to standard Illumina protocols

value: ESCs

value: RGd2_clone 6

tag: growth

value: negative control

tag: line

value: RGd2 clonal line 6

tag: ChIP

value: input


title: 16h_H3Kme3

tag: cell type

tag: genotype/variation

value: withdrawn from 2i for 16h


title: HUVECs siCont+DF rep1

source_name: HUVECs siCont disturbed flow (DF) 24 hrs

value: Control siRNA


title: HUVECs siMAGI1 rep1


title: DMSO_vs_SU5416high

value: DMSO

source_name: Endothelial cells SU5416 treated (high dose)


title: DMSO_vs_SU5416low

source_name: Endothelial cells SU5416 treated (low dose)


title: HUVECs siMAGI1+DF rep2


title: HUVECs siMAGI1+DF rep3


title: 25h Rex1-low H3K4me3 (FACS-sorted)

value: withdrawn from 2i for 25h, Rex1-low population


title: 2i_H3K4me3