title: Growth period 2, Control 1 [TnseqMMC13]


title: AVF-CKD 1

status: Public on Jun 27 2018

type: SRA

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

country: USA

institute: The Mayo Clinic

library_source: transcriptomic

data_processing:
TopHat v2.1.0 for alignment
FeatureCounts to quantify expression
edgeR for defining differentially expressed genes
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv format containg raw gene counts and RPKM normalize expression values

molecule: total RNA

organism: Mus musculus

source_name: venous limb of AVF

extract_protocol:
trizol and Qiagen total RNA kit
TruSeq RNA Sample Prep Kit v2

treatment_protocol: sham and AVF-CKD surgery

tag: time point

value: harvested 7 days after surgery

tag: protocol

value: AVF-CKD surgery


title: MicroRNA-seq preB young 1

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
small RNA
MicroRNA_counts.txt

data_processing:
Libraries were sequenced on the IlluminaHiSeq1000/2500 platforms using the default RTA analysis software.
Sequencing reads were trimmed using trim galore v0.4 using default parameters to remove the standard Illumina adapter sequence. Reads were mapped to the mouse GRCm38 genome assembly using bowtie2 v2.2.5 using default parameters. BAM files imported to SeqMonk and reads were extended by 200bp at their 5’ end to approximate the true insert size.
RNA-seq: Reads were mapped using Hisat2. Seqmonk V1.39 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was used for quality control, visualization and quantification of raw read counts. Total RNA was quantified over genes, whilst nuclear RNA was quantified using the active transcription pipeline which counts reads over intronic sequences.   MicroRNA-seq: Annotations from Ensembl and miRBase were merged and deduplicated. Reads were mapped using bowtie 2, and strand-specific raw read counts were generated using Seqmonk.  ATAC-seq: Reads were mapped with bowtie2. Peaks were called with MACS2 (--nomodel --shif -25 --extsize 50 –q 0.01) and filtered to exclude any for which the read counts with mapping quality score > 30 was less than 64, or that overlapped with a blacklisted region. For each condition (young and aged) peaks present in 3 out of 4 replicates were accepted and any peaks closer than 100bp to each other were merged. Raw read counts were generated over the union of peaks in young and aged used featureCounts (Liao et al., 2014).  ChIP-seq: Reads were mapped using bowtie2. Peaks were called using MACS2 with default parameters for narrow peaks for all datasets except H3K27me3 for which we used MACS1.4 to call broad peaks. Similar to ATAC-seq, peaks with low numbers of high quality reads or overlapping blacklisted regions were filtered out, and peaks for each condition were accepted if they were present in both replicates. Raw read counts over the union of peaks from young and aged were generated using featureCounts.  Hi-C/Promoter Capture Hi-C: Reads were mapped and filtered using HiCUP (Wingett et al., 2015),and Hi-C was then analysed using HOMER (Heinz et al., 2010). Interactions for promoter capture HiC were called using Chicago (Cairns et al., 2016).
Genome_build: GRCm38
RNA report: Genomic locations and raw read counts over genes (total RNA), or specifically counted over introns as a measure of active transcription (nuclear RNA). Assumed opposing strand specificity.
MicroRNA report: Genomic locations and raw, strand-specific read counts over microRNAs.
ATAC ChIP report: Read counts over union of MACS peaks from young and aged cells; peaks called by MACS2 except for H3K27me3 for which broad peaks were called with MACS1.4.
Hi-C report: Scores for PC1 from principle component analysis of interaction profiles for 250 kb bins genome-wide. Scores are aligned with H3K4me3 ChIP-seq data such that a positive score indicates an active A compartment, and a negative score an inactive, B compartment.
PCHi-C report: Chicago interaction scores for the union of significant interactions (threshold score >= 5) in aged and young. Genomic locations of the HindIII fragments at both ends of the interaction are provided, as well as the gene(s) overlapping the bait and other end of the interaction (for bait-to-bait interactions) and Chicago scores for young and aged.

source_name: bone marrow

growth_protocol: All cells were depleted of non-B lineage cells by magnetic cell sorting, and then flow sorted for pro-B and pre-B cells, directly from bone marrow single cell suspensions from young and aged mice

extract_protocol:
RNA-seq: For nuclear RNA-seq nuclei were isolated from 1-10 x 106 flow sorted B lymphocytes by incubation in 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% NP40 for 5 min on ice followed by centrifugation at 500 x g. Total and nuclear RNA was isolated with a RNeasy mini kit (Qiagen) and treated with Turbo DNAse (Ambion).  Total RNA was depleted of ribosomal RNA using a Ribo-Zero Gold rRNA removal kit (Human/Mouse/Rat:Illumina) according to the manufacturer’s instructions.  miRNA-seq: Short RNAs were isolated from 1-10 x 106 flow sorted B lymphocytes using a mirVANA kit (Ambion/ThermoFisher).  ATAC-seq: ATAC-seq was performed directly on 5 x 104 flow sorted B lymphocytes.  ChIP-seq: Flow sorted B lymphocytes were fixed in 1% formaldehyde for 10 min at RT, quenched with 125mM glycine, washed with PBS and pellets snap frozen for storage at -80°C. Cells were lysed (150mM NaCl/25mM Tris pH 7.4/5mM EDTA/0.1% Triton/1% SDS/protease inhibitors; + 20mM Sodium Butyrate for H3K27ac), chromatin sonicated and diluted 5-10 times (0.01% SDS/1.1% Triton/1.2mM EDTA/16.7mM Tris pH 8.1/167mM NaCl; or for H3K27ac in RIPA buffer: 10 mM Tris-HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated with antibody overnight at 4°C before addition of protA-G magnetic beads. For H3K27ac, antibody was instead pre-incubated with beads and washed with RIPA buffer before incubation with chromatin at 4°C overnight. Beads were washed once with Low Salt buffer (0.1% SDS, 0.1% SDS, 2mM EDTA, 20mM Tris pH 8.0, 150mM NaCl), twice with High Salt buffer (0.1% SDS, 0.1% SDS, 2mM EDTA, 20mM Tris pH 8.0, 500mM NaCl) and twice with TE (10mM Tris pH 8.0, 1mM EDTA). For CTCF the last High Salt buffer was substituted with LiCl Buffer (0.25M LiCl, 1% IGEPAL, 1% deoxycholic acid, 1mM EDTA, 10mM Tris, pH 8.1). For H3K27ac the first 3 washes were performed with RIPA buffer. DNA was eluted in 0.1M NaHCO3/1% SDS and reverse-crosslinked with Proteinase K (Ambion); ChIP and input DNA was purified using the QIAquick PCR Purification Kit (Qiagen).  Hi-C/Promoter Capture Hi-C: Hi-C and Promoter CHi-C libraries were generated as described (Schoenfelder et al., 2015), with modifications as described below. 3.2-3.5 x 107 pre-B cells, pooled from several FACS sorts, were used for each library. DNA digestion was performed with 1500 units HindIII (NEB) per 5 million cells. After the biotin fill-in, in-nucleus ligation was performed as described previously (Nagano et al., 2015) for four hours at 16°C (5.5 ml 50 mM Tris-HCl, 10 mM MgCl2, 1 mM ATP, 10 mM DTT, 100 µg/ml BSA + 50 units T4 DNA ligase (Life Technologies)). An additional Proteinase K incubation (65 µl of 10mg/ml) for two hours was included after the overnight incubation, preceding RNase A treatment, two sequential phenol/chloroform (Sigma) extractions and DNA precipitation including three 70% ethanol washes. Biotin removal from non-ligated fragment ends was followed by phenol/chloroform purification and DNA precipitation.
RNA-seq: Paired-end strand-specific libraries were generated as described (Parkhomchuk et al., 2009) except polyA+ RNA selection was omitted, first strand cDNA synthesis was performed with random hexamer primers, and double-stranded cDNA was fragmented with a Covaris E220 sonicator.   miRNA-seq: Libraries were generated using the NEBNext small RNA library prep set for Illumina with 15 cycles of PCR. Transfer RNA and ribosomal RNA derived fragments were removed from the libraries by ‘double-sided’ AMPure XP size selection as described in the user manual.  ATAC-seq: Atac-seq was performed as described in Buenrostro et al. (2015).  ChIP-seq: Library preparation was performed from 0.2-0.8 ng of purified DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with the following modifications: Illumina Tru-Seq adaptors were used and library amplification was performed with the KAPA PCR Amplification kit (KAPA, Cat. KK2501) using 15 cycles.   Hi-C/Promoter Capture Hi-C: Libraries were generated essentially as described in Schoenfelder et al. (2015).

tag: strain

tag: tissue

value: bone marrow

tag: age of mouse (months)

value: 3 months

tag: cell type

value: flow sorted pre-B cells

tag: markers


title: MMC Starter Culture 3 [TnseqMMC6]

city: Ann Arbor

first: Lyle

middle: A

last: Simmons

state: MI

address: 830 N University Ave

department: MCDB

institute: University of Michigan

description: processed data file: MMC_processed_data.csv

library_source: genomic

data_processing:
Samples were sequenced on an Illumina Hiseq 2500 using Hiseq control software-2.2.38 (TnseqMMC1-24) or 2.2.68 (TnMP1-33)
Base calling was performed using RTAVersion-1.18.61 (TnseqMMC1-24) or 1.18.66.3 (TnMP1-33)
Sequencing reads were trimmed to 43 nucleotides to remove the sequence from the transposon outside the inverted repeat
sequencing reads were mapped to PY79 genome coordinates using BWA and the reference genome "tn_site_ref.fa"
Coverage was summed for each transposon insertion site using Rstudio
Genome_build: The PY79 genome build was used to generate a transposon insertion specific reference genome; File name = "tn_site_ref.fa"
Supplementary_files_format_and_content: Processed data files include coverage for transposon insertion sites for each sample, transposon insertion site coordinate in PY79 genome (in bp), and the locus tag or gene name for each transposon insertion

molecule: genomic DNA

organism: Bacillus subtilis PY79

source_name: MMC Starter Culture 3

growth_protocol:
growth conditions prior to sample extraction: Transposon insertion library grown to OD600 of about 0.8 in LB + 100 μg/mL spectinomycin
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

extract_protocol:
Genomic DNA was isolated using a silica spin column
Sequencing libraries were constructed by digesting genomic DNA with MmeI, ligating adaptors containing illumina specific sequences, and amplifying transposon/genomic DNA junctions via PCR

treatment_protocol: Samples were treated with 15 ng/mL mitomycin C (MMC), vehicle control, 50 μg/mL methyl methane sulfonate (MMS), or 25 ng/mL phleomycin (Phleo) as indicated

tag: treatment

tag: growth period

value: none; Starter culture


title: MicroRNA-seq preB young 2

description:
small RNA
MicroRNA_counts.txt


title: MMC Starter Culture 2 [TnseqMMC5]

source_name: MMC Starter Culture 2


title: MicroRNA-seq proB young 4

description:
small RNA
MicroRNA_counts.txt

value: flow sorted pro-B cells


title: sham 5

source_name: jugular vein

value: sham


title: sham 6


title: MicroRNA-seq proB young 3

description:
small RNA
MicroRNA_counts.txt


title: sham 4


title: AVF-CKD 2


title: MicroRNA-seq proB young 2

description:
small RNA
MicroRNA_counts.txt


title: sham 3


title: MMC Library 3 [TnseqMMC3]

source_name: MMC Library 3

growth_protocol:
growth conditions prior to sample extraction: Transposon insertion library isolated from LB agar plates containing 100 μg/mL spectinomycin to select for cells with a transposon
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: none; Transposition library


title: MicroRNA-seq proB young 1

description:
small RNA
MicroRNA_counts.txt


title: MMC Library 1 [TnseqMMC1]

source_name: MMC Library 1


title: sham 2


title: H9 hESC-derived NPCs_KD

city: Bangalore

first: Gaiti

last: Hasan

state: karnataka

address: GKVK Campus Rd

country: India

institute: NCBS,TIFR

data_processing:
HiSeq Control and Real-Time Analysis Software was used for basecalling
Reads (FASTQ sequences) obtained after sequencing were aligned to the annotated UCSC human genome (GRCh37/hg19) using HISAT2 (Version-2.0.5)
These aligned SAM files were converted to BAM files using SAMtools (Version- 1.3)
These aligned BAM files were converted to Sorted BAM files using SAMtools (Version- 1.3)
The resulting alignment data from SAMtools were then fed to CuffDiff2.We set a corrected p-value, referred to as the q-value cut-off of 0.05 and Fold change >/= 1.5(+/-) to identify differentially expressed genes.
Read counts for each transcript or exon were also calculated independently using python based package HTSeq (Version 0.9.1)
These read counts were then used as inputs for the differential analysis with DESeq and EdgeR.
Genome_build: UCSC human genome (GRCh37/hg19)
Supplementary_files_format_and_content: Differential Expression result by CuffDiff, DESeq & EdgeR are given as supplementary files in .txt format.

organism: Homo sapiens

source_name: H9 hESC-derived NPCs_KD

growth_protocol: NPCs were plated onto Matrigel-coated plates in maintenance medium containing 1 : 1 DMEM/F12 neurobasal medium supplemented with 1:200 N2, 1:100 B27, 3 μM CHIR99021, 0.5 mM purmorphamine and 150 μM ascorbic acid (Sigma, St Louis, MO, USA). Neural precursor cells (NPCs) were then passaged enzymatically with Accutase (Invitrogen, Carlsbad, CA, USA) and freeze thawed as per requirement (protocol adapted from Reinhardt et al. 2013).

extract_protocol:
Total RNA was isolated from hNPCs using TRIzol as per manufacturer’s instructions. The RNA was run on a Bio-analyzer chip (Agilent) to ensure integrity.
Approximately 500 ng of total RNA was used per sample to prepare libraries (RIN values>9) using a TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer’s instructions. The prepared libraries were run on a DNA1000 chip of a Bio-analyzer to check their size. Libraries were then quantified by qPCR and run on an Illumina Hiseq2000 platform, for a single end and 75bp read protocol by SciGenome.

treatment_protocol: Lenti  virus mediated knockdown was done using tetracyclin inducible ShERWOOD-UltramiR short hairpin RNA (shRNA)

value: Human embryonic stem cell (H9 hESC) derived neural progenitor cells

tag: passage

tag: genotype

value: STIM1 Knockdown


title: H9 hESC-derived NPCs_KD3


title: H9 hESC-derived NPCs_NTC4

source_name: H9 hESC-derived NPCs_NTC

value: shRNA Control (Non-Targeted)


title: SCNT_rep2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) with TopHat v2.0.14 coupled with Bowtie v2.1.0. The mapped reads were subjected to Cufflinks v2.2.1 with the reference annotation (UCSC gene models) to calculate the FPKM values of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: the processed data files contain the FPKM values of each gene (gene id, FPKM value)

source_name: mouse blastocysts generated with somatic nuclear transffer

growth_protocol: B6D2F1/J (BDF1) mice were used for the collection of recipient oocytes for SCNT. For mouse embryonic fibroblast (MEF) cell preparation, Xist KO female mice maintained in 129S1/SvImj background (Marahrens et al., 1997) were mated with CAST/EiJ males to generate Xist heterozygous KO embryos in 129/CAST F1 background. Somatic cell nuclear transfer was carried out as described previously (Matoba et al., 2014; Ogura et al., 2000). IVF was performed using Xist KO oocytes (129S1/Svj background) and WT sperm (CAST/EiJ background)

extract_protocol:
Six IVF or SCNT embryos of the early blastocyst stage (96 hours after fertilization or activation) were directly lysed and used for cDNA synthesis using the SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 634936).
After amplification, the cDNA samples were fragmented using a Covaris M220 sonicator (Covaris). Sequencing libraries were made with the fragmented cDNA using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer’s instructions (New England Biolabs, E7370).

value: 129S1/Svj x CAST/EiJ


title: H9 hESC-derived NPCs_KD4


title: SCNT_rep1

value: mouse blastocysts generated with somatic nuclear transffer


title: sham 1


title: H9 hESC-derived NPCs_NTC3


title: IVF_rep1

source_name: mouse blastocysts generated with in vitro fertilization


title: IVF_rep2

value: mouse blastocysts generated with in vitro fertilization


title: MMC Starter Culture 1 [TnseqMMC4]

source_name: MMC Starter Culture 1


title: MicroRNA-seq proB aged 4

description:
small RNA
MicroRNA_counts.txt

value: 18-22 months


title: H9 hESC-derived NPCs_WT4

source_name: H9 hESC-derived NPCs_WT

value: Wild Type


title: H9 hESC-derived NPCs_WT3


title: MMC Library 2 [TnseqMMC2]

source_name: MMC Library 2


title: H9 hESC-derived NPCs_WT1


title: H9 hESC-derived NPCs_NTC2


title: KO3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contamination was removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 76
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

molecule: polyA RNA

source_name: Lung alveolar macrophages

growth_protocol: Experiments were conducted with sex-matched 8-12 week-old mice with C57BL/6 background

extract_protocol:
Cell lysis was performed with buffer RLT (Qiagen), containing 10µ/ml β-mercaptoethanol and RNA was isolated with RNeasy Plus Mini Kit (Qiagen).
RNA concentration and integrity were determined with an Agilent 2100 Bioanalyzer (Caliper Life Science)
RNASeq libraries were sequenced (single-end mode and length of 61 bp) on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.

treatment_protocol: Experiments were done in mice under steady-state conditions

value: Vhl(flox/flox) / CD11c (cre/+)

value: None (Steady-state)

tag: age

value: 8-12 weeks


title: KO1


title: JSP1


title: JSP2


title: JSP3


title: KO2


title: CREminus1

value: Vhl(flox/flox) / CD11c (+/+)


title: CREminus3


title: CREminus2


title: Ileum_Balb/c_female_repl3

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

label: biotin

source_name: distal ileum, BALB/c mouse, female

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Male and female wild-type B6 and BALB/c mice were purchased from Harlan (Harlan, Horst, the Netherlands) at an age of eight weeks. Mice were co-housed (five mice per cage) in isolated ventilated cages to limit environmental influences. The animals had free access to food (low fat diet, according to D12450B diet formulation, prepared by Research Diets Services, Wijk bij Duurstede, the Netherlands) and water. Between an age of 3 and 5 months all mice were sacrificed by cervical dislocation under anesthesia (isoflurane and oxygen). Subsequently approximately 1 cm of the distal ileum was removed for microarray analysis. All female mice were sacrificed during the diestrus phase of their ovarian cycle to ensure low stable levels progesterone and estrogens.

extract_protocol: RNA was purified using TRIzol (Life Technologies, Calsbad, CA, USA) followed by an additional round of purification with RNeasy Microkit columns (Qiagen, Venlo, the Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice did not receive any specific treatment

tag: Sex

value: female

tag: mouseid

value: standard, low fat diet (formulation according to Research Diets Inc.:D12450B)

value: distal ileum

value: wildtype

value: Balb/c


title: Ileum_C57Bl/6_male_repl2

source_name: distal ileum, C57bl/6 mouse, male

value: male


title: Ileum_C57Bl/6_female_repl1

source_name: distal ileum, C57bl/6 mouse, female


title: Ileum_Balb/c_female_repl2


title: LUHMES_day 15_rotenone_100nM_24hr_rep3

city: Baltimore

first: Lena

last: Smirnova

address: 615 N. Wolfe St

department: Environmental Health & Engineering

institute: Johns Hopkins University

scan_protocol: The arrays were scanned in the Agilent G2600D SureScan Microarray Scanner using scan protocol AgilentG3_GX_1color for gene expression arrays.

data_processing: Agilent’s Feature Extraction Software Version 11.5.1.1 was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data. Txt-files from Feature Extraction Software were exported for further analysis with R version 3.5 (https://www.R-project.org/) and Bioconductor version 3.7 (Huber et al. 2015, Gentleman et al. 2004). In a first step, the arrays gMedianSignal were imported, normexp background corrected (Ritchie et al. 2007, Silver et al. 2009) and quantile normalized between arrays (Bolstad et al. 2003). Primary QC by principal components analysis revealed a batch effect on a subset of arrays, which were processed at a different time point with a different washing procedure, which was corrected by parametric empirical Bayes frameworks for adjusting data for batch effects as implemented in ComBat (Johnson et al. 2007).  Probes were then filtered out if they are not least 10% brighter than the 95% percentile of the negative control probes on each array on at least three arrays (original 62,976 probes, after 54,135 probes). In a next step control probes were filtered out (after 51,849 probes) and duplicate probes were summarized (after 44,414 probes). Individual probes which were either labeled by the Agilent Feature Extractor Software as not to be used, Non-uniform outlier or Population outlier were removed as well (174 probes over all arrays). In the last step, probes, which did not map to Entrez-ID, were removed (31,664 probes left) and probes were averaged per Entrez-ID (21,733 unique Entrez-IDs left). Differential expression was estimated by empirical Bayes moderation of the standard errors towards a common value (Empirical Bayes moderated t-test) (Smyth et al. 2004).

source_name: day 15 of differentiated LUHMES in 3D, Rotenone 100 nM, 24 hours

label_protocol: One hundred nanograms of total RNA was processed for cDNA synthesis and labeling and hybridization to Agilent SurePrint G3 Human Gene Expression v2 8x60K Arrays according to Agilent’s One Color Microarray-Based Analysis (Low Input QuickAmp Labeling) protocol

growth_protocol: LUHMES were differentiated on gyratory shaker at 80 rpm, 50 mm orbit diameter in differentiation medium (Advance DMEM/F12 supplemented with cAMP, GDNF, tetracycline, N2)

extract_protocol: RNA was isolated with Mirvana microRNA isolation kt

treatment_protocol: On day 7 of differentiation LUHMES were treated with 50 or 100 nM rotenone from 100mM stock in DMSO. DMSO was diluted the same way to reach the same amount as for 100 nM rotenone. LUHMES were treated either for 12 or 24 hours. Samples were collected immediately after treatment or after rotenone wash-out and 7 day recovery - on day 15.

tag: cell line

value: LUHMES dopaminergic cell line

tag: toxicant

value: Rotenone, 100 nM

tag: day

value: day 15

tag: exposure duration


title: Ileum_Balb/c_male_repl1

source_name: distal ileum, BALB/c mouse, male


title: Colon_C57Bl/6_female_repl5

source_name: proximal colon, C57bl/6 mouse, female

growth_protocol: Male and female wild-type B6 and BALB/c mice were purchased from Harlan (Harlan, Horst, the Netherlands) at an age of eight weeks. Mice were co-housed (five mice per cage) in isolated ventilated cages to limit environmental influences. The animals had free access to food (low fat diet, according to D12450B diet formulation, prepared by Research Diets Services, Wijk bij Duurstede, the Netherlands) and water. Between an age of 3 and 5 months all mice were sacrificed by cervical dislocation under anesthesia (isoflurane and oxygen). Subsequently approximately 1 cm of the proximal colon was removed for microarray analysis. All female mice were sacrificed during the diestrus phase of their ovarian cycle to ensure low stable levels progesterone and estrogens.

value: proximal colon


title: Ileum_Balb/c_female_repl4


title: Colon_C57Bl/6_male_repl4

source_name: proximal colon, C57bl/6 mouse, male


title: LUHMES_day 15_DMSO_rep3

hyb_protocol: Agilent’s One Color Microarray-Based Analysis (Low Input QuickAmp Labeling) protocol

source_name: day 15 of differentiated LUHMES in 3D, DMSO

value: DMSO


title: LUHMES_day 15_rotenone_50nM_24hr_rep3

source_name: day 15 of differentiated LUHMES in 3D, Rotenone 50 nM, 24 hours

value: Rotenone, 50 nM


title: Ileum_Balb/c_male_repl3


title: Ileum_C57Bl/6_male_repl5


title: Ileum_Balb/c_female_repl5


title: Ileum_C57Bl/6_male_repl3


title: Ileum_Balb/c_male_repl2


title: Ileum_C57Bl/6_male_repl4


title: Ileum_C57Bl/6_female_repl3


title: LUHMES_day 15_rotenone_50nM_12hr_rep1

description: this sample was on a slide which was repeated. Batch correction is needed to compare with the rest of the samples

source_name: day 15 of differentiated LUHMES in 3D, Rotenone 50 nM, 12 hours


title: Ileum_C57Bl/6_female_repl2


title: Ileum_Balb/c_female_repl1


title: LUHMES_day 15_rotenone_100nM_24hr_rep1


title: LUHMES_day 15_rotenone_50nM_24hr_rep1


title: Ileum_C57Bl/6_male_repl1


title: LUHMES_day 15_rotenone_50nM_12hr_rep2


title: LUHMES_day 15_DMSO_rep2


title: Colon_Balb/c_male_repl4

source_name: proximal colon, BALB/c mouse, male


title: LUHMES_day 15_rotenone_50nM_24hr_rep2


title: LUHMES_day 15_DMSO_rep1


title: LUHMES_day 15_rotenone_100nM_24hr_rep2


title: LUHMES_day 15_rotenone_50nM_12hr_rep3


title: Colon_Balb/c_female_repl5

source_name: proximal colon, BALB/c mouse, female


title: LUHMES_day 8_rotenone_100nM_24hr_rep3

source_name: day 8 of differentiated LUHMES in 3D, Rotenone 100 nM, 24 hours

value: day 8


title: LUHMES_day 8_rotenone_100nM_24hr_rep2


title: Colon_C57Bl/6_female_repl4


title: Colon_C57Bl/6_male_repl2


title: Colon_C57Bl/6_male_repl3


title: Colon_Balb/c_female_repl4


title: Colon_C57Bl/6_female_repl3


title: LUHMES_day 8_rotenone_50nM_24hr_rep2

source_name: day 8 of differentiated LUHMES in 3D, Rotenone 50 nM, 24 hours


title: LUHMES_day 8_rotenone_50nM_24hr_rep3


title: Colon_Balb/c_male_repl3


title: leaf_M.sexta_oviposition_S.exigua_feeding_rep3

city: Berlin

first: Tobias

last: Lortzing

state: Berlin

address: Haderslebener Str. 9

department: Biology

country: Germany

institute: Freie Universität Berlin

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer’s protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Data were analyzed using the “limma” software packages from Bioconductor in “R” (R Core Team; Ritchie et al. 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed. For the data-upload, all raw data were background-corrected and normalized across all arrays. In the publication, a detection limitwas set at the 10% quantile of fluorescence signal intensity of each array. All structural spots, as well as oligos that  were not above this detection limit in any of the arrays, were removed from further analysis. Subsequently, the expression levels were background-corrected after removal of the non-expressed genes using the normexp method and normalized between the arraysusing quantile normalisation.

organism: Nicotiana attenuata

source_name: leaf, M. sexta oviposited S. exigua fed

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacture’s protocol.

growth_protocol: Nicotiana attanuata plants originated from a 15x WT inbred line collected in Utah and were grown from seed at a 16/8 h light/dark cycle and a photon irradiance between 190 - 250 µmol/ m s

extract_protocol: For each microarray sample, leaf material from three or four independent biological replicates was pooled. Leaf material was ground under liquid nitrogen and RNA was extracted with the NucleoSpin® RNA Plant kit (Macherey-Nagel GmbH & Co. KG) according to the manufacturer’s instructions using double the amount of RAP lysis buffer. RNA was DNase digested using TURBO DNA-free™ (AmbionTM) according to the manufacturer’s instructions.

treatment_protocol: Plants received different combinations of oviposition and herbivory by M. sexta and S. exigua. Oviposition by M. sexta was standardized to 1-3 eggs, S. exigua laid 1-2 egg clutches. Right before their natural hatching time, eggs were gently removed using a soft brsuh or tweezers. Feeding treatment: either 3 M. sexta or 20 S. exigua larvae were enclosed in a clip cage on a leaf two below the sink-source transition leaf, systemic to the oviposited leaf. Controls received an empty clip cage. The leaves, local to feeding or on the respective leaf position on control plants, were harvested after 24h of feeding.

tag: line

value: 15x WT inbred line

tag: treament

value: M. sexta oviposited S. exigua fed

value: leaf


title: Colon_Balb/c_female_repl3

tag: tissue

tag: strain


title: LUHMES_day 8_rotenone_50nM_12hr_rep3

source_name: day 8 of differentiated LUHMES in 3D, Rotenone 50 nM, 12 hours


title: LUHMES_day 8_rotenone_50nM_12hr_rep2


title: leaf_M.sexta_oviposition_S.exigua_feeding_rep1


title: Colon_C57Bl/6_female_repl2


title: Colon_Balb/c_male_repl2


title: leaf_S.exigua_oviposition_M.sexta_feeding_rep3

source_name: leaf, S. exigua oviposited M. sexta fed

value: S. exigua oviposited M. sexta fed


title: Colon_C57Bl/6_male_repl1


title: Colon_Balb/c_female_repl2

value: female


title: LUHMES_day 8_DMSO_rep3

source_name: day 8 of differentiated LUHMES in 3D, DMSO


title: LUHMES_day 8_rotenone_50nM_12hr_rep1


title: leaf_M.sexta_oviposition_ M.sexta_feeding_rep3

source_name: leaf, M. sexta oviposited M. sexta fed

value: M. sexta oviposited M. sexta fed


title: LUHMES_day 8_rotenone_50nM_24hr_rep1


title: COV362_THZ1_250nM_rep2

city: Auburndale

first: Mei

last: Zeng

state: MA

address: 360 Longwood Avenue

department: cancer biology

institute: Dana Farber Cancer Institute

description:
Cov_THZ1_250nM_1
processed data file: THZ1_analysis_Cov_all_fpkm_exprs_norm.txt

data_processing:
Fastq files were aligned to human genome build hg19 using HiSat with default parameters.
Transcripts were assembled and FPKM values were generated using cuff quant and cuffnorm from the cufflinks pipeline (Trapnell et al., Nat. Biotechnol. 28, 511-515, 2010).
FPKM values were then normalized to synthetic ERCC spike-in RNAs as described previously (Loven et al., Cell 151, 476-482, 2012).
Genome_build: hg19
Supplementary_files_format_and_content: THZ1_analysis_Ku_all_fpkm_exprs_norm.txt ; THZ1_analysis_Cov_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

growth_protocol: KURAMOCHI cells (RPMI supplemented with 10% Fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin) and COV362 cells (DMEM supplemented with 10% Fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin)were cultured at 37 ºC and 5% CO2.

extract_protocol:
KURAMOCHI and COV362 cells were lysed, homogenized using Qiashredder columns (Qiagen), and total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cell count normalized RNA samples were mixed with the ERCC RNA Spike-In Mix #1 (Life Technologies) prior to library preparation.
Libraries for Illumina sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced on an Illumina NextSeq 500 (single end 75 bp reads) .

treatment_protocol: Cells were treated with DMSO, 50 nM THZ1, 250 nM THZ1 for six hours.

tag: cell type

value: human ovarian cancer cell line

tag: genotype/variation

value: untransduced control

tag: culture condition

value: DMEM + 10% Fetal Bovine Serum + 1% Pen/Strep

value: THZ1_250nM for 6 hours


title: leaf_S.exigua_oviposition_M.sexta_feeding_rep2


title: leaf_M.sexta_oviposition_S.exigua_feeding_rep2


title: leaf_S.exigua_oviposition_M.sexta_feeding_rep1


title: LUHMES_day 8_DMSO_rep1

value: LUHMES dopaminergic cell line


title: COV362_THZ1_250nM_rep1

description:
Cov_THZ1_250nM_0
processed data file: THZ1_analysis_Cov_all_fpkm_exprs_norm.txt

tag: treatment


title: LUHMES_day 8_DMSO_rep2


title: COV362_THZ1_50nM_rep2

description:
Cov_THZ1_50nM_1
processed data file: THZ1_analysis_Cov_all_fpkm_exprs_norm.txt

value: THZ1_50nM for 6 hours


title: COV362_THZ1_50nM_rep1

description:
Cov_THZ1_50nM_0
processed data file: THZ1_analysis_Cov_all_fpkm_exprs_norm.txt


title: Colon_Balb/c_male_repl1

value: male

value: standard, low fat diet (formulation according to Research Diets Inc.:D12450B)

value: wildtype

value: Balb/c


title: COV362_DMSO_rep2

description:
Cov_DMSO_1
processed data file: THZ1_analysis_Cov_all_fpkm_exprs_norm.txt

value: DMSO for 6 hours


title: LUHMES_day 8_rotenone_100nM_24hr_rep1

value: Rotenone, 100 nM

value: day 8


title: Input from U2OS FLAG-RepID FL stable cells

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

data_processing:
For RepID ChIP, the MACS peak calling program was used comparing reads from the ChIP –seq experiment to genomic input reads from the same cell line, with default parameters, and a p-value = 1e-9.
For nascent strand peak calling the SICER program was used. Nascent strand reads were called by comparison to HCT116 genomic reads using a window size of 200bp, gap size of 600pb, and FDR of 0.00001. For ChiP sequencing peak calling, the SICER program was used except for H4K16Ac ChIP, which are called peaks by broad MACS. For peak calling, used same length sequenced genomic control (101bp or 125bp)
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

source_name: Colon carcinoma

growth_protocol: Cancer cells were grown in DMEM medium, 10% FBS

extract_protocol:
DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using each antibodies. Enriched DNA molecules were then amplified randam primer with klenow fragment and sequenced by Illumina Genome Analyzer IIx.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).
Illumina paired-end sequencing

value: Cultured cancer cell line

tag: chip antibody


title: U2OS H3K4me3 ChIP-seq

description: ChipSeq for H3K4me3

source_name: Osteosarcoma

value: H3K4me3 antibody (9751P, Cell Signaling)


title: U2OS CUL4A ChIP-seq

description: ChipSeq for CUL4A

value: CUL4A antibody (ab92554, Abcam)


title: U2OS H3K9me3 ChIP-seq

description: ChipSeq for H3K9me3

value: H3K9me3 antibody (13969P, Cell Signaling)


title: GnRH antagonist sample 3

city: shanghai

first: Mingjie

last: Wang

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

hyb_protocol: Labeled cRNAs were hybridized onto the microarray according to manufacture's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quatified using Agilent Feature Extraction Software (version 10.7.1.1)

data_processing: The data were quantile normalized and background adjusted using  package marray under R 3.4.1.

source_name: endometrial tissue_GnRH antagonist treated

label_protocol: Agilent standard protocol

growth_protocol: Tissue samples were frozen at –80°C before RNA extraction.

extract_protocol: Total RNA extracted using Trizol following the manufacture's instructions.

tag: subject status

value: patients with IVF/ICSI cycles

tag: gender

value: female

tag: subject group

value: GnRH antagonist protocol

value: endometrial tissue


title: COV362_DMSO_rep1

description:
Cov_DMSO_0
processed data file: THZ1_analysis_Cov_all_fpkm_exprs_norm.txt

value: human ovarian cancer cell line

value: untransduced control

value: DMEM + 10% Fetal Bovine Serum + 1% Pen/Strep


title: leaf_M.sexta_oviposition_ M.sexta_feeding_rep1

value: 15x WT inbred line

value: M. sexta oviposited M. sexta fed

value: leaf


title: KURAMOCHI_THZ1_250nM_rep1

description:
Ku_THZ1_250nM_0
processed data file: THZ1_analysis_Ku_all_fpkm_exprs_norm.txt

value: KURAMOCHI

value: RPMI + 10% Fetal Bovine Serum + 1% Pen/Strep

value: THZ1_250nM for 6 hours


title: leaf_M.sexta_feeding_rep3

source_name: leaf, M. sexta fed

value: M. sexta fed


title: U2OS CDT2 ChIP-seq

description: ChipSeq for CDT2

value: Cultured cancer cell line

value: CDT2 antibody (ab72264, Abcam)


title: Colon_Balb/c_female_repl1

tag: Sex

tag: mouseid

value: standard, low fat diet (formulation according to Research Diets Inc.:D12450B)

value: proximal colon

tag: genotype

value: wildtype

value: Balb/c


title: Input from HCT116 RepID KO cells

tag: cell line


title: GnRH antagonist sample 1

value: patients with IVF/ICSI cycles

value: female

value: GnRH antagonist protocol

value: endometrial tissue


title: Colon_C57Bl/6_female_repl1

source_name: proximal colon, C57bl/6 mouse, female


title: leaf_M.sexta_oviposition_ M.sexta_feeding_rep2

value: 15x WT inbred line


title: leaf_S.exigua_oviposition_S.exigua_feeding_rep3

source_name: leaf, S. exigua oviposited S. exigua fed

value: S. exigua oviposited S. exigua fed


title: leaf_M.sexta_feeding_rep1

value: leaf


title: GnRH antagonist sample 2


title: GnRH agonist sample 2

source_name: endometrial tissue_GnRH agonist treated

value: GnRH agonist long protocol


title: GnRH agonist sample 3


title: leaf_S.exigua_oviposition_S.exigua_feeding_rep1


title: KURAMOCHI_THZ1_50nM_rep1

description:
Ku_THZ1_50nM_0
processed data file: THZ1_analysis_Ku_all_fpkm_exprs_norm.txt

value: KURAMOCHI

value: human ovarian cancer cell line

value: untransduced control

value: RPMI + 10% Fetal Bovine Serum + 1% Pen/Strep

value: THZ1_50nM for 6 hours


title: Input from HCT116 WT cells

value: Cultured cancer cell line


title: KURAMOCHI_THZ1_50nM_rep2

description:
Ku_THZ1_50nM_1
processed data file: THZ1_analysis_Ku_all_fpkm_exprs_norm.txt


title: DPBS_3

city: Seoul

first: Suji

last: Kim

state: Gwanak-gu

address: 1, Gwanak-ro

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

data_processing:
RTA(Real Time Analysis) software used for basecalling.
To estimate expression levels and to find alternative spliced transcripts, the RNA-seq reads were mapped to the genome of sus scrofa using TopHat (Trapnell et al., 2009), which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks software (Trapnell et al., 2010) in default options.
Raw data were calculated as FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments) of each transcript in each sample cufflinks software. We excluded the transcripts with zeroed FPKM values more than on for total samples. We added 1 with FPKM value of the filtered transcript to facilitate log2 transformation. Filtered data was transformed by logarithm and normalized by quantile normalization method. For each transcript, we conducted independent t-test between case and control. Each transcript was determined using independent t-test.
Genome_build: Sscrofa11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sus scrofa

source_name: porcine alveolar macrophage cells

growth_protocol: Porcine alveolar macrophages (PAMs, 3D4/31, ATCC CRL-2844) was cultured in Roswell Park Memorial Institute medium (RPMI) 1640 (Gibco, USA) with 10% fetal bovine serum (FBS; Gibco), penicillin (100U/mL), and streptomycin (100 µg/mL). Cells were cultivated in a humidified incubator with 5% CO2 at 37℃.

extract_protocol:
total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 12h-cluture of PAMs at a concentration of 1×106 cells/well in 6-well cultures plates containing 2% FBS, penicillin (100U/mL), and streptomycin (100 µg/mL), cells were stimulated with the recombinant proteins of Apx toxins at 10µg/ml and DPBS as a negative control. Following centrifugation at 125×g for 5min at 20℃, the treated cells were incubated at 37℃ under 5% CO2 atmosphere for 24h.

value: lung

tag: age

value: 27 days

tag: agent

value: DPBS


title: DPBS_2

value: wildtype


title: KURAMOCHI_DMSO_rep1

description:
Ku_DMSO_0
processed data file: THZ1_analysis_Ku_all_fpkm_exprs_norm.txt

value: DMSO for 6 hours


title: ApxIVAC2_1

value: antigenic epitopes of actinobacillus pleuropneumoniae IVA


title: ApxIVAC1_3


title: KURAMOCHI_DMSO_rep2

description:
Ku_DMSO_1
processed data file: THZ1_analysis_Ku_all_fpkm_exprs_norm.txt


title: HCT116 RepID KO SKP2 ChIP-seq

description: ChipSeq for SKP2

value: SKP2 antibody (ab68455, Abcam)


title: ApxIVAC1_1


title: HCT116 RepID KO NS

description: HCT116 RepID KO clone nascent strand DNA

data_processing:
Library strategy: Nascent DNA
For RepID ChIP, the MACS peak calling program was used comparing reads from the ChIP –seq experiment to genomic input reads from the same cell line, with default parameters, and a p-value = 1e-9.
For nascent strand peak calling the SICER program was used. Nascent strand reads were called by comparison to HCT116 genomic reads using a window size of 200bp, gap size of 600pb, and FDR of 0.00001. For ChiP sequencing peak calling, the SICER program was used except for H4K16Ac ChIP, which are called peaks by broad MACS. For peak calling, used same length sequenced genomic control (101bp or 125bp)
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq


title: ApxIIANt_1

value: antigenic epitopes of actinobacillus pleuropneumoniae IIA


title: HCT116 WT SKP2 ChIP-seq

description: ChipSeq for SKP2


title: ApxIACt_2

value: antigenic epitopes of actinobacillus pleuropneumoniae ApxIA


title: ApxIVAC2_2


title: U2OS WT NS

description: unsynchronized untreated U2OS nascent strand DNA


title: ApxIACt_1


title: Control sample 3

source_name: endometrial tissue_healthy control

value: patients with IVF/ICSI cycles

value: female

value: untreated healthy control

value: endometrial tissue


title: ApxIIANt_3


title: leaf_S.exigua_oviposition_S.exigua_feeding_rep2

tag: line

value: 15x WT inbred line

tag: treament

value: S. exigua oviposited S. exigua fed

value: leaf


title: Control sample 2

tag: tissue


title: GnRH agonist sample 1

value: GnRH agonist long protocol


title: leaf_S.exigua_feeding_rep2

source_name: leaf, S. exigua fed

value: S. exigua fed


title: leaf_M.sexta_oviposition_rep1

source_name: leaf, M. sexta oviposited

value: M. sexta oviposited


title: leaf_M.sexta_oviposition_rep2


title: leaf_S.exigua_oviposition_rep2

source_name: leaf, S. exigua oviposited

value: S. exigua oviposited


title: leaf_S.exigua_oviposition_rep3


title: leaf_S.exigua_feeding_rep3


title: Subject 11118 baseline

status: Public on Jun 26 2018

city: Boston

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression data from bronchial epithelial cells collected by bronchoscopic brushing at baseline.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene10sthsentrezg R package (version 16.0.0).

source_name: Bronchial epithelial cells

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: The brushes were immediately placed in TRIzol reagent (Invitrogen) after removal from the bronchoscope and kept at -80°C until RNA isolation was performed. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA). Integrity of the RNA samples was assessed by Agilent BioAnalyzer, and purity of the RNA was confirmed using a NanoDrop spectrophotometer.

treatment_protocol: Study participants were asked to refrain from cigarette smoking for at least two days (verified by exhaled CO < 6 ppm) and then smoke three cigarettes in the span of one hour. Subjects then underwent fiberoptic bronchoscopy after 24 hours where samples were collected. In like manner, subjects abstained from smoking and underwent bronchoscopy at a separate time at least 6 weeks from the post-smoking bronchoscopy to serve as an unexposed baseline sample (also verified by exhaled CO < 6 ppm). In both instances, bronchial brushings were collected from the 1st and 2nd subsegmental branches of the left lower lobe.

tag: smoke exposure

value: baseline

tag: rin


title: leaf_S.exigua_feeding_rep1


title: leaf_S.exigua_oviposition_rep1


title: Subject 11116 post-ASE

description: Gene expression data from bronchial epithelial cells collected by bronchoscopic brushing 24 hours after acute smoke exposure (ASE)..

value: post-ASE

value: male


title: Subject 11118 post-ASE


title: Subject 11117 post-ASE


title: Subject 11119 baseline


title: Subject 11116 baseline


title: Subject 11120 baseline


title: Control sample 1


title: leaf_M.sexta_oviposition_rep3


title: Subject 11120 post-ASE


title: KURAMOCHI_THZ1_250nM_rep2

description:
Ku_THZ1_250nM_1
processed data file: THZ1_analysis_Ku_all_fpkm_exprs_norm.txt

value: KURAMOCHI

tag: cell type

value: human ovarian cancer cell line

tag: genotype/variation

value: untransduced control

tag: culture condition

value: RPMI + 10% Fetal Bovine Serum + 1% Pen/Strep

value: THZ1_250nM for 6 hours


title: leaf_control_rep2

source_name: leaf, undamaged control

value: undamaged control


title: Subject 11119 post-ASE


title: Subject 11117 baseline

value: female


title: Subject 11115 post-ASE


title: Subject 11111 baseline


title: Subject 11115 baseline


title: Subject 11111 post-ASE


title: leaf_control_rep1

value: 15x WT inbred line


title: Subject 11110 baseline


title: Subject 11110 post-ASE


title: Subject 11108 post-ASE


title: Subject 11108 baseline


title: Subject 11092 baseline


title: Subject 11102 post-ASE


title: Subject 11103 baseline


title: Subject 11096 baseline


title: Subject 11109 baseline


title: Subject 11091 baseline


title: Subject 11091 post-ASE


title: Subject 11102 baseline


title: Subject 11086 post-ASE


title: Subject 11096 post-ASE


title: Subject 11103 post-ASE


title: Subject 11092 post-ASE


title: Subject 11084 baseline


title: Subject 11080 post-ASE


title: Subject 11077 baseline


title: Subject 11085 post-ASE


title: Subject 11078 baseline


title: Subject 11083 post-ASE


title: Subject 11084 post-ASE


title: Subject 11086 baseline


title: Subject 11083 baseline


title: Subject 11080 baseline


title: Subject 11078 post-ASE


title: Subject 11077 post-ASE


title: Subject 11085 baseline


title: Subject 11075 baseline


title: Subject 11070 post-ASE


title: Subject 11075 post-ASE


title: Subject 11070 baseline


title: Subject 11069 post-ASE


title: Subject 11068 post-ASE


title: Subject 11062 baseline


title: Subject 11069 baseline


title: Subject 11057 post-ASE


title: leaf_M.sexta_feeding_rep2

value: M. sexta fed


title: Subject 11062 post-ASE


title: Subject 11057 baseline


title: Subject 11059 post-ASE


title: Subject 11051 post-ASE


title: Subject 11051 baseline


title: Subject 11038 baseline


title: Subject 11038 post-ASE


title: Subject 11039 baseline


title: Subject 11068 baseline


title: Subject 11056 post-ASE


title: Subject 11052 post-ASE


title: Subject 11056 baseline


title: Subject 11059 baseline


title: Subject 11041 post-ASE


title: Subject 11049 post-ASE


title: Subject 11037 baseline


title: Subject 11039 post-ASE


title: Subject 11037 post-ASE


title: Subject 11052 baseline


title: Subject 11049 baseline


title: Subject 11035 post-ASE


title: Subject 11041 baseline


title: Subject 11035 baseline


title: Subject 11034 baseline


title: Subject 11030 baseline


title: Subject 11032 post-ASE


title: Subject 11032 baseline


title: Subject 11029 post-ASE


title: Subject 11027 baseline


title: Subject 11034 post-ASE


title: Subject 11029 baseline


title: Subject 11023 post-ASE


title: Subject 11027 post-ASE


title: Subject 11028 baseline


title: Subject 11024 baseline


title: Subject 11023 baseline


title: Subject 11019 post-ASE


title: Subject 11024 post-ASE


title: Subject 11016 baseline


title: Subject 11020 baseline


title: Subject 11018 baseline


title: Subject 11018 post-ASE


title: Subject 11030 post-ASE


title: Subject 11019 baseline


title: Subject 11020 post-ASE


title: Subject 11028 post-ASE


title: Subject 11016 post-ASE


title: Subject 11017 baseline


title: Subject 11014 baseline


title: Subject 11109 post-ASE


title: Subject 11014 post-ASE


title: Subject 11013 post-ASE


title: Subject 11017 post-ASE


title: Subject 11013 baseline


title: Subject 11012 post-ASE


title: Subject 11011 post-ASE


title: Subject 11011 baseline


title: Subject 11009 post-ASE


title: Subject 11007 post-ASE


title: Subject 11008 baseline


title: Subject 11009 baseline


title: Subject 11008 post-ASE


title: Subject 11003 baseline


title: Subject 11004 post-ASE


title: Subject 11005 post-ASE


title: Subject 11007 baseline


title: Subject 11006 baseline


title: Subject 11003 post-ASE


title: Subject 11005 baseline


title: Subject 11006 post-ASE


title: Subject 11002 post-ASE


title: Subject 11012 baseline


title: leaf_control_rep3

value: leaf


title: Subject 11004 baseline


title: Subject 11002 baseline


title: Genomic DNA from nasal epithelial cells [ESS063_A1]

type: genomic

city: Davis

first: Hong

last: Ji

state: CA

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

description: Nasal epithelial cells obtained by nasal brushing

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: RnBeads

label: Cy5 and Cy3

source_name: Nasal epithelial cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen Allprep micro kit according to manufacturer’s  instructions.

value: Nasal epithelial cells

value: Male

tag: diagnosis

value: asthma


title: Genomic DNA from nasal epithelial cells [ESS093_S1]

tag: gender

value: Female

value: control


title: Genomic DNA from nasal epithelial cells [ESS055_S1]


title: Genomic DNA from nasal epithelial cells [ESS059_A1]


title: Genomic DNA from nasal epithelial cells [ESS097_S1]


title: Genomic DNA from nasal epithelial cells [ESS097_A1]


title: Genomic DNA from nasal epithelial cells [ESS059_S1]


title: Genomic DNA from nasal epithelial cells [ESS093_A1]


title: Genomic DNA from nasal epithelial cells [ESS061_A1]


title: Genomic DNA from nasal epithelial cells [ESS055_A1]


title: Genomic DNA from nasal epithelial cells [ESS047_S1]


title: Genomic DNA from nasal epithelial cells [ESS053_A1]


title: Genomic DNA from nasal epithelial cells [ESS061_S1]


title: Genomic DNA from nasal epithelial cells [ESS047_A1]


title: Genomic DNA from nasal epithelial cells [ESS045_A1]


title: Genomic DNA from nasal epithelial cells [ESS035_S1]


title: Genomic DNA from nasal epithelial cells [ESS033_S1]


title: Genomic DNA from nasal epithelial cells [ESS063_S1]


title: Genomic DNA from nasal epithelial cells [ESS049_A1]


title: Genomic DNA from nasal epithelial cells [ESS041_S1]


title: Genomic DNA from nasal epithelial cells [ESS029_S1]


title: Genomic DNA from nasal epithelial cells [ESS039_A1]


title: Genomic DNA from nasal epithelial cells [ESS039_S1]


title: Genomic DNA from nasal epithelial cells [ESS033_A1]


title: Genomic DNA from nasal epithelial cells [ESS045_S1]


title: Genomic DNA from nasal epithelial cells [ESS049_S1]


title: Genomic DNA from nasal epithelial cells [ESS053_S1]


title: Genomic DNA from nasal epithelial cells [ESS035_A1]


title: Genomic DNA from nasal epithelial cells [ESS041_A1]


title: Genomic DNA from nasal epithelial cells [ESS025_A1]


title: Genomic DNA from nasal epithelial cells [ESS023_A1]


title: Genomic DNA from nasal epithelial cells [ESS029_A1]


title: Genomic DNA from nasal epithelial cells [ESS025_S1]


title: Genomic DNA from nasal epithelial cells [ESS015_A1]


title: Genomic DNA from nasal epithelial cells [ESS021_S1]


title: Genomic DNA from nasal epithelial cells [ESS027_A1]


title: Genomic DNA from nasal epithelial cells [ESS017_A1]


title: Genomic DNA from nasal epithelial cells [ESS017_S1]


title: Genomic DNA from nasal epithelial cells [ESS021_A1]


title: SNU475 S110 D56 NOE

city: Los Angeles

first: Gangning

last: Liang

address: 925 W 34th St

institute: University of Southern California

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

data_processing: BeadStudio software v3.2

growth_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

extract_protocol: Standard Illumina Protocol

treatment_protocol: Standard Illumina Protocol

tag: treatment

tag: day

tag: msssi

value: N


title: SNU475 S110 D28 +M.SssI

value: Y


title: Genomic DNA from nasal epithelial cells [ESS013_A1]


title: Genomic DNA from nasal epithelial cells [ESS023_S1]


title: SNU475 S110 D56 +M.SssI


title: Genomic DNA from nasal epithelial cells [ESS019_S1]


title: Genomic DNA from nasal epithelial cells [ESS013_S1]


title: Genomic DNA from nasal epithelial cells [ESS027_S1]


title: Genomic DNA from nasal epithelial cells [ESS011_S1]


title: Genomic DNA from nasal epithelial cells [ESS011_A1]


title: Genomic DNA from nasal epithelial cells [ESS007_A1]


title: SNU475 S110 D14 NOE


title: SNU475 PBS  +M.SssI

value: PBS


title: SNU475 S110 D28 NOE


title: Genomic DNA from nasal epithelial cells [ESS019_A1]


title: SNU475 S110 D7 NOE


title: Genomic DNA from nasal epithelial cells [ESS015_S1]


title: Genomic DNA from nasal epithelial cells [ESS009_A1]


title: Genomic DNA from nasal epithelial cells [ESS007_S1]


title: SNU475 S110 D21 +M.SssI


title: SNU475 S110 D0 +M.SssI


title: Genomic DNA from nasal epithelial cells [ESS005_S1]


title: SNU475 S110 D14 +M.SssI


title: Genomic DNA from nasal epithelial cells [ESS005_A1]


title: SNU475 S110 D7 +M.SssI


title: SNU475 S110 D21 NOE


title: SNU398 PBS  +M.SssI


title: Genomic DNA from nasal epithelial cells [ESS003_S1]


title: SNU398 S110 D0 +M.SssI


title: SNU398 S110 D7 NOE


title: Genomic DNA from nasal epithelial cells [ESS009_S1]


title: SNU398 S110 D21 +M.SssI


title: Genomic DNA from nasal epithelial cells [ESS001_A1]


title: SNU398 S110 D14 NOE


title: HepG2 S110 D0 +M.SssI


title: Genomic DNA from nasal epithelial cells [ESS001_S1]


title: HepG2 S110 D7 NOE


title: SNU475 S110 D0 NOE


title: SNU398 S110 D7 +M.SssI


title: HepG2 S110 D0 NOE


title: HepG2 S110 D21 +M.SssI


title: SNU475 PBS  NOE


title: SNU398 S110 D0 NOE


title: SNU398 S110 D14 +M.SssI


title: HepG2 S110 D14 +M.SssI


title: Total RNA - sh309 - Replicate C

city: Liegge

first: pierre

last: close

address: Avenue de l'hopital

department: GIGA-Institute

country: Belgium

institute: University of Liege

description:
sh309_C_RNA
Related to sample Ribosome-Protected Fragments - shELP3 - Replicate C

data_processing:
Library strategy: Ribo-Seq
Illumina bcl2fastq was used to generate fastq files with adapters trimmed
Fastx toolkit was used to trim reads to 55bp
Reads mapping to rRNA and tRNA were discarded using Bowtie
Alignment to mouse genome was performed with Tophat 2.1.1 using the genes.gtf from iGenomes
Gene read counts were generated using HTSeq count in union mode
Genome_build: mm10 (from iGenomes)
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for all samples

source_name: B16 melanoma cell line

growth_protocol: DMEM + 10% FBS + 1% Pen-strep + 1% L-glutamine

extract_protocol:
TruSeq Ribo Profile (Mammalian) protocol - Illumina
TruSeq Ribo Profile (Mammalian) Library Prep Kit - Illumina

treatment_protocol: transduction with shRNA lentivirus expressing either non-relevant shRNA (shCTL) or Elp3-specific shRNA (sh309)

value: melanoma cell line

tag: rna fraction

value: Total RNA after rRNA depletion

tag: shRNA treatment

tag: replicate

value: C


title: SNU398 S110 D21 NOE

tag: cell line


title: HepG2 PBS  NOE


title: HepG2 PBS  +M.SssI


title: Total RNA - sh309 - Replicate A

description:
sh309_A_RNA
Related to sample Ribosome-Protected Fragments - shELP3 - Replicate A

value: A


title: Total RNA - sh309 - Replicate B

description:
sh309_B_RNA
Related to sample Ribosome-Protected Fragments - shELP3 - Replicate B

value: B


title: Total RNA - shCTL - Replicate C

description:
shCTL_C_RNA
Related to sample Ribosome-Protected Fragments - shCTRL - Replicate C

value: shControl


title: SNU398 PBS  NOE


title: HepG2 S110 D14 NOE


title: HepG2 S110 D7 +M.SssI


title: CD8+ 24h rep 2 S

city: Jerusalem

first: Itamar

last: Simon

state: APO/FPO IRAQ / AFGHANISTAN / MIDDLE EAST

address: Hadassah Ein Kerem

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University medical school

data_processing:
Library strategy: DNA-seq
Sequencing reads were aligned to mouse genome (mm9) using bowtie2.  Unmapped or discordant pairs were removed.
Duplicates were removed using Picard markduplicates.
RT measurements were performed as described (Yehuda et al. 2017).  Every 200 G1 phase reads were binned in order to establish genomic windows. Corresponding S phase reads were counted in order to determine an S/G1 ratio for each window. Ratio data was normalized by subtracting the mean and dividing by the standard deviation. Continuous data was smoothed and interpolated using the Matlab csaps function (10e-16) at a resolution of 100kb (approximate average size of the windows). Continuous segments containing under 15 informative windows were removed from the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files containing normalized replication timing data

growth_protocol: C57Bl/6J mouse spleen was processed and erythrocytes were lysed (155mM NH4Cl, 10mM KHCO3, 0.1mM EDTA). For each experiment, 3X106 splenocytes were moved to a 24 well plate and activated for 24-48h in RPMI medium (BI) containing 1µg/ml anti CD3 (2C11, BioLegend) and supplemented with penicillin, streptomycin, and 10% v/v heat-inactivated (56°C, 30 min) FBS (BI). Activated splenocytes were stained with anti CD8-Pacific blue (J3.6.7, BioLegend) 1:500 and anti CD90.2-APC (H12, BioLegend) 1:500.

extract_protocol:
Cells were sorted by FACS into S and G1 phase portions
Library preparation was done similar to Blecher-Gonen et al. (Blecher-Gonen et al. 2013) with some changes. Briefly, Sonicated DNA was subjected to a 50µl end repair reaction using 1µl End repair mix (E6050L, NEB), cleaned by 1.8X AmpureXP beads, followed by a 50µl A-tail reaction using 2µl Klenow fragment exo- (M0212L, NEB). The products were cleaned by 1.8X beads and were ligated by 2µl quick ligase (M2200, NEB) to 0.75µM illumina compatible forked indexed adapters. Ligation products were size selected by 0.7X PEG (considering the PEG in the ligation buffer) in order to remove free adaptors. 12-19 cycles of amplification were performed by PFU Ultra II Fusion DNA polymerase (600670, Agilent) with the following Primers:   P7 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC 3’,   P5 5' CAAGCAGAAGACGGCATACGAGAT 3’.   Amplified DNA was size selected for 300-700bp fragments by taking the supernatant after using 0.5X beads (which removed fragments greater than 700bp) followed by a 1.0X beads cleaning (which removed remaining primers and adapter dimers). The final quality of the library was assessed by Qubit and TapeStation. Libraries were pooled and sequenced on NextSeq (illumina) for 75 bp paired-end sequencing, generating 10M reads per each library (60M per experiment for triplicates of G1 and S).

tag: phase

value: S


title: CD8+ 24h rep 1 G1


title: CD8+ 24h rep 3 S


title: CD8+ 24h rep 3 G1


title: CD8+ 24h rep 2 G1


title: CD8+ 24h rep 1 S


title: Total RNA - shCTL - Replicate A

description:
shCTL_A_RNA
Related to sample Ribosome-Protected Fragments - shCTRL - Replicate A


title: Ribosome-Protected Fragments - sh309 - Replicate C

description:
sh309_C_RPF
Related to sample Total RNA - shELP3 - Replicate C

value: Ribosome-protected fragments


title: Ribosome-Protected Fragments - sh309 - Replicate A

description:
sh309_A_RPF
Related to sample Total RNA - shELP3 - Replicate A


title: Ribosome-Protected Fragments - shCTL - Replicate C

description:
shCTL_C_RPF
Related to sample Total RNA - shCTRL - Replicate C


title: HepG2 S110 D21 NOE


title: Ribosome-Protected Fragments - shCTL - Replicate B

description:
shCTL_B_RPF
Related to sample Total RNA - shCTRL - Replicate B


title: Ribosome-Protected Fragments - shCTL - Replicate A

description:
shCTL_A_RPF
Related to sample Total RNA - shCTRL - Replicate A


title: Total RNA - shCTL - Replicate B

description:
shCTL_B_RNA
Related to sample Ribosome-Protected Fragments - shCTRL - Replicate B


title: lung in presence of distal tumor 6879 batch 1

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_tumorbearing_Mouse ID 6879_1

data_processing:
Pseudoalignment with salmon, version ,0.9.1
Import and summarize salmon generated counts with tximport, version 1.6.0
Analyze differential expression with DESeq2 BioConductor package, version 1.18.1
Genome_build: mm10
Supplementary_files_format_and_content: comma separated format, rawCounts matrix file contains raw counts as generated by Salmon and imported by tximport (these counts were used for the DESeq2 analysis), tpm matrix contains transcripts per million normalized counts as calculated by tximport

source_name: lung

growth_protocol: Female FVB mice 7 weeks of age were purchased from Taconic Biosciences (Hudson, NY). All experiments were conducted in accordance with regulations of the Children’s Hospital institutional animal care and use committee (protocol 15-11-3062R) and Brigham and Women’s Hospital animal care protocol committee (2017N000056). Mice were 8 weeks of age at time of injections. Met1 breast cancer cell line was orthotopically injected (250,000 cells/mouse in 20 µl PBS) into the inguinal mammary fat pads. 2 weeks after injection mice were sacrified, 20mg from tumors and lungs were snap frozen, and RNA was extracted.

extract_protocol:
Frozen samples were incubated with 600 ul of Lysis Buffer (RNeasey Plus Mini kit, Qiagen) and 20U of RNAse inhibitors/sample (Applied Biosystems), and immediately disrupted and homogenized with a rotor-stator homogenizer. RNA was extracted using the RNeasey Plus Mini Kit, according to the manufacturer’s instructions. Final RNA was resuspended in 50 ul of RNase-free water and 20U of RNAse inhibitors/sample.
Purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score > 7 as well as RNA samples with a RIN < 7 but DV200 > 50% were fragmented at 94C for 8min according to manufacturer’s recommendation. RNA samples with RIN < 7 and DV200 < 50% were not fragmented and RT primers were annealed at 65C for 1min. Libraries were prepared using Roche Kapa Biosystems RiboErase and RNA HyperPrep sample preparation kits from 100ng of RNA. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: tumor present

value: yes

tag: strain

value: FVB

tag: preparation batch

tag: age

value: 10 weeks


title: Genomic DNA from nasal epithelial cells [ESS003_A1]

tag: tissue

value: Nasal epithelial cells

value: Male

value: asthma


title: lung in presence of distal tumor 6881 batch 1

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_tumorbearing_Mouse ID 6881_1


title: lung in presence of distal tumor 6880 batch 1

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_tumorbearing_Mouse ID 6880_1


title: normal lung 6893 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_normal_NA_Mouse ID 6893_2

value: no


title: normal lung 6888 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_normal_NA_Mouse ID 6888_Repet 2


title: breast tumor 6880 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
Met1 breast_tumor_Mouse ID 6880_2

source_name: mammary tumor


title: Ribosome-Protected Fragments - sh309 - Replicate B

description:
sh309_B_RPF
Related to sample Total RNA - shELP3 - Replicate B

tag: cell type


title: breast tumor 6881 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
Met1 breast_tumor_Mouse ID 6881_2


title: normal lung 6886 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_normal_NA_Mouse ID 6886_Repet 2


title: Slfn2 KO + IFNβ 1

city: CHICAGO

first: Mariafausta

last: Fischietti

state: ILLINOIS

address: 303 E. Superior Street

department: Hematology/Oncology Robert H Lurie Comprehensive Cancer Center

institute: Northwestern University

data_processing:
Adapters were trimmed using cutadapt version 1.13
Trimmed reads were aligned to mouse reference genome mm10 using STAR version STAR_2.5.2a
Count files were generated using htseq-count version version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each Sample

source_name: Mouse embryonic fibroblasts

growth_protocol: The immortalized Slfn2 WT and Slfn2 KOMEFs were cultured in DMEM supplemented with 10% FBS and antibiotics and incubated at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Slfn2 WT and Slfn2 KO MEFs were plated in duplicate/triplicate and were left untreated or were treated for 6 hours with 5x103 IU/ml of mouse IFNβ

value: Mouse embryonic fibroblasts

tag: genotype

value: Slfn2 KO

value: IFNbeta


title: Slfn2 KO untreated 1

value: untreated


title: Slfn2 KO untreated 2


title: Slfn2 WT + IFNβ 2

value: Slfn2 WT


title: Slfn2 KO + IFNβ 2


title: Slfn2 WT + IFNβ 3


title: breast tumor 6877 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
Met1 breast_tumor_Mouse ID 6877_2


title: lung in presence of distal tumor 6877 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_tumorbearing_Mouse ID 6877_2


title: normal lung 6887 batch 2

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_normal_NA_Mouse ID 6887_2


title: Slfn2 WT untreated 2


title: Slfn2 WT untreated 3


title: normal lung 6888 batch 1

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_normal_NA_Mouse ID 6888_Repet 1


title: normal lung 6886 batch 1

description:
RNA extracted with RNeasey Plus Mini kit, Qiagen
lung_normal_NA_Mouse ID 6886_Repet 1


title: pre-b rep 3 G1

source_name: pre-b

growth_protocol: Cells isolated from the bone marrow of female C57BL6 mouse (10 weeks old) were grown in RPMI 1640 media (Gibco) supplemented with 10% fetal bovine serum (Hyclone), penicillin–streptomycin (Gibco), L-glutamine (Gibco) and 50 μM of β-Mercaptoethanol (Gibco) on irradiated ST2 feeder cells. IL-7 conditioned medium (collected from J558L-IL7 secreting cells provided by A. Rolink) was added to the cells to select for pre-B cell populations for14 days.


title: pre-b rep 2 S


title: pre-b rep 3 S


title: pre-b rep 1 G1


title: pre-b rep 2 G1


title: Slfn2 WT + IFNβ 1


title: Slfn2 WT untreated 1


title: SSC rep 2 G1

source_name: SSC

growth_protocol: SSC culture was prepared from the testis of 4-7 days old F1 C57/Bl6 crossed with DBA male mice, according to Kubota et al. (Kubota and Brinster 2008) with minor modifications. Testis cells suspensions were obtained using trypsin (BI) and DNAse (Sigma). Thy1+ cells were isolated using magnetic microbeads conjugated with anti-Thy-1 antibody (Miltenyi Biotec). Cells were examined for their replenishment potential in busulfan treated NODSCID mice.


title: SSC rep 1 S


title: PGC Male rep 3 S

source_name: PGC

growth_protocol: Oct4-GFP+/+, Sox2-GFP+/- and M2rtTA+/+ mice were obtained from Jackson Labs. Oct4-GFP+/+ mice and Sox2-GFP+/- mice were bred to M2rtTA mice and females were sacrificed on day 13.5 of pregnancy. GFP positive cells were isolated from E13.5 gonads of either Oct4-GFP+/+ or Sox2-GFP+/- mouse embryos, resulting a pure population of PGCs (Yabuta et al. 2006), according to the following procedure. Embryos were dissected in PBS under the microscope. GFP-positive gonads were chosen by observation in fluorescent microscope and 4-8 embryos were processed per experiment. Gonads and mesonephros were first dissected and then separated into single cells using trypsin (BI) and 700µg/ml DNAse (sigma), followed by neutralization using FBS (BI). Cells were washed with PBS (BI), and filtered through 35µm mesh into 5ml polystyrene tubes (BD). GFP+ cells were isolated using FACSARIA III (BD) using cold conditions


title: SSC rep 1 G1


title: SSC rep 3 G1


title: pre-b rep 1 S


title: PGC Male rep 1 S


title: PGC Male rep 3 G1


title: PGC Male rep 2 S


title: PGC Female rep 2 S


title: PGC Female rep 2 G1


title: SSC rep 2 S


title: PGC Male rep 1 G1


title: EPN-PFA SAMPLE 644

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'

label: biotin/DNP

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: diagnosis

value: EPN-PFA

tag: Sex

value: M

tag: institute

value: SK

tag: os

tag: OS status

tag: pfs

tag: pfs status


title: PGC Female rep 1 S

value: S


title: MEF 1X10^4 rep 3 S

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts (MEFs) were cultured in DMEM medium (BI) supplemented with penicillin, streptomycin, L-Glutamine and 20% v/v heat-inactivated (56°C, 30 min) FBS (BI).


title: MEF 1X10^4 rep 2 S


title: MEF 1X10^5 rep 2 S


title: EPN-PFA SAMPLE 541

value: SJ

value: wt


title: SSC rep 3 S


title: MEF 1X10^3 rep 3 S


title: MEF 1X10^3 rep 2 S


title: MEF 1X10^5 rep 1 S


title: MEF 1X10^4 rep 1 S


title: PGC Male rep 2 G1


title: PGC Female rep 1 G1


title: MEF 1X10^5 rep 3 G1


title: MEF 1X10^3 rep 1 S


title: MEF 1X10^4 rep 3 G1


title: MEF 1X10^3 rep 3 G1


title: MEF 1X10^5 rep 2 G1


title: MEF 1X10^3 rep 2 G1


title: MEF 1X10^4 rep 2 G1


title: MEF 1X10^5 rep 3 S


title: Edge1.3

city: Vancouver

first: Evelyn

last: Sun

state: BC

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina GAIIx
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the PA14 genome using bowtie2
Bam-sam file conversion/sorting was conducted using samtools
read count tables were generated using htseq-count v.2.5
Genome_build: UCBPP-PA14 (GenBank gene annotations)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: bacteria_surfing colony_edge

growth_protocol: Surfing colonies were grown in synthetic cystic fibrosis media (SCFM) with 0.3% agar and 0.4% mucin wt/vol. Planktonic cells were grown in liquid SCFM without mucin (swimming)

extract_protocol:
RNA stabilized using RNAprotect Bacteria (Qiagen), extracted using Rneasy Mini Kit (Qiagen), DNAase treated using TURBO DNA-free kit (Thermo Fisher), rRNA depletion conducted with Ribozero Bacteria kit (Illumina - USA)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

tag: growth condition

value: surfing colony (edge)

tag: molecule subtype

value: ribosomally depleted RNA


title: Edge1.2


title: Edge1.1


title: MEF 1X10^4 rep 1 G1

tag: phase


title: MEF 1X10^5 rep 1 G1


title: Planktonic1.2

source_name: bacteria_planktonic cells

value: planktonic cells


title: MEF 1X10^3 rep 1 G1


title: Center1.3

source_name: bacteria_surfing colony_center

value: surfing colony (center)


title: Center1.1


title: Center1.2


title: center3

description: ribosomally depleted RNA

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the PA14 genome using bowtie2
Bam-sam file conversion/sorting was conducted using samtools
read count tables were generated using htseq-count v.2.5
Genome_build: UCBPP-PA14 (GenBank gene annotations)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

source_name: surfing colony (center)

growth_protocol: Surfing colonies were grown in synthetic cystic fibrosis media (SCFM) with 0.3% agar and 0.4% mucin wt/vol. Swimming cells were grown in SCFM with 0.3% agar without mucin (swimming)


title: center2

description: ribosomally depleted RNA


title: center1

description: ribosomally depleted RNA


title: swim3

description: ribosomally depleted RNA

source_name: swimming cells

value: swimming cells


title: edge3

description: ribosomally depleted RNA

source_name: surfing colony (edge)


title: swim2

description: ribosomally depleted RNA


title: edge2

description: ribosomally depleted RNA


title: swim1

description: ribosomally depleted RNA


title: Planktonic1.1


title: Planktonic1.3


title: edge1

description: ribosomally depleted RNA


title: NF2-associated Vestibular Schwannoma_20

city: beijing

first: zhao

last: fu

address: No. 6 Tiantan Xili Dongcheng District

institute: Beijing Neurosurgical Institute

description: Gene expression date from NF2 VS

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

source_name: Vestibular Schwannoma

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disease state

value: NF2-associated VS

tag: gender

tag: age at onset of nf2 symptoms

tag: age at diagnosis

value: VS


title: NF2-associated Vestibular Schwannoma_22

description: Gene expression date from NF2 VS

value: F

tag: tissue


title: NF2-associated Vestibular Schwannoma_24

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_15

description: Gene expression date from NF2 VS


title: EPN-PFA SAMPLE 388

tag: age


title: NF2-associated Vestibular Schwannoma_21

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_27

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_14

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_28

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_29

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_10

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_25

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_09

description: Gene expression date from NF2 VS


title: Sporadic Vestibular Schwannoma_09

description: Gene expression date from sporadic VS

value: Vestibular Schwannoma


title: NF2-associated Vestibular Schwannoma_17

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_16

description: Gene expression date from NF2 VS


title: NF2-associated Vestibular Schwannoma_19

description: Gene expression date from NF2 VS


title: Normal never_10

description: Gene expression date from normal never

source_name: Brachial plexus

value: control

value: normal control vestibular nerve


title: NF2-associated Vestibular Schwannoma_08

description: Gene expression date from NF2 VS


title: Sporadic Vestibular Schwannoma_02

description: Gene expression date from sporadic VS


title: NF2-associated Vestibular Schwannoma_11

description: Gene expression date from NF2 VS


title: Sporadic Vestibular Schwannoma_10

description: Gene expression date from sporadic VS


title: Sporadic Vestibular Schwannoma_06

description: Gene expression date from sporadic VS


title: Sporadic Vestibular Schwannoma_05

description: Gene expression date from sporadic VS


title: Sporadic Vestibular Schwannoma_08

description: Gene expression date from sporadic VS


title: Sporadic Vestibular Schwannoma_07

description: Gene expression date from sporadic VS


title: Sporadic Vestibular Schwannoma_01

description: Gene expression date from sporadic VS


title: Sporadic Vestibular Schwannoma_04

description: Gene expression date from sporadic VS


title: sRNA-cbp80-rep1

city: college station

first: Xiuren

last: Zhang

state: Texas

address: 2123 tamu

department: biochemistry & biophysics

institute: texas a&m university

data_processing:
Adapters were trimmed by FASTX-Toolkit (ver. 0.0.14)
sRNAs with lengths between 19- to 28-nt were selected and mapped using bowtie (version 1.1.2) to the Arabidopsis genomic sequences
sRNAs reads mapped to transposons or miRNAs were count by BED Tools (v2.26) with 1 bp overlapping
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: Tab-delimited text files include raw reads counts for each Sample.

organism: Arabidopsis thaliana

source_name: 10-day-old seedlings

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) reagent from 10-day-old seedlings.
sRNAs of 19-24 nt were gel-purified and ligated to a pair of adapters at the 5’ and 3’ ends by using T4 RNA ligase (NEB). sRNAs with adapters were transcribed into cDNA and amplified by Illumina sequencing-compatible primers.

tag: genotype

value: 10-day-old seedlings


title: sRNA-se_atxr-rep1


title: sRNA-se-rep1

value: se


title: sRNA-hyl1-rep1


title: sRNA-Col-rep1

value: Col


title: sRNA-atxr-rep1

value: atxr


title: sRNA-cbp80_atxr-rep2


title: sRNA-cbp80_atxr-rep3


title: sRNA-hyl1_atxr-rep1


title: sRNA-hyl1_atxr-rep2


title: sRNA-se_atxr-rep2


title: sRNA-cbp80_atxr-rep1


title: sRNA-hyl1_atxr-rep3


title: Sporadic Vestibular Schwannoma_03

description: Gene expression date from sporadic VS


title: sRNA-cbp80-rep2


title: sRNA-cbp80-rep3


title: Normal never_06

description: Gene expression date from normal never

value: M


title: Normal never_08

description: Gene expression date from normal never


title: Normal never_09

description: Gene expression date from normal never


title: sRNA-hyl1-rep2


title: sRNA-atxr-rep3


title: sRNA-hyl1-rep3


title: sRNA-se-rep3


title: se_2_atxr_rep3

data_processing:
All reads were mapped using TopHat2 (ver. 2.1.1) to the Arabidopsis genomic sequences with default parameters.
Reads mapped to selected genomic features were counted by HTSeq (ver.0.6.1) with default parameters.
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: Tab-delimited text files include raw reads counts for each Sample.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) reagent from 10-day-old seedlings.
Total RNA was extracted by RNeasy Plant Kit (Qiagen) with DNaseI treatment; and Ribosome depletion libraries were generated by Ribo-Zero Plant and TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s manual.


title: sRNA-Col-rep3


title: se_2_rep3


title: sRNA-atxr-rep2


title: se_2_rep2


title: se_2_atxr_rep2


title: sRNA-se_atxr-rep3


title: se_2_rep1


title: se_2_atxr_rep1


title: hyl1_atxr_rep3


title: sRNA-Col-rep2


title: EPN-PFA SAMPLE 326

tag: diagnosis

value: EPN-PFA

value: UK


title: hyl1_atxr_rep2


title: hyl1_atxr_rep1


title: hyl1_rep3


title: AdultMB-006

description: Gene expression in difference of subgroup

hyb_protocol: Each Slide was hybridized with 1.65μg 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=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: medulloblastoma

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).

value: Male

tag: subgroup

tag: pathology

value: CMB


title: AdultMB-008

value: WNT


title: hyl1_rep2


title: Col_0_rep3


title: hyl1_rep1


title: AdultMB-009

value: SHH

value: DNMB


title: AdultMB-007

value: Female

value: LCMB


title: AdultMB-011


title: AdultMB-012


title: Col_0_rep1


title: AdultMB-010

value: AMB


title: AdultMB-013


title: AdultMB-005


title: cbp80_atxr_rep3


title: Col_0_rep2


title: cbp80_atxr_rep1


title: cbp80_atxr_rep2


title: AdultMB-004


title: cbp80_rep3


title: cbp80_rep2


title: cbp80_rep1


title: atxr_rep3


title: AdultMB-003


title: AdultMB-002


title: atxr_rep1


title: K27me1_se-2_rep2

data_processing:
ChIP-seq reads were also mapped to the Arabidopsis genomic sequences with Bowtie (version 1.1.2), allowing up to 2 mismatches.
Only uniquely mapped reads were retained and sorted by samtools.
ChIP binding peaks were called by MACS2 (v2.1.1).
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: bedgraph files of ChIP peak calling by MACS2 (v2.1.1)

extract_protocol:
Three grams of 10-day seedlings were crosslinked with 1% formaldehyde. Lysates were clarified from sonicated protein-DNA complexes were isolated with selected antibodies. For histone modifications ChIP, Dynabeads Protein A or G Magnetic Beads (Thermo Fisher Scientific) with the anti-H3K9me2 (Abcam, cat #Ab1220); H3 (Millipore, cat # 04-745); anti-H3K27me1 (Millipore, cat #07-448) antibodies are used; Anti-FLAG M2 magnetic beads (Sigma-Aldrich, M8823) were used for FM-SE.
ChIP-seq libraries were generated using the Ovation Ultralow DR Multiplex System (NuGEN), two to ten microgram of ChIPed DNA were used as the starting DNA and 18 cycles were used for the library amplification step.

tag: chip antibody

value: anti-H3K27me1; Millipore; Cat# 07-448; lot# 2500674


title: K27me1_se-2_atxr_rep1

value: se-2 atxr5 atxr6


title: K27me1_se-2_atxr_rep2

value: 10-day-old seedlings


title: K27me1_Col-0_rep1


title: K9me2_se-2_rep2

value: anti-H3K9me2; Abcam; Cat# Ab1220; lot# 138716-4


title: AdultMB-001


title: SNU475_D56_rep2_RNA

description: SGI-110 treated, D56

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: SGI-110 treated, D56

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

growth_protocol: Human carcinoma cell lines were obtained from the American Type Culture Collection (ATCC; www.atcc.org) and cultured according to standard mammalian tissue culture protocols and sterile technique.

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.

treatment_protocol: SNU398, SNU475 and HepG2 cells were purchased form the American Type Culture Collection (ATCC; www.atcc.org), and treated with three daily consecutive doses of SGI-110 (Astex Pharmaceuticals, Dublin, CA) at 100 nM (72 h total exposure). Cells were harvested at subsequent time points.

tag: cell line

tag: time point

value: Day 56


title: K9me2_se-2_rep1


title: K27me1_Col-0_rep2


title: K27me1_se-2_rep1


title: K27me1_atxr_rep2

value: atxr5 atxr6


title: SNU475_D56_rep1_RNA

description: SGI-110 treated, D56


title: K9me2_se-2_atxr_rep2


title: K9me2_se-2_atxr_rep1


title: K9me2_kyp

value: kyp


title: K9me2_Col-0_rep1


title: K27me1_atxr_rep1


title: SNU475_D31_rep1_RNA

description: SGI-110 treated, D31

source_name: SGI-110 treated, D31

value: Day 31


title: K9me2_Col-0_rep2


title: SNU475_D24_rep1_RNA

description: SGI-110 treated, D24

source_name: SGI-110 treated, D24

value: Day 24


title: SNU475_D17_rep1_RNA

description: SGI-110 treated, D17

source_name: SGI-110 treated, D17

value: Day 17


title: SNU475_D24_rep2_RNA

description: SGI-110 treated, D24


title: SNU475_D31_rep2_RNA

description: SGI-110 treated, D31


title: SNU475_D17_rep2_RNA

description: SGI-110 treated, D17


title: K9me2_Col-0_for_kyp


title: SNU475_D3_rep2_RNA

description: SGI-110 treated, D3

source_name: SGI-110 treated, D3

value: Day 3


title: SNU475_D10_rep2_RNA

description: SGI-110 treated, D10

source_name: SGI-110 treated, D10

value: Day 10


title: K9me2_atxr_rep2


title: SNU475_D10_rep1_RNA

description: SGI-110 treated, D10


title: Input_kyp


title: SNU475_D3_rep1_RNA

description: SGI-110 treated, D3


title: H3-se-2_rep2

value: anti-H3; Millipore; cat#  MABE923; lot# Q2366893


title: H3-se-2_rep1


title: H3-se-2_atxr_rep1


title: H3-se-2_atxr_rep2


title: SNU475_D0_rep2_RNA

description: Untreated

source_name: Untreated

value: untreated


title: H3-atxr_rep1


title: FM-SE-ChIP

value: Flag-4Myc(FM)-SE transgenic line in se-2

value: Flag M2; Sigma-Aldrich; cat# M8823; lot# SLBM0090V


title: H3-atxr_rep2


title: H3-Col-0_rep2


title: Input-Col-0_for_kyp


title: Col-0-FM-ChIP


title: Bisul-se-2-atxr

data_processing:
BS-seq reads were aligned with Bismark version 0.14.3;
After removal of the PCR duplicates, the methylation information was obtained using bismark_methylation_extractor with cutoff at least 4 coverage depth;
Wig files of methylation level were generated through swDMR version 1.0.0
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: Wig files of methylation level mC/(mC+Un_mC)

extract_protocol:
Total DNA from 10-day-old seedlings were extracted by CTAB, RNase treated and purified with phenol:chloroform followed by Ethanol precipitation.
Approximately 1 ug of genomic DNA were used to generate libraries using premethylated adapters (NEXTFlex Bisulfite-Seq Adapters, Bioo Scientific #511911).The adaptor-ligated fragments were purified by QIAQuick column (QIAGEN) and bisulfite converted using the EpiTect Kit (Qiagen) following the manufacturer’s instructions. The converted DNA was later enriched by PCR using the Pfu Turbo Cx Polymerase (Agilent), using the specific primers provided by Bios Scientific for enrichment.


title: K9me2_atxr_rep1


title: Bisul-hyl1-atxr


title: Bisul-atxr

value: atxr


title: H3-Col-0_rep1


title: Bisul-se-2


title: SNU398_D24_rep2_RNA

description: SGI-110 treated, D24


title: SNU398_D17_rep2_RNA

description: SGI-110 treated, D17


title: SNU398_D17_rep1_RNA

description: SGI-110 treated, D17


title: SNU475_D0_rep1_RNA

description: Untreated


title: Bisul-Col-0


title: SNU398_D10_rep1_RNA

description: SGI-110 treated, D10


title: SNU398_D10_rep2_RNA

description: SGI-110 treated, D10


title: SNU398_D24_rep1_RNA

description: SGI-110 treated, D24


title: Bisul-hyl1


title: SNU398_D0_rep2_RNA

description: Before SGI-110 treatment


title: SNU398_D3_rep1_RNA

description: SGI-110 treated, D3


title: HepG2_D24_rep2_RNA

description: SGI-110 treated, D24


title: SNU398_D0_rep1_RNA

description: Before SGI-110 treatment


title: OFAII-D8-01

city: Oslo

first: Thomas

last: Sæther

state: Oslo

address: Sognsvannsveien 9

department: Dept. of Molecular Medicine

country: Norway

institute: University of Oslo

description: processed data file: Sample RPKM data.xlsx

data_processing:
For pre-alignment quality control the software FastQC v0.10.1 was used. The mean library size was ~18 million read pairs, with no difference between groups or time points.
Alignment of cDNA sequenced reads was done using Tophat v2.0.8, Samtools v0.1.18, and Bowtie v2.1.0 with default settings.
Reads were counted by Cufflinks v2.1.1 and presented as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Differentially expressed genes were identified using one-way ANOVA and an RPKM cut-off set to 5.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: Sample_RPKM_data.xlsx: Excel file includes gene RPKM values for all samples.
Supplementary_files_format_and_content: QC_table.xlsx: Excel file includes quality control data for all samples.

source_name: Adipocytes

growth_protocol: The SGBS cells were maintained in basal medium (DMEM/nutrient mix F-12; D6421, Sigma-Aldrich) supplemented with 2 mg/L of biotin, 1 mg/L of D-pantothenate, 4 mM L-glutamine, penicillin/streptomycin (50 U/mL; 50 μg/mL), and 10% non-inactivated fetal calf serum (F7524; Sigma-Aldrich).

extract_protocol:
RNA was isolated using the RNeasy Mini kit (#74104, Qiagen) with the following modifications: Lysates from cells with high-fat content, such as SGBS cells on day 8, were mixed 1:1 in 70% ethanol in high salt solution (0.45 M NaCl/0.24 M Na-acetate), before applied to the columns. RNA quality was assessed on a BioAnalyzer 2100, using the Agilent RNA 6000 Nano Kit (#5067-1511; Agilent Technologies Inc, Santa Clara, CA). The RIN values (RNA integrity number) varied between 9.80 and 10.00, with an average of 9.95.
Illumina sequencing libraries were prepared according to the strand-specific TruSeq RNA Sample Preparation Guide (revision D).

treatment_protocol: Human Simpson-Golabi-Behmel syndrome (SGBS) cells were differentiated into adipocytes essentially as described by Wabitsch et al., Int J Obes Relat Metab Disord 25:8-15, 2001. Briefly, cells were seeded at low passage (P6-P8) at 0.8×10e5 cells/well in 12-well plates and grown to confluence (day 0). From day 0 to day 4, the cells were exposed to adipogenic medium (Quickdiff; 3FC supplemented with 25 nM dexamethazone, 0.5 mM isobutylmethylxanthine, and 2 μM rosiglitazone, 25 μM (7E)-9-oxohexadec-7-enoic acid:BSA, or 25 μM (10E)-9-oxohexadec-10-enoic acid:BSA, followed by continuous culturing in 3FC (basal medium supplemented with 10 μg/mL human transferrin, 20 nM human insulin, 100 nM cortisol, and 0.2 nM triiodothyronine). Medium was renewed every fourth day.

value: SGBS

tag: cell type

value: Simpson-Golabi-Behmel syndrome pre-adipocyte cell line

tag: agonist treatment

value: (10E)-9-oxohexadec-10-enoic acid

tag: differentiation day

value: Day 8


title: CTRL-D0-02

value: Day 0


title: OFAI-D8-04

value: (7E)-9-oxohexadec-7-enoic acid


title: ROSI-D8-02

value: Rosiglitazone


title: ROSI-D8-01


title: OFAI-D8-03


title: ROSI-D8-03


title: OFAII-D8-02


title: OFAI-D8-01


title: HepG2_D24_rep1_RNA

description: SGI-110 treated, D24


title: CTRL-D0-01


title: HepG2_D3_rep2_RNA

description: SGI-110 treated, D3


title: HepG2_D10_rep2_RNA

description: SGI-110 treated, D10


title: SNU398_D3_rep2_RNA

description: SGI-110 treated, D3


title: OFAI-D8-02


title: ROSI-D8-04


title: HepG2_D17_rep1_RNA

description: SGI-110 treated, D17


title: HepG2_D17_rep2_RNA

description: SGI-110 treated, D17


title: HepG2_D10_rep1_RNA

description: SGI-110 treated, D10


title: HepG2_D0_rep2_RNA

description: Before SGI-110 treatment


title: HepG2_D3_rep1_RNA

description: SGI-110 treated, D3


title: BAT_NCD8

city: Cologne

first: Jan-Wilhelm

last: Kornfeld

state: NRW

address: Gleueler Strasse 50

institute: Max-Planck-Institute for Metabolism Research

data_processing:
Quality control of the raw FASTQ files using FastQC_v0.10.1
Alignment of reads against reference genome using tophat-2.0.10.Linux_x86_64
Alignment of RNA-Seq reads with the STAR aligner
Call of FPKM values per transcript using cufflinks-2.2.1.Linux_x86_64
Differential expression analysis on gene level using DESeq2 (R-3.2.2)
Genome_build: GRCm38.p5; Ensmbl Build 87

source_name: brown adipose tissue

extract_protocol:
RNA was isolated using the mirVANA Kit (Thermo Fisher) according to manufacturer’s protocols for total RNA isolation and rRNA depleted using NEBNext rRNA depletion kit
Libraries were prepared according to NEB´s instructions accompanying the NEBNExt Ultra  II Directional RNA  Library Prep Kit (New England Biolabs).

tag: strain

value: brown adipose tissue

tag: treatment

value: normal chow diet feeding


title: BAT_warm4

value: exposure to 22°C


title: BAT_warm7


title: BAT_HFD2

value: high-fat diet feeding


title: BAT_NCD6


title: BAT_HFD6


title: BAT_cold2

value: exposure to 4°C for 24h