title: Cell_line_SiHa_2hyp

source_name: Cervical cancer cell line, 2% O2, hyp

value: Exposed to hypoxic condition (2% O2, 5% CO2) for 24 h at 37C


title: WGBS of Sus scrofa: skeletal muscle at E100, replicate2

status: Public on Sep 01 2020

type: SRA

city: Shenzhen

first: Zhonglin

last: Tang

state: GuangDong

address: No.7, Pengfei road, Dapeng District

department: Agricultural Genome Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

data_processing:
Illumina Covaris S220 software used for basecalling.
After transforming the Sus scrofa reference genome to a bisulfite-converted version (C-to-T and G-to-A conversion) and then indexing it using bowtie2, the bisulfite-treated clean reads were mapped to the reference genome using the Bismark software (v 0.12.5) was used to perform alignments with default parameters
The sequencing depth and coverage of the methylcytosine were summarized after deletion of the duplicated reads. The methylation level of each CpG site was defined as the number of methylated reads (C) divided by the total number of methylated reads (C) and unmethylated reads (T) at the same positions in the reference genome.
Genome_build: Suscrofa 11.1
Supplementary_files_format_and_content: C_level_result.txt.gz

molecule: genomic DNA

organism: Sus scrofa

source_name: skeletal muscle

extract_protocol:
Total DNA for WGBS was extracted and fragmented by sonication to 200−300 bp using a Covaris S220 (Covaris, Woburn, MA, USA), followed by end repair and A-ligation. After ligation to cytosine-methylated barcodes, the DNA fragments were treated twice with bisulfite using an EZ DNA Methylation-GoldTM Kit (Zymo Research, Orange, CA, USA).
The libraries were then prepared according to the Illumina standard DNA methylation analysis protocol. The WGBS libraries were sequenced on the Illumina HiSeq X Ten platform (Illumina, CA, USA) and 150-bp paired-end reads were generated.

tag: strain

value: Landrance


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A10_AD002_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOp

tag: Sex

value: male

tag: age


title: Cell_line_SiHa_0.5hyp

type: RNA

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization in BeadStudio 3.1.3.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cervical cancer cell line, 0.5% O2, hyp

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using miRNeasy MiniKit (Quiagen), according to the manufacturers’ instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were seeded (1.5x10^6 cells for HeLa, 1.7x10^6 cells for SiHa) in 10 cm plastic dishes 24 hours before exposure to hypoxia at 0.2%, 0.5% 1%, 2% and 5% O2 for 24 hours at 37⁰C, all with 5% CO2, by using an Invivo2200 chamber (Ruskinn Technology Ltd) with accurate O2 and CO2 controls. Normoxic controls (95% air , 5% CO2) were included for all hypoxia experiments.

tag: cell line

value: SiHa

tag: histology

value: squamous cell carcinoma

tag: treatment

value: Exposed to hypoxic condition (0.5% O2, 5% CO2) for 24 h at 37C


title: Cell_line_SiHa_0.5ctrl

source_name: Cervical cancer cell line, 0.5% O2, ctrl

value: Exposed to normoxic (control) condition (95% air , 5% CO2) for 24 h at 37C


title: RNAseq_N2_14hr

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

library_source: transcriptomic

data_processing:
RNA-seq data were mapped to the C. elegans ce10 genome using the qAlign function (splicedAlignment=TRUE) from the QuasR package in R
Gene expression was quantified using qCount function from the QuasR package in R
Counts were scaled by total mapped library size for each sample
A pseudocount of 8 was added and counts were log2-transformed
Genome_build: ce10
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Wormbase identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample.

organism: Caenorhabditis elegans

source_name: synchronized population

growth_protocol: a population of L1 synchronized by egg prep and M9 incubation was grown on OP50 containing agar plates at room temperature. Worms were collected hourly by washing of worms with M9 and washing 3 times in M9.

extract_protocol:
RNA was extracted using Trizol and conventional Phenol / Chlorophorm extraction.
Illumina TruSeq mRNA-Seq Sample Prep Kit (Stranded - high input), followed by the Hiseq50 Cycle Single-end reads on HiSeq2500 protocol

tag: timepoint

tag: tissue

value: L1 arrested C. elegans larvae


title: RNAseq_N2_10hr


title: Cell_line_SiHa_0.2hyp

source_name: Cervical cancer cell line, 0.2% O2, hyp

value: Exposed to hypoxic condition (0.2% O2, 5% CO2) for 24 h at 37C


title: WGBS of Sus scrofa: skeletal muscle at E100, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H9_AD010_indexed


title: RNAseq_N2_9hr

value: 9 h


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A10_AD007_indexed


title: RNAseq_N2_12hr


title: RNAseq_N2_8hr

value: 8 h


title: WGBS of Sus scrofa: skeletal muscle at E95, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H9_AD006_indexed


title: WGBS of Sus scrofa: skeletal muscle at E95, replicate2


title: RNAseq_N2_7hr

value: 7 h


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_3_CEMBA180605_5D_4_A10_AD004_indexed


title: RNAseq_N2_6hr

value: 6 h


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H8_AD001_indexed


title: WGBS of Sus scrofa: skeletal muscle at E95, replicate1


title: WGBS of Sus scrofa: skeletal muscle at E90, replicate3


title: RNAseq_N2_11hr


title: RNAseq_N2_5hr

value: 5 h


title: WGBS of Sus scrofa: skeletal muscle at E90, replicate2


title: RNAseq_N2_4hr

value: 4 h


title: WGBS of Sus scrofa: skeletal muscle at E90, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD012_indexed


title: RNAseq_N2_3hr

value: 3 h


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H8_AD010_indexed


title: RNAseq_N2_2hr

value: 2 h


title: Cell_line_SiHa_0.2ctrl

source_name: Cervical cancer cell line, 0.2% O2, ctrl


title: Cell_line_HeLa_2hyp

value: HeLa

value: adenocarcinoma

value: Exposed to hypoxic condition (2% O2, 5% CO2) for 24 h at 37C


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H9_AD007_indexed

value: MOp

value: male


title: Cell_line_HeLa_2ctrl

source_name: Cervical cancer cell line, 2% O2, ctrl


title: Cell_line_HeLa_0.5ctrl


title: Cell_line_HeLa_1ctrl

source_name: Cervical cancer cell line, 1% O2, ctrl


title: Cell_line_HeLa_5ctrl

source_name: Cervical cancer cell line, 5% O2, ctrl


title: RNAseq_N2_1hr

value: 1 h


title: WGBS of Sus scrofa: skeletal muscle at E85, replicate3

value: Landrance


title: PBMC_OND_rep27

city: milan

first: massimo

last: acquaviva

state: mi

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Hospital

data_processing:
Microarray raw data originating from Illumina HumanRef-8 v2 and HumanHT-12 v4 arrays were pre-processed and normalized independently using the limma package and then merged into a single integrated dataset according to the common probes. Raw intensities were background subtracted and filtered according to detection pvalues (p<0.05 in at least 20% of samples) and then normalized using quantile normalization. Pre-processed data were log2 transformed and inspected for the presence of hidden batch effects using DASC. Batch correction and cross-platform integration of the two independently normalized datasets was performed using Combat.
[Matrix-merged-normalized-batch.corrected.txt]  quantile normalized and batch corrected signals.

source_name: blood

label_protocol: Reverse transcription and biotinylated cRNA synthesis were performed using the Illumina TotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using Trireagent (Ambion) and stored at -80°C. Quantification and quality analyses of RNA were performed at a Bioanalyzer 2100 (Agilent).

treatment_protocol: Peripheral blood mononuclear cells were collected from healthy subjects, untreated MS and CIS individuals and other neurological diseases.

tag: disease

value: other neurological disease

tag: disease staging

tag: illumina chip

value: HumanHT-12 v4

tag: dataset partition

value: Independent Test set

value: blood

tag: cell type

value: PBMC


title: WGBS of Sus scrofa: skeletal muscle at E85, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H8_AD012_indexed


title: WGBS of Sus scrofa: skeletal muscle at E80, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H9_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H8_AD007_indexed


title: mBrain_F1_DMR_LR-EM-seq_5mC

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

institute: New England Biolabs

description: LR-EM-seq (PacBio)

data_processing:
library strategy: LR-EM-seq (Long Range Enzymatic Methyl-seq)
Illumina sequencing: basecalls were performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq. Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
Pacbio SMRT sequencing: Circular Consensus Sequences were extracted from the raw movie data and converted into fastq file using SMRT Link (version 6.0.0.47841) CCS protocol for Sequel runs or using the SMRT portal (version 2.3.0.140893) “RS_ReadsOfInsert” protocol for RSII runs. Reads that were shorter than the expected amplicon sizes were removed from downstream analysis
Oxford Nanopore sequencing: Raw fast5 data from the MinION were generated using Min- KNOW version 18.12 and base called using Guppy base caller Version 2.1.3.
Trimmed Illumina reads of the whole genome 5mC/5hmC sequencing experiments were mapped to a composite reference including the sequences of mouse genome (mm9), lambda, XP12, pUC19 and T4 using the Bismark program with the default bowtie2 setting. The aligned reads were then subjected to two post-processing QC steps: 1, alignment pairs that shared the same alignment start positions (5’ ends) were regarded as PCR duplicates and were discarded; 2,  reads that alinged to the mouse genome and contain excessive cytosines in non-CpG context (e.g., more than 5 in 150bp) were removed because they likely resulted from conversion errors. The remaining good quality alignments were then used for cytosine methylation and hydroxymethylation calling by Bismark methylation extractor.
Long reads generated by Pacbio SMRT sequencing and Oxford Nanopore sequencing were mapped to the mouse reference genome (mm9) using the Bismark program with the following parameters: –bowtie2 -N1 -L15 –score min L,0,-0.6. The modification states of individual cytosine sites were called by the bismark methylation extrator program. We then extracted the context specific methylation information of individual molecules using custome perl scripts and plotted in R.
SNPs were called using the Samtools
Genome_build: mouse (mm9)
Supplementary_files_format_and_content: tab-delimited text files include genomic coordinates, modification calls and sequence contexts of covered cytosines.

source_name: brain cortex tissue

growth_protocol: E14 ES cells were grown in GMEM media (Thermo Fisher Scientific) containing 10% FBS (Gemcell), 1% non-essential amino acids (NEAA) (Hyclone), 1% sodium pyruvate (Thermo Fisher Scientific), 50 μM β-mercaptoethanol (Sigma), and 1 LIF (Millipore). To maintain the undifferentiated state, ES cells were grown on 0.1% gelatin- coated culture dishes (Stem Cell Technologies).

extract_protocol:
Mouse genomic DNA’s were extracted with a DNeasy Blood and Tissue Kit (QIAGEN) according to the manufacturer's instructions.
(Illumina) DNA was sheared to 250 bp fragments with a Covaris S2 sonicator. Enzymatic 5mC libraries were prepared using the NEBNext Enzymatic Methyl-seq Kit (E7120S, NEB) according to the manufacturer’s instructions. WGBS libraries were prepared using NEBNext Ultra II Kit (NEB) according to the manufacturer’s instructions. Enzymatic 5hmC libraries were prepared using the NEBNext Ultra II Kit (NEB) with the following modifications: (1) after sonication and prior to end repair, fragmented DNA was first glucosylated with BGT (NEB); (2) Pyrrolo-dC adaptors were used instead of 5-mC adapters, and (3) APOBEC-5hmC treatment was applied after adapter ligation and before PCR.
(PacBio) PacBio SMRT libraries were prepared using PacBio Amplicon template preparation and sequencing protocol. Libraries were loaded onto SMRT cells using the MagBead method and were sequenced on a PacBio RSII machine with 5.5-hour movie or on a PacBio Sequel machine with 10-hour movie.
(Nanopore) Oxford Nanopore libraries were prepared using the 1D Native barcoding genomic DNA kit (EXP-NBD103 and SQK-LSK108 kits, Oxford Nanopore Technologies).  For each sample, end-repair and dA-tailing was performed using the NEBNext Ultra II End repair/dA-Tailing module (E7546, NEB), following Oxford Nanopore protocol, except that the incubation time was increased to 20 min. Samples were barcoded using the EXP-NBD103 kit (Oxford Nanopore Technologies) and were pooled in equimolar amounts. The Nanopore adapter ligation was performed according to the manufacturer’s protocol. The library was sequenced for a total of 11h on a MinION (Oxford Nanopore Technologies) using a FLO-MIN106 Rev D flow cell.

treatment_protocol:
(APOBEC-5mC) 1 to 200 ng of mouse E14 genomic DNA was mixed with 1% unmethylated lambda DNA, 1% XP12 phage DNA, and 0.1% CpG methylated pUC19 DNA, then incubated with TET2 enzyme (EM-seq component E7130A, NEB) for 30 min at 37oC) followed by a 30 min incubation with T4 BGT (NEB) 37oC. Oxidized genomic DNA was incubated additional 30 min with Proteinase K (NEB) and subsequently purified with a Genomic DNA Clean Concentrator (Zymo Research). Purified DNA was then denaturated at 90oC in presence of 29% of formamide, for 10 minutes, and deaminated with APOBEC3A (EM-seq components E7133AA and E7134AA, NEB) for 3 hours.
(APOBEC-5hmC) 1 to 200 ng of mouse E14 genomic DNA was mixed with 1% unmethylated lambda DNA, 1% T4gt phage DNA, and 0.1% CpG methylated pUC19 DNA, then treated with BGT (NEB) for 2 h at 37oC. Glucosylated genomic DNA was incubated additional 30 min with Proteinase K (NEB) at 37oC, and then purified with a Genomic DNA Clean Concentrator kit (Zymo Research). Purified DNA was then denaturated at 90oC in presence of 29% of formamide, for 10 minutes, and deaminated by APOBEC3A (EM- seq components E7133AA and E7134AA, NEB) for 16 hours.
(bisulfite 1) EpiTect Bisulfite Kit (Qiagen) was used according to the manufacturer's instructions
(bisulfite 2) EZ DNA Methylation-Gold Kit (Zymo Research) was used according to the manufacturer's instructions

tag: strain background

value: F1 of Cast (female) X 129 (male)

tag: tissue source

value: brain cortex

tag: modification type

value: 5mC (5mC+5hmC)

value: APOBEC 5mC


title: PBMC_OND_rep25


title: mBrain_cast_DMR_LR-EM-seq_5mCbrain tissue

description: LR-EM-seq (PacBio)

value: Cast/EiJ (Cast)


title: Cell_line_HeLa_1hyp

source_name: Cervical cancer cell line, 1% O2, hyp

value: HeLa

value: Exposed to hypoxic condition (1% O2, 5% CO2) for 24 h at 37C


title: Cell_line_HeLa_5hyp

source_name: Cervical cancer cell line, 5% O2, hyp

value: adenocarcinoma

value: Exposed to hypoxic condition (5% O2, 5% CO2) for 24 h at 37C


title: Cell_line_HeLa_0.5hyp

value: Exposed to hypoxic condition (0.5% O2, 5% CO2) for 24 h at 37C


title: PBMC_OND_rep26


title: Cell_line_HeLa_0.2ctrl

value: Exposed to normoxic (control) condition (95% air , 5% CO2) for 24 h at 37C


title: WGBS of Sus scrofa: skeletal muscle at E85, replicate2

tag: strain

value: Landrance


title: PBMC_OND_rep24

value: other neurological disease


title: WGBS of Sus scrofa: skeletal muscle at E80, replicate1


title: mBrain_129_DMR_LR-EM-seq_5mC

description: LR-EM-seq (PacBio)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD010_indexed

tag: brain region

value: MOp

value: male


title: mBrain_LR-EM-seq_5hmC

description: LR-EM-seq (PacBio)

source_name: genomic DNA of normal brain

value: BALB/cJ

value: brain

value: APOBEC 5hmC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD008_indexed

tag: Sex


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD007_indexed

tag: age


title: WGBS of Sus scrofa: skeletal muscle at E75, replicate3


title: WGBS of Sus scrofa: skeletal muscle at E75, replicate2


title: PBMC_OND_rep23

value: HumanHT-12 v4

value: Independent Test set

value: blood

value: PBMC


title: mBrain_LR-EM-seq_5mC

description: LR-EM-seq (PacBio)

value: 5mC (5mC+5hmC)

value: APOBEC 5mC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H9_AD001_indexed


title: hpr1∆ rep B

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description: 3' READS library

data_processing:
library strategy: 3' READS
Prep for mapping (removal of adapters, counting and removal of initial Ts, discarding reads with ambiguous base calls): python3
Mapping to yeast genome build Sac cer3 (first 17 non-A bases; accepting perfect matches and unique reads only): Bowtie (Langmead et al., 2009)
Discard mapped reads with fewer initial Ts than there are As in the adjacent genome: python3
Tally reads by UTR position if they map to the first 400nt after an ORF end: python3
Genome_build: Sac cer 3
Supplementary_files_format_and_content: tab-delimited text files with isoform expression percentages for every position in the first 400 nt after yeast genes

organism: Saccharomyces cerevisiae

source_name: hpr1∆_yeast cells

growth_protocol: Growth in the specified culture medium to mid-log phase except for diauxic cells, which were cultured for approximately 72 hours

extract_protocol:
Hot acid phenol RNA extraction followed by Qiagen RNeasy purification
3' READS starting with 25µg total RNA (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

tag: genotype

value: Wild-type RPO21-FRB hpr1<delta>

tag: growth medium

value: YPD

tag: culture stage

value: log phase


title: WGBS of Sus scrofa: skeletal muscle at E75, replicate1


title: PBMC_OND_rep22


title: PBMC_OND_rep21


title: PBMC_OND_rep20


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD004_indexed


title: WGBS of Sus scrofa: skeletal muscle at E70, replicate3


title: spt4∆ rep B

description: 3' READS library

source_name: spt4∆_yeast cells

value: Wild-type RPO21-FRB, spt4<delta>


title: hpr1∆ rep A

description: 3' READS library

value: Wild-type RPO21-FRB, hpr1<delta>


title: PBMC_OND_rep19

value: other neurological disease


title: WGBS of Sus scrofa: skeletal muscle at E70, replicate2

source_name: skeletal muscle

value: Landrance


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD006_indexed

source_name: C57BL/6J Male P56 Mouse Brain

value: MOp

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD001_indexed


title: spt4∆ rep A

description: 3' READS library


title: WGBS of Sus scrofa: skeletal muscle at E70, replicate1


title: PBMC_OND_rep18

value: Training Set


title: Rpb1-E1103G ("faster") rep B

description: 3' READS library

source_name: Rpb1-E1103G ("faster")_yeast cells


title: PBMC_OND_rep17


title: WGBS of Sus scrofa: skeletal muscle at E65, replicate3


title: Rpb1-E1103G ("faster") rep A

description: 3' READS library


title: WGBS of Sus scrofa: skeletal muscle at E65, replicate2


title: PBMC_OND_rep16


title: Rpb1-L1101S ("fast") rep B

description: 3' READS library

source_name: Rpb1-L1101S ("fast")_yeast cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H6_AD010_indexed


title: WGBS of Sus scrofa: skeletal muscle at E65, replicate1


title: PBMC_OND_rep14


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H9_AD002_indexed


title: PBMC_OND_rep15


title: WGBS of Sus scrofa: skeletal muscle at E60, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H5_AD006_indexed


title: WGBS of Sus scrofa: skeletal muscle at E60, replicate2


title: PBMC_OND_rep13


title: Rpb1-F1086S ("slow") rep B

description: 3' READS library

source_name: Rpb1-F1086S ("slow")_yeast cells


title: WGBS of Sus scrofa: skeletal muscle at E60, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H5_AD010_indexed


title: PBMC_OND_rep12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H6_AD001_indexed


title: WGBS of Sus scrofa: skeletal muscle at E55, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H6_AD006_indexed


title: Rpb1-H1085Q ("slower") rep A

description: 3' READS library

source_name: Rpb1-H1085Q ("slower")_yeast cells


title: PBMC_OND_rep10


title: PBMC_OND_rep11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H5_AD007_indexed


title: Sorbitol rep B

description: 3' READS library

source_name: Sorbitol_yeast cells

value: Wild-type RPO21-FRB

value: YPD + 1M Sorbitol


title: WGBS of Sus scrofa: skeletal muscle at E55, replicate2


title: PBMC_OND_rep9

value: HumanHT-12 v4


title: Rpb1-L1101S ("fast") rep A

description: 3' READS library


title: WGBS of Sus scrofa: skeletal muscle at E55, replicate1


title: Rpb1-F1086S ("slow") rep A

description: 3' READS library


title: WGBS of Sus scrofa: skeletal muscle at E50, replicate2


title: PBMC_OND_rep7

value: blood


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H6_AD007_indexed


title: WGBS of Sus scrofa: skeletal muscle at E50, replicate1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H5_AD004_indexed


title: PBMC_OND_rep6

value: PBMC


title: Rpb1-H1085Q ("slower") rep B

description: 3' READS library


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H5_AD001_indexed


title: PBMC_OND_rep5


title: WGBS of Sus scrofa: skeletal muscle at E45, replicate3


title: YPGal rep A

description: 3' READS library

source_name: YPGal_yeast cells

value: YP + 2% Galactose


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H6_AD002_indexed


title: Cell_line_HeLa_0.2hyp

source_name: Cervical cancer cell line, 0.2% O2, hyp

tag: cell line

value: HeLa

tag: histology

value: adenocarcinoma

tag: treatment

value: Exposed to hypoxic condition (0.2% O2, 5% CO2) for 24 h at 37C


title: WGBS of Sus scrofa: skeletal muscle at E45, replicate2


title: PBMC_OND_rep4

tag: disease

tag: disease staging

tag: tissue


title: YPD diauxic rep B

description: 3' READS library

source_name: YPD diauxic_yeast cells

value: YPD

value: diauxic


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H7_AD002_indexed


title: PBMC_OND_rep3

source_name: blood

tag: illumina chip

tag: dataset partition

tag: cell type


title: PBMC_OND_rep8


title: WGBS of Sus scrofa: skeletal muscle at E50, replicate3


title: WGBS of Sus scrofa: skeletal muscle at E45, replicate1


title: WGBS of Sus scrofa: skeletal muscle at E40, replicate3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H4_AD010_indexed


title: YPD diauxic rep A

description: 3' READS library


title: PBMC_OND_rep1


title: PBMC_HC_rep60

value: healthy control

value: Independent Test set


title: WGBS of Sus scrofa: skeletal muscle at E40, replicate1

value: Landrance


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H4_AD007_indexed

value: MOp


title: PBMC_OND_rep2

value: other neurological disease


title: WGBS of Sus scrofa: skeletal muscle at E40, replicate2


title: PBMC_HC_rep59


title: MCF7_2_Exp4_Abemaciclib+SR11302_2 7 days

city: Melbourne

first: Shom

last: Goel

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Novogene pipeline
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited .txt file of read counts generated by Novogene

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of RNA-seq was between 60-70%.

extract_protocol:
Total RNA was isolated from cell lines using a Nucleospin RNA Plus kit (Macherey-Nagel).
Novogene pipeline

treatment_protocol: DMSO, Abemaciclib (500 nM), and SR11302 (20 uM) for 7 days for all cell lines.

value: MCF7 breast carcinoma cell line

value: abemaciclib + SR11302

tag: treatment length

value: 7 days


title: MCF7_2_Exp4_Abemaciclib+SR11302_1 7 days


title: WGBS of Sus scrofa: skeletal muscle at E33, replicate3

tag: strain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H4_AD006_indexed

tag: brain region

value: male


title: WGBS of Sus scrofa: skeletal muscle at E80, replicate2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H3_AD006_indexed

tag: Sex


title: WGBS of Sus scrofa: skeletal muscle at E33, replicate2


title: PBMC_HC_rep58

value: HumanHT-12 v4

value: blood


title: MCF7_2_Exp4_Abemaciclib_2 7 days

value: abemaciclib


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H4_AD004_indexed

tag: age


title: WGBS of Sus scrofa: skeletal muscle at E33, replicate1


title: PBMC_HC_rep57

value: PBMC


title: MCF7_2_Exp4_Abemaciclib_1 7 days


title: BP-30h

city: Nanjing

first: Chen

last: Ling

address: 163 Xianlin Avenue

institute: Nanjing University

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:(1) Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW:  4:10) (2) Remove trailing low quality or N bases (below quality 3) (TRAILING:3) (3) Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa:  2: 30: 7) (4) Drop reads below the 26 bases long (5) Discard those reads that can not form paired
The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the clean reads.
Cell Ranger uses an aligner called STAR, which peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read that is compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it is considered uniquely (confidently) mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting.
Cell Ranger takes as input the expected number of recovered cells, N (see -- expect-cells). Let m be a robust estimate of the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group (library) and, if the reference contains multiple genomes, for each genome.
Genome_build: Danio_rerio_Ensemble_95（GRCz11)
Supplementary_files_format_and_content: gene-barcode expression matrix

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
The zebrafish embryo was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument(10x Genomics, USA) to generate single cell Gel bead in Emulsion (GEMs).
ScRNA-seq libraries were prepared using the GemCode Single-Cell 3’ Gel Bead, Chip and Library Kits (10x Genomics, USA) as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.

treatment_protocol: Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages (gasturla, segmentation and pharyngula) , zebrafish embryo were collected.

value: embryonic single cell suspension

tag: exposed pollutants

value: 100ppb BPA


title: PBMC_HC_rep55


title: MCF7_2_Exp4_DMSO_2 7 days

value: DMSO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H6_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H3_AD007_indexed


title: MCF7_2_Exp4_DMSO_1 7 days


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD012_indexed


title: BP-12h


title: PBMC_HC_rep54


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H4_AD001_indexed


title: BP-8h


title: CK-30h


title: PBMC_HC_rep52


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H3_AD010_indexed


title: CK-12h


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H4_AD002_indexed


title: 548_PDX-Combo

city: Bethesda

first: Haobin

last: Chen

state: MD

address: Building 10-CRC, Room 3-5848

department: NCI/CCR

institute: NIH

data_processing:
RNA-Seq reads were processed using the Snakemake-based lcdb-wf transcriptomics pipelinev1.3c (https://github.com/lcdb/lcdb-wf). Quality was assessed using FastQScreen and FastQC, and adapter sequences and low quality base pairs were trimmed usingcutadapt. Trimmed reads were then mapped to the human reference genome (gencode v30)using HISAT2 (v.2.1.0), and transcript levels were quantified using the thefeatureCounts method from RSubRead (v1.6.4). Normalized read counts generated usingDESeq2 (v1.28.0).
Genome_build: Gencode Release 30 (GRCh38.p12)
Supplementary_files_format_and_content: Count matrix (tab-delimited)

molecule: polyA RNA

source_name: PDX-Combo

growth_protocol: Subcutaneous implantation in NOD-SCID mice

extract_protocol:
Tumor cells were isolated from PDX using a magnetic-activated cell sorting method (Mouse Cell Depletion Kit, Miltenyi Biotec) Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Library was constructed using the Illumina TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: Oral gavaging daily for 7 days

value: Isolated tumor cells

tag: tumor type

value: Small cell lung cancer

tag: treatment type

tag: treatment duration

tag: mouse strain

value: NOD-SCID


title: PBMC_HC_rep51

value: healthy control

value: Independent Test set


title: 517_PDX-Combo


title: PBMC_HC_rep56


title: CK-8h


title: PBMC_HC_rep50


title: 537_PDX-Combo


title: 555_PDX-Combo


title: Liver circRNA-sequencing

city: hangzhou

first: wenjie

last: zhang

address: xuelin street

institute: Zhejiang Sci-Tect University

data_processing:
Total RNA was pretreated to enrich circRNA using CircRNA Enrichment Kit (Cloud-seq, Inc., USA).
The reads were aligned to the genome (ASM401019v1)  with bowtie2 software and circRNAs were detected and identified with find_circ software.
Raw junction reads for all samples were normalized by total reads number and log2 transformed.
Genome_build: Chiloscyllium plagiosum
Supplementary_files_format_and_content: Number of raw junction read

organism: Chiloscyllium plagiosum

source_name: liver

extract_protocol: RNA extraction protocol

value: liver


title: PBMC_HC_rep45.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H3_AD001_indexed

value: MOp


title: 522_PDX-Combo


title: PBMC_HC_rep53


title: PBMC_HC_rep41

value: Training Set


title: 545_PDX-Combo

value: 7 days


title: PBMC_HC_rep42


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD010_indexed

value: male


title: Captivity 6

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

data_processing:
Paired-end sequencing was conducted on an Illumina NextSeq 500 platform to generate 2x150 paired end (PE) reads.
Reads from each sample were mapped against the newly aasembled reference transcriptome PRJNA639785 using Hisat2 software. Only reads showing unique match were counted as valid alignments. The resulting count table was analysed using edgeR (v 3.20.9) library in R environment. Transcripts showing an expression level of a minimum value of 3 CPM in at least 3 samples in both groups were considered as consistently expressed and were further used for differential expression analysis.
Genome_build: genome sequence available at PRJNA639785
Supplementary_files_format_and_content: Matrix table with raw counts for each sample and locus detected.

organism: Isostichopus badionotus

source_name: Body wall

extract_protocol:
Captive sea cucumbers were washed with cold sterile distilled water to remove excess of sea salt and were quickly eviscerated to leave only the body wall. The body wall of each animal was cut into several pieces of approximately 1 cm^2 and each piece was immersed in 1 ml of RNAlater™ stabilization solution (Ambion©, Cat. AM7021). Each portion was pooled, snap frozen in liquid N2 and stored at -80°C until its use.
Total RNA with a RIN score >7.0 was accepted for cDNA library preparation. mRNA isolation, cDNA synthesis and library preparation were performed using the TruSeq Stranded mRNA Sample Preparation Kit® (Illumina©, RS-122-2101).

tag: environment

value: Captivity adapted

value: Body wall

tag: Stage

value: adult


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H3_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H3_AD012_indexed


title: Captivity 5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD007_indexed


title: 508_PDX-mTORi

source_name: PDX-mTORi

value: Everolimus


title: Captivity 4

value: Captivity

value: juvenile


title: PBMC_HC_rep40

tag: disease

tag: disease staging

value: HumanHT-12 v4

value: blood

value: PBMC


title: 541_PDX-mTORi

value: Isolated tumor cells

value: Small cell lung cancer

value: NOD-SCID


title: Captivity 3

tag: tissue


title: PBMC_HC_rep39

value: healthy control

tag: illumina chip

tag: dataset partition


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD008_indexed

value: MOp


title: Captivity 2


title: 542_PDX-mTORi

tag: cell type


title: 524_PDX-Combo


title: PBMC_HC_rep38

value: Training Set


title: Captivity 1


title: 506_PDX-mTORi

value: 7 days


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD006_indexed

value: male

tag: strain


title: hiHeps-2

city: Beijing

first: Qiming

last: Wang

address: No.5 Yiheyuan Road Haidian District

institute: School of Life Sciences, Peking University

description: reprogrammed cells

data_processing:
Sequence reads were trimmed by Trimmomatic with parameters ILLUMINACLIP:/path/to/adapters/TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:10 MINLEN:36
Trimmed clean reads were mapped to human reference genome hg19 by STAR with default parameters
The gene count matrix of all samples was generated by function featureCounts of R package Rsubread.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each sample

source_name: reprogrammed cells

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

value: reprogrammed human induced hepatocytes

tag: cell line

tag: batch


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD004_indexed

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: Sex

tag: age


title: 516_PDX-mTORi

tag: tumor type

tag: treatment type


title: PBMC_HC_rep37


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H1_AD010_indexed


title: PBMC_HC_rep36


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H8_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H1_AD007_indexed


title: 505_PDX-mTORi

tag: treatment duration

tag: mouse strain


title: hiHeps-1

description: reprogrammed cells


title: F-PHHs-2

description: Freshly isolated primary hepatocytes

source_name: Freshly isolated primary hepatocytes

value: Freshly isolated primary hepatocytes

value: batch 2


title: F-PHHs-1

description: Freshly isolated primary hepatocytes

value: batch 1


title: 536_PDX-BETi

source_name: PDX-BETi


title: hFLCs-2

description: human fetal liver cells

source_name: human fetal liver cells

value: human fetal liver cells


title: 518_PDX-BETi


title: PBMC_HC_rep33


title: PBMC_HC_rep34


title: PBMC_HC_rep6.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H1_AD006_indexed


title: 550_PDX-BETi


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H1_AD004_indexed


title: hFLCs-1

description: human fetal liver cells


title: 562_PDX-BETi


title: iPSCs

description: pluripotent stem cells

source_name: pluripotent stem cells

value: Induced pluripotent stem cells

value: iPSCs


title: PBMC_HC_rep5.1

value: HumanHT-12 v4

value: blood


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD001_indexed


title: 523_PDX-BETi

value: Isolated tumor cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H2_AD002_indexed


title: PBMC_HC_rep4.1

value: PBMC


title: H1

description: pluripotent stem cells

value: Embryonic stem cells


title: EPS2-Heps-4

description: Differentiated cells

source_name: Differentiated cells

value: Extended pluripotent stem cells 2 derived hepatocytes

value: batch 4


title: PBMC_HC_rep35

value: healthy control

value: Training Set


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H11_AD004_indexed

value: MOp

value: male


title: PBMC_HC_rep3.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H6_AD012_indexed


title: 549_PDX-Vehicle

source_name: PDX-Vehicle

value: Small cell lung cancer

value: Vehicle

value: 7 days

value: NOD-SCID


title: 547_PDX-Vehicle


title: EPS2-Heps-3

description: Differentiated cells

value: batch 3


title: PBMC_HC_rep2.1


title: PBMC_SP_rep26

value: multiple sclerosis

value: Independent test set


title: EPS2-Heps-2

description: Differentiated cells

value: batch 2


title: 544_PDX-Vehicle

value: Isolated tumor cells


title: EPS2-Heps-1

description: Differentiated cells

value: batch 1


title: PBMC_SP_rep25

value: HumanHT-12 v4

value: blood

value: PBMC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H11_AD006_indexed


title: 560_PDX-Vehicle


title: EPS1-S1-2

description: Differentiated cells

value: Extended pluripotent stem cells 1 derived primed stem cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H1_AD008_indexed


title: 565_PDX-Vehicle


title: PBMC_SP_rep17

value: Training Set


title: EPS1-S1-1

description: Differentiated cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H11_AD007_indexed

value: MOp


title: PBMC_SP_rep16


title: 515_PDX-Vehicle


title: PBMC_SP_rep18


title: EPS1-Heps-4

description: Differentiated cells

value: Extended pluripotent stem cells 1 derived hepatocytes

value: batch 4


title: PBMC_PP_rep35

value: primary-progressive multiplle sclerosis

value: Independent Test Set


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H1_AD002_indexed

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H11_AD012_indexed


title: 519_PDX-Vehicle

value: Small cell lung cancer

value: Vehicle

value: 7 days

value: NOD-SCID


title: EPS1-Heps-2

description: Differentiated cells

value: batch 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H1_AD001_indexed


title: HeLa cells, siPDCD2_2

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

data_processing:
Reads containing adapter sequences (>11 nt) were removed from the dataset, and low quality bases at read termini were trimmed using the fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html), discarding short reads (<32 nt) after trimming.
Tophat was used to perform a spliced alignment to the human reference genome build hg19.
After mapping, CoCo (Deschamps-Francoeur et al., 2019) was used to assign reads to features while correcting read counts for nested genes and multiple mapping reads. DESeq2 was used for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with read counts for every gene and every sample

source_name: HeLa cells

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% of tetracycline-free fetal bovine serum.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies)
RNA-seq libraries were prepared for stranded paired-end 100 sequencing using Illumina TruSeq total RNA Sample Prep Kit with 1 ug of total RNA.

treatment_protocol: siRNAs (non target or against PDCD2) were transfected with Lipofectamine 2000 at a final concentration of 25 nM .

value: HeLa

tag: sirna

tag: genotype


title: HeLa cells, siPDCD2_1


title: HeLa cells, siNT_2

value: siNT

value: control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H11_AD002_indexed


title: EPS1-Heps-1

description: Differentiated cells

value: batch 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H11_AD001_indexed


title: PBMC_PP_rep33

tag: disease

value: multiple sclerosis

tag: disease staging

value: HumanHT-12 v4

value: blood

value: PBMC


title: HeLa cells, siNT_1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H10_AD010_indexed

value: MOp


title: EPS-HPLCs-2

description: Differentiated cells

value: Extended pluripotent stem cells 1 derived hepatic progenitor liked cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H10_AD007_indexed


title: PBMC_PP_rep31

value: primary-progressive multiplle sclerosis

tag: illumina chip

value: Independent Test Set

tag: tissue


title: EPS-HPLCs-1

description: Differentiated cells

tag: cell type


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H10_AD006_indexed

value: male

tag: strain


title: Failed Ventricle 3 RNA-Seq

city: Chicago

first: Anthony

middle: Martin

last: Gacita

state: IL

address: 303 E Superior St. Lurie 7-240

department: Center for Genetic Medicine

institute: Northwestern Univeristy Feinberg School of Medicine

description:
RNA-seq from Failed Left Ventricle Tissue
RNA_Seq_Differential_Genes.txt
TRID60_RNA-seq

data_processing:
RNA-Seq (CAGE)
Reads were aligned to hg19 using STAR (v2.5.2)
CAGEr was used to find CAGE-tag transcriptional start sites
CAGEfightR was used to cluster singals and do downstream analysis
See publication for detailed data processing steps
Genome_build: hg19
Supplementary_files_format_and_content: Promoter_Table_All_Info.txt contains all of the information for promoter clusters
Supplementary_files_format_and_content: Enhancer_Table_All_Info.txt contains all of the information for enhancer clusters
RNA-Seq
Reads were trimmed with trimmomatic
Reads were aligned to hg19 using STAR (v2.5.2)
HT-seq Count was used to assign reads to transcripts.
EdgeR was used to normalize counts calculate differential expression.
Differentially expressed genes were filtered for an FDR p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: RNA_Seq_Differential_Genes.txt contains statistics for differential gene expression as outputted by EdgeR.

source_name: Human Left Ventrice Tissue

extract_protocol:
RNA was extracted from tissue using TRIzol and the Aurum Total RNA Mini Kit (Bio-Rad, Hercules, CA; 7326820).
TruSeq Sranded mRNA-Seq Library Prep (Illumina)

tag: phenotype

value: Heart Failure


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H10_AD001_indexed


title: EPS1-Heps-3

description: Differentiated cells

value: Extended pluripotent stem cells 1 derived hepatocytes

tag: cell line

tag: batch

value: batch 3


title: EPS cells-2

description: Extended pluripotent stem cells

source_name: Extended pluripotent stem cells

value: Extended pluripotent stem cells 1


title: Failed Ventricle 2 RNA-Seq

description:
RNA-seq from Failed Left Ventricle Tissue
RNA_Seq_Differential_Genes.txt
TRID53_RNA-seq


title: PBMC_PP_rep23

source_name: blood

tag: dataset partition

value: Training Set


title: PBMC_PP_rep34


title: PBMC_PP_rep22


title: Failed Ventricle 1 RNA-Seq

description:
RNA-seq from Failed Left Ventricle Tissue
RNA_Seq_Differential_Genes.txt
TRID33_RNA-seq


title: Healthy Ventricle 3 RNA-Seq

description:
RNA-seq from Healthy Left Ventricle Tissue
RNA_Seq_Differential_Genes.txt
LV7_RNA-seq

value: Healthy


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G9_AD010_indexed

tag: brain region

tag: Sex

tag: age


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G9_AD012_indexed


title: Red Delicious

city: Srinagar

middle: Z.

last: Masoodi

state: Jammu and Kashmir

address: Shalimar Campus

department: Division of Plant BiotechnologyDivision of Plant Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir

description: RD

data_processing:
The generated data was aligned to the Malus domestica genome using Hisat2. The resultant bam were subsequently processed by the Subread pipeline
Genome_build: GCF_000148765.1
Supplementary_files_format_and_content: counts.matrix (Tab delimited files contatining raw read counts)

organism: Malus domestica

source_name: Leaf

extract_protocol:
Using CTAB based modified method
RNA libraries were prepared for sequencing using standard  Illumina protocols

value: Leaf

tag: developmental stage

value: Walnut stage

tag: cultivar

value: Red Delicious

tag: scab resistance

value: Susceptible


title: PBMC_PP_rep21

value: multiple sclerosis

value: HumanHT-12 v4

value: blood


title: Healthy Ventricle 2 RNA-Seq

description:
RNA-seq from Healthy Left Ventricle Tissue
RNA_Seq_Differential_Genes.txt
LV6_RNA-seq


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H10_AD012_indexed

value: MOp


title: EPS cells-1

description: Extended pluripotent stem cells


title: PBMC_PP_rep20

value: primary-progressive multiplle sclerosis

value: PBMC


title: PBMC_PP_rep32

value: Independent Test Set


title: Healthy Ventricle 1 RNA-Seq

description:
RNA-seq from Healthy Left Ventricle Tissue
RNA_Seq_Differential_Genes.txt
LV5_RNA-seq


title: Prima

description: PR

value: Prima

value: Resistant


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H10_AD002_indexed

value: male


title: Ambri

description: AM

value: Ambri


title: PBMC_PP_rep19

value: Training Set


title: Failed Ventricle 4 RNA-Seq

description:
RNA-seq from Failed Left Ventricle Tissue
RNA_Seq_Differential_Genes.txt
TRID74_RNA-seq

value: Heart Failure


title: PBMC_PP_rep18


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G7_AD004_indexed


title: Mahraji

description: MH

value: Leaf

value: Mahraji


title: PBMC_PP_rep24


title: PBMC_RR_rep108

value: relapse-remitting multiple sclerosis

value: Independent test set


title: Florina

description: FL

value: Walnut stage

value: Florina


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G9_AD007_indexed


title: PBMC_RR_rep107

value: multiple sclerosis

value: HumanHT-12 v4

value: blood


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G8_AD004_indexed

value: MOp


title: SW6ODC1

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

description:
rawcounts.txt
normcounts.txt

data_processing:
Illumina Casava2.2 software used for basecalling.
Sequenced reads were mapped to rn6 whole genome using STAR v2.5.3a with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.24.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include rawcount values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values(cpm = count per millions) for each Sample

source_name: CRC cell line

growth_protocol: Human CRC and non-malignant cells were obtained from ATCC or Public Health England with a corresponding authentication certificate. The cells were cultured in a humidified incubator at 37°C and 5% CO2 in culture medium supplemented with 10% foetal bovine serum (S1810-500, Biowest, Nuaillé, France) and 1% penicillin/streptomycin (4-01F00-H, BioConcept, Allschwil, Switzerland). Culture media: RPMI-1640 Glutamax medium (61870-010, Gibco, Paisley, UK) for DLD1; DMEM Glutamax medium (31966-021, Gibco) for SW620, HCT116, LS174T, HT29, SW48; EMEM medium (M2279-500ML, Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol:
RNA extraction was performed with the RNA easy® Plus kit (74134, Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Illumina TruSeqHT stranded mRNA kit

treatment_protocol: Drugs were dissolved in DMSO, stored at -80 and an aliquot was thawn prior to each. Drugs were dissolved at concentrations resulting in in vitro experimental conditions 0.15% DMSO maximum in culture medium. Drug stocks: 20 mg/mL regorafenib (R-8024), 15 mg/mL erlotinib (E-4007), 20 mg/mL vemurafenib (V-2800) and 1 mg/mL BEZ-325 (N-4288) from LC laboratories (Woburn, MA, USA); 20 mg/mL selumetinib (HY-50706), 10 mg/mL AZD-4547 (HY-13330, 10 mg/mL GDC-0994 (HY--15947), 20 mg/mL folinic acid (HY-17556) and 5 mg/mL oxaliplatin (HY-17371)  from MedChemExpress (Monmouth Junction, NJ, USA); 10 mg/mL vatalanib (S1101) and 10 mg/mL crenolanib (S2730) from Selleck Chemicals (Houston, TX, USA); 10 mg/mL 5-fluorouracil (F6627) from Sigma-Aldrich; 4 mg/mL Zaltrap® from Sanofi. Single drugs or pre-mixed drug combinations were incubated with the 2D cell cultures for 2h at day 1 post-seeding

tag: treatment

value: ODC (regorafenib, vemurafenib)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G9_AD004_indexed


title: SW6CTRL2

description:
rawcounts.txt
normcounts.txt

value: CTRL


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G9_AD002_indexed


title: SW6CTRL1

description:
rawcounts.txt
normcounts.txt


title: Vista Bella

description: VB

value: Vista Bella

value: Susceptible


title: PBMC_RR_rep106

tag: disease

value: PBMC


title: PBMC_RR_rep105

tag: disease staging


title: SW4ODC2

description:
rawcounts.txt
normcounts.txt

value: ODC (vemurafenib, crenolanib)


title: wt_FIPs5

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HiSAT2 (v 2.0.1) (Pertea et al., 2016) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015).
Aligned reads were quantified using featurecount (v1.4.6) (Liao et al., 2014) per gene ID against Gencode version 10 (Mudge and Harrow, 2015).
Differential gene expression analysis was done using the R package DEseq2 (v 1.6.3).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited file with logCPM gene counts

source_name: mouse fibro-inflammatory progenitors (FIPs)

growth_protocol: All 20 samples were prepared from the PDGFRb+ cells of gonadal white adipose tissue of Mural-Zfp423TG and control mouse after 1-month high-fat diet (60% kcal from fat) feeding. Stromal vascular fraction (SVF) cells were isolated from gWAT of 8-week-old male mice (n=10 mice each genotype which were housed in thermoneutrality (30°C). Then, FIPs (CD45-CD31-PDGFRb+LY6C+) and APCs (CD45-Cd31-PDGFRb+LY6C-CD9-) were sorted form the SVF cells using FACS prior to the Total RNA isolation. The RNA of the same cell type from two independent mice were pooled to get enough amounts of RNA for RNA-seq.

extract_protocol:
Total RNA from freshly FACS-sorted cells was extracted and purified using the RNAqueous Micro total RNA isolation kit (ThermoFisher Scientific, #AM1931). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA).
Starting from total RNA, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) is used to isolate pure mRNA. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. With NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770), cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).

value: control

value: FIP


title: wt_FIPs3


title: SW4ODC1

description:
rawcounts.txt
normcounts.txt


title: wt_FIPs4


title: SW6ODC2

description:
rawcounts.txt
normcounts.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_H10_AD004_indexed

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: male


title: SW4CTRL2

description:
rawcounts.txt
normcounts.txt


title: wt_FIPs1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G7_AD001_indexed


title: PBMC_RR_rep103

value: relapse-remitting multiple sclerosis

tag: illumina chip


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G8_AD010_indexed


title: wt_APCs5

source_name: adipogenic visceral adipocyte precursor cells

value: APC


title: LSODC2

description:
rawcounts.txt
normcounts.txt

value: ODC (regorafenib, GDC-0994)


title: SW4CTRL1

description:
rawcounts.txt
normcounts.txt


title: PBMC_RR_rep102

value: Independent test set

tag: tissue


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G7_AD008_indexed


title: PBMC_RR_rep101

value: multiple sclerosis

tag: cell type


title: PBMC_RR_rep100

value: HumanHT-12 v4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G7_AD007_indexed

tag: strain


title: wt_APCs3


title: LSODC1

description:
rawcounts.txt
normcounts.txt


title: wt_APCs4


title: wt_APCs2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G8_AD006_indexed


title: wt_FIPs2


title: wt_APCs1


title: PBMC_RR_rep99

value: blood


title: LSCTRL2

description:
rawcounts.txt
normcounts.txt


title: PBMC_RR_rep104


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G7_AD002_indexed

value: MOp


title: tg_FIPs5

value: Mural-Zfp423 transgenic


title: PBMC_RR_rep98


title: LSCTRL1

description:
rawcounts.txt
normcounts.txt

value: CTRL


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G8_AD012_indexed


title: HTODC2

description:
rawcounts.txt
normcounts.txt

value: ODC (regorafenib, AZD-4547, vatalanib)


title: PBMC_RR_rep96


title: HTODC1

description:
rawcounts.txt
normcounts.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G9_AD008_indexed


title: tg_FIPs4


title: PBMC_RR_rep97


title: HTCTRL2

description:
rawcounts.txt
normcounts.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G6_AD012_indexed


title: tg_FIPs2


title: PBMC_RR_rep94


title: PBMC_RR_rep95


title: tg_FIPs3


title: HCTODC2

description:
rawcounts.txt
normcounts.txt

value: ODC (regorafenib, vemurafenib, GDC-0994)


title: tg_FIPs1


title: HCTODC1

description:
rawcounts.txt
normcounts.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G7_AD006_indexed


title: PBMC_RR_rep92

value: PBMC


title: tg_APCs5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G7_AD012_indexed


title: HTCTRL1

description:
rawcounts.txt
normcounts.txt


title: HCTCTRL2

description:
rawcounts.txt
normcounts.txt


title: tg_APCs4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G6_AD010_indexed


title: PBMC_RR_rep91


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G6_AD007_indexed


title: PBMC_RR_rep90


title: HCTCTRL1

description:
rawcounts.txt
normcounts.txt


title: DLDODC2

description:
rawcounts.txt
normcounts.txt

value: ODC (regorafenib, selumetinib)


title: tg_APCs2


title: tg_APCs3


title: PBMC_RR_rep89


title: DLDODC1

description:
rawcounts.txt
normcounts.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G4_AD010_indexed


title: PBMC_RR_rep88


title: PBMC_RR_rep93


title: PBMC_RR_rep87


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G5_AD012_indexed


title: DLDCTRL1

description:
rawcounts.txt
normcounts.txt


title: tg1_input

data_processing:
The raw reads were aligned to the mouse reference genome (GRCm38/mm10) using default parameters in BWA v0.7.12 (Li and Durbin, 2009).
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 (Li et al., 2009) and Sambamba version 0.6.6 (Tarasov et al., 2015).
Library complexity was measured using BEDTools version 2.26.0 (Quinlan and Hall, 2010) and meets ENCODE data quality standards (Landt et al., 2012).
Relaxed peaks were called using MACS version 2.1.0 (Feng et al., 2012) with a p-value of 1x10-2 for H2K27ac and SPP version 1.4 (Kharchenko et al., 2008) with an IDR = 0.01 for each replicate and pseudoreplicates. For H3K27ac peak calls that are either observed in both pseudoreplicates were used for subsequent analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: ChIP-seq BigWig files were generated using MACS version 2.1.0; Scores represent the ChIP-seq fold change over control

growth_protocol: FIPs isolated from control and Mural-Zfp423TG mice were prepared and cultured as preciously described (Hepler et al., eLife, 2018). After isolation, FIPs were cultured in ITS media (60% low glucose DMEM, 40% MCDB-201 media, 2% endotoxin-free FBS, 1% insulin-transferrin-selenium premix, 0.1 mM L-ascorbic acid-2-2phosphate, 10ng/mL FGF basic, 1% penicillin/streptomycin, and 1% gentamicin) until experiments were performed.

extract_protocol:
Chromatin Immunoprecipitation (ChIP) was performed as described (Luo, et al. Mol Cell). FIP cells from control or Mural-Zfp423TG mice were cross-linked with 1% formaldehyde in PBS for 10 minutes at 37 °C and quenched in 125 mM glycine in PBS for 5 minutes at 4 °C. The FIP cells were then lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]) to obtain nuclear material. Crude nuclear pellets were collected by centrifugation and resuspended in lysis buffer (5 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]), and incubated on ice for 10 minutes. The chromatin fragmentation was performed at 4 °C by Bioruptor 300 using the setting of 10 cycles of 30 seconds on and 60 seconds off to generate chromatin fragments of 200-500 bp in length. The soluble chromatin fragments were diluted 1:10 with dilution buffer (20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2mM EDTA, 150 mM NaCl, 1 mM DTT, and Protease inhibitor cocktail [Sigma, #P8340]) and pre-cleared using Protein G Sepharose 4 Fast Flow (GE Healthcare Bio-sciences, #17-0618-01) for 1 hour at 4 °C. The pre-cleared samples were incubated with anti-p65 antibody (Cell Signaling technology, #8242) at 4 °C for overnight before the addition of Protein G Sepharose 4 Fast Flow (GE Healthcare Bio-sciences, #17-0618-01) at 4 °C for 2 hours to capture the antibody-protein-DNA complexes. The immunoprecipitated material was consecutively washed with low salt wash buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, and Protease inhibitor cocktail [Sigma, #P8340]), high salt wash buffer (20 mM Tris-HCl pH 7.9, 2mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, and Protease inhibitor cocktail [Sigma, #P8340]), LiCl wash buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, and Protease inhibitor cocktail [Sigma, #P8340]), and 1x Tris-EDTA (TE). After eluted using elution buffer (100 mM NaHCO3, 1% SDS), the immunoprecipitated material was digested with RNase (Roche, #11119915001) and proteinase K (ThermoFisher Scientific, #EO0491) prior to the purification and concentration of the immunoprecipitated genomic DNA by ChIP DNA Clean & Concentrator kit (Zymo Research, #D5201).
ChIP-seq libraries were generated using Nebnext NGS DNA Library Preparation for Illumina kit (New England BioLabs, E7645) following the manufacturer’s protocol.

treatment_protocol: FIPs isolated from both control and Mural-Zfp423TG mice were subject to LPS (100ng/mL, 2 hours treatment and ChIP assay were performed after the treatment.

tag: antibody

value: Input (IgG control)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G4_AD004_indexed


title: PBMC_RR_rep86


title: tg1_chd4

value: NF-κB p65 (D14E12) XP® Rabbit mAb (Cell Signaling Technology, #8242)


title: PBMC_RR_rep85


title: c1_input

value: control


title: c1_chd4


title: PC3_Res_88

city: Ann Arbor

first: Evan

middle: T

last: Keller

state: MI

address: 2800 Plymouth Rd

institute: University of Michigan

data_processing:
Samples were sequenced on Illumina HiSeq 2500 for DU145 cell line and Illumina HiSeq 4000 with single end option for PC3 cell line.
Samples were aligned to Human genome hg38 using bowtie alignment tool.
Poor quality cells were removed as determined using the Fluidigm Singular package.
Genome_build: Human genome hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts

growth_protocol: Cells were cultered in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Cells were trypsinized in 0.05% Trypsin EDTA for 5-10 mins at 37°C and washed with media.  The cell suspension was loaded into the Fluidigm C1TM machine and processed into single cell cDNA libraries according to the manufacturer protocol.
Full length mtotal RNA-seq libraries were generated from single cells captured using the Fluidigm C1TM Single Cell mtotal RNA Seq IFC, 10-17 um and Fluidigm C1TM Single-Cell Reagent Kit for mtotal RNA Seq.  Full length cDNA was converted into sequence ready libraries using SMART-seq v4 Ultra Low Input total RNA kit for Fluidigm C1TM System and SeqAmpTM DNA Polymerase.  Library preparation was completed using Nextera XT DNA library prep kit.

treatment_protocol: Docetaxel resistance was maintained with the addition of 10 nM docetaxel in DMSO in growth media while sensitive cells were maintained with the addition of a final concentration of 0.1% DMSO.

tag: docetaxel

value: Resistant

tag: disease state

value: Prostate cancer

tag: cell line


title: PC3_Res_89


title: PBMC_RR_rep84

data_processing:
Microarray raw data originating from Illumina HumanRef-8 v2 and HumanHT-12 v4 arrays were pre-processed and normalized independently using the limma package and then merged into a single integrated dataset according to the common probes. Raw intensities were background subtracted and filtered according to detection pvalues (p<0.05 in at least 20% of samples) and then normalized using quantile normalization. Pre-processed data were log2 transformed and inspected for the presence of hidden batch effects using DASC. Batch correction and cross-platform integration of the two independently normalized datasets was performed using Combat.
[Matrix-merged-normalized-batch.corrected.txt]  quantile normalized and batch corrected signals.

extract_protocol: Total RNA was extracted using Trireagent (Ambion) and stored at -80°C. Quantification and quality analyses of RNA were performed at a Bioanalyzer 2100 (Agilent).

value: relapse-remitting multiple sclerosis

tag: dataset partition


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G6_AD004_indexed

first: Joseph

tag: brain region

tag: Sex

value: male


title: PC3_Res_90


title: Mm_EPI_HFD_AA_006

first: Alexander

last: Banks

address: 330 Brookline Ave, CLS 738

department: Endocrinology

institute: Beth Israel Deaconess Medical Center

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v2.20.0) and aligned to the mm10 mouse genome by with HISAT2 (v2.0.5)
PCR duplicates and low-quality reads were filtered by Picard (v2.9.2)
Filtered reads were assigned to the annotated transcriptome and quantified using featureCounts  (v1.5.2)
Normalization and differential expression analysis were performed using EdgeR (v 3.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was isolated from cells or tissues using TRIzol reagent (Thermo Fisher) followed by a Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer’s instructions.
400ng of total RNA was used as input for RNA-seq Library construction, which consisted of rRNA removal via the NEBNext rRNA depletion kit (E6310X) and conversion to cDNA using the NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (E6111L), both per manufacturer’s instructions. cDNA was diluted 1:15 and subsequently tagmented and amplified for 12 cycles using the Nextera XT DNA Library Preparation Kit (Illumina FC-131).
Individual libraries were QC’d by Qubit and Agilent Bioanalyzer, pooled, and sequenced at a final loading concentration of 1.8 pM on a NextSeq500 (36bp x 36bp paired-end reads).

tag: genotype

value: epididymal white adipose

tag: diet

value: high-fat diet


title: tg_APCs1

value: APC


title: PBMC_RR_rep83

last: acquaviva

address: Via Olgettina, 60

institute: San Raffaele Hospital

value: multiple sclerosis

value: HumanHT-12 v4

value: Independent test set

value: blood


title: PBMC_RR_rep82


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G5_AD010_indexed

value: MOp

tag: age


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G6_AD002_indexed


title: Mm_EPI_HFD_AA_003


title: PBMC_RR_rep81

value: PBMC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G5_AD006_indexed


title: DLDCTR2

description:
rawcounts.txt
normcounts.txt

tag: treatment

value: CTRL


title: Mm_EPI_HFD_AA_002


title: PC3_Res_84


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G4_AD012_indexed


title: PC3_Res_85


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G5_AD007_indexed


title: PBMC_RR_rep73

tag: disease

value: Training Set


title: Mm_EPI_HFD_WT_003

value: WT


title: PC3_Res_87


title: PBMC_RR_rep71

tag: disease staging


title: Mm_EPI_HFD_AA_004


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G5_AD001_indexed


title: PC3_Res_82


title: PC3_Res_83


title: PC3_Res_81


title: Mm_EPI_HFD_WT_001


title: PBMC_RR_rep72

tag: illumina chip


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G6_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G4_AD001_indexed


title: PC3_Res_86


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G5_AD002_indexed


title: PBMC_RR_rep70

tag: tissue


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G4_AD002_indexed


title: PBMC_RR_rep69

tag: cell type


title: MyTrMaSt_CBE_5 [4KO_CBE100_5]

city: Rehovot

first: Ayelet

last: Vardi

state: Hamerkaz

address: Herzl St 234

country: Israel

institute: Weizmann Institute of science

data_processing:
massively parallel single-cell RNA-sequencing (MARS-Seq)
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200)
Reads were mapped to genome
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Read count was performed with HTSeq-count
UTAP: User-friendly Transcriptome Analysis Pipeline. Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran and Dena Leshkowitz (in revision BMC Bioinformatics)
Genome_build: mm10
Supplementary_files_format_and_content: Raw_counts, Normalized, Differentially_expressed

extract_protocol:
Brain tissue was homogenized using a GentleMACS dissociator and mRNA was isolated using the RNeasy mini kit. RNA concentration (260/230 and 260/280 nm ratios)  were measured using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was evaluated using an RNA screen tape on a Tapestation 2200 (Agilent, Santa Clara, California, USA).
A bulk variation of MARSseq was used to construct RNAseq libraries: Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Science. American Association for the Advancement of Science; 2014;343:776–9.

tag: strain/genotype

value: MyTrMaSt Null

value: 19 days

value: conduritol B-epoxide (CBE)

value: Brain


title: PC3_Res_80

value: Resistant

value: Prostate cancer


title: PBMC_RR_rep80

city: milan

first: massimo

value: relapse-remitting multiple sclerosis


title: PC3_Res_79


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G3_AD006_indexed

value: male

tag: strain


title: Mm_EPI_HFD_WT_005

value: epididymal white adipose

value: high-fat diet


title: PBMC_RR_rep68

value: multiple sclerosis

value: HumanHT-12 v4


title: PC3_Res_78

tag: docetaxel


title: MyTrMaSt_CBE_4 [4KO_CBE100_4]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G3_AD010_indexed

value: MOp


title: MyTrMaSt_CBE_3 [4KO_CBE100_3]


title: PBMC_RR_rep67

value: blood

value: PBMC


title: Mm_EPI_HFD_WT_002


title: MyTrMaSt_CBE_2 [4KO_CBE100_2]


title: PC3_Res_77

tag: disease state


title: PBMC_RR_rep66

value: Training Set


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G2_AD006_indexed


title: PC3_Res_76

tag: cell line


title: PC3_Res_75


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G3_AD004_indexed


title: MyTrMaSt_PBS_3 [4KO_PBS100_3]

value: PBS


title: PBMC_RR_rep65

tag: dataset partition


title: PBMC_RR_rep63


title: MyTrMaSt_CBE_1 [4KO_CBE100_1]

value: MyTrMaSt Null


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G3_AD007_indexed

tag: brain region


title: PBMC_RR_rep64


title: MyTrMaSt_PBS_2 [4KO_PBS100_2]

value: 19 days


title: PC3_Res_74


title: PBMC_RR_rep62


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G3_AD001_indexed

tag: Sex


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD010_indexed


title: MyTrMaSt_PBS_1 [4KO_PBS100_1]


title: PC3_Res_73


title: PC3_Res_72


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD012_indexed


title: WT_CBE_3 [CBE100_3]

value: conduritol B-epoxide (CBE)


title: PC3_Res_71


title: PBMC_RR_rep60


title: WT_CBE_2 [CBE100_2]

value: Brain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G2_AD012_indexed


title: PC3_Res_70

value: Resistant


title: PBMC_RR_rep59


title: WT_CBE_1 [CBE100_1]


title: PC3_Res_69

value: Prostate cancer


title: WT_PBS_3 [PBS100_3]


title: WT_PBS_2 [PBS100_2]


title: PBMC_RR_rep58

value: relapse-remitting multiple sclerosis


title: PC3_Res_67


title: PC3_Res_68


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD006_indexed

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G4_AD007_indexed


title: PBMC_RR_rep57


title: IRMOE5

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Mouse muscle  RNA-seq by Illumina NextSeq 500

data_processing:
Reads were aligned to the mouse genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: muscle

extract_protocol:
Muscle RNA of Control or IRMOE mice was extracted by homogenizing tissues in TRIzol, treating with chloroform, and precipitating in 70% ethanol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: IRMOE


title: PC3_Res_66


title: PC3_Res_65


title: IRMOE6


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD004_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: PBMC_RR_rep61


title: PC3_Res_64


title: IRMOE4


title: PBMC_RR_rep53


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G2_AD002_indexed


title: PC3_Res_63


title: IRMOE3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G2_AD001_indexed


title: PC3_Res_62


title: PBMC_RR_rep56


title: PBMC_RR_rep51


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G11_AD006_indexed


title: IRMOE2


title: PC3_Res_61


title: PBMC_RR_rep55


title: PBMC_RR_rep50


title: IRMOE1


title: PC3_Res_60


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD001_indexed


title: PBMC_RR_rep49


title: CTRL6

value: control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD008_indexed


title: CTRL5


title: PBMC_RR_rep48

value: multiple sclerosis


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G11_AD010_indexed


title: PBMC_RR_rep47

value: HumanHT-12 v4


title: PC3_Res_58


title: CTRL4


title: PC3_Res_57


title: PBMC_RR_rep46


title: PC3_Res_56


title: CTRL3


title: PBMC_RR_rep45


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G11_AD012_indexed

value: MOp


title: PBMC_RR_rep44

value: blood


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G11_AD007_indexed


title: PC3_Res_54


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G10_AD006_indexed


title: PBMC_RR_rep43

value: PBMC


title: IFNg_3

city: Guangzhou

first: Bodu

last: Liu

state: State...

address: School of Life Sciences, Sun Yat-sen U East Camp, High. Edu. Meg. Cntr.

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
HTSeq-count was used to quantify gene/transcript levels
DESeq2 was used to normalize the expression levels
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values of genes for each sample

source_name: Mammary tumor

extract_protocol:
Mammary tumors were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols of TruSeq RNA Library Prep Kit v2 kit

value: treat with IFNg alone


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G11_AD002_indexed


title: PBMC_RR_rep42

value: Training Set


title: PC3_Res_53


title: PBMC_RR_rep54


title: IFNg_1


title: PBMC_RR_rep34.1


title: PC3_Res_52


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G10_AD007_indexed


title: IFNg_2


title: PC3_Res_51


title: CTRL2

city: Boston


title: PBMC_RR_rep16.1


title: MPLA_3

value: treat with MPLA alone


title: PC3_Res_55


title: CTRL1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G10_AD004_indexed


title: PC3_Res_50


title: MPLA_2


title: PBMC_RR_rep14.1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G11_AD001_indexed


title: PBMC_RR_rep12.2


title: WT_PBS_1 [PBS100_1]

value: 19 days

value: PBS


title: PBMC_RR_rep11.2


title: PC3_Res_47


title: MPLA_IFNg_2

value: treat with MPLA and IFNg


title: PC3_Res_49

value: Resistant


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G10_AD010_indexed


title: PC3_Res_46

value: Prostate cancer


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G10_AD002_indexed


title: MPLA_IFNg_1


title: PBMC_RR_rep1.1

value: relapse-remitting multiple sclerosis


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F9_AD006_indexed

value: male


title: MPLA_1


title: PBMC_RR_rep52


title: Vehicle_3

value: treat with vehicle


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F9_AD012_indexed


title: PBMC_CIS_rep56

value: clinically isolated syndrome

value: Independent test set


title: Vehicle_2


title: PC3_Res_45


title: PC3_Res_44


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G10_AD001_indexed


title: PC3_Res_48


title: PC3_Res_59


title: Vehicle_1


title: MPLA_IFNg_3


title: PBMC_RR_rep1.2

value: multiple sclerosis

value: HumanHT-12 v4


title: PBMC_CIS_rep55

value: blood


title: PC3_Res_42


title: PBMC_CIS_rep54

value: PBMC


title: Inguinal tdTomato- GFP+ cells from inguinal WAT

data_processing:
Data was analyzed using Cell Ranger (v3.1.0) to perform demultiplexing, aligning reads, filtering, clustering, and gene expression analyses, using default parameters.
Genome_build: mm10 + GFP
Supplementary_files_format_and_content: The processed data files contain the unfiltered barcodes, matrix, and genes.

source_name: inguinal white adipose tissue

extract_protocol:
The cells were isolated from inguinal WAT as previously described (Hepler et al. Elife 2017).  The library was generated according to manufacturer's instructions (10X Genomics).
According to 10x Genomics’ protocol, sequenced R1=26cycles R2=58cycles, i7=8cycles

value: 8 weeks old

tag: genotype

value: MuralChaser mice

value: gonadal white adipose tissue

value: tdTomato- GFP+ cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F9_AD001_indexed

value: MOp


title: PBMC_CIS_rep57


title: PBMC_CIS_rep53


title: PC3_Res_41


title: PBMC_CIS_rep48

value: Training set


title: E14_5.4kb_5hmC

city: Ipswich

first: Zhiyi

last: Sun

address: 240 County Road

institute: New England Biolabs

description: LR-EM-seq (Illumina, PacBio, Nanopore)

data_processing:
library strategy: LR-EM-seq (Long Range Enzymatic Methyl-seq)
Illumina sequencing: basecalls were performed using Illumina RTA software (v2.4.11 and v3.4.4) and fastq files were generated from the BCL files using Picard’s basecallstofastq. Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
Pacbio SMRT sequencing: Circular Consensus Sequences were extracted from the raw movie data and converted into fastq file using SMRT Link (version 6.0.0.47841) CCS protocol for Sequel runs or using the SMRT portal (version 2.3.0.140893) “RS_ReadsOfInsert” protocol for RSII runs. Reads that were shorter than the expected amplicon sizes were removed from downstream analysis
Oxford Nanopore sequencing: Raw fast5 data from the MinION were generated using Min- KNOW version 18.12 and base called using Guppy base caller Version 2.1.3.
Trimmed Illumina reads of the whole genome 5mC/5hmC sequencing experiments were mapped to a composite reference including the sequences of mouse genome (mm9), lambda, XP12, pUC19 and T4 using the Bismark program with the default bowtie2 setting. The aligned reads were then subjected to two post-processing QC steps: 1, alignment pairs that shared the same alignment start positions (5’ ends) were regarded as PCR duplicates and were discarded; 2,  reads that alinged to the mouse genome and contain excessive cytosines in non-CpG context (e.g., more than 5 in 150bp) were removed because they likely resulted from conversion errors. The remaining good quality alignments were then used for cytosine methylation and hydroxymethylation calling by Bismark methylation extractor.
Long reads generated by Pacbio SMRT sequencing and Oxford Nanopore sequencing were mapped to the mouse reference genome (mm9) using the Bismark program with the following parameters: –bowtie2 -N1 -L15 –score min L,0,-0.6. The modification states of individual cytosine sites were called by the bismark methylation extrator program. We then extracted the context specific methylation information of individual molecules using custome perl scripts and plotted in R.
SNPs were called using the Samtools
Genome_build: mouse (mm9)
Supplementary_files_format_and_content: tab-delimited text files include genomic coordinates, modification calls and sequence contexts of covered cytosines.

source_name: E14 embryonic stem cells

extract_protocol:
Mouse genomic DNA’s were extracted with a DNeasy Blood and Tissue Kit (QIAGEN) according to the manufacturer's instructions.
(Illumina) DNA was sheared to 250 bp fragments with a Covaris S2 sonicator. Enzymatic 5mC libraries were prepared using the NEBNext Enzymatic Methyl-seq Kit (E7120S, NEB) according to the manufacturer’s instructions. WGBS libraries were prepared using NEBNext Ultra II Kit (NEB) according to the manufacturer’s instructions. Enzymatic 5hmC libraries were prepared using the NEBNext Ultra II Kit (NEB) with the following modifications: (1) after sonication and prior to end repair, fragmented DNA was first glucosylated with BGT (NEB); (2) Pyrrolo-dC adaptors were used instead of 5-mC adapters, and (3) APOBEC-5hmC treatment was applied after adapter ligation and before PCR.
(PacBio) PacBio SMRT libraries were prepared using PacBio Amplicon template preparation and sequencing protocol. Libraries were loaded onto SMRT cells using the MagBead method and were sequenced on a PacBio RSII machine with 5.5-hour movie or on a PacBio Sequel machine with 10-hour movie.
(Nanopore) Oxford Nanopore libraries were prepared using the 1D Native barcoding genomic DNA kit (EXP-NBD103 and SQK-LSK108 kits, Oxford Nanopore Technologies).  For each sample, end-repair and dA-tailing was performed using the NEBNext Ultra II End repair/dA-Tailing module (E7546, NEB), following Oxford Nanopore protocol, except that the incubation time was increased to 20 min. Samples were barcoded using the EXP-NBD103 kit (Oxford Nanopore Technologies) and were pooled in equimolar amounts. The Nanopore adapter ligation was performed according to the manufacturer’s protocol. The library was sequenced for a total of 11h on a MinION (Oxford Nanopore Technologies) using a FLO-MIN106 Rev D flow cell.

tag: strain background

value: E14 embryonic stem cells

tag: tissue source

value: embryo

tag: modification type

value: APOBEC 5hmC


title: PC3_Res_40

value: Resistant

value: Prostate cancer


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F9_AD002_indexed

value: male

tag: age


title: PC3_Res_39


title: PBMC_CIS_rep47

tag: disease

tag: disease staging

value: clinically isolated syndrome


title: E14_5.4kb_5mC

description: LR-EM-seq (Illumina, PacBio, Nanopore)

value: 5mC (5mC+5hmC)

tag: treatment

value: APOBEC 5mC


title: PC3_Res_43


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F8_AD012_indexed


title: PC3_Res_38


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F9_AD007_indexed


title: PBMC_CIS_rep46

value: multiple sclerosis

tag: illumina chip

value: HumanHT-12 v4

tag: tissue

value: blood

tag: cell type


title: mBrain_5hmC

description: Illumina

source_name: genomic DNA of normal brain

value: BALB/c

value: brain


title: PBMC_CIS_rep45

value: PBMC


title: PC3_Res_37

tag: docetaxel


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F8_AD007_indexed

value: MOp

tag: strain


title: mHeart_5hmC

description: Illumina

source_name: genomic DNA of normal heart

value: heart


title: mSpleen_5hmC

description: Illumina

source_name: genomic DNA of normal spleen

value: spleen


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F8_AD001_indexed


title: PC3_Res_36

tag: disease state

tag: cell line


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F9_AD008_indexed

tag: brain region


title: PBMC_CIS_rep44

tag: dataset partition

value: Training set


title: PC3_Res_35


title: PBMC_CIS_rep43


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F8_AD004_indexed

tag: Sex


title: PC3_Res_34


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F7_AD004_indexed


title: J1_ES_TKO_5hmC

description: Illumina

source_name: genomic DNA of J1 embryonic stem cells

tag: strain background

value: J1 embryonic stem cells

value: embryo

value: APOBEC 5hmC


title: E14_APOBEC_5hmC

description: Illumina

value: E14 embryonic stem cells

tag: tissue source


title: PC3_Res_33

value: Resistant

value: Prostate cancer


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F6_AD007_indexed

value: male


title: PC3_Res_32


title: E14_BS2_5mC

description: Illumina

tag: modification type

value: 5mC (5mC+5hmC)

value: Bisulfite 2


title: E14_BS1_5mC

description: Illumina

value: Bisulfite 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F7_AD010_indexed

tag: age


title: E14_APOBEC_5mC

description: Illumina

value: APOBEC 5mC


title: PC3_Res_31


title: TG_p65

value: Mural-Zfp423 transgenic

tag: antibody

value: NF-κB p65 (D14E12) XP® Rabbit mAb (Cell Signaling Technology, #8242)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F4_AD001_indexed

value: MOp


title: 3T3_5hmC

description: Illumina

source_name: genomic DNA of NIH/3T3 fibroblast cells

value: NIH/Swiss

value: NIH/3T3 fibroblast cells


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G1_AD002_indexed


title: PC3_Res_30


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F7_AD012_indexed


title: PC3_Res_29


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F5_AD004_indexed


title: TG_input

value: Input (IgG control)


title: PC3_Res_28


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F6_AD012_indexed


title: PC3_Res_27


title: WT_p65

value: control


title: WT_input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F4_AD012_indexed


title: KO testis, repeat 4

city: Worcester

first: Julie

last: Zhu

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

data_processing:
data were processed as described previously (Wang et al., 2016)
Illumina Casava1.7 software used for basecalling.
The paired reads were aligned to the mouse genome (ensemble GRCm38) using Hisat2 (version 2.1.0) with default parameters.
featureCounts was used to generate the gene count matrix
edgeR was use for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include CPM values calculated by edgeR with gene annotation

source_name: testis

extract_protocol:
Library was constructed as described (Vallaster et al., 2016)
Library was constructed as described (Vallaster et al., 2016)
Library was constructed as described (Vallaster et al., 2016)

value: testis

tag: genotype

value: Rlim-KO

tag: batch

tag: gender


title: PC3_Res_25


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F5_AD012_indexed


title: PC3_Res_24


title: KO testis, repeat 3

tag: tissue


title: PC3_Res_23


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F5_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F6_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F5_AD007_indexed


title: D29_G3_591017 H rep2

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: The Jenner Institute, University of Oxford

data_processing: Probes were background corrected using negative control probes followed by quantile normalization using the neqc method of Shi et al. (2010) [PMID:20929874].

source_name: Whole Blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit

extract_protocol: Blood samples (2.5mL) were collected from consenting volunteers into PAXgene tubes. Blood samples were incubated at room temperature for 2 hours to precipitate RNA and stored at -80°C until extraction. Total RNA was purified according to the manufacturer’s protocol, including DNAse digestion for 15 minutes at room temperature, and eluted into 100 uL of the supplied elution buffer. Excess globin transcripts were removed from the samples using Human GLOBINclear kits (Life Technologies), prior to amplification.

tag: subject

tag: day

tag: vaccinegroup

tag: efficacy

value: P


title: D29_G3_591025 rep1


title: D29_G4_591011 L rep2

value: NP


title: PC3_Res_22

tag: docetaxel

value: Resistant

tag: disease state

value: Prostate cancer

tag: cell line


title: PC3_Res_26


title: D29_G4_593310 K rep2


title: D57_G3_591025 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F4_AD010_indexed

tag: brain region

tag: Sex

value: male

tag: strain


title: PC3_Res_21


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F4_AD004_indexed


title: KO testis, repeat 2


title: WT testis, repeat 2

value: WT


title: WT testis, repeat 3


title: KO testis, repeat 1


title: PC3_Res_20


title: WT testis, repeat 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F5_AD002_indexed


title: D0_G1_591013 rep1


title: D0_G2_591012 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_G11_AD008_indexed


title: D1_G1_591015 rep1


title: C-1_G4_593310 rep1


title: D57_G4_591022 rep1


title: D29_G1_591024 rep1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180605_5D_1_CEMBA180605_5D_2_F6_AD004_indexed


title: PC3_Res_19


title: D29_G4_591020 rep1


title: D29_G4_593303 rep1