title: Dnmt3a KO iEpiSC #8_methylseq

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
Libraries were sequenced on the HiSeq2500 (2×100 bp paired-end reads, illumina) or Nextseq500 100 bp, single read, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
For WGBS analysis, the trimmed reads were mapped to the mouse genome (mm10) by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the mapped reads with high mapping quality (MAPQ>=20) were used for extraction of methylated cytosines by the Bismark methylation extractor with --ignore 10 --ignore_3prime 5 options (single-end reads) or with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options (paired-end reads).
For allelic methylation analysis, the trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For caluculation of allelic methylation levels, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For allelic methylation analysis with methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph columns: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.
Supplementary_files_format_and_content: ProcessedDataMatrixRPKMfin.STAR.txt:Tab-delimited text file includes RPKMs for each sample.

source_name: iEpiSCs

growth_protocol: MEFs were isolated from E14.5 embryos and were cultured in DMEM (Nacalai tesque) with 2 mM L-glutamine (Nacalai tesque), 100× nonessential amino acids (NEAA) (Nacalai tesque), 100 U/ml penicillin, 100 mg/ml streptomycin (P/S) (Nacalai tesque) and 10% Fetal Bovine Serum (FBS) (GIBCO). ESCs and iPSCs are maintained on feeders (mitomycin C (Kyowa Hakko Kirin Co., Ltd.)-treated MEFs) in knockout DMEM (GIBCO) with 2 mM L-glutamine, 100×NEAA, 100 U/ml penicillin, 100 g/ml streptomycin (P/S), 15% Fetal Bovine Serum (FBS), 0.11 mM β-mercaptoethanol (GIBCO) and 1000 U/ml human recombinant leukemia inhibitory factor (LIF) (Wako). EpiSCs were cultured in DMEM/F12+L-Glu (GIBCO), NEAA, P/S, 0.11 mM β-mercaptoethanol, 20% KnockOut Serum Replacement (KSR) (GIBCO), which was supplemented with 10 ng/ml Human Recombinant Fibroblast Growth Factor (basic) (rh bFGF) (wako), and 10 M Y-27632 (wako). iEpiSCs were maintained in DMEM/F12+L-Glu supplemented with B27 (GIBCO) and N2 cell-supplements (GIBCO), NEAA, P/S, 0.11 mM β-mercaptoethanol, 15% FBS, which was supplemented with 10 ng/ml rh bFGF, 20 ng/ml Recombinant Activin A (R&D), 200 ng/ml anti-LIF antibody (Funakoshi).

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) or NucleoSpin RNA plus (MACHEREY-NAGEL) for RNA.
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: iEpiSCs

tag: passage

tag: strains

tag: gender

value: Male

tag: analysis method

value: Methylseq


title: P304_8

status: Public on Jun 18 2019

type: SRA

city: Freiburg

first: Nadim

last: Aizarani

address: Stübeweg 51

department: Independent group leaders

country: Germany

institute: MPI-IE

library_source: transcriptomic

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the reference transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.
Supplementary_files_format_and_content: Normalhumanliverdata.RData: A count table or expression matrix for all the normal human liver cells. Use readRDS function to load data in R.

molecule: total RNA

organism: Homo sapiens

source_name: Liver tissue

growth_protocol: Cells were isolated from human liver specimens obtained from surgical resections

extract_protocol:
Liver specimens were perfused and treated with collagenase followed by Percoll purifcation/clean up steps
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hasimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

tag: tissue

value: normal liver resection specimen

tag: cause of resections

value: Colorectal cancer metastasis


title: Donor HU1020 (AKA BD405A) HBV mono-infected, 8 days

city: Princeton

first: Alexander

last: Ploss

state: NJ

address: Washington Road

department: Molecular Biology

country: USA

institute: Princeton University

data_processing:
The samples were run on two HiSeq 2500 Rapid Run mode flowcells. Basecalling was performed by Illumina RTA version 1.18.64.0. BCL files were then converted to fastq format using Illumina’s bcl2fastq version 1.8.4. Reads that aligned to phiX using Bowtie 1.1.1 (Langmead et al., 2009) were removed as well as reads that failed Illumina’s default chastity filter. The fastq files from each lane were then combined before splitting the reads from each sample using the barcode sequences allowing 1 mismatch, using the barcode_splitter program, version 0.18.2 (Leach and Parsons, 2017).
A reference genome was created using the NCBI GRCh38 human reference (iGenomes), the NCBI GRCm38 mouse reference (iGenomes), the NCBI U95551.1 Hepatitis B virus subtype ayw, complete genome, and the NCBI M21012.1 Hepatitis delta virus RNA, complete genome. The reference sequences (fasta) and gene annotations (gtf) were combined to form a single unified reference. The read alignment, quantification, and differential expression analysis was done using a locally installed instance of the Galaxy workflow platform (Afgan et al., 2016). The reads for each sample were then aligned to the combined reference using STAR (Galaxy Version 2.5.2b-1) with default parameters (Dobin et al., 2013). Quantification for each gene was then done using featurecounts (Galaxy Version 1.6.0.1) with default settings (Liao et al., 2014).
Genome_build: A reference genome was created using the NCBI GRCh38 human reference (iGenomes), the NCBI GRCm38 mouse reference (iGenomes), the NCBI U95551.1 Hepatitis B virus subtype ayw, complete genome, and the NCBI M21012.1 Hepatitis delta virus RNA, complete genome.
Supplementary_files_format_and_content: Tabular files of ENSEMBL gene ID and counts

organism:
Homo sapiens
Mus musculus

source_name: SACC-PHHs

growth_protocol: All SACC-PHHs were grown in Hurel Maintenance media containing 5% fetal bovine serum (FBS) and 1% v/v penicillin/streptomycin.

extract_protocol:
Total RNA extracted using Qiagen Rneasy Mini Kit per manufacturer's directions.
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Nano chip (Agilent Technologies, CA); only samples with RNA Integrity Number (RIN) greater than 9.0 were used for RNA-seq.  The poly-A containing RNA transcripts were enriched from 1μg of total RNA for each sample using oligo-dT bead, and further converted to cDNA then Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Wafergen Biosystems, CA) according to the manufacturer's protocol.  Different DNA barcodes were added to each RNA-seq library.  The libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, and quantified by Qubit fluorometer (Invitrogen, CA).  The RNA-seq libraries were pooled at equal molar amount and sequenced on Illumina HiSeq 2500 Rapid flowcells as single-end 75 nucleotide reads following the standard protocol.  Raw sequencing reads were filtered by Illumina HiSeq Control Software, and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: PHHs (188,000 cells/well) were seeded along with 3T3 J mouse (30,000 cells/well) in a 24 well format.  Seven to ten days after seeding, SACC-PHHs were challenged with respective viruses.

tag: cell type

value: Primary human hepatocytes co-cultured with mouse 3T3J non-parenchymal cells

tag: treatment

value: Mono-infected with HBV (MOI = 4,000)


title: Dnmt3a WT iEpiSC #7_methylseq

country: Japan

library_source: genomic

molecule: genomic DNA

organism: Mus musculus


title: P304_7


title: Dnmt3a KO iEpiSC #5_methylseq


title: Donor HU1020 (AKA BD405A) uninfected, 8 days

value: Uninfected


title: dCas9 gControl ChIP-seq

city: Paris

first: Sebastian

last: Baumgarten

address: 25, Rue du Dr. Roux

department: Parasites and Insect Vectors

country: France

institute: Institut Pasteur

description: Plasmodium falciparum dCas ChIP

data_processing:
For m6A-seq, dCas9 ChIP-seq and mRNA-seq: Sequencing reads were aligned to the P. falciparum genome using bwa ‘mem’ allowing only unique read mappings (option ‘-c 1’). Optical duplicates and alignments with a quality score < 20 were removed using samtools’ ‘rmdup’ and ‘view’, respectively
For m6A-seq and dCas9 ChIP-seq bedGraph coverage plots, deeptool’s 'bamCompare' was used to normalize the read coverage per genome position (option ‘--bs 1’) in the respective input and ChIP samples to the total number of mapped reads in each library (option ‘--normalizeUsingRPKM’). Normalized input coverage per bin was subtracted from the IP values (option ‘--ratio subtract’)
Significant m6A peaks (FDR ≤ 0.05) were called using macs2 using the de-duplicated and quality filtered alignment files with options ‘--no-model’ and '--ext-size 150' for every replicate separately. Overlapping enriched regions among replicates at each time point were identified using bedtools ‘multiinter’ and were only retained if they were present in ≥ two of the four replicates.
Strand specific gene counts were calculated from the quality-filtered bam alignment files using 'htseq-count'
Genome_build: Plasmodium falciparum v28 (plasmoDB.org)
Supplementary_files_format_and_content: m6A-seq and dCas9 ChIP-seq bedGraph files contain input normalized IP enrichments (IP minus input) at single nucleotide resolution; m6A peak files are in bed format and indicate tje start and end position of a significantly enriched m6A peaks at each time point (FDR ≤ 0.05).

organism: Plasmodium falciparum 3D7

source_name: cell culture

extract_protocol:
Red blood cell cultures (~4% hematocrit) were crosslinked for 10 min by direct addition of methanol-free formaldehyde (1% final concentration) and the cross-linking reaction was quenched using glycine. Red blood cells were lysed using 0.15% saponin and parasite cells were collected by centrifugation (3250 g, 4°C, 5 min). Following nuclei extraction, chromatin was sheared to ~ 200nt fragment lenght by sonication and the HA-tagged dCas9 was immunoprecipitated overnight at 4 °C using anti HA antibodies (Abcam #ab9110) coupled to magnetic beads. Following stringent washes, dCas9-DNA complexes were reverse crosslinked and DNA was precipitated using phenol:chloroform:isoamyl alcohol.
DNA sequencing libraries were prepared using the Diagenode MicroPlex Library Preparation kit (Diagenode # C05010014) according to the manufacturer’s instructions and sequenced on an Illumina NextSeq 500 platform with a 1x150 bp single-end read layout.

tag: strain

tag: develoment stage

value: 12 hpi

tag: genotype/variation

value: control (gControl)


title: Donor HU1019 (AKA BD330)  uninfected, 28 days


title: Dnmt3a WT iEpiSC #4_methylseq


title: NORM.4: Normal sample 4

type: RNA

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

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

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

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for Human GeneChip Gene 2.0 ST transcript annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/ genecodet.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Only genes identified by probesets with 4 or more specifc probes within were retained.  The gained CDF results a umich GENCODEG-like annotation that retains only unambiguous signals for lncRNA and coding genes that partially overlap in thier genomic position.

label: biotin

source_name: Highly purified PCs from healthy donor

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

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

value: Bone marrow plasma cells

tag: diagnosis

value: healthy donor

value: normal karyotype


title: dCas9 gPfMT-A70 ChIP-seq

description: Plasmodium falciparum dCas ChIP

value: knock-down (gPfMT-A70 )


title: RNA-Seq_siSA2_rep2

city: Madrid

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description: Poly A+ RNA

data_processing:
ChIP-Seq processing. Alignment of sequences to the reference mouse genome (mm9, February 2009) was performed using ‘Bowtie2’ under default settings (Langmead and Salzberg, 2012) . Duplicates were removed using Picardtools (version 2.13.2) and peak calling was carried out using MACS2 (version 2.1.1.20160309) after setting the qvalue (FDR) to 0.05 and using the ‘--extsize’ argument with the values obtained in the ‘macs2 predictd’ step (Zhang et al., 2008).
RNA-Seq processing. Fastq files with 51-nt single-end sequenced reads were quality-checked with FastQC (S. Andrews, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the mouse genome (mm9) with Nextpresso (Graña et al., 2018) executing TopHat-2.0.0 using Bowtie 0.12.7 and Samtools 0.1.16 allowing two mismatches and five multi-hits. Transcript assembly, estimation of their abundances and differential expression were calculated with Cufflinks 1.3.0 using the mouse genome annotation dataset NCBIM37/mm9 from Ensembl. To account for multiple-hypothesis testing, the estimated significance level (P value) was adjusted using Benjamini–Hochberg FDR correction. We consider significant those changes with FDR < 0.05.
HiC processing. HiC was performed as described (Rao et al., 2014) using MboI enzyme. Libraries from two different experiments were generated and sequenced per condition. (>200 million reads each). Data were processed using TADbit (Serra et al., 2017) for read quality control, read mapping, interaction detection, interaction filtering, and matrix normalization. After a FastQC protocol to discard artifacts, the remaining reads were mapped to the reference mouse genome (mm10) using a fragment-based strategy in TADbit, after discarding non- informative contacts -including self-circles, dangling-ends, errors, random breaks or duplicates
Genome_build: mm9 for ChIP-seq/RNA-seq; mm10 for HiC
Supplementary_files_format_and_content: bigwig files were generated using the tool bamCoverage of deeptools

molecule: polyA RNA

source_name: mES cells SA2 depleted

growth_protocol: mESCs were grown in DMEM containing 10% fetal calf serum in the presence of LIF (serum-grown condition). MEK inhibitor PD0325901 (1μM) and GSK3 inhibitor CHIR99021 (3μM) were added (2i-grown). In both cases plates were coated with 0.1% gelatin and no feeder cells were present.

extract_protocol:
For ChIP-seq experiments, lysates were clarified from sonicated nuclei and cohesin-DNA complexes were isolated with antibody. HiC was performed as described (Rao et al., 2014) using MboI enzyme. For RNA-Seq,  RNA was extracted using the RNeasy Mini Kit and treated with DNaseI.
ChIP-Seq liibraries were prepared as follows: From 5 to 15 ng of immunoprecipitated chromatin (as quantitated by fluorometry) were electrophoresed on an agarose gel and independent sample-specific fractions of 100–200 bp were taken. Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers.  Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. HiC libraries were performed as described (Rao et al., 2014) using MboI enzyme. For RNA-seq libraries, RNA was extracted as described and treated with DNaseI (Ambion). polyA+RNA was purified with the Dynabeads mRNA purification kit (Invitrogen), randomly fragmented and converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: ES cells

tag: passages


title: P304_4


title: RNA-Seq_siSA2_rep1

description: Poly A+ RNA


title: NORM.2: Normal sample 2


title: NORM.1: Normal sample 1


title: P304_5


title: Donor HU1019 (AKA BD330)  HBV/HDV co-infected for 28 days

value: Co-infected with HBV (MOI = 4,000) and HDV (MOI = 1,000)


title: Donor HU1019 (AKA BD330)  HBV/HDV co-infected for 28 days, replicate


title: MM.021: MM at diagnosis, sample 2

source_name: Highly purified PCs from MM patient

value: Multiple myeloma (MM)


title: m6A-seq 36hpi gPfMT-A70 Rep1

description: Plasmodium falciparum dCas m6A-seq

extract_protocol:
Infected red blood cells (iRBCs) were collected by centrifugation and washed once with Dulbecco’s phosphate-buffered saline (DPBS) (Thermo Fisher # 14190-144) at 37 °C. iRBCs were lysed in 0.075 % saponin in DPBS at 37 °C, and the parasite cell pellet was washed once with DPBS and then resuspended in 700 μL QIAzol reagent (Qiagen # 79306). Total RNA was extracted using the miRNeasy Mini Kit (Qiagen # 217004), including an on-column DNase I digestion and exclusion of small RNA (< 200 nt) according to the manufacturer’s protocol.
mRNA is enriched from total RNA using oligo dT beads and fractionated to ~100nt using Mg2+. m6A methyated RNA fragments are enriched by m6A immunoprecipiation and strand specific libraries of m6A and mRNA-input fragments  are prepared using the Illumina TruSeq stranded mRNA library kit (Illumina # 20020594) following the manufacturer's instructions. Sequencing was performed on an Illumina NextSeq 500 platform with a 1x150 bp single-end read layout.

value: 36 hpi


title: Donor HU1019 (AKA BD330)  HBV mono-infected for 28 days


title: RNA-Seq_siSA1_rep3

description: Poly A+ RNA

source_name: mES cells SA1 depleted


title: m6A-seq 36hpi gPfMT-A70 Rep2

description: Plasmodium falciparum dCas m6A-seq


title: RNA-Seq_siSA1_rep2

description: Poly A+ RNA


title: Donor HU1019 (AKA BD330)  uninfected, 8 days


title: P304_1


title: P304_2


title: P304_6


title: m6A-seq 36hpi gControl Rep1

description: Plasmodium falciparum dCas m6A-seq


title: Donor HU1019 (AKA BD330)  HBV mono-infected for 8 days


title: m6A-seq 24hpi gPfMT-A70 Rep2

description: Plasmodium falciparum dCas m6A-seq

value: 24 hpi


title: P301_32


title: Donor HU1019 (AKA BD330)  HBV/HDV co-infected for 8 days, replicate


title: P301_31


title: NORM.3: Normal sample 3


title: m6A-seq 24hpi gPfMT-A70 Rep1

description: Plasmodium falciparum dCas m6A-seq


title: RNA-Seq_Control_rep2

description: Poly A+ RNA

source_name: mES cells


title: Donor HU1019 (AKA BD330)  HBV/HDV co-infected for 8 days


title: RNA-Seq_siSA1_rep1

description: Poly A+ RNA


title: m6A-seq 24hpi gControl Rep2

description: Plasmodium falciparum dCas m6A-seq


title: Donor HU1007 (AKA Sample 3) uninfected, 28 days


title: P301_29


title: HiC_Serum_siSA2_rep2

description: Digested/Ligated genomic DNA


title: HiC_Serum_siSA2_rep1

description: Digested/Ligated genomic DNA


title: m6A-seq 36hpi gControl Rep2

description: Plasmodium falciparum dCas m6A-seq


title: Donor HU1007 (AKA Sample 2) uninfected, 28 days


title: P301_28


title: m6A-seq 24hpi gControl Rep1

description: Plasmodium falciparum dCas m6A-seq


title: HiC_Serum_siSA1_rep2

description: Digested/Ligated genomic DNA


title: m6A-seq 12hpi gPfMT-A70 Rep2

description: Plasmodium falciparum dCas m6A-seq


title: P301_27


title: RNA-Seq_Control_rep3

description: Poly A+ RNA


title: m6A-seq 12hpi gPfMT-A70 Rep1

description: Plasmodium falciparum dCas m6A-seq


title: P301_26


title: m6A-seq 12hpi gControl Rep2

description: Plasmodium falciparum dCas m6A-seq


title: Donor HU1007 (AKA Sample 3) HBV mono-infected for 28 days


title: Donor HU1007 (AKA Sample 2) HBV mono-infected for 28 days


title: HiC_Serum_siSA1_rep1

description: Digested/Ligated genomic DNA


title: m6A-seq 12hpi gControl Rep1

description: Plasmodium falciparum dCas m6A-seq


title: RNA-Seq_Control_rep1

description: Poly A+ RNA


title: P301_25


title: Donor HU1007 (AKA Sample 1) HBV mono-infected for 28 days


title: P301_24


title: HiC_Serum_siC_rep1

description: Digested/Ligated genomic DNA


title: Donor HU1007 (AKA Sample 1) uninfected, 28 days


title: P301_23


title: Leaves, Man-72h-2

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.5
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.9.1
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using NGSQCToolkit Version 2.3.3
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Read counts of genes and their isoformes were calculated by featureCounts Version 1.5.2
Genome_build: GCA_000512265.2
Supplementary_files_format_and_content: tab-delimited text file includes the values of read count for each sample (genome annotation is provided by Annuum.v.2.0.gff3.gz in http://peppergenome.snu.ac.kr/)

organism: Capsicum annuum

source_name: Leaves, Man-72h

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

tag: cultivar

tag: age

value: six weeks

tag: stress

value: Mannitol

tag: time

value: Leaves


title: Donor HU1007 (AKA Sample 2) uninfected, 8 days

value: Primary human hepatocytes co-cultured with mouse 3T3J non-parenchymal cells


title: HiC_2i_rep2

description: Digested/Ligated genomic DNA

source_name: mES cells + 2i

value: ES cells with 2i


title: P301_22

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: ChIP_Suz12_siSA2_10-human_rep2

description: genomic DNA

value: ES cells with 20% of human chromatin

tag: chip antibody


title: HiC_2i_rep1

description: Digested/Ligated genomic DNA


title: Leaves, Man-72h-1


title: Donor HU1007 (AKA Sample 3) HBV mono-infected for 8 days

value: Mono-infected with HBV (MOI = 4,000)


title: Donor HU1007 (AKA Sample 1) uninfected, 8 days

value: Uninfected


title: P301_20


title: ChIP_Suz12_siSA2_10-human_rep1

description: genomic DNA


title: P301_21


title: Leaves, Man-24h-2

source_name: Leaves, Man-24h


title: HiC_Serum_siC_rep2

description: Digested/Ligated genomic DNA


title: Leaves, Man-72h-3


title: Donor HU1007 (AKA Sample 2) HBV mono-infected for 8 days


title: Donor HU1007 (AKA Sample 3) uninfected, 8 days


title: Donor HU1007 (AKA Sample 1) HBV mono-infected for 8 days


title: Leaves, Man-24h-1


title: P301_19


title: P301_18


title: isolated cDC2s pSS_15

city: Utrecht

first: Ana

middle: Pinheiro

last: Lopes

state: Utrecht

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_15

data_processing:
miRNA profiling data was analyzed using the ExpressionSuite Software (Life Technologies) according to the comparative threshold cycle (CT) method.
Low expressed miRNAs (CT > 27) were set at 27.
The expression of each sample was normalized by the mean expression of the four reference sncRNAs (miR-17, miR-191, RNU48, U6-snRNA).
The miRNA expression normalized to the reference sncRNAs was calculated using 2^-deltaCt, where deltaCt = (Ct_miRNA − meanCt_sncRNAs)
Relative expression was depicted as FC compared to one randomly selected healthy control (HC_03), which was set at 1.
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Non-normalized data reports raw CT value.
Fold Change data reports the relative expression of each sample compared to a randomly selected healthy control sample (HC_03) for the 143 expressed miRNAs.

label: TaqMan

source_name: peripheral blood

label_protocol: Samples were prepared using theTaqman OpenArray Human microRNA protoco,l panel version miRBase 20.1 (Life Technologies catalog number 4470187)

extract_protocol: Total RNA was purified using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

treatment_protocol: Peripheral blood CD1c-expressing cDC2s were isolated using magnetic-activated cell sorting using CD1c (BDCA-1)+ Dendritic Cell Isolation Kit (Miltenyi Biotec)

value: Female


title: Leaves, Man-12h-3

source_name: Leaves, Man-12h


title: ChIP_Suz12_siSA1_10-human_rep2

description: genomic DNA


title: P301_17


title: Leaves, Man-24h-3


title: Leaves, Man-12h-2


title: ChIP_Suz12_Control_10-human_rep2

description: genomic DNA


title: isolated cDC2s pSS_14

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_14

value: Male


title: Leaves, Man-12h-1


title: isolated cDC2s pSS_13

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_13


title: ChIP_Suz12_Control_10-human_rep1

description: genomic DNA


title: Leaves, Man-6h-3

source_name: Leaves, Man-6h


title: P301_15


title: ChIP_serum_SMC1

description: genomic DNA

value: ES cells

value: custom made antibody for SMC1


title: isolated cDC2s pSS_12

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_12


title: isolated cDC2s pSS_11

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_11


title: P301_14


title: Leaves, Man-6h-2


title: ChIP_serum_SA2

description: genomic DNA

value: custom made antibody for SA2 (STAG2)


title: Leaves, Man-6h-1


title: P301_13


title: ChIP_Suz12_siSA1_10-human_rep1

description: genomic DNA


title: P301_12


title: isolated cDC2s pSS_10

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_10


title: ChIP_serum_SA1

description: genomic DNA

value: custom made antibody for SA1 (STAG1)


title: isolated cDC2s pSS_09

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_09


title: ChIP_serum_INPUT

description: genomic DNA


title: isolated cDC2s pSS_08

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_08


title: P301_16


title: Leaves, Man-3h-2

source_name: Leaves, Man-3h


title: P301_11


title: ChIP_Ring1b_Control_5-human

description: genomic DNA

value: ES cells with 5% of human chromatin

value: Ring1B (gift from L. Di Croce)


title: P301_10


title: ChIP_Input_siSA2_10-human_rep2

description: genomic DNA


title: MM.042: MM at diagnosis, sample 8

value: Bone marrow plasma cells

value: Multiple myeloma (MM)


title: P301_9


title: isolated cDC2s pSS_07

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_07


title: Leaves, NaCl-72h-3

source_name: Leaves, NaCl-72h

value: six weeks

value: NaCl

value: Leaves


title: ChIP_Input_siSA2_10-human_rep1

description: genomic DNA


title: isolated cDC2s pSS_05

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_05


title: Leaves, NaCl-72h-2


title: ChIP_Input_siSA2_5-human

description: genomic DNA


title: isolated cDC2s pSS_04

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_04


title: P301_8

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: Leaves, NaCl-72h-1


title: P301_7


title: ChIP_Input_siSA1_10-human_rep2

description: genomic DNA

value: ES cells with 20% of human chromatin


title: P301_6


title: Leaves, NaCl-24h-3

source_name: Leaves, NaCl-24h


title: Leaves, Man-3h-3

value: Mannitol


title: isolated cDC2s pSS_03

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_03

value: Female


title: isolated cDC2s pSS_02

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_02


title: Leaves, Man-3h-1


title: ChIP_Input_siSA1_5-human

description: genomic DNA


title: P301_5

source_name: Liver tissue


title: Leaves, NaCl-24h-1


title: Leaves, NaCl-24h-2


title: isolated cDC2s pSS_06

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_06


title: Leaves, NaCl-12h-3

source_name: Leaves, NaCl-12h


title: isolated cDC2s HC_06

description:
isolated cDC2s
healthy control
HC_06


title: isolated cDC2s pSS_01

description:
isolated cDC2s
primary Sjögren's Syndrome patient
pSS_01


title: ChIP_Input_siSA1_10-human_rep1

description: genomic DNA


title: IGROV1 Cisplatin Resistant Replicate 2 (IGROV1_CR_704)

city: Washington

first: Wenge

last: Zhu

state: DC

address: 800 22nd Street NW, , Science & Engineering Hall 8480

department: School of Medicine and Health Sciences

institute: George Washington University

description: IGROV1 cisplatin resistant ovarian cancer cell line

data_processing:
Alignment of paired end reads was performed using the STAR Aligner v. 2.5.1a, default parameters.
Read Counting of bam alignment files was performed using HTSeq (htseq-count) to generate raw per-gene read counts.
DESeq, R package, was used to generate normalized reads, Log2FoldChange, and differential expression statistics
Genome_build: Ensembl Human: GRCh38.p7, and corresponding GTF file.
Supplementary_files_format_and_content: Two matrix files are provided, one containing raw read counts and the other containing normalized read counts.

source_name: ovarian cancer cell line

growth_protocol: WT cells was treat with cisplatin for 4 hours, followed by release to cisplatin free medium for three weeks, we repeated the cisplatin treatment in the medium with the increased concentration of cisplatin. After 5 months treatment (six cycles), we identified cells that were able to grow in the medium with high concentration of cisplatin and named these cisplatin resistant cells as IGROV1 CR

extract_protocol:
RNA isolation was completed using the Qiagen miRNeasy Mini Kit according to the manufacturer’s protocol
RNA samples are converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).  Briefly, Total RNA samples are concentration normalized, and poly-adenylated RNA is purified using oligo-dT attached to magnetic beads.  Purified mRNA is fragmented using heat in the presence of divalent cations. Fragmented RNA is converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix.  A single 'A' base is added to the cDNA and forked adaptors that include index, or barcode, sequences are attached via ligation. The resulting molecules are amplified via polymerase chain reaction (PCR). During PCR the polymerase stalls when a dUTP base is encountered in the template. Since only the second strand includes the dUTP base, this renders the first strand the only viable template, thereby preserving the strand information. Final libraries are quantified, normalized and pooled.  Pooled libraries are bound to the surface of a flow cell, and each bound template molecule is clonally amplified up to 1000-fold to create individual clusters.  Four fluorescently labeled nucleotides are then flowed over the surface of the flow cell and incorporated into each nucleic acid chain.  Each nucleotide label acts as a terminator for polymerization, thereby ensuring that a single base is added to each nascent chain during each cycle.  Fluorescence is measured for each cluster during each cycle to identify the base that was added to each cluster. The dye is then enzymatically removed to allow incorporation of the next nucleotide during the next cycle.

treatment_protocol: Both IGROV1 WT or IGROV1 CR cells were collected in narmal growth medium in log growth phase and without any treatment.

tag: cisplatin response

value: Resistant

tag: uid


title: ChIP_Input_Control_10-human_rep1

description: genomic DNA


title: P301_4


title: isolated cDC2s HC_04

description:
isolated cDC2s
healthy control
HC_04

tag: gender


title: isolated cDC2s HC_05

description:
isolated cDC2s
healthy control
HC_05


title: ChIP_Input_Control_5-human

description: genomic DNA


title: GFPday8rep2

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
fastqc
The mouse transcriptome index was generated by RSEM with bowtie 2 and then the raw reads were aligned to the transcriptome index
Per-gene read counts were calculated using RSEM GC normalized using EDAseq
Genes with mean read counts over all traits and replicates of less than 20 were discarded leading to a final set of 15,130 genes
DESeq2 for differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file; see RNAseqprocesseddata_description.txt for a description of the file contents.

growth_protocol: OG2MEF cells were transduced twice by pMX-Sox2, Klf4 along with Oct4 or Oc6 or engineered Oct4 (YR or Oct4defSox2)  or GFP retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to highly efficient chemically defined (iCD1) reprogramming medium. The iCD media switch day was defined as day 0 and cells were cultured with daily media change.

extract_protocol:
Total RNA was isolated with TRIzol
TruSeq Nano RNA sample prep kit (Illumina) was used for library constructions.

tag: transduction

value: GFP

value: reprogramming cells

tag: day of reprogramming


title: Leaves, NaCl-12h-1

tag: tissue


title: IGROV1 Cisplatin Resistant Replicate 1 (IGROV1_CR_703)

value: IGROV1 cisplatin resistant ovarian cancer cell line


title: IGROV1 Wild Type Replicate 2 (IGROV1_WT_702)

description: IGROV1 wild type ovarian cancer cell line

value: Susceptible


title: GFPday8rep1

tag: cell type


title: ChIP_Input_Control_10-human_rep2

description: genomic DNA

tag: strain


title: isolated cDC2s HC_02

description:
isolated cDC2s
healthy control
HC_02


title: isolated cDC2s HC_03

description:
isolated cDC2s
healthy control
HC_03


title: Leaves, NaCl-6h-3

source_name: Leaves, NaCl-6h


title: GFPday5rep2


title: IGROV1 Wild Type Replicate 1 (IGROV1_WT_701)

value: IGROV1 wild type ovarian cancer cell line


title: GFPday5rep1


title: Leaves, NaCl-6h-2


title: Leaves, NaCl-6h-1


title: P301_3

tag: cause of resections


title: P9-6

city: Cambridge

first: Christopher

middle: WJ

last: Smith

address: Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
Ribozero, paired-end reads mRNA-seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

data_processing:
Read Trimming and adapter removal performed with Trimmomatic (version 0.36).
Read alignment and gene expression quantification was performed with RSEM (v 1.2.31) and STAR (v 2.5.2a).
Differential expression analysis was carried out with DESeq2 package ( version 1.16.1 ) with R version 3.4.1.
TPM values were obtained from RSEM (genes.results files).
Alternative splicing analysis was carried out using rMATS version 3.2.5.
Genome_build: Ensembl Rnor_6.0 release-89
Supplementary_files_format_and_content: Table_TPM_values_per_gene_per_sample.txt: Tab-delimited text file includes TPM values for each gene on each sample.

organism: Rattus norvegicus

source_name: Aorta

growth_protocol: SMCs were grown in DMEM supplemented with Glutamax (Invitrogen) and 10% FBS. Cells were split 1:2 for zero or 9 passages.

extract_protocol:
Tri-reagent (Sigma/9424).
Ribozero, TruSeq

treatment_protocol: Dissected rat aorta tissue was treated with collagenase & elastase to produce single cell suspensions which were then plated in culture dishes. RNA was harvested form tissue, single cells, passage 0 and passage 9 cells.

value: Aorta smooth muscle cell

tag: sample type

value: Cultured cells at passage 9


title: isolated cDC2s HC_01

description:
isolated cDC2s
healthy control
HC_01


title: P9-5


title: GFPday3rep2


title: Leaves, NaCl-3h-3

source_name: Leaves, NaCl-3h


title: P9-4


title: GFPday3rep1


title: Leaves, NaCl-12h-2


title: Leaves, NaCl-3h-1


title: GFPday1rep2


title: P0-3

value: Cultured cells at passage 0


title: Leaves, Heat-72h-3

source_name: Leaves, Heat-72h

value: six weeks

value: Heat


title: P0-2


title: GFPday1rep1


title: P301_30


title: P0-1


title: GFPday0rep2


title: Leaves, Heat-72h-2

value: Leaves


title: GFPday0rep1


title: SC2

value: Primary single cell


title: Leaves, NaCl-3h-2

value: NaCl


title: Leaves, Heat-24h-3

source_name: Leaves, Heat-24h


title: InputDay1

data_processing:
fastqc
Reads were aligned to mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive –end-to-end.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read was retained.
Samtools was used to discard reads with mapping quality < 10
Peaks were called using MACS2 with options --call-summits --to-large -p 0.0001 –bdg options.
For each binding location, the read coverage for all libraries was calculated using the bedtools multicov function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed followed by bedGraphToBigWig.

growth_protocol: OG2MEF cells were transduced twice by pMX-Sox2, Klf4 along with Oct4 or Oc6 or engineered Oct4 (YR or Oct4defSox2) retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to highly efficient chemically defined (iCD1) reprogramming medium. The iCD media switch day was defined as day 0 and cells were cultured for next 7 days with daily media change.

extract_protocol:
Reprogramming cells (7.5-10 x 10e6 cells per sample were collected by trypsinization at day 1, 5 and 7 days post transduction and washed twice with PBS (Gibco). Cells were resuspended in PBS at a density of 5 x 105/mL and then chemically crosslinked by the addition of 1% formaldehyde for 10 min at room temperature with gentle rotation. Crosslinking was stopped by the addition of glycine to a final concentration of 125 mM for 5 min at room temperature. Cells were washed twice with 10 mL cold PBS and lysed in 10 mL Lysis Buffer 1 (150 mM NaCl, 0.5% NP40; 1 mM EDTA, 10% glycerol, 0.25% triton-X100, freshly added complete proteinase inhibitor cocktail in 15 mL tubes at 4°C for 10 min with gentle rocking. The lysate was centrifuged for 10 min at 1350 x g at 4°C. The supernatant was discarded and the pellet was resuspended in 10 mL lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, protease inhibitor) incubated at 4°C for 10 min. The procedure was repeated using 10 mL lysis buffer 3 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, protease inhibitor) and 10 min rocking at RT. Nuclei were collected by centrifugation and washed twice with sonication buffer (10 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, protease inhibitor) and finally suspended in sonication buffer. Samples were sonicated using a Covaris S220 machine with settings to obtain DNA fragments with a length from 150 to 500 bp using microTUBEs (130 μL) for 5 cycles of 30 sec ON and 60 sec OFF using default settings recommended for microTUBEs. 10% Triton-X100 was added and the lysate was centrifuged at high speed (20000 x g for 10 min at 4°C). 1/10 of the supernatant was stored as input control. ChIP was performed in an automated fashion using the IP-Star compacted automated system (Diagenode) using 6 ug ChIP-grade antibodies (Oct4 or Oct6) and 50 ul protein G Dynabeads (Invitrogen). The coupling time for beads and antibody was 5 hours followed by incubation with lysate for 15 hours at 4°C. Automated wash steps of 10 minutes at 4°C were performed in the following order: low salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 150 mM NaCl) , high salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 500 mM NaCl), LiCl buffer (500 mM LiCl, 50 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% NP-40, 0.5% Na-deoxycholate), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) with final elution in 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS buffer. The eluted chromatin and input samples were reverse‐crosslinked by overnight incubation at 65°C. Samples were treated with RNaseA (0.2 mg/ml final concentration) at 37°C for 2h followed by proteinase K (0.2 ug/ml final conc.) at 55°C for 3 hours. DNA was extracted by phenol:chloroform:isoamyl alcohol (25:24:1) and phase separated using heavy phase-lock tubes (TianGen) by centrifugation at 10000 rpm for 10 min at RT and precipitated with 100% ethanol with 20 μg/μl glycogen as co-precipitant. The precipitate was washed with 80% ethanol and finally eluted in 20ul water. DNA concentration was determined using Qubit dsDNA HS assay kit.
The libraries were generated using the Trueseq Nano DNA kit (Illumina)

tag: antibody vendor, cat#, lot#


title: SC1


title: InputDay5


title: Leaves, Heat-72h-1


title: T9

value: Primary tissue


title: Control-agricultral soil in livestock ZZ replicate1

city: Beijing

first: Qun

last: Gao

state: Beijing

address: Shuang Qing Road

department: Environmental sicence and engineering

country: China

institute: Tsinghua University

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: soil metagenome

source_name: Microbes in Control-agricultral soil

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Microbial genomic DNA in each sample was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: different livestock farms

value: ZZ

tag: status after 5 years

value: Control-agricultral soil


title: Control-agricultral soil in livestock HZ replicate1

value: HZ


title: P304_3

value: normal liver resection specimen

value: Colorectal cancer metastasis


title: Leaves, Heat-24h-1

tag: cultivar

tag: age


title: Leaves, Heat-24h-2

tag: stress

tag: time


title: Compost in livestock HZ replicate4

organism: compost metagenome

source_name: Microbes in Compost

value: Compost


title: T8


title: Compost-amended soil in livestock HZ replicate2

source_name: Microbes in Compost-amended soil

value: Compost-amended soil


title: Manure in livestock ZZ replicate1

organism: manure metagenome

source_name: Microbes in Manure

value: Manure


title: Control-agricultral soil in livestock ZZ replicate2


title: SC3

value: Aorta smooth muscle cell


title: Compost in livestock CP replicate1

value: CP


title: Leaves, Heat-12h-3

source_name: Leaves, Heat-12h


title: Sox2_YRSK_d5

value: reprogramming cells

tag: chip antibody

value: Sox2 Antibody

value: Cell Signaling Technology; #2748; 2


title: Sox2_YRSK_d1


title: T7


title: Leaves, Heat-12h-2

value: six weeks

value: Heat

value: Leaves


title: Control-agricultral soil in livestock CP replicate2


title: Control-agricultral soil in livestock CP replicate1


title: Sox2_O6SK_d1


title: Leaves, Heat-6h-3

source_name: Leaves, Heat-6h


title: Sox2_O4SK_d5


title: Compost-amended soil in livestock CP replicate3


title: Leaves, Heat-12h-1


title: NEG3

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

description:
10- to 12-week-old endstage KPf/fC mice.
processed data file: RNAseq all_gene_count.txt
processed data file: RNAseq NEG_GFP_fdr.txt

data_processing:
RNA-seq fastq files were processed into transcript-level summaries using kallisto.
Transcript-level summaries were processed into gene-level summaries by adding all transcript counts from the same gene.
Gene counts were normalized across samples using DESeq normalization, and the gene list was filtered based on mean abundance, which left 13,787 genes for further analysis.
Differential expression was assessed with an R package limma applied to log2-transformed counts.
Statistical significance of each test was expressed in terms of local false discovery rate lfdr using the limma function eBayes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FPKM matrix of expression and DESeq2 differential gene set.
Supplementary_files_format_and_content: RNAseq all_gene_count.txt: Normalised transcript counts (DESeq2).
Supplementary_files_format_and_content: RNAseq NEG_GFP_fdr.txt: limma differential expression results.

source_name: Msi2-reporter KPf/fC pancreas tumor

extract_protocol:
Tumors were isolated and dissociated into single cell suspension. EpCAM+/GFP+ and EpCAM+/GFP- cells were FACS sorted and flash frozen in RNA lysis buffer.
Total RNA was assessed for quality using an Agilent Tapestation, and all samples had RIN 7.9. RNA libraries were generated from 65 ng of RNA using Illumina’s TruSeq Stranded mRNA Sample Prep Kit following manufacturer’s instructions, modifying the shear time to 5 minutes.

tag: strain/background

value: Mixed (C57BL/6, Agouti)

tag: genotype/variation

value: Msi2-reporter het; Ptf1a-Cre het; KrasG12D het; p53f/f

value: 10-12 weeks

value: Pancreatic adenocarcinoma

tag: cell population

value: Pancreatic cancer non-stem cells (Musashi2-reporter negative)


title: Sox2_O4SK_d1

tag: day of reprogramming


title: Leaves, Heat-6h-1

tag: tissue


title: NEG2


title: Leaves, Heat-3h-3

source_name: Leaves, Heat-3h


title: X422

city: Toronto

first: Ming-Sound

last: Tsao

address: 101 College Street, PMCRT 14-401

country: Canada

institute: University Health Network

description: xenograft

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization

source_name: xenograft

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

growth_protocol: surgical section of primary tumor was implanted subcutaneously into NOD/SCID mouse to form xenograft tumors

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: xenograft


title: Leaves, Heat-3h-2


title: NEG1


title: Leaves, Heat-3h-1


title: X410

description: xenograft


title: Control-agricultral soil in livestock ZZ replicate4

value: ZZ

value: Control-agricultral soil


title: Compost-amended soil in livestock CP replicate4

value: Compost-amended soil


title: GFP3

value: Pancreatic cancer stem cells (Musashi2-reporter positive)


title: Sox2_O6SK_d5

tag: cell type


title: Compost-amended soil in livestock JG replicate3

value: JG


title: Compost-amended soil in livestock ZZ replicate4


title: Leaves, Cold-72h-3

source_name: Leaves, Cold-72h

value: Cold


title: GFP2


title: Leaves, Heat-6h-2


title: X328

description: xenograft


title: Compost-amended soil in livestock DX replicate4

value: DX


title: Compost-amended soil in livestock HZ replicate1

value: HZ


title: X267

description: xenograft


title: X356

description: xenograft


title: X271

description: xenograft


title: X322

description: xenograft


title: Compost in livestock ZZ replicate3

value: Compost


title: X188

description: xenograft


title: Control-agricultral soil in livestock JG replicate4


title: GFP1


title: Leaves, Cold-72h-2

value: six weeks


title: Leaves, Cold-72h-1

value: Leaves


title: Heart, MI 256 (scRNA-seq)

city: Edinburgh

first: Mairi

last: Brittan

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: University of Edinburgh

data_processing:
*I1_001.fastq.gz: contains the 8 nt sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 75  nt RNA sequence.
Raw reads were aligned to the mouse reference genome mm10 (Ensembl 84) using the 10X Genomics Cell Ranger Single Cell 2.1.0 pipeline.
The output filtered feature-barcode matrix (containing detected cellular barcodes only) together with the corresponding feature and barcode sequences files for each sample from the Cell Ranger pipeline were read into R (v3.5.2) using the Seurat (v2.3) package, which returned a unique molecular identified (UMI) count matrix. The matrices from the eight samples were used to create the corresponding objects and then aggregated to generate a single Seurat object with the raw count matrix stored. The aggregated raw count matrix is provided here as the processed data with the column names as the cell names and row names as the feature/gene names.
Genome_build: mm10 (Ensembl 84)
Supplementary_files_format_and_content: Aggregated_raw_read_counts.txt

source_name: cardiac endothelial cells

extract_protocol:
Single cell suspensions were processed using the 10X Genomics ChromiumTM Single Cell 3’ Assay, during which the cells were partitioned into Gel Bead-In-Emulsions (GEMs) and polyadenylated (polyA) transcripts were captured.
Cells were incubated in GEMs with primers containing an Illumina R1 primer sequence, a 16 bp 10X barcode, a 10 bp Unique Molecular Identifier (UMI) and a poly-dT primer sequence and full-length cDNAs were generated from the captured polyA transcripts. cDNAs were then amplified by PCR followed by enzymatic fragmentation and size selection for optimised amplicons. P5, P7, i7 sample index and R2 primer sequence were added during library construction via end-repair, A-tailing, adaptor ligation and PCR.

treatment_protocol: iCreERT2 activity was induced using a single intraperitoneal injection of 150 mg/ kg tamoxifen in 200 μl peanut oil resulting in Brainbow2.1 transgene (RFP, nuclear GFP, YFP or membranous CFP) expression in Pdgfb-lineage ECs. At 14 days post-tamoxifen, myocardial infarction MI was induced by permanent ligation of the left anterior descending coronary artery in the MI group. At 7 days post-MI (21 days post-tamoxifen), hearts from the healthy control and MI groups were harvested into ice-cold sterile collection media. Ventricles were extracted, finely minced and digested to obtain single cell suspensions. Cells were FACS-sorted using antibodies against CD31 and Podoplanin, and CD31+Confetti+Podoplanin- cells were selected for further processing.

tag: strain

tag: developmental stage

value: adult

tag: condition

value: 7-day post MI

value: heart

value: cardiac endothelial cells


title: Heart, MI 255 (scRNA-seq)


title: Compost-amended soil in livestock HZ replicate3


title: Leaves, Cold-24h-3

source_name: Leaves, Cold-24h


title: Leaves, Cold-24h-2


title: iEpiSC_B1_RNAseq

data_processing:
Libraries were sequenced on the HiSeq2500 (2×100 bp paired-end reads, illumina) or Nextseq500 100 bp, single read, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
For WGBS analysis, the trimmed reads were mapped to the mouse genome (mm10) by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the mapped reads with high mapping quality (MAPQ>=20) were used for extraction of methylated cytosines by the Bismark methylation extractor with --ignore 10 --ignore_3prime 5 options (single-end reads) or with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options (paired-end reads).
For allelic methylation analysis, the trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For caluculation of allelic methylation levels, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For allelic methylation analysis with methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.
Supplementary_files_format_and_content: ProcessedDataMatrixRPKMfin.STAR.txt:Tab-delimited text file includes RPKMs for each sample.

source_name: iEpiSCs

growth_protocol: MEFs were isolated from E14.5 embryos and were cultured in DMEM (Nacalai tesque) with 2 mM L-glutamine (Nacalai tesque), 100× nonessential amino acids (NEAA) (Nacalai tesque), 100 U/ml penicillin, 100 mg/ml streptomycin (P/S) (Nacalai tesque) and 10% Fetal Bovine Serum (FBS) (GIBCO). ESCs and iPSCs are maintained on feeders (mitomycin C (Kyowa Hakko Kirin Co., Ltd.)-treated MEFs) in knockout DMEM (GIBCO) with 2 mM L-glutamine, 100×NEAA, 100 U/ml penicillin, 100 g/ml streptomycin (P/S), 15% Fetal Bovine Serum (FBS), 0.11 mM β-mercaptoethanol (GIBCO) and 1000 U/ml human recombinant leukemia inhibitory factor (LIF) (Wako). EpiSCs were cultured in DMEM/F12+L-Glu (GIBCO), NEAA, P/S, 0.11 mM -mercaptoethanol, 20% KnockOut Serum Replacement (KSR) (GIBCO), which was supplemented with 10 ng/ml Human Recombinant Fibroblast Growth Factor (basic) (rh bFGF) (wako), and 10 M Y-27632 (wako). iEpiSCs were maintained in DMEM/F12+L-Glu supplemented with B27 (GIBCO) and N2 cell-supplements (GIBCO), NEAA, P/S, 0.11 mM β-mercaptoethanol, 15% FBS, which was supplemented with 10 ng/ml rh bFGF, 20 ng/ml Recombinant Activin A (R&D), 200 ng/ml anti-LIF antibody (Funakoshi).

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) or NucleoSpin RNA plus (MACHEREY-NAGEL) for RNA.
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: iEpiSCs

tag: passage

value: F1 (129X1/SvJ and MSM/Ms)

tag: gender

value: Male

tag: analysis method

value: RNAseq


title: iEpiSC_F1_RNAseq


title: iPSC_13_RNAseq

source_name: iPSCs

value: iPSCs


title: iPSC_9_RNAseq


title: Leaves, Cold-24h-1

tag: cultivar


title: Heart, Healthy 240 (scRNA-seq)

value: healthy


title: Leaves, Cold-12h-3

source_name: Leaves, Cold-12h

tag: age


title: Leaves, Cold-12h-2

tag: stress


title: Heart, Healthy 228 (scRNA-seq)


title: iPSC_1_RNAseq


title: Heart, Healthy 239 (scRNA-seq)


title: Leaves, Cold-12h-1

tag: time


title: Heart, Healthy 227 (scRNA-seq)


title: Leaves, Cold-6h-3

source_name: Leaves, Cold-6h


title: EpiSC_12_male_RNAseq

source_name: EpiSCs

value: EpiSCs


title: Heart, MI 250 (scRNA-seq)


title: Heart, MI 244 (scRNA-seq)


title: Control-agricultral soil in livestock ZZ replicate3

source_name: Microbes in Control-agricultral soil

tag: different livestock farms

value: ZZ

tag: status after 5 years

value: Control-agricultral soil


title: Leaves, Cold-6h-2

value: Cold


title: iEpiSCs_F1_methylseq

value: Methylseq


title: P102

description:
NEBNext12
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

data_processing:
Read Trimming and adapter removal performed with Trimmomatic (version 0.36).
Read alignment and gene expression quantification was performed with RSEM (v 1.2.31) and STAR (v 2.5.2a).
Differential expression analysis was carried out with DESeq2 package (version 1.16.1) with R version 3.4.1.
TPM values were obtained from RSEM (genes.results files).
Alternative splicing analysis was carried out using rMATS version 3.2.5.
Genome_build: Ensembl Rnor_6.0 release-89
Supplementary_files_format_and_content: Table_TPM_values_per_gene_per_sample.txt: Tab-delimited text file includes TPM values for each gene on each sample.

source_name: PAC1 cell line

growth_protocol: Rat PAC1 pulmonary artery SMCs were grown in DMEM supplemented with Glutamax (Invitrogen) and 10% FBS. To encourage the cells toward a more differentiated state they were sub-cultured at a 1:10 dilution once per week and for the more proliferative state they were sub-cultured 1:20 twice per week. (M. Llorian, et al., 2016)

extract_protocol:
Tri-reagent (Sigma/9424) and Zymo direct-zol columns (Zymo Research/R2050).
Poly A selection using NEB Ultra II kit.

treatment_protocol: For siRNA transfection, differentiated PAC1 cells were seeded at 10e5 cells per well and 24 h later transfected with 90 nM of siRNA (C2/Dharmacon for control and RBPMS siRNA/Stealth siRNA RSS363828/ThermoFisher) and oligofectamine. Cells were transfected 24 h later using lipofectamine 2000 with the same concentration of siRNAs. Total RNA was harvested 48 h after the second hit. For overexpression, three pInducer22-RBPMSA lentiviral populations were generated with dedifferentiated PAC1 cells. Populations were either not treated or treated with Doxycycline at 1μg/ml for 24 h, when total RNA was harvested.

tag: cell line

value: Pulmonary artery smooth muscle cell line

tag: cell differentiation state

value: Proliferative

tag: treatment

value: No Doxycycline


title: iEpiSCs_B1_methylseq

tag: tissue


title: Control-agricultral soil in livestock CP replicate3

value: CP


title: X149

description: xenograft

value: xenograft


title: Leaves, Cold-6h-1

value: six weeks

value: Leaves


title: Control-agricultral soil in livestock JG replicate2

value: JG


title: Control-agricultral soil in livestock DX replicate1

value: DX


title: Control-agricultral soil in livestock HZ replicate3

value: HZ


title: Manure in livestock CP replicate3

value: Manure


title: iPSC_7_RNAseq

value: iPSCs

value: F1 (129X1/SvJ and MSM/Ms)

value: Male

value: RNAseq


title: Manure in livestock JG replicate1


title: iPSCs_No13_methylseq


title: P91

description:
NEBNext11
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

tag: cell type


title: Compost-amended soil in livestock DX replicate3

source_name: Microbes in Compost-amended soil

value: Compost-amended soil


title: Manure in livestock ZZ replicate3

source_name: Microbes in Manure

value: ZZ


title: Compost in livestock ZZ replicate1

source_name: Microbes in Compost

value: Compost


title: Leaves, Cold-3h-3

source_name: Leaves, Cold-3h

value: Cold


title: D105

description:
NEBNext09
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: Pulmonary artery smooth muscle cell line

value: Proliferative

value: Doxycycline


title: P84

description:
NEBNext10
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: No Doxycycline


title: iPSCs_No1_methylseq

tag: strain

value: Methylseq


title: iPSCs_No7_methylseq


title: Leaves, Cold-3h-1

value: six weeks

value: Leaves


title: Compost-amended soil in livestock ZZ replicate3


title: Leaves, Abio-mock-72h-3

source_name: Leaves, Abio-mock-72h

value: Abio-mock


title: D87

description:
NEBNext07
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: EpiSCs_No12_XY_methylseq

value: EpiSCs


title: Control-agricultral soil in livestock HZ replicate2

value: HZ

value: Control-agricultral soil


title: Compost in livestock JG replicate1

value: JG


title: KD3

description:
NEBNext06
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: Differentiated

value: RBPMS siRNA


title: Leaves, Abio-mock-72h-2


title: S/L_ESCs_No12_XY_methylseq

source_name: ESCs

value: ESCs

value: F1 (129X1/SvJ and MSM/Ms)

value: Male


title: D94

description:
NEBNext08
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: Pulmonary artery smooth muscle cell line


title: Compost in livestock HZ replicate3

value: Compost


title: KD2

description:
NEBNext05
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: Leaves, Abio-mock-72h-1


title: Leaves, Cold-3h-2

value: Cold


title: Leaves, Abio-mock-24h-2

source_name: Leaves, Abio-mock-24h


title: Dnmt3a WT_Lung_methylseq

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina) or Nextseq500 (75 bp or 86bp, single read, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
For WGBS analysis, the trimmed reads were mapped to the mouse genome (mm10) by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the mapped reads with high mapping quality (MAPQ>=20) were used for extraction of methylated cytosines by the Bismark methylation extractor with --ignore 10 --ignore_3prime 5 options (single-end reads) or with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options (paired-end reads).
For allelic methylation analysis, the trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For caluculation of allelic methylation levels, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For allelic methylation analysis with methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.
Supplementary_files_format_and_content: ProcessedDataMatrixRPKM.txt:Tab-delimited text file includes RPKMs for each sample.

growth_protocol: MEFs were isolated from E14.5 embryos and were cultured in DMEM (Nacalai tesque) with 2 mM L-glutamine (Nacalai tesque), 100× nonessential amino acids (NEAA) (Nacalai tesque), 100 U/ml penicillin, 100 mg/ml streptomycin (P/S) (Nacalai tesque) and 10% Fetal Bovine Serum (FBS) (GIBCO).

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) or NucleoSpin RNA plus (MACHEREY-NAGEL) for RNA.
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: Lung


title: Dnmt3a WT_Liver_methylseq

value: Liver

value: Methylseq


title: Dnmt3a WT_Heart_methylseq

value: Heart


title: C3

description:
NEBNext03
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: C2 siRNA


title: Leaves, Abio-mock-24h-3

value: six weeks

value: Abio-mock

value: Leaves


title: Leaves, Abio-mock-24h-1


title: iPSCs_No9_methylseq

value: iPSCs


title: Dnmt3a WT_Limb_methylseq

value: Limb


title: Leaves, Abio-mock-12h-3

source_name: Leaves, Abio-mock-12h


title: C2

description:
NEBNext02
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: Differentiated


title: C1

description:
NEBNext01
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt


title: Leaves, Abio-mock-12h-2


title: Compost in livestock JG replicate2

value: JG


title: KD1

description:
NEBNext04
PolyA, paired-end 150 mRNA-Seq.
processed data file: Table_TPM_values_per_gene_per_sample.txt

value: RBPMS siRNA


title: Manure in livestock DX replicate4

value: DX

value: Manure


title: Dnmt3a WT_Brain_methylseq

value: Brain

value: Male


title: Leaves, Abio-mock-12h-1


title: Compost-amended soil in livestock DX replicate2

value: Compost-amended soil


title: E41 high TBPH exposure

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: ORD

institute: US EPA

data_processing:
base calling was done by Illumina Real Time Analysis (RTA) v2.7.7
read quality was checked for each sample using FastQC
raw reads were mapped to the transcript sequences of Fundulus heteroclitus’ reference genome from NCBI using BWA default paired-end read mapping protocol
the reads that were not mapped in-pair were filtered out
total read count of each transcript was reported and normalized by EpiCenter
RPKM data were derived from the normalized read counts
Genome_build: version 3.02
Supplementary_files_format_and_content: RPKM data in the tab-delimited text format

organism: Fundulus heteroclitus

source_name: embryo

growth_protocol: Adult killifish (~100 - 200 fish) were collected using baited traps at an uncontaminated estuarine site in Barnstable, MA (‘Scorton Creek’; Nacci et al. 2010). Fish were returned to US EPA ORD aquarium facilities (Narragansett, RI), and maintained in ~300 – ~600 L flowing sea water tanks for > six months or up to two years, and then used as breeding stock. These stocks provided hundreds of embryos that were collected following unstimulated or manually induced spawning events, held at 23° C overnight, then screened to remove dead or abnormal embryos. Typically, batches of normally developed embryos from a single tank of breeding stock were used in a single ELA

extract_protocol:
Total RNA was isolated from embryos using the MagMAX™-96 Total RNA Isolation kit (ThermoFisher, Waltham, MA) following the manufacturer’s protocol supplied with the kit, except as noted below. Homogenization of embryos was performed in 1.5 ml microcentrifuge tubes using a Bullet Blender© Storm 24 homogenizer (Next Advance, Troy, NY) with a 3.2 mm stainless steel bead added to each sample. Each embryo was homogenized in 100 µl of MagMax Lysis/Binding solution supplemented with 0.7 µl β-mercaptoethanol. Contaminating DNA was removed from samples using the supplied Turbo DNase. Both the duration of DNase treatment and incubation temperature were increased, to 20 min and 37 °C, to increase the effectiveness of digestion. RNA was eluted from the magnetic beads using 25 µl of Elution Buffer. During the elution step, samples were incubated at 37 °C
Libraries were prepared (n = 16 per treatment) using the TruSeq Stranded mRNA Library Prep Kit for Neoprep (Illumina, San Diego, CA) according to the manufacturer’s protocol.  One hundred ng RNA was used as input into the automated NeoPrep System (Illumina, San Diego, CA).  The NeoPrep is able to prepare libraries for up to 16 samples.  Samples were blocked by treatment for a multiplex level of 16 samples.  This level of multiplexing provides a theoretical sequencing depth of 18.75 M sequences per sample. Following library preparation, individual samples were quantified using the Qubit fluorometer (Thermofisher), normalized to 10 nM and pooled

treatment_protocol: Each ELA used embryos exposed individually from one to seven days post-fertilization (dpf) in ten mL of amended sea water. Following these early developmental exposures, embryos were flash frozen by immersion in liquid nitrogen and archived at -80° C until genomic or chemical analysis or allowed to develop until seven days post hatching (dph)

value: embryos

value: high dose of TBPH solution


title: Leaves, Abio-mock-6h-2

source_name: Leaves, Abio-mock-6h


title: E42 high TBPH exposure


title: E40 high TBPH exposure


title: YRday5rep2

tag: transduction

value: reprogramming cells

tag: day of reprogramming


title: E39 high TBPH exposure


title: Compost in livestock HZ replicate2

value: HZ

value: Compost


title: YRday1rep2


title: Leaves, Abio-mock-6h-1

value: six weeks

value: Abio-mock


title: YRday3rep2


title: Compost in livestock CP replicate2

value: CP


title: MEF

value: fibroblasts


title: E38 high TBPH exposure


title: Compost-amended soil in livestock ZZ replicate2

value: ZZ


title: Control-agricultral soil in livestock JG replicate3

value: JG

value: Control-agricultral soil


title: Compost-amended soil in livestock JG replicate4


title: Compost in livestock ZZ replicate2


title: YRday0rep2


title: E37 high TBPH exposure


title: Control-agricultral soil in livestock JG replicate1


title: Leaves, Abio-mock-3h-3

source_name: Leaves, Abio-mock-3h

value: Leaves


title: YRday8rep2


title: Oct6WTday8rep2


title: Compost in livestock JG replicate3


title: Leaves, Abio-mock-6h-3


title: Control-agricultral soil in livestock HZ replicate4


title: Leaves, Abio-mock-0h-1

source_name: Leaves, Abio-mock-0h


title: Leaves, Abio-mock-3h-2


title: Leaves, Abio-mock-0h-2


title: E35 high TBPH exposure


title: Oct6WTday5rep2


title: E34 high TBPH exposure


title: Leaves, Abio-mock-0h-3


title: E36 high TBPH exposure


title: Manure in livestock CP replicate2

value: Manure


title: E32 low TBPH exposure

value: low dose of TBPH solution


title: Oct6WTday0rep2


title: Leaves, Abio-mock-3h-1


title: E33 high TBPH exposure


title: Oct6WTday3rep2


title: Compost in livestock DX replicate1

value: DX


title: Compost-amended soil in livestock DX replicate1

value: Compost-amended soil


title: Oct6WTday1rep2


title: E31 low TBPH exposure

value: embryos


title: Manure in livestock CP replicate4


title: Oct4WTday5rep2


title: 20160310_206693960817_immuno031016_10.RCC

city: Charlestown

first: Michael

last: Whalen

state: MA

address: 149 13th Street Room 6303

department: Department of Pediatrics

institute: Massachusetts General Hospital

data_processing: The raw Nanostring nCounter genes were normalized using NanoStringDiff(Wang et al., 2016), adjusting for positive controls, housekeeping genes and background level.

source_name: brain

extract_protocol: Microglia isolated by FACS were stored in RNAlater Stabilization Solution (AM7020, Invitrogen) at -80°C until further processing. Total RNA from the sorted cells was extracted using miRNeasy Micro Kit from Qiagen (Redwood City, CA) for purification of total RNA from small amounts of cells according to the manufacturer's instructions. mRNA expression analysis with the NanoString nCounter® Mouse Inflammation v2 Panel was performed according to the manufacturer's protocol (NanoString Technologies Inc., Seattle, WA).

tag: injury


title: 20160310_206693960817_immuno031016_11.RCC


title: Oct4WTday8rep2


title: Manure in livestock ZZ replicate4


title: E30 low TBPH exposure


title: E29 low TBPH exposure


title: E28 low TBPH exposure


title: Oct4WTday1rep2


title: 20160310_206693960817_immuno031016_09.RCC


title: 20141015_cci_01_12.RCC


title: Oct4WTday0rep2


title: Oct4WTday3rep2


title: Manure in livestock HZ replicate2


title: 20141015_cci_01_11.RCC


title: Manure in livestock HZ replicate3


title: E26 low TBPH exposure


title: E27 low TBPH exposure


title: YRday5rep1


title: 20141015_cci_01_10.RCC


title: Compost in livestock ZZ replicate4


title: YRday8rep1


title: YRday3rep1


title: 20141015_cci_01_08.RCC


title: E25 low TBPH exposure


title: Compost in livestock JG replicate4


title: Compost in livestock HZ replicate1


title: Control-agricultral soil in livestock DX replicate2


title: YRday1rep1


title: Control-agricultral soil in livestock DX replicate3


title: E24 low TBPH exposure


title: 20141015_cci_01_09.RCC


title: Compost in livestock DX replicate2


title: 20141015_cci_01_07.RCC


title: YRday0rep1


title: Manure in livestock JG replicate2


title: E22 low TBPH exposure


title: Oct6WTday8rep1


title: 20141015_cci_01_06.RCC


title: E21 low TBPH exposure


title: Oct6WTday5rep1


title: E20 low TBPH exposure


title: Compost-amended soil in livestock CP replicate2


title: E19 low TBPH exposure


title: 20141015_cci_01_04.RCC

value: sham


title: E23 low TBPH exposure


title: Oct6WTday1rep1

value: reprogramming cells


title: 20141015_cci_01_03.RCC


title: Compost in livestock CP replicate3


title: 20141015_cci_01_02.RCC


title: 20141015_cci_01_05.RCC


title: Compost in livestock CP replicate4


title: fruiting body, replicate 3

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 9.5.3). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.1 of CLC Genomics Workbench Tool (v. 9.5.3). Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: Auriculariopsis ampla NL-1724 v1.0 (Auramp1)
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Schizophyllum amplum

growth_protocol: Auriculariopsis ampla was grown on solid sterilized poplar (Populus alba) bark and solid wood pieces plugged into MEA in 250 ml glass beakers. Cultures were incubated for 14 days in the dark at 30°C, then transferred to room temperature 60 cm under a light panel of 6 Sylvania Activa 172 Daylight tubes, with a 12 hr light/dark cycle and >90% relative humidity. Primordia started to develop 7 days after the transfer to light.

extract_protocol:
Total RNA was extracted using the Quick-RNA Miniprep kit (Zymo Research), following the manufacturer’s protocol
Library generation was performed using the TrueSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions. RNA quality and quantity were assessed using RNA ScreenTape and Reagents on TapeStation (all from Agilent); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (ThermoFisher) treated and the mRNA was purified based on PolyA selection and fragmented. First strand cDNA synthesis was performed using SuperScript II (ThermoFisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. Purification was done using AmPureXP Beads (Beackman Coulter). DNA concentration of each library was determined using the KAPA Library Quantification Kit for Illumina (KAPA Biosystems)

treatment_protocol: Vegetative mycelium, stage 1 and 2 primordia, young and mature fruiting bodies were flash-frozen in liquid nitrogen and stored at -80°C.

tag: group


title: E18 low TBPH exposure


title: E17 low TBPH exposure


title: Compost-amended soil in livestock JG replicate2


title: Compost-amended soil in livestock HZ replicate4

value: HZ


title: Oct4WTday8rep1


title: E16 solvent control

value: solvent control


title: Oct6WTday3rep1


title: 20141015_cci_01_01.RCC


title: fruiting body, replicate 2


title: Oct4WTday5rep1


title: Oct4WTday3rep1


title: Manure in livestock JG replicate4


title: young fruiting body, replicate 3


title: E15 solvent control


title: Oct4WTday1rep1


title: fruiting body, replicate 1


title: Manure in livestock HZ replicate4


title: Oct6WTday0rep1


title: E13 solvent control


title: Manure in livestock DX replicate2


title: young fruiting body, replicate 1


title: E11 solvent control


title: E12 solvent control


title: young fruiting body, replicate 2


title: Oct4WTday0rep1


title: InputDay7

tag: chip antibody

tag: antibody vendor, cat#, lot#


title: stage 2 primordium, replicate 3


title: E10 solvent control


title: oct4YR_YRSK_d5

value: Oct4 Antibody

value: Santa Cruz biotech; sc-8628 X; 12415


title: E14 solvent control


title: Manure in livestock DX replicate1


title: stage 2 primordium, replicate 2


title: Manure in livestock CP replicate1

value: CP


title: E9 solvent control


title: Compost-amended soil in livestock ZZ replicate1


title: stage 2 primordium, replicate 1


title: E43 high TBPH exposure

value: high dose of TBPH solution


title: Control-agricultral soil in livestock DX replicate4


title: oct4YR_YRSK_d1


title: Manure in livestock JG replicate3


title: stage 1 primordium, replicate 3


title: oct6WT_O4SK_d5

value: Oct6 Antibody

value: Santa Cruz biotech;sc-11661 X; G0608


title: E8 solvent control


title: Compost-amended soil in livestock CP replicate1


title: E7 solvent control


title: stage 1 primordium, replicate 2


title: stage 1 primordium, replicate 1


title: E6 solvent control


title: E5 solvent control


title: oct4WT_O4SK_d5


title: oct4WT_O4SK_d7


title: Manure in livestock DX replicate3


title: Control-agricultral soil in livestock CP replicate4

value: Control-agricultral soil


title: Compost in livestock DX replicate3

value: Compost


title: oct6WT_O4SK_d1

value: Santa Cruz biotech;sc-11661 X; G0606


title: vegetative mycelium, replicate 3


title: oct4WT_O4SK_d1


title: Compost-amended soil in livestock JG replicate1

value: JG


title: vegetative mycelium, replicate 2


title: E4 solvent control


title: E3 solvent control


title: E1 solvent control


title: vegetative mycelium, replicate 1


title: E2 solvent control


title: MCF-7

city: Hong Kong

first: Ui-soon

last: Khoo

address: Queen Mary hospital

department: Pathology

country: Hong Kong

institute: University of Hong Kong

data_processing:
Sequencing reads were first filtered for adapter sequence and low quality sequence followed by retaining only reads with read length ≥ 40bp.
sequencing reads were filtered for rRNA sequence
Reads were mapped to the reference genome (Human Genome GRCh38) using STAR (Version 2.5.2) with default parameters
The expression was quantified by RSEM (Version 1.2.31)
Genome_build: Human Genome GRCh38
Supplementary_files_format_and_content: excel file showing TPM and normalized reads

source_name: breast cancer cell

growth_protocol: MCF-7 and MCF-7 eIF4E OE cells were cultured in DMEM containing 10% (v/v) FBS and 1% (v/v) antibiotics (penicillin, 100 U/ml; streptomycin sulfate, 100 ug/ml). ZR-75 and ZR-75 eIF4E OE were cultured in phenol-free modified IEME supplemented with 10% (v/v) FBS and 1% (v/v) PS. All cells were maintained in 370C humidified atmosphere supplemented with 5% CO2.

extract_protocol:
Trizol total RNA extraction
cDNA libraries were prepared by KAPA Stranded mRNA-Seq Kit (KR0960-v3.15)

tag: passage

tag: er status

value: positive


title: ZR-75


title: ZR-75 eIF4E overexpression


title: Manure in livestock HZ replicate1

value: Manure


title: E48 high TBPH exposure

value: embryos


title: Manure in livestock ZZ replicate2

value: ZZ


title: MCF-7 eIF4E overexpression


title: E47 high TBPH exposure


title: E46 high TBPH exposure


title: siControl A549 VSV

city: Guangzhou

first: Shaochun

last: Yuan

address: 132 Waihuan East Road

institute: Sun yat-sen university

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality
The expression of transcripts was quantified as reads per kilobase of exon model per million mapped reads (RPKM). Subsequently, gene enrichment analysis was conducted using the DAVID tool.
Genome_build: hg19
Supplementary_files_format_and_content: The excel file include RPKM values for each sample

source_name: A549 cells

extract_protocol:
Total RNA was isolated using TRIZOL Reagent (Invitrogen). cDNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: epithelial

tag: genotype

value: DDX23 knockdown


title: siDDX23 A549  VSV


title: E45 high TBPH exposure


title: siDDX23 A549

value: control cells


title: siControl A549


title: E44 high TBPH exposure


title: UCC2003 Lactulosucrose vs Ribose Dye Swap

first: Laura

last: Ruiz-Aceituno

state: Madrid

address: Nicolas Cabrera, 9

department: CIAL

institute: CSIC

description:
Sample 8
Biological replicate 2

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).  Data processing  DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 WT

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 cultures were grown separately in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of  4-galactosyl kojibiose,  kojibiose, lactulose, lactulosucrose or ribose as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) untill OD600 was 0.5.  Growth protocol  Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (Pokusaeva et al., 2009)(van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, 2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

value: WT

tag: carbon source

value: Bifidobacterium breve UCC2003 grown on Lactulosucose

value: Bifidobacterium breve UCC2003 grown on Ribose


title: UCC2003 Lactulosucrose vs Ribose

description:
Sample 7
Biological replicate 1


title: UCC2003 Lactulose vs Ribose Dye Swap

description:
Sample 6
Biological replicate 2

value: Bifidobacterium breve UCC2003 grown on Lactulose


title: UCC2003 Kojibiose vs Ribose Dye Swap

description:
Sample 2
Biological replicate 2

value: Bifidobacterium breve UCC2003 grown on Kojibiose


title: SKIN_HV3

status: Public on Jun 17 2019

city: Seoul

first: Doyoung

last: Kim

address: 50-1 Yonsei-ro Seodaemun-gu

department: Dermatology

institute: Yonsei University College of Medicine

description:
SKIN_HV3
Healthy volunteer
Single-cell RNA-Seq

data_processing:
CellRanger (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v2.3.4).
Two different groups (disease vs. healthy volunteers, pre- vs. post-treatment) were aligned using canonical correlation analysis by Seurat package (v2.3.4).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.h5: Filtered gene expression matrices with cells identified as cell barcodes and the values representing gene UMI counts.

source_name: Skin biopsy from HV3

extract_protocol: Samples were prepared using 10X Genomics Chromium 5' kit and 3' kit (v2).

tag: disease diagnosis

value: Healthy

value: Skin

tag: manipulation

value: Freshly isolated


title: SKIN_HV4

description:
SKIN_HV4
Healthy volunteer
Single-cell RNA-Seq

source_name: Skin biopsy from HV4


title: UCC2003 4-Galactosyl kojibiose vs Ribose

description:
Sample 3
Biological replicate 1

value: Bifidobacterium breve UCC2003 grown on 4-Galactosyl kojibiose


title: SKIN_HV5

description:
SKIN_HV5
Healthy volunteer
Single-cell RNA-Seq

source_name: Skin biopsy from HV5


title: SKIN_HV2

description:
SKIN_HV2
Healthy volunteer
Single-cell RNA-Seq

source_name: Skin biopsy from HV2