title: 24h NRG rep8

city: Antwerp

first: Ligia

middle: Monica

last: Mateiu

address: Universiteitsplein 1

department: Center for Molecular Neurology

country: Belgium

institute: VIB

data_processing:
The raw reads were trimmed and cleaned of adapters using  BBMap version 38.70 BBDuk (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 int=f ziplevel=9)
Sequencing quality was assessed with FASTQC software
Reads were mapped using STAR 2.7.1a (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --readFilesCommand zcat --outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000)
Gene expression levels were generated with featurecounts - SUBREAD v1.5.1 for the uniquely mapped reads
Genome_build: ENSEMBL HG38, release 98

source_name: microvascular endothelial cells

extract_protocol:
total mRNA was isolated using the mirVana isolation kit (Ambion® by Life Technologies)
QuantSeq 3’ mRNA-Seq Library Prep kit for Illumina (Lexogen) sequenced on NextSeq 500/500 High output Kit v2 (150 cycles)

value: 24h NRG


title: VC_WT_log_4

status: Public on May 15 2020

type: SRA

city: Boston

first: Satoshi

last: Kimura

state: Massachusetts

address: 181 Longwood Avenue

country: USA

institute: Brigham and Women's Hospital

description: total tRNA

library_source: transcriptomic

data_processing:
3’ linker sequences and one nucleotide at the 5’ end was trimmed
Bowtie v. 1.2.2 with default settings was used for mapping reads to reference tRNA sequences retrieved from tRNAdb (http://trnadb.bioinf.uni-leipzig.de/DataOutput/Search)
Two sequences in V. cholerae (tdbD00003706, tdbD00008082) and three sequences in E. coli (tdbD00007320, tdbD00010329, and tdbD00011810) were eliminated from the reference sequences due to extremely low coverage.
Mpileup files were made using the samtools mpileup command without any filtration (option, -A –ff 4 -x -B -q 0 -d 10000000 -f).
The frequency of misincorporation was calculated in each mpileup file. 5’ end termini of the mapped reads were piled up using the bedtools genomecov command (-d -5 -ibam).
To calculate the termination frequency, the number of 5’ termini at any given position was divided by the total number of mapped termini at the given position along with all upstream positions (5’ side).
genome build: Sequencing data of Vibrio cholerae and Escherichia coli are mapped to VCtRNA.fa and ECtRNAs.fa, respectively. These reference files are available at https://drive.google.com/open?id=1EsilghrGGcKp2cwND6Q1oPLk_cI2cWww
processed data files format and content: Tab-delimited text files containing frequencies of RT-signatures (misincorporation and termination) observed in tRNAs. Each row and column represents species and positions of tRNAs, respectively.

molecule: total RNA

organism: Vibrio cholerae

extract_protocol:
Bacterial cells in a culture medium or cecal fluid were harvested by centrifugation. Total RNA was immediately extracted from cell pellets with Trizol according to the manufacture’s instruction.
The tRNA fraction was cut out from 10% TBE-Urea gels and recovered by isopropanol precipitation. tRNA fraction (250 ng) was deacylated in 500 ul of 100 mM Tris-HCl pH 9.0 at 37 °C for 1 hr and recovered by isopropanol precipitation. After dephosphorylation with alkaline phosphatase from calf intestine (New England Biolabs), tRNAs were ligated to 100 pmol of 5’ adenylated and 3’ end-blocked DNA oligo (3’ linker) using truncated T4 RNA ligase at 25 °C for 2.5 hr in 25% PEG 8000. The ligated product was purified on a 10 % TBE-Urea polyacrylamide gel (Thermo Fisher Scientific) as above. Half of the recovered ligated tRNAs were reverse transcribed with 5 pmol TGIRT-III (InGex) in 100 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 450 mM NaCl, 5 mM MgCl2, 5 mM DTT, 1 mM dNTPs, and 1.25 pmol primer (ocj485) at 60 °C for 1 hr. After the elimination of template RNAs by alkali treatment, cDNA was purified on a 10 % TBE-Urea polyacrylamide gel. The single stranded cDNA was then circularized using 50 U of CircLigase II(Epicenter) at 60 °C for 1 hr, followed by addition of another 50 U of CircLigase II for an additional 1 hr at 60 °C. cDNA was amplified using Phusion DNA polymerase (New England Biolabs) with o231 primer and index primers. After 12-18 rounds of PCR amplification, the product was gel purified from an 8 % TBE-Urea polyacrylamide gel (Thermo Fisher Scientific).

tag: strain

tag: growth phase

value: log phase

tag: genotype

value: WT


title: CONT

city: Seoul

first: Youngkyung

last: Cho

department: Biological Science

country: South Korea

institute: Seoul National University

data_processing:
Filtering: Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Sequence alingment: Filtered reads were mapped to GRCm38 (ensembl) using the aligner STAR v.2.4.0b. Reads were aligned with Tophat (v2.1.1) and Fragments per kilobase of exon per million reads (FPKMs) were calculated using Cufflinks (v2.1.1). Cuffdiff (v2.1.1) was used for normalization.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: 427.1.86 thymoma cells

growth_protocol: DMEM with 10% FBS

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen) according to manufacturer's instructions. The quality of the RNA was assessed by a Agilent 2100 BioAnalyzer. Then mRNA was enriched using Oligo dT magnetic beads for library preparation.  Libraries were prepared for 100bp paired-end sequencing using TruSeq RNA Library Preparation kit (Illumina, CA, USA) according to manufacturer's instructions.
mRNA molecules were purified and fragmented from 2μg of total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×100bp) using Illumina HiSeq2500 (Illumina, CA, USA).

treatment_protocol: 427.1.86 cells which are stably transfected with pSUPER vector were deprived serum for 2 h and then treated DMSO (CONT) or 1 µM of PMA (CONT+PMA) for 2 h to compare the conditions increased EICD upon the PMA-induced shedding. 427.1.86-SPPL2b knockdown cells (KD) were treated with 1 µM of PMA for 2 h after serum deprivation for 2 h to exclude the other effect of PMA. 427.1.86-SPPL2b knockdown cells were transfected with GFP vector alone (KD/GFP) or GFP vector and Flag-N55 (KD/GFP+N55) and GFP-positive cells were sorted using FACS. Using KD/GFP and KD/GFP+N55, we analyzed the direct effect of EICD.

value: wild type

tag: passage

tag: treated with

value: pSUPER vector and DMSO


title: RNA-seq_t2iLGoY-D13_rep1

city: Melbourne

first: Fernando

last: Rossello

state: VIC

address: L 10, 305 Grattan Street

country: Australia

institute: The University of Melbourne

data_processing:
Cellranger mkref (v2.1.0) was run to create a reference using the modified GTF annotation file and the  hg19 genome (GRCh37, CellRanger reference version 1.2.0, genome build GRCh37.p13, which contained the Sendai virus KLF4, MYC and SeV sequences as extra chromosomes, also accounted for as extra annotations on the annotation file).
Low quality sequencing reads and were filtered and trimmed with Trimmomatic (v 0.36, Phred score of 6 consecutive bases below 15, minimum read length of 36nt) and mapped to a custom version of hg19 human genome (with modifications described above with STAR (v 2.4.2a).
Gene read counting was performed with featureCounts (v1.5.2, unstranded) against the custom version of Ensembl’s GRCh37 annotation with modifications described above.
Genome_build: hg19
Supplementary_files_format_and_content: Each sample gene (rows) read counts matrices

organism: Homo sapiens

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed and a few types of naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time.

extract_protocol:
Reprogramming intermediates and hiPSCs were isolated by FACS (Supplementary Table 4) and RNA extraction was performed using the RNeasy micro kit (Qiagen, Cat#74004) from ∼2–20 × 10^4 cells with QIAcube (Qiagen). The concentrations of RNA were measured by a Qubit RNA HS Assay Kit (ThermoFisher, Cat#Q32855) on a Qubit 2.0 Fluorometer (ThermoFisher).
~25 ng of RNA was used for library construction with the SPIA kit (NuGen) and subsequently sequenced by HiSeq 1500 or HiSeq 3000 sequencer (Illumina). Sequencing libraries were single-end with 50 nt length and a targeted number of reads of 20-30 million.

tag: source cell type

value: human fibroblasts

tag: cell type

value: reprogramming intermeidates or hiPSCs

tag: cell subtype/time point


title: 25rP1

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

data_processing:
The reads were trimmed for quality and length using custom scripts.  The trimmed reads were aligned to the hg38 (UCSC genome) with Gencode annotation for the same version of the genome using HiSAT2.  The alignments were processed with StringTie to generate gene specific count matrix for all the samples.
The count matrices were then processed using DESeq2 in R to determine significantly differentially expressed genes.
The results were visualized using R
Genome_build: hg38
Supplementary_files_format_and_content: tpm matrix file where each row is the gene, and each column is the sample.

source_name: Resting CD4+ T cells following ex vivo PMA/ionomycin activation, Sortseq

growth_protocol: Resting CD4+ T cells were isolated from ART-treated, virally suppressed, HIV-1-infected individuals using magnetic negative selection.

extract_protocol:
Resting CD4+ T cells were sorted by HIV-1 RNA SortSeq into  single cells into RNA preserving buffer. RNA was reverse crosslinked with proteinase K and SDS under 50°C for 1 hour. RNA was extracted by Quick-RNA Microprep (Zymo Research) with a built-in on-column DNase treatment step.
Total RNA from single cells was extracted followed by a ribosomal RNA depletion step using the SMARTer Stranded Total RNA-Seq Kit Pico Input Mammalian v2. Samples with different barcodes were pooled into one Hiseq4000 2x150 platform, targeting an estimated reads of 20-40 million per sample.

treatment_protocol: Cells were treated with PMA (1 µg/ml) and ionomycin (1 µM) for 16-18 hours in the presence of enfurvitide to induce HIV-1 RNA expression without causing new rounds of infection in vitro.

value: Resting CD4+ T cells

tag: treatment

value: PMAionomycine for 16 hours under enfuvirtide

tag: individual


title: 24h NRG rep6


title: 24h NRG rep7


title: 23rN6


title: 23rN5


title: RNA-seq_5iLAF-D21_rep2


title: RNA-seq_Primed-P3_rep1


title: RNA-seq_Primed-P3_rep2


title: VC_WT_CF_3

description: total tRNA

value: cecal fluid


title: 8h NRG rep8

value: 8h NRG


title: VC_WT_log_1

description: total tRNA


title: VC_WT_24h_3

description: total tRNA

value: stationary phase


title: 24h NRG rep5


title: VC_WT_log_3

description: total tRNA


title: RNA-seq_Primed-D21_rep2


title: 23rN4


title: RNA-seq_NHSM-D21_rep2


title: 8h NRG rep7


title: VC_WT_24h_2

description: total tRNA


title: 27rP1


title: 8h NRG rep6


title: 23rN3


title: 8h NRG rep5


title: Differentiating spermatogonia rep2

city: East lansing

first: Yuan

last: Wang

state: MI

address: 474 S Shaw Ln

institute: Michigan State University

data_processing:
Paired-end RNA-seq reads with 150 bp in each end were aligned to the Mus musculus genome (GRCm38) using Subread( The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013)
reads in each gene were counted through feature Counts v1.5.3
Differentially expressed gene expression analysis and KEGG pathway analysis  We used DESeq2 (Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550. https://doi.org/10.1186/s13059-014-0550-8.) to call differentially expressed genes with FDR < 0.05 and fold change > 2.
KEGG pathway enrichment was performed with KOBAS(KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nuc. Acids Res. 39, 316–322. https://doi.org/10.1093/nar/gkr483.).
Genome_build: GRCm38
Supplementary_files_format_and_content: abundance measurements in xlsx file format

source_name: testes

growth_protocol: undifferentiated spermatogonia were maintained in Stempro34  supplemented with 20 ng/ml β-FGF , 103 U/ml ESGRO, and 20 ng/ml GDNF/EGF

extract_protocol:
cells were collected in Trizol for RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: treated with 100 µM retinoic acid

tag: tissue

value: testes

value: retinoic acid

tag: culture

value: in vitro differentiated


title: control rep8

value: control


title: VC_WT_log_2

description: total tRNA


title: RNA-seq_5iLAF-D21_rep1


title: RNA-seq_NHSM-D21_rep1


title: RNA-seq_Primed-D21_rep1


title: 23rP2


title: Differentiating spermatogonia rep1


title: 22rP1


title: control rep7


title: 23rP1


title: Undifferentiated spermatogonia rep2

value: DMSO

value: in vitro cultured


title: 02rP1


title: control rep6


title: control rep5


title: 10rP1


title: 23rN1


title: 159rN6


title: 24h NRG rep4

value: 24h NRG


title: RNA-seq_Fibroblast-D7_rep1


title: 159rN4


title: RNA-seq_NHSM-D13_rep2


title: RNA-seq_Fibroblast-D3_rep2


title: RNA-seq_NHSM-D13_rep1


title: RNA-seq_5iLAF-D13_rep2


title: RNA-seq_Fibroblast-D7_rep2


title: RNA-seq_Fibroblast-D3_rep1


title: Undifferentiated spermatogonia rep1


title: ATAC_P10_NM_REP_2

library_source: genomic

data_processing:
ATAC sequencing reads (pair-end 51nt reads) were adaptor-trimmed and filtered by base quality and length using Cutadapt v 1.852using -a CTGTCTCTTATACACATCT, -A CTGTCTCTTATACACATCT, -q 20, and --minimum-length 18 options. Read pairs passing filters were mapped to the complete human genome [hg19 human genome (UCSC version, December 2011)] using Bowtie2 with -X 2000, --no-mixed and --no-discordant options.
Mapped sample reads were filtered for multi-mappers (mapping quality < 10) and reads mapped to mitochondrial DNA using Jvarkit’s54 samjs. PCR duplicates were discarded using Picard’s (http://broadinstitute.github.io/picard) MarkDuplicates tool. Sequencing reads aligned to known genomic blacklisted regions were also not considered for further analysis
Peak calling was performed on each biological replicate with MACS2 callpeak subcommand56 using --nomodel -f BAM --keep-dup all --gsize hs --shift -100 --extsize 200 --SPMR -B options. For downstream analysis we use an “intersect and rescue” approach. This approach consisted of intersecting each time point and reprogramming media biological replicates peak sets (bedtools intersect)57, subcommand (-wa -wb -F/-f 0.3) and then filtering those peaks with a fold change over background of more than 5 fold change (FC) and at least 3 FC in the other replicate. This created two intersection peaksets (major to 5 FC in replicate 1 and major to 3 FC in replicate 2 and vice versa), which were then combined and merged with bedtools merge (a minimum of 1 bp overlap). The union peakset of both replicates for each timepoint and reprogramming media was then reduced by merging all peaks within 100 bp. Finally, a consensus peak set of all time points and reprogramming media was created using bedtools merge as described above.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files are the output of macs2 callpeaks. Format is is BED6+4 (details about the format can be found at https://genome.ucsc.edu/FAQ/FAQformat.html#format12 and https://github.com/taoliu/MACS/). Macs2 specific columns are: 5th display integer score (int(-10*log10qvalue)), 7th fold change at peak summit relative to background, 8th  -log10pvalue at peak summit, 9th -log10qvalue at peak summit and 10th relative peak summit position to peak start. Detailed information can be found at MACS webiste (https://github.com/taoliu/MACS/).  BigWig files were created using UCSCs bedGraphToBigWig from the normalised bedgraph file output from MACS2.

molecule: genomic DNA

source_name: human fibroblasts

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=5, c-MYC MOI=15, KLF4 MOI=6. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed and naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time.

extract_protocol:
Reprogramming intermediates and hiPSCs were isolated by FACS (Supplementary Table 4) and ~65k cells were washed and lysed in ATAC-seq lysis buffer (10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 10 mM Tris pH 7.4). The transposition reaction was then carried out by using 22.5 μl of UltraPure Distilled Water (ThermoFisher, Cat#10977-015), 25 μl of Tagment DNA Buffer (Illumina, Cat#15027866) and 2.5 μl of Tagment DNA Enzyme 1 (Illumina, Cat#15027865) for each sample, and then incubated for 30 min at 37°C, followed by immediate purification using a MinElute Reaction Cleanup Kit (Qiagen, Cat#28204) according to the manufacturer’s instructions.
11 μl of transposed DNA, 25μl of the NEBNext High-Fidelity 2x PCR Master Mix (Cat#M0541S) and 1.25μM of the adaptor sequences as published previously were used in a 50 μl PCR reaction. PCR parameters were: 72°C for 5 min, 98°C for 30 s and 9 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The prepared libraries were purified using a MinElute PCR purification kit (Qiagen, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s specifications, where library fragments ranging from 200 to 700 bp were selected and sequenced on an Illumina HiSeq 1500 in 2x51 cycle paired-end mode

value: human naive induced pluripotent stem cells

tag: passages

value: Passage 10


title: RNA-seq_Primed-D13_rep2


title: 159rN3


title: 24h NRG rep3


title: SLN111_D1

city: Berkeley

first: Zoë

last: Steier

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

description: Biological replicate 1, stained with 111 antibody panel.

data_processing:
Library strategy: CITE-seq
Sequencing reads were processed with CellRanger v3.1.0 with feature barcoding to produce UMI count matrices.
Cellranger was used to aggregate samples without read depth normalization for cells stained with the same antibody panel (e.g. SLN111_matrix.mtx.gz, SLN208_matrix.mtx.gz).
Genome_build: mm10
Supplementary_files_format_and_content: *_barcodes.tsv.gz: Cell barcodes.
Supplementary_files_format_and_content: *_features.tsv.gz: Genes and proteins, where proteins include both ADT and HTO.
Supplementary_files_format_and_content: *_matrix.mtx.gz: UMI count matrix for all cell barcodes and features.
Supplementary_files_format_and_content: *_raw_feature_bc_matrix.h5: compressed format UMI count matrix of all sequenced barcodes, incuding empty droplets.

molecule: polyA RNA

source_name: spleen and lymph nodes

extract_protocol:
Stained and washed cells from one sample were loaded into a single lane of the 10x Genomics Chromium Single Cell 3' v3 kit.
CITE-seq library construction was performed following the 10x Genomics Chromium Single Cell 3' v3 protocol to prepare RNA, antibody-derived-tag (ADT) and hashtag-oligo (HTO) libraries.

treatment_protocol: Cells were stained in RPMI + 10% FBS with pooled BioLegend TotalSeq-A antibodies according to the manufacturer's instructions. Spleen and lymph node cells  were stained with different hashtag antibodies and pooled just prior to loading.

value: spleen and lymph nodes

tag: age

value: 5 weeks

tag: molecule subtype

value: polyA RNA and protein


title: SLN208_D2

description: Biological replicate 2, stained with 208 antibody panel.


title: VC_WT_24h_1

description: total tRNA

value: WT


title: 24h NRG rep1


title: 8h NRG rep3


title: SLN111_D2

description: Biological replicate 2, stained with 111 antibody panel.


title: 24h NRG rep2


title: 8h NRG rep4


title: 159rN1

value: Resting CD4+ T cells

value: PMAionomycine for 16 hours under enfuvirtide


title: ATAC_P10_PM_REP_2

value: human primed induced pluripotent stem cells


title: 8h NRG rep2

value: 8h NRG


title: 159rN5


title: SLN208_D1

description: Biological replicate 1, stained with 208 antibody panel.


title: RNA-seq_Primed-D13_rep3

value: human fibroblasts

value: reprogramming intermeidates or hiPSCs


title: ATAC_P3_NM_REP_2

value: Passage 3


title: 159rN2


title: ATAC_P3_PM_REP_2


title: control rep4

value: control


title: PhSpMo2

city: New York

first: Olga

last: Ossipova

state: NY

address: 1 Gustave L Levy Place Anbg 25-90 PO Box 1020

institute: Mount Sinai Hospital

description: 40 ng of PhSpMo into each blastomere at the 4-cell stage

data_processing:
The original raw data from Illumina HiSeqTM were transformed to Sequenced Reads by base calling. Raw data were recorded in FASTQ files.
Base Quality and Phred score relationship were evaluated with the Illumina CASAVA v1.8 software
Raw reads were filtered to remove reads containing adapters or reads of low quality.
The sequences wer mapped to the Xenopus genome using hisat2
The files were sorted using the Samtools.The sequences were counted using HTSeq.
Genome_build: Xenopus XL-9.1_v1.8.3.2
Supplementary_files_format_and_content: Excel, contains the counts;

organism: Xenopus laevis

source_name: marginal zone (mesoderm) explant

growth_protocol: ectoderm explants and  frog embryo culture

extract_protocol:
RNAeasy column (Qiagen)
mRNA was enriched using oligo(dT) beads; mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. Then a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment was performed.
Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/μl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were then fed into HiSeq2000 machines according to activity and expected data volume.
quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).

treatment_protocol: RNA overexpression or MO oligos depletion

tag: developmental stage

value: st 10.5, gastrula

tag: treated or not

value: PhSpMo-injected


title: scRNA Human Blood IFN lambda

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description:
human_blood_ifnlambda
Healthy Donor Patient
Exp ID: 190723_0257_B4
Lab data ID: F4L
mRNA
read1_26/i7index_8/read2_98

data_processing:
Raw sequencing data were processed with Cell Ranger software (version 3.0.2). Cell Ranger output files were loaded into R for analysis using the Seurat package. Low quality cells were removed based on % mitochondrial gene expression. Data were integrated, normalized, and transformed for downstream analysis. Clustering was performed using the UMAP algorithm. Cell clusters were annotated using the SingleR algorithm. Unclassified cells were removed from downstream analysis. Gene expression was subsequently determined in each cluster. Data were visualized using ggplot2.
Genome_build: Mouse: mm10 (GRCm38); Human: GRCh38
Supplementary_files_format_and_content: barcodes.tsv: Cell Ranger count raw_feature_bc_matrix barcodes.
Supplementary_files_format_and_content: features.tsv: Cell Ranger count raw_feature_bc_matrix features.
Supplementary_files_format_and_content: matrix.mtx: Cell Ranger count raw_feature_bc_matrix matrix.

source_name: Peripheral Blood

extract_protocol:
Spleens were isolated and smashed through a 70uM sterile filter to obtain single cell suspensions. Red blood cells (RBCs) were lysed using ACK lysing buffer. Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. For human samples, cells were isolated from whole blood of healthy volunteers using ErythroClear RBC depletion kit (STEMCELL). Cells were resuspended in RPMI supplemented with 10% FBS and 1% Pen/Strep. Cells were treated with recombinant interferon for 4 hours as indicated.
Isolated cells were encapsulated using microfluidics technology, and barcoded using a unique molecular identifier (UMI).
scRNAseq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.

tag: diagnosis

value: Healthy

value: Peripheral Blood

value: Immune cells

value: IFN lambda


title: scRNA Human Blood Untreated

description:
human_blood_untreated
Healthy Donor Patient
Exp ID: 190731_0260_B3
Lab data ID: F44
mRNA
read1_26/i7index_8/read2_98

value: Untreated


title: ATAC_D21_NM_REP_2

value: human naive intermediates

value: Passage 0


title: 159rP1

value: Resting CD4+ T cells


title: PhSpMo1


title: control rep2


title: scRNA Human Blood IFN alpha

description:
human_blood_ifnalpha
Healthy Donor Patient
Exp ID: 190723_0257_B5
Lab data ID: F4A
mRNA
read1_26/i7index_8/read2_98

value: IFN alpha


title: control rep3


title: control rep1


title: Co2

description: no treatment

value: control untreated


title: ATAC_D21_PM_REP_2

value: human primed intermediates


title: Co1

description: no treatment


title: ATAC_D13_PM_REP_2


title: ATAC_D13_NM_REP_2


title: ATAC_D7_FM_REP_2

value: human fibroblasts intermediates


title: FlagPin_1

description: 1.5 ng of Flag-Pinhead RNA

source_name: ectodermal explant

value: st 11, gastrula

value: FlagPinhead RNA overexpression


title: SC_RNA-seq_RSet

data_processing:
Cellranger mkref (v2.1.0) was run to create a reference using the modified GTF annotation file and the  hg19 genome (GRCh37, CellRanger reference version 1.2.0, genome build GRCh37.p13, which contained the Sendai virus KLF4, MYC and SeV sequences as extra chromosomes, also accounted for as extra annotations on the annotation file).
Sequencing single cell samples were aligned to the created custom reference and UMI counting were performed using cellranger count (v2.10, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.0/what-is-cell-ranger).
Genome_build: hg19
Supplementary_files_format_and_content: Gene/cell read counts matrices are contained in compressed Market Exchange Format (MEX) for sparse matrices. Feature, in this case genes, and cell barcodes  are gzipped TSV files, corresponding to row and column indices of count matrices respectively. For more information, please refer to: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

growth_protocol: To generate human primed and naïve iPSCs used for this study, somatic cell reprogramming with the Cytotune 2.0 kit, experiments were performed according to the manufacturer’s instructions (Invitrogen). Briefly, human dermal fibroblast (adult) were seeded at ~5x104 cells per well of a 6-well plate in fibroblast medium containing DMEM (Gibco), 10% FBS (Hyclone), 1% nonessential amino acids (Gibco), 1mM GlutaMAX (Gibco), Pen-strep (Gibco), 0.1mM 2-mercaptoethanol (Gibco) and 1mM sodium pyruvate (Gibco) . After 2 days, cells were transduced with Sendai viruses in fibroblast medium with multiplicity of infections (MOIs) as follows, KOS MOI=10, c-MYC MOI=10, KLF4 MOI=12. After 24 hours, the medium was replaced with fresh fibroblast medium and media were changed every other day thereafter. On day 7, cells were trypsinized and seeded onto a layer of iMEF feeders at ~0.5x105~1x105 per flask in fibroblast medium. The next day, the cells were switched to primed and naive media. 21-24 days after transduction, cells were passaged and expanded. Reprogramming intermediates were collected at the indicated time.

extract_protocol:
day 0, day 3, day 7, day 13 primed, day 13 naive, day 21 primed, day 21 naive, hiPSC primed (passage 3) and hiPSC naive (passage 3) were collected and cryopreserved. These collected samples were then subjected to FACS, for D0, D3, D7, D13 primed, D13 naive, D21 primed and D21 naive samples were sorted for PI negative, TRA-1-85 positive cells to remove dead cells and iMEF cells, while hiPSC primed (passage 3) and hiPSC naive (passage 3) samples were sorted for PI negative, TRA-1-85 positive, CD13 negative, F11R positive, TRA-1-60 positive, EPCAM positive cells to get rid of dead cells and iMEF cells as well as differentiated cells. Three samples were prepared (Fig. 1b) for subsequent library preparation, sample one contained cells isolated from D0, 3 and 7, samples two and three contained cells for primed (D13, D21, hiPSCs) and naive reprogramming (D13, D21, hiPSCs) respectively, and a small number of mixed D0, 3 and 7 cells were added to sample two and three to capture the full reprogramming trajectories and also to account for potential batch effects. The collected cells were isolated, encapsulated and library constructed using Chromium controller (10x Genomics) as per the manufacturer's instructions "Chromium Single Cell 3' Reagent Kit V2 User Guide", 10X Genomics document number CG00052 Revision 3.
A total of 12 cDNA amplification cycles were used. A total of 16 cycles of library amplification were used. Sequencing was carried out using an Illumina NextSeq 500 using SBS V2 chemistry in a high-output mode according to the recommendations outlined by 10x Genomics "Chromium Single Cell 3' Reagent Kit V2 User Guide", 10x Genomics document number CG00052 Revision 3, with the exception that the second read was extended to 115b instead of 98b. Libraries were diluted according to the manufacturer's instruction "NextSeq 500 System User Guide" Illumina document number 15046563 v02 and loaded at 1.8pM. Chromium barcodes were used for demultiplexing and FASTQ files were generated from the mkfastq pipeline using the Cellranger program (v2.1.0). Alignment and UMI counting were performed to the hg19 genome as per the snRNA-seq. The same experimental procedure and the computational pipeline were also applied to generate the RSeT reprogramming scRNA-seq library shown in Extended Data Fig. 4d,e.

value: Reprogramming intermediates and hiPSCs


title: RNA-seq_Primed-D13_rep1

value: human fibroblasts

value: reprogramming intermeidates or hiPSCs


title: SC_RNA-seq_Primed


title: ATAC_D3_FM_REP_2


title: FlagPin_2

description: 1.5 ng of Flag-Pinhead RNA


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep2

city: Goteborg

first: Shadi

last: Rahimi

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description:
no8N2D_S9_L002_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep2

data_processing:
Pre-processing of paired-end Illumina RNA reads was performed using GEO2RNAseq pipeline. Briefly, quality of reads was analyzed before and after trimmung using FastQC (v. 0.11.8). Quality control of reads was performed with Trimmomatic (v. 0.36). Mapping reads to reference genomes was performed using HiSat2. The ammonium and nitrate-enriched sequences were mapped on the reference genome of the Clostridium_beijerinckii (NCBI Assembly accession: ASM83310v2; GCF_000833105.2) and Clostridium butyricum (NCBI Assembly accession: ASM145606v2; GCF_001456065.2), respectively. In total 284,907,998 2x75 bp sequences were mapped on the reference genomes. Each sample was sequenced four times to ensure sufficient sequencing depth. Samples contained between 2,904,757 to 4,678,797 reads. The SAMtools package was used to convert, sort and index sequence alignment files for downstream data analysis. Gene abundances were estimated per sample using featureCounts tool.
Supplementary_files_format_and_content: csv including raw gene counts

organism: Clostridium butyricum

extract_protocol:
Total RNA extraction was performed through RNeasy Mini Kit (Qiagen), and the quality examination was performed by Bioanalyzer (Agilent) through Agilent RNA 6000 Nano Kit.
After removing rRNA from total RNA samples through Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina), library was prepared through TruSeq mRNA stranded Bacteria HT (Illumina).

treatment_protocol: Two two-chamber H-Cell MECs (Adams & Chittenden Scientific Glass) were used for conducting bioelectrochemcial experiments. 50 ml of 10 g/L NaCl and graphite felt anode (3.75 cm2 and 2 mm thickness) were used in the anodic chamber. The anode chamber and the cathode chamber (volume 50 mL) were separated using a membrane (Nafion 117, perfluorinated membrane, 0.007in. thick). Wastewater supplemented with 1% glucose, a graphite rod cathode (2.4 cm length and 0.6 cm diameter), an Ag/AgCl (3M NaCl) reference electrode (Bioanalytical Systems, Inc. BASi) were used as the cathodic compartment. 5 ×106 cells/ml from B. subtilis and OE-NasDEF were inoculated to 50 ml of wastewater for B. subtilis + MC and OE-NasDEF+ MC systems, respectively and MC system was used as the control setup without additional bacteria inoculation. Anode and cathode were contacted via wire (0.025 cm diameter) to the outside of the MEC. The MEC was connected to a two-channel potentiostat/galvanostat (MLab) to record the current and potential during 48 h of run. The MEC was operated at 37 °C. Nitrogen gas sparged into the cathodic compartment to enhance anaerobic condition.

tag: protocol


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep4

description:
no8N2D_S9_L004_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep4


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep4

description:
no8N2C_S8_L004_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep4


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep1

description:
no8N2D_S9_L001_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep1


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep3

description:
no8N2D_S9_L003_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep3


title: SC_RNA-seq_Naive


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep3

description:
no8N2C_S8_L003_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep3


title: Cocaps1

description: no treatment


title: SC_RNA-seq_D0_D7


title: Cocaps2

description: no treatment


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep1

description:
no8N2C_S8_L001_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep1


title: Delta-luxR-Delta-05185-1 (paired-end)

city: Bloomington

first: Julia

middle: C

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

description:
Sample 10
countstable.paired-end.txt.gz

data_processing:
Read sequences were de-multiplexed using bcl2fastq (software versions 2.1.0.31).
Sequencing reads were trimmed for quality and adapters using Trimmomatic (v0.38 for all samples) with the following parameters: ILLUMINACLIP:adapters.fa:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:30
Reads were mapped to the genome using bowtie2 (v2.3.4.3).
Read counts for genes and intergenic regions were determined with custom perl scripts
Genome_build: Vibrio harveyi ATCC BAA-1116 with the refseq IDs CP000789.1, CP000790.1, and CP000791.1
Supplementary_files_format_and_content: Processed data files are tab-delimited files indicating the number of reads (either single-end or paired-end) associated with a gene or intergenic region. Intergenic regions are given by molecule,strand,begin-end and are 100 bps long

organism: Vibrio campbellii

source_name: Bacterial lysate

growth_protocol: Cells were grown at 30 °C to an OD600 of 1.0

extract_protocol:
RNA was extracted using Trizol and chloroform
Total RNA was first treated with RiboMinus Transcriptome Isolation Kit (Bacteria) (ThermoFisher Scientific, cat#K155004) to remove excess ribosomal RNA
All libraries were prepared using ScriptSeq RNA-Seq Library Preparation kit (Illumina, cat#SSV21124) according to manufacturer’s protocol
For all samples, sequencing barcodes selected from TruSeq Dual Index Sequencing Primer Box, Paired-End (Illumina cat#PE-121-1003) were added to the libraries during construction for multiplexing. The barcoded libraries were cleaned with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit4 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), then pooled
Pooled libraries were sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005)
Samples 1-8 were sequenced on single-end 75 cycle run
Samples 9-10 were sequenced on paired-end 75 cycle run

tag: strain

value: ATCC BAA-11121

tag: genotype


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep4

description:
N1C_S2_L004_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep4


title: RNAseq_C. butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep2

description:
no8N2C_S8_L002_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep2


title: Delta-luxR-Delta-05185-2 (paired-end)

description:
Sample 10
countstable.paired-end.txt.gz


title: Delta-luxR-Delta-05185-3 (paired-end)

description:
Sample 10
countstable.paired-end.txt.gz


title: Delta-luxR-3 (paired-end)

description:
Sample 9
countstable.paired-end.txt.gz

value: {delta}luxR (KM669)


title: ATAC_P3_NM_REP_1

value: human naive induced pluripotent stem cells

value: Passage 3


title: ATAC_P10_PM_REP_1

value: human primed induced pluripotent stem cells

value: Passage 10


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep3

description:
N1C_S2_L003_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep3


title: 8h NRG rep1

value: 8h NRG


title: ATAC_P10_NM_REP_1


title: ATAC_D21_NM_REP_1

value: human naive intermediates

value: Passage 0


title: IA synovial 5

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

data_processing:
Reads were trimmed for adaptors and sequence quality. Trimmed reads were aligned to human b37.3 reference genome using omicsoft sequence aligner (Hu et al., 2012).
Aligned reads were quantified using EM algorithm with UCSC transcriptome model accessed on September 26, 2014 (Li et al., 2010).
Genome_build: human b37.3 reference genome
Supplementary_files_format_and_content: tab-delimited processed data matrix file contains feature counts for all samples and features

source_name: inflammatory arthritis_synovial fluid

growth_protocol: Synovial fluid was isolated from patients and synovial fluid mononuclear cells were isolated using a density gradient seperation. CD141+DC were magnetically sorted using CD141 antibody conjugated microbeads and used for RNA isolation

extract_protocol:
Total RNA was extracted from CD141+DC synovial fluid samples and healthy control peripheral blood and the quality of all RNA samples was evaluated using an Agilent Bioanalyzer.
RNA samples were reverse transcribed and sequencing libraries constructed using NuGen Ovation Universal RNA-Seq System (CAT# 0402-A01) according to the manufacturer’s protocol.  The resulting sequencing libraries were analyzed using the Caliper LabChip GX and quantified using KAPA qPCR.  Libraries were then normalized and pooled in one batch of 6 and one batch of 5.  Each pool was clustered and sequenced on an Illumina NextSeq500 instrument using 2x100 bp paired-end reads, following the manufacturer’s protocols.

tag: subject status

value: inflammatory arthritis

value: synovial fluid

value: CD141+ dendritic cell


title: Delta-luxR-2 (paired-end)

description:
Sample 9
countstable.paired-end.txt.gz


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep2

description:
N1C_S2_L002_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep2


title: IA synovial 4


title: ATAC_D0_FM_REP_2

value: Passage 5


title: ATAC_D21_PM_REP_1

value: human primed intermediates


title: Delta-luxR-1 (paired-end)

description:
Sample 9
countstable.paired-end.txt.gz


title: ATAC_D13_PM_REP_1


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-connected, ammonium-enriched wastewater, rep1

description:
N1C_S2_L001_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-connected using ammonium-enriched wastewater-rep1


title: 06936-3_S48 (single-end)

description:
Sample 8
countstable.single-end.txt.gz

value: ATCC BAA-11120


title: ATAC_D13_NM_REP_1


title: IA synovial 3


title: IA synovial 2


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep4

description:
N1D_S1_L004_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep4


title: 06936-2_S47 (single-end)

description:
Sample 8
countstable.single-end.txt.gz


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep3

description:
N1D_S1_L003_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep3


title: ATAC_D7_FM_REP_1

value: human fibroblasts intermediates


title: 06936-1_S46 (single-end)

description:
Sample 8
countstable.single-end.txt.gz


title: IA synovial 6


title: ATAC_D3_FM_REP_1


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep2

description:
N1D_S1_L002_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep2


title: RNAseq_C. butyricum: B. subtilis cocultured cathodic MEC-disconnected, ammonium-enriched wastewater, rep1

description:
N1D_S1_L001_R1_001
RNA-Seq of Clostridium butyricum: B. subtilis cocultured cathodic MEC-disconnected using ammonium-enriched wastewater-rep1


title: IA synovial 1


title: 06912-3_S63 (single-end)

description:
Sample 7
countstable.single-end.txt.gz

value: ATCC BAA-11119


title: 06912-2_S62 (single-end)

description:
Sample 7
countstable.single-end.txt.gz


title: ATAC_D0_FM_REP_1

value: human fibroblasts


title: ATAC_P3_PM_REP_1


title: healthy peripheral 5

source_name: healthy_peripheral blood

value: healthy

value: peripheral blood


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep4

description:
no8A1D_S7_L004_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep4

organism: Clostridium beijerinckii


title: H9_BMP4_3'READS

city: Philadelphia

first: Bin

last: Tian

address: 3601 Spruce Street

department: Program in Gene Expression and Regulation; Center for Systems and Computational Biology

institute: Wistar Institute

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to hg19 or mm9 using bowtie2
reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis. Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for each pAs

source_name: human embryonic stem cell

extract_protocol:
TRIzol
3'READS: The 3’READS procedure has been described in (Hoque et al, 2013; Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer.

value: hESC


title: 06912-1_S61 (single-end)

description:
Sample 7
countstable.single-end.txt.gz


title: healthy peripheral 2


title: H9_3'READS

value: Untreated


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep2

description:
no8A1D_S7_L002_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep2


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep1

description:
no8A1D_S7_L001_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep1


title: N2RAmZB_34370

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

data_processing:
Raw reads in fastq format were mapped and quantified using RSEM (v1.2.9)
Reads were mapped to mm10 version of mouse genome
Raw counts and TPM(Transcripts per million) per gene across samples were reported
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: raw counts and TPM files in .xls format

source_name: Spleenocytes

growth_protocol: Single-cell suspensions of MZB cells were isolated from the spleens of 10-14 week old mice using an antibody cocktail and subjected to FACS.

extract_protocol:
Qiagen Rneasy micro kit (#74004)
Ovation RNA-Seq System V2

value: spleen

value: MZB

value: Adult 10-14 weeks old

value: Mixed Background


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep3

description:
no8A1D_S7_L003_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep3


title: healthy peripheral 6


title: N2RAmZB_34362


title: 02618-2_S53 (single-end)

description:
Sample 6
countstable.single-end.txt.gz

value: ATCC BAA-11118


title: RMB375_pTh17+IL12 OT2 NKG2Dko

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
in vitro generated NKG2D-/- Th17 cells
RMB375

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by feature featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: 8 day cultured Th17 cells, sorted as Thy1.1 OT-II NKG2D-/-

growth_protocol: Naive CD4+ T cells were isolated from lymph nodes and spleen of OT-II and OT-II x NKG2D-/- mice and were co-cultured and activated in vitro with OVA323-339 and a-CD28, in the presence of APCs, and differentiated with IL-2, IL-12 and a-IL-4 in the case of Th1 and IL-1b, IL-6, IL-23, a-IFNg and a-IL4 in the case of Th17. IL-12 was added to the Th17 culture after the second triggering event. Co-cultured cells were subjected to two rounds of polarization (day 0 and day 5), harvested on day 8 and sorted with the help of congenic markers as Thy1.2+ NKG2D+ OT-II and Thy1.1+ OT-II x NKG2D-/- before being subjected to RNA isolation.

extract_protocol:
Total RNA was purified with NucleoSpin RNA Kit (Macherey-Nagel) from in vitro generated and FACS sorted Th1 and Th17 cells. RNA quality was determined on a Bioanalyzer using the RNA 6000 Nano Kit (Agilent).
For poly-A dependent cDNA synthesis and a first amplification step the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) was used. After quality control (High sensitivity DNA Kit, Agilent) and concentration measurement (Qubit dsDNA HS Assay Kit, Invitrogen), 150 pg of the purified cDNA was used for tagmentation and library completion with the Nextera XT library preparation kit (Illumina). In the following, 2x75 nucleotides paired-end sequencing was performed on a NextSeq 500 using a mid-output flow cell.

value: Th17 cells

value: OT-II x NKG2D-/-

value: LN/spleen


title: 02617-3_S51 (single-end)

description:
Sample 5
countstable.single-end.txt.gz

value: ATCC BAA-11117


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep4

description:
no8A1C_S6_L004_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep4


title: 02618-1_S52 (single-end)

description:
Sample 6
countstable.single-end.txt.gz


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep3

description:
no8A1C_S6_L003_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep3


title: healthy peripheral 4

value: CD141+ dendritic cell


title: N2RAmZB_34363


title: healthy peripheral 1


title: RMB373_pTh17+IL12 OT2 WT NKG2D+

description:
in vitro generated WT Th17 cells, sorted as NKG2D+
RMB373

source_name: 8 day cultured Th17 cells, sorted as Thy1.2 OT-II NKG2D+

value: C57BL/6 x OT-II


title: 02617-2_S50 (single-end)

description:
Sample 5
countstable.single-end.txt.gz


title: RMB372_pTh17+IL12 OT2 NKG2Dko

description:
in vitro generated NKG2D-/- Th17 cells
RMB372


title: N2WTmZB_33875

value: WT


title: 02618-3_S54 (single-end)

description:
Sample 6
countstable.single-end.txt.gz


title: N2WTmZB_34066


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep2

description:
no8A1C_S6_L002_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep2


title: 02617-1_S49 (single-end)

description:
Sample 5
countstable.single-end.txt.gz


title: RNAseq_C. beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep1

description:
no8A1C_S6_L001_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis OE-NasDEF cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep1


title: N2WTmzB_34359


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep4

description:
A2C_S4_L004_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep4


title: RMB367_pTh17+IL12 OT2 WT NKG2D+

description:
in vitro generated WT Th17 cells, sorted as NKG2D+
RMB367


title: ATAC-seq_N2RA51193-2

data_processing:
Raw reads in fastq format were processed using Computational Suite For Bioinformaticians and Biologists (CSBB-v3.0)
Raw reads were mapped to mm10 version of Mouse genome
CSBB uses fastqc for quality check, Boiwtie2 for mapping and MACS2 for peak calling
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: Bigwigs files were generated using deeptools and peaks were called using MACS2

extract_protocol:
Nuclei were isolated from purified MZBs as described by Buenrostro et al (2013)
ATAC-Seq (Buenrostro et al, 2013)


title: 02611-2_S59 (single-end)

description:
Sample 4
countstable.single-end.txt.gz

value: ATCC BAA-11116


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep3

description:
A2C_S4_L003_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep3


title: 02611-1_S58 (single-end)

description:
Sample 4
countstable.single-end.txt.gz


title: ATAC-seq_N2RA828-2


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep2

description:
A2C_S4_L002_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep2


title: RMB366_Th1 OT2 NKG2Dko

description:
in vitro generated NKG2D-/- Th1 cells
RMB366

source_name: 8 day cultured Th1 cells, sorted as Thy1.1 OT-II NKG2D-/-

value: Th1 cells


title: RMB370_pTh17+IL12 OT2 WT NKG2D+

description:
in vitro generated WT Th17 cells, sorted as NKG2D+
RMB370


title: ATAC-seq_N2RAMZB-4


title: RMB364_Th1 OT2 WT NKG2D+

description:
in vitro generated WT Th1 cells, sorted as NKG2D+
RMB364

source_name: 8 day cultured Th1 cells, sorted as Thy1.2 OT-II NKG2D+


title: 02610-2_S56 (single-end)

description:
Sample 3
countstable.single-end.txt.gz


title: RMB361_Th1 OT2 WT NKG2D+

description:
in vitro generated WT Th1 cells, sorted as NKG2D+
RMB361


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-connected, nitrate-enriched wastewater, rep1

description:
A2C_S4_L001_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-connected using nitrate-enriched wastewater-rep1


title: RMB363_Th1 OT2 NKG2Dko

description:
in vitro generated NKG2D-/- Th1 cells
RMB363


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep4

description:
A1D_S3_L004_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep4


title: 02610-3_S57 (single-end)

description:
Sample 3
countstable.single-end.txt.gz


title: ATAC-seq_N2WT51195-2


title: 00050-3_S42 (single-end)

description:
Sample 2
countstable.single-end.txt.gz


title: RMB358_Th1 OT2 WT NKG2D+

description:
in vitro generated WT Th1 cells, sorted as NKG2D+
RMB358


title: 02611-3_S60 (single-end)

description:
Sample 4
countstable.single-end.txt.gz


title: ATAC-seq_N2WT828-2


title: RMB369_pTh17+IL12 OT2 NKG2Dko

description:
in vitro generated NKG2D-/- Th17 cells
RMB369


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep2

description:
A1D_S3_L002_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep2


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep1

description:
A1D_S3_L001_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep1


title: ATAC-seq_N2WTMZB-4


title: 00050-2_S41 (single-end)

description:
Sample 2
countstable.single-end.txt.gz


title: 00050-1_S40 (single-end)

description:
Sample 2
countstable.single-end.txt.gz


title: ATAC-seq_N2WTMZB-2


title: PLN3_BEC (scRNA-seq)

city: Palo Alto

first: Kevin

last: Brulois

address: 3801 Miranda Ave

institute: Stanford University

data_processing:
Cell Ranger v3.0.2 (10X Genomics) was for alignment and generation of UMI count matrices.
BEC were selected by supervised gating on a tSNE plot based on canonical markers.
BEC classifications are based on graph-based clustering using the findClusters function from the Seurat R package (detailed description in Brulois et al. [PMID: TBD])
Male and female cells in the PLN1 sample were identified in silica based on the pooled expression of Y-chromosomal genes and expression of the female specific Xist (detailed description in Brulois et al. [PMID: TBD])
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrices (MTX) and associated features and barcodes (TSV). Cell-level meta data (CSV).

source_name: Peripheral lymph node

extract_protocol:
Axillary, inguinal and brachial peripheral lymph nodes from 25-30 mice per replicate were dissociated. BEC were sorted as CD31+ gp38- CD45- CD11a- EpCAM- Ter119-
Cells were processed using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics). Libraries were sequenced on a NextSeq 500 using the High Output Kit v2 (150 cycles; Illumina).

value: Mixed

tag: Sex

value: Female

value: Peripheral lymph node

value: blood vessel endothelial cells (BEC)


title: ATAC-seq_N2RAMZB-2

value: spleen

tag: cell type

value: MZB


title: LuxR-3_S39 (single-end)

description:
Sample 1
countstable.single-end.txt.gz

value: {delta}luxR (KM669)


title: 02610-1_S55 (single-end)

description:
Sample 3
countstable.single-end.txt.gz


title: RMB360_Th1 OT2 NKG2Dko

description:
in vitro generated NKG2D-/- Th1 cells
RMB360


title: 16-0128

city: Hershey

first: Elizabeth

middle: Anne

last: Proctor

address: 500 University Dr

department: Neurosurgery

institute: Pennsylvania State University

data_processing:
Gene expression was mapped using the STAR/RSEM pipeline, using Mus musculus GRCm38.93 as a reference (available for download in GTF format from Ensembl).
We estimated variance-mean dependence in count data and tested for differential expression based on a model using the negative binomial distribution with the DESeq package in R from the Bioconductor repository.
From the 48 original samples, 6 outliers were identified by principal component analysis (PCA), and later confirmed by quality control to be contaminated or feature low read counts. These samples were excluded from further analysis.
Genome_build: Mus musculus GRCm38.93
Supplementary_files_format_and_content: CSV: log2-scaled gene transcript abundance

source_name: kidney

growth_protocol: Male C57BL/6J mice (Jackson Laboratories, Bar Harbor, ME) weighing 23.4 ± 0.1 g were individually housed in Nalgene polycarbonate cages (11.5 in x 7.5 in x 5 in) fitted with HEPA-filter cage tops and Shepherds Specialty Blend bedding (ScottPharma, Marlborough, MA) under standard laboratory conditions (25 ± 2 °C; 12:12 hour light-dark cycle, lights on at 0600 h). Rodent laboratory chow (Harlan Teklad 7012; Madison, WI) and water were provided ad libitum. Each cage was supplied with a Nalgene Mouse House (Nalgene Nunc, Rochester, NY), maple wood product (Product #W0002; Bio-Serv, Frenchtown, NJ), and stainless steel ring attached to the wire lid for environmental enrichment. Clean cages, fresh food and water were provided weekly.  All procedures were approved by the Institutional Animal Care and Use Committee at the United States Army Research Institute of Environmental Medicine. In conducting this research, the investigators adhered to the Guide for the Care and Use of Laboratory Animals in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility.

extract_protocol:
Qiagen RNeasy with DNase
Kapa mRNA Hyperprep

treatment_protocol: under isoflurane anesthesia, mice were intraperitoneally implanted with radiotelemetry transmitters (1.1 g, model G2 Emitter; Starr Life Sciences Corp., Inc., Oakmont, PA) to measure body core temperature (Tc; ± 0.1 °C) and general activity (counts). Surgical analgesia was provided with a subcutaneous buprenorphine injection (0.05 mg/kg) just prior to surgery, and again 24 and 48 hours post-procedure. The mice recovered from surgery in approximately 7-10 days as assessed by return to pre-surgical body weight, normal food and water consumption, and stable circadian Tc and activity rhythms9. Tc and activity were continuously monitored at 1-minute intervals throughout recovery and experimentation using the VitalView system (Starr Life Sciences Corp., Inc., Oakmont, PA).

value: Male

tag: stress

value: heat

tag: injection

value: saline

tag: time point

value: Tcmax


title: PLN2_BEC (scRNA-seq)

value: Balb/c

tag: tissue


title: RNAseq_C. beijerinckii: B. subtilis cocultured cathodic MEC-disconnected, nitrate-enriched wastewater, rep3

description:
A1D_S3_L003_R1_001
RNA-Seq of Clostridium beijerinckii: B. subtilis cocultured cathodic MEC-disconnected using nitrate-enriched wastewater-rep3


title: LuxR-1_S37 (single-end)

description:
Sample 1
countstable.single-end.txt.gz


title: PLN1_BEC (scRNA-seq)

value: Male and female


title: LuxR-2_S38 (single-end)

description:
Sample 1
countstable.single-end.txt.gz


title: WT 2

city: Copenhagen N

first: Hans

middle: H.

last: Wandall

state: Denmark

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file.
SOAPnuke software is used to filter reads (remove reads with adaptors; remove reads in which unknown bases(N) are more than 5%; remove low quality reads (a read is defined as low quality, if the percentage of bases for which quality  is lesser than 15 is greater than 20% in a read).
After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format.
For initial assessment, HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) is used to map clean reads to reference genome (HISAT2 v2.0.4).
For gene expression analysis, clean reads are mapped to reference using Bowtie2 (v2.2.5), and then gene expression level is calculated using RSEM (v1.2.12). RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample, as well as corresponding gene name, gene ID, and transcript ID.

source_name: Keratinocyte cell line (N/TERT-1)

growth_protocol: N/TERT-1 cells were grown in KSFM supplemented with 25 ug/mL bovine pituitary extract, 0.2 ng/mL epidermal growth factor, and CaCl2 to a final Ca2+ concentration of 0.3 mmol/L. The cells were passaged 2 times per week, after reaching approximately 40 % confluency, and seeded at 5.000/cm2

extract_protocol:
Total RNA was extracted from cells that reached 80 % confluency using the RNeasy® kit (Qiagen). RNA integrity and quality were determined using Bioanalyzer instrumentation (Agilent Technologies).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: To achieve higher confluency, medium was replaced with growth medium (KSFM supplemented with 25 ug/mL bovine pituitary extract, 0.2 ng/mL epidermal growth factor, and CaCl2 to a final Ca2+ concentration of 0.3 mmol/L) mixed 1:1 with DFK medium (DMEM/HAM's F12 (1:1) supplemented with 25 ug/mL bovine pituitary extract and 0.2 ng/mL epidermal growth factor), after reaching 60 % confluency.

value: Wild Type

tag: replicate

value: Technical


title: WT 1


title: 16-0122

value: control


title: poly(A) mRNA MDSC_p50ko_IFNg R2

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

data_processing:
Reads were adapter-trimmed according to the Illumina pipeline (Bcl2fastq)
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 150bp
Transcripts abundance were quantified using HTSeq (PMID: 25260700)
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm9 (NCBI Build 37),  transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained using edgeR

source_name: Monocytic Myeloid Derived Suppressor Cells (M-MDSC) replicate 2

growth_protocol: CD11b+Ly6C+ Monocytic Myeloid Derived Suppressor Cells (M-MDSC) were obtained by serial selection using magnetic separation from tumor-bearing C56Bl6/J mice, 28 days after injection of murine fibrosarcoma (MN/MCA1). In details, myeloid suppressor populations were first enriched by  serial negative selections with CD19 and CD11c microbeads, and then positively selected with Ly6G microbeads. Remaining cells were positively selected with CD11b+ microbeads. The purity of the cell populations evaluated by flow cytometry exceeded 90%.

extract_protocol: The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small fragments using divalent cations and elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.  cDNA fragments were end-repaired and a single ‘A’ base was added before adapter ligation. The products were then purified and enriched by PCR to create the final cDNA library.

treatment_protocol: 5 million M-MDSC were plated in RPMI1640 containing 10% FBS and left untreated or stimulated with 200U/ml interferon gamma for 4 hours.

value: M-MDSC (28 post injection)

tag: treatment

value: Interferon-treated


title: POGLUT1 KO 2

value: POGLUT1 KO

value: Biological (clonal cell line 2)

tag: clone name


title: 16-0085

value: poly I:C

value: 1 day


title: poly(A) mRNA MDSC_p50ko_IFNg R1

source_name: Monocytic Myeloid Derived Suppressor Cells (M-MDSC) replicate 1

value: Untreated


title: POFUT1 KO 2

value: POFUT1 KO


title: poly(A) mRNA MDSC_p50kot_UT R2


title: POGLUT1 KO 1

value: Biological (clonal cell line 1)


title: POFUT1 KO 1


title: pSUC2-PreBuds-3

city: College Park

first: James

middle: N

last: Culver

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

description: polysomal RNA from PPV infected Pre-CID Bud tissue

data_processing:
Reads were mapped to the PPV-D isolate Penn7 (GenBank accession EF640935) using the CLC Genomics Workbench v10.0.1 Map to reads tool and parameters (            Masking mode = No masking            Match score = 1            Mismatch cost = 2            Cost of insertions and deletions = Linear gap cost            Insertion cost = 3            Deletion cost = 3            Length fraction = 0.5            Similarity fraction = 0.8            Global alignment = No            Auto-detect paired distances = Yes            Non-specific match handling = Ignore            Output mode = Create reads track            Create report = No            Collect un-mapped reads = No - CLC Bio, Aarhus, Denmark)
Low frequency variants were called against the PPV-D isolate Penn7 (GenBank accession EF640935) using the CLC Genomics Workbench v10.0.1 Low frequency variant caller tool and parameters (            Required significance (%) = 1.0            Ignore positions with coverage above = 100,000            Restrict calling to target regions = Not set            Ignore broken pairs = Yes            Ignore non-specific matches = Reads            Minimum coverage = 10            Minimum count = 2            Minimum frequency (%) = 0.5            Base quality filter = No            Read direction filter = No            Relative read direction filter = Yes            Significance (%) = 1.0            Read position filter = No            Remove pyro-error variants = No            Create track = Yes            Create annotated table = No            Create report = No - CLC Bio, Aarhus, Denmark)
Variants were filtered on  CLC Genomics with the following parameters (Criteria = 'Forward/reverse balance < .7501',           Criteria = 'Forward/reverse balance > .2499999',           Criteria = 'Reference allele contains no' - - CLC Bio, Aarhus, Denmark)
Amino acid changes were identified using the CLC genomics Workbench Amino Acid Changes tool with parameters (CDS track = PPV Penn7 (CDS)            Sequence track = PPV Penn7 (Genome) protein cistrons            mRNA track = Not set            Filter synonymous variants = No            Genetic code = 1 Standard            Filter CDS regions with no variants = No
Genome_build: PPV-D isolate Penn7 (GenBank accession EF640935)
Supplementary_files_format_and_content: tab-delimited text files include Chromosome, Region, Type, Reference, Allele, Reference allele, Length, Linkage, Zygosity, Count, Coverage, Frequency, Probability, Forward read count, Reverse read count, Forward/reverse balance, Average quality, Read count, Read coverage, # unique start positions, # unique end positions, BaseQRankSum, Read position test probability, Read direction test probability, Homopolymer length, Homopolymer, QUAL, Coding region change, Amino acid change, Amino acid change in longest transcript, Coding region change in longest transcript, Other variants within codon, and Non-synonymous.

organism: Prunus domestica

source_name: Pre-CID Buds of Prunus domesitica L leaves

growth_protocol: Transgenic plum trees expressing promoter:His6FLAG-RPL18 were maintained in the plant biosafety level 3 containment facility at the USDA facility at Fort Detrick, Frederick, MD, USA. Plants in the quarantine greenhouse were subjected to a cycle of 60 days of cold dormancy (4°C) followed by 84-90 days of growth at normal greenhouse temperatures (27°C). Leaf samples were collected at two, four, six, and twelve weeks post cold induced dormancy over two consecutive vegatative growth periods

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothereitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue. Samples were centrifuged at 16,000 g for 15 min at 4°C. The supernatant was loaded onto an 8 mL 1.6 M sucrose cushion. The polysome fraction was pelleted by centrifuging the samples at 170,000 g for 18 h at 4 °C. The pellet was resuspended in 1 mL of PEB. 50 μl of Anti-FLAG magnetic beads (Sigma Chemical Company, St. Louis, MO, USA) was added to the resuspended pellet and incubated at 4°C overnight with gentle rocking. The beads were recovered using their magnetic property and were washed four times in wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). Polysome-RNA complexes were eluted by treatment of the magnetic beads with 100 μl of Elution Buffer (100 μl wash buffer, 10 μl of 5 mg/mL FLAG3 peptide—Sigma Chemical Company, St. Louis, MO USA, 0.5 μl of 2 U/ml RNAse OUT—Thermo Fisher Scientific Cleveland, OH, USA). RLT buffer plus β-mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA, USA) was added to the eluted complexes. A 0.5 × volume of 100% ethanol was then added, and the sample transferred to Qiagen RNeasy columns. Washes and RNA elutions were performed according to the manufacturer’s instructions. Isolated RNA was measured on a NanoDrop 2000 and with the Qubit RNA Assay Kit (Thermo Fisher Scientific, Cleveland, OH, USA). Quality of the RNA was analyzed using an RNA ScreenTape assay (Agilent Technologies, Palo Alto, CA, USA).
Library preparation and paired-end sequencing on the Illumina HiSeq system was done by Genewiz (South Plainfield, NJ, USA).

treatment_protocol: PPV_D isolate Penn7 (EF640935) was used in this study. A Myzus persicae aphid colony was maintained inside containment and transmissions were conducted using symptomatic P. persica cv. GF 305 peach leaves as the inoculum source for aphid transmission to P. domestica L. transgenic plant lines.

tag: cultivar

value: Prunus domestica L 'Stanley'

value: Pre-CID Buds

tag: infection status

value: PPV infected


title: pSUC2-PreBuds-2

tag: developmental stage


title: 16-0047

value: Male

value: saline

value: Tcmax


title: poly(A) mRNA MDSC_p50ko_UT R1


title: pSUC2-PreBuds-1


title: 16-0036

value: heat


title: poly(A) mRNA MDSC_wt_IFNg R2

source_name: Monocytic Myeloid Derived Suppressor Cells (M-MDSC)  replicate 2

value: wild type


title: 16-0033

value: control


title: MGAT1 KO 2

value: MGAT1 KO


title: poly(A) mRNA MDSC_wt_IFNg R1

value: M-MDSC (28 post injection)


title: 16-0062


title: 16-0027


title: MGAT1 KO 1


title: COSMC KO 2

value: C1GALT1C1 KO

value: Biological (clonal cell line 2)


title: pSUC2-PostBuds-2

description: polysomal RNA from PPV infected Post-CID Bud tissue

source_name: Post-CID Buds of Prunus domesitica L leaves

value: Post-CID Buds


title: poly(A) mRNA MDSC_wt_UT R2

value: Interferon-treated


title: poly(A) mRNA MDSC_wt_UT R1

value: Untreated


title: 16-0019

value: poly I:C

value: 1 day


title: pSUC2-PostBuds-3

description:
polysomal RNA from PPV infected Post-CID Bud tissue
Analysis produced no results due to low 10-fold coverage

value: Prunus domestica L 'Stanley'


title: 16-0021


title: pSUC2-6GP2-3

description: phloem polysomal RNA from PPV infected 6-week-old leaf tissue

source_name: 6 week old Prunus domesitica L leaves

value: 6 weeks GP2

value: PPV infected


title: 16-0018

value: Male


title: CORE1 KO 1

value: C1GALT1 KO

value: Biological (clonal cell line 1)


title: ChIP_SEQ_PECs_p50ko_UT

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 4.1.2 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters and bw=100. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

source_name: Peritoneal Exudate Macrophages (PEC)

growth_protocol: PEC were harvested from mice injected with 500 L of 3% (wt/vol) thioglycollate medium (Difco) 4 days before isolation

extract_protocol: ChIP-Seq library preparation was performed as described in Ostuni et al., Cell 2013

treatment_protocol: 50 million PECs were plated in RPMI1640 containing 10% FBS and left untreated or stimulated with 200U/ml interferon gamma for 4 hours.

value: Peritoneal Exudate Macrophages (PEC)

tag: chip antibody

value: anti-STAT1 (Santa Cruz, sc-592)


title: pSUC2-6GP2-2


title: pSUC2-PostBuds-1


title: B4GALT5 KO 2

value: B4GALT5 KO


title: B4GALT5 KO 1


title: pSUC2-6GP1-3

value: 6 weeks GP1


title: ChIP_SEQ_PECs_WT_IFNg

value: wild type


title: 16-0009

value: heat


title: pSUC2-6GP1-2


title: PolyA_PEC_p50ko_IFNy_R2

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 250bp
Transcripts abundance were quantified using HTSeq (PMID: 25260700)
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained using edgeR

treatment_protocol: 5 million PECs were plated in RPMI1640 containing 10% FBS and left untreated or stimulated with 200U/ml interferon gamma for 4 hours.


title: siCINP

city: Tianjin

first: jintang

last: dong

address: Weijin road

country: China

institute: Nankai university

data_processing:
Basecalling and data filtering based on the BGI methord.
We use Bowtie2 to map clean reads to reference gene and use HISAT to reference hg19 genome.
FPKM  method is used in calculated expression level
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: bladder carcinoma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Roche) from the cells.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: K12 cells transfected siCINP and siCtrl respectively

tag: cell line


title: ChIP_SEQ_PECs_p50ko_IFNg

tag: strain


title: PolyA_PEC_p50ko_IFNy_R1

tag: genotype


title: Marmoset_Stomach_Input

city: Utrecht

first: Menno

middle: P

last: Creyghton

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
Genome_build: Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in .bw

organism: Callithrix jacchus

extract_protocol: TruSeq DNA sample preparation kit (Illumina)

value: Stomach


title: COSMC KO 1

value: C1GALT1C1 KO


title: pSUC2-6GP1-1


title: CORE1 KO 2

value: Biological (clonal cell line 2)


title: 15-0148

value: saline

value: Tcmax


title: pSUC2-4GP2-3

description: phloem polysomal RNA from PPV infected 4-week-old leaf tissue

source_name: 4 week old Prunus domesitica L leaves

value: Prunus domestica L 'Stanley'

value: 4 weeks GP2


title: 16-0002

value: control

value: 1 day


title: pSUC2-4GP2-2

value: PPV infected


title: 16-0017

value: Male

value: poly I:C


title: 15-0130


title: pSUC2-4GP2-1


title: PolyA_PEC_p50ko_UT_R1

value: Peritoneal Exudate Macrophages (PEC)

value: Untreated


title: 15-0132


title: ChIP_SEQ_PECs_WT

value: anti-STAT1 (Santa Cruz, sc-592)


title: PolyA_PEC_wt_IFNy_R1

value: wild type

value: Interferon-treated


title: Marmoset_Pancreas_Input

value: Pancreas


title: 15-0126

value: heat


title: PolyA_PEC_wt_IFNy_R2


title: PolyA_PEC_p50ko_UT_R2


title: 15-0122


title: pSUC2-6GP2-1

value: 6 weeks GP2


title: 16-0008


title: pSUC2-4GP1-2

value: 4 weeks GP1


title: Marmoset_Spleen_Input

value: Spleen


title: PolyA_PEC_wt_UT_R1


title: Marmoset_Kidney_Input

value: Kidney


title: PolyA_PEC_wt_UT_R2


title: pSUC2-4GP1-1

value: Prunus domestica L 'Stanley'


title: 15-0121

value: control

value: Tcmax


title: Marmoset_Heart_Input

value: Heart


title: 15-0111

value: Male


title: 15-0120

value: poly I:C


title: pSUC2-2GP2-3

description: phloem polysomal RNA from PPV infected 2-week-old leaf tissue

source_name: 2 week old Prunus domesitica L leaves

value: 2 weeks GP2

value: PPV infected


title: pSUC2-2GP2-1


title: Marmoset_Colon_Input

value: Colon


title: pSUC2-4GP1-3


title: Marmoset_SkeletalMuscle_Input

value: SkeletalMuscle


title: Marmoset_Stomach_H3K4me3_1

value: Stomach


title: DSCAM-AS1 LNA rep2

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

data_processing:
Raw reads were assessed for Phred quality scores using FASTQC program and low bases and adaptor sequences were trimmed off using Fqtrim retaining only reads of 75 bass length. Then, clean reads were aligned against the human reference genome (GRCh38.p10 assembly) with Gencode v27 annotation (gencode.v27.annotation.gtf.gz) using STAR v2.5.1b. STAR was run in two-pass mode allowing alignment to the transcriptome coordinates by setting the option --quantMode to TranscriptomeSAM.
Next, the expression levels in read counts, TPM, and FPKM units were then estimated at both genes and isoforms levels by running RSEM on the alignment files in default parameters.
Differentially expressed genes and isoforms upon DSCAM-AS1 silencing as compared to the control condition were identified using the DESeq2 R package (v1.26.0) in default parameters. The expression at isoform level was summarized to gene-level using the tx-import bioconductor package and the resulting count matrices were provided to DESeq2. Prior to DE analysis, lowly expressed genes and isoforms were discarded from the analysis and only genes or isoforms with more than 10 normalized read counts in at least one condition (3 out of 6 samples) were considered for further downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene-level or isoform-level raw read counts for each sample.
Supplementary_files_format_and_content: tab-delimited text files include gene-level or isoform-level TPM read counts for each sample.

source_name: Breast cancer cell lines

growth_protocol: MCF-7 cells were routinely grown in DMEM (Life Technologies, 31053–028) supplemented with 10% heat-inactivated FBS (Euroclone, ECS0180L) and 2 mM L-glutamine (ThermoFisher Scientific, 25030–024). Batches of human cell lines were purchased from ATCC. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Total RNA used for downstream RNA-seq analysis was isolated from MCF-7 cells using the RNeasy Mini Kit, according to the manufacture’s protocol (Qiagen, 74104).
RNA quality check (RNA integrity number (RIN) > 8) was achieved with Fragment Analyzer (Advanced Analytical Technologies, Inc, Ankeny, IA, USA) and quantified with Qubit (Qubit™ RNA HS Assay Kit, ThermoFisher Scientific,Waltham, MA, USA;Q32852). Two ug of RNA were polyA+ selected and RNA-Seq libraries were constructed using Illumina TruSeq RNA sample prep kit (TruSeq™ RNA Sample Prep Kit v2-Set B, Illumina, RS-122-2002). Paired-end (PE) cluster generation was performed using cBot on Flow Cell v3 (TruSeq PE Cluster Kit v3-cBot-HS, Illumina, PE-401-3001). Sequencing of libraries was performed on the HiSeq sequencing system (Illumina, San Diego, CA, USA).

treatment_protocol: MCF-7 cells were detached and transfected in suspension with LNAs (20 nM final concentration) using Lipofectamine3000 (ThermoFisher Scientific, L3000015), according to the manufacturer's protocol. Custom-designed LNA GapmeRTM from Exiqon were used to target all the DSCAM-AS1 lncRNA isoforms (LNA_1 5'-ATGGCAGTTGGAGGAG-3', LNA_2 5'-ACAGAGAAGGACATGG-3' and LNA_3 5'-AAGTAGCTTCATCTTT-3'); Negative control A - LNA longRNA GapmeR™ was used as a control LNA (5'-AACACGTCTATACGC-3'; Exiqon, 300611-00). Experiments were performed 48 hours after LNA transfection.

value: Breast cancer cell line

value: DSCAM-AS1 LNA


title: DSCAM-AS1 LNA rep3


title: 15-0055

value: heat


title: DSCAM-AS1 LNA rep1


title: Marmoset_Spleen_H3K4me3_1


title: 15-0051

value: saline


title: 15-0034

value: 1 day


title: pSUC2-2GP1-2

value: 2 weeks GP1


title: siCtrl


title: pSUC2-2GP1-1

value: Prunus domestica L 'Stanley'


title: 15-0033

value: control


title: Marmoset_Pancreas_H3K4me3_1

value: Pancreas


title: Marmoset_SkeletalMuscle_H3K4me3_1


title: 15-0028


title: pSUC2-12GP2-2

description: phloem polysomal RNA from PPV infected 12-week-old leaf tissue

source_name: 12 week old Prunus domesitica L leaves

value: 12 weeks GP2


title: Control LNA rep2

value: Control LNA


title: pSUC2-12GP2-3


title: Control LNA rep1


title: Marmoset_Liver_H3K4me3_1

value: Liver


title: pSUC2-2GP1-3


title: 15-0027

value: Male

value: poly I:C


title: pSUC2-12GP1-3

value: 12 weeks GP1

value: PPV infected


title: 15-0025


title: si-CLOCK ZT44

city: Yongin-si

first: Sunyoung

last: Park

state: Gyeonggi-do

address: 1920, Yonggu-daero

institute: Amorepacific corporation

description: data column (in the'FPKM_all_samples.xlsx'): 4_FPKM

data_processing:
Sequence reads were mapped to hg19 by TopHat (v2.0.11) using Bowtie2 (v2.1.0)
FPKM abundances were estimated by Cufflink (v2.1.1) with -G option
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft Excel file include FPKM values of 4 samples

source_name: NHEK_CLOCK siRNAs

growth_protocol: Human epidermal keratinocytes, neonatal (NHEKs), were purchased from Lonza (Clonetics Lonza, Walkersville, MD) and maintained in Keratinocyte Growth Medium (KGM)-Gold supplemented with BulletKit (Lonza). The cells were cultured at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNAs were extracted using the TRIzol reagent (Invitrogen)), and poly-A containing mRNAs were purified and converted into a cDNA library.
Subsequent cluster generation and DNA sequencing following the instructions of the illumina® TruSeq RNA sample preparation kit (Illumina, San Diego, CA).

treatment_protocol:
The cells were transfected with either scrambled or CLOCK siRNAs for 8 h and incubated overnight in the growth medium. The cells were then synchronized with serum-rich medium for 2 h at ZT 0.
For UV irradiation, the cells were treated with 20 mJ/cm2 UVB using BIO-SUN UV-H (VILBER LOURMAT, France) at ZT 20, and the cells were cultured back in fresh KBM. The cells were harvested at ZT 32 and 44.

value: NHEK

value: Human epidermal keratinocytes, neonatal

tag: passages

tag: transfected with

value: CLOCK siRNAs for 8 h


title: Marmoset_Colon_H3K4me3_1

value: Colon


title: si-scrambled ZT44

description: data column (in the'FPKM_all_samples.xlsx'): 2_FPKM

source_name: NHEK_scrambled siRNAs

tag: cell type

value: scrambled siRNAs for 8 h


title: pSUC2-12GP1-2


title: 15-0014

tag: Sex

tag: stress

value: heat

value: saline

value: Tcmax


title: si-scrambled ZT32

description: data column (in the'FPKM_all_samples.xlsx'): 1_FPKM


title: iRasDox_3_3'READS

source_name: mouse embryonic stem cell

value: mESC

value: Doxycyline

tag: protocol


title: pSUC2-12GP1-1

value: Prunus domestica L 'Stanley'


title: pSUC2-12GP2-1

value: 12 weeks GP2


title: 14-0183

source_name: kidney

tag: injection

tag: time point


title: p35S-PreBuds-3

value: Prunus domestica L 'President'

value: Pre-CID Buds


title: 15-0016

value: Male

value: control


title: 14-0172

value: 1 day


title: p35S-PreBuds-2

value: PPV infected


title: iRas_2_3'READS

tag: treatment

value: Untreated


title: iRasDox_2_3'READS


type: RNA

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description: Gene expression in the liver tissue of the 0 g group, 2 days after the SARA challenge, Cattle No. 24

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: 0 g group_2 days after the SARA challenge

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 500 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the rumen epithelium using Trizo (Invitrogen) according to the manufacturer's instructions.

tag: breed

value: Holstein

tag: animal id

value: Cattle No. 24

tag: sample group

value: 0 g group

value: 2 days after the SARA challenge

tag: tissue

value: Liver tissue


title: si-CLOCK ZT32

description: data column (in the'FPKM_all_samples.xlsx'): 3_FPKM

value: NHEK

value: Human epidermal keratinocytes, neonatal

value: CLOCK siRNAs for 8 h


title: iRas_3_3'READS

value: mESC


title: 14-0163

value: heat

value: saline

value: Tcmax


title: p35S-PostBuds-3

tag: cultivar

value: Prunus domestica L 'President'

tag: developmental stage

value: Post-CID Buds

tag: infection status


title: p35S-PostBuds-2

tag: genotype


title: p35S-PreBuds-1

value: Pre-CID Buds


description: Gene expression in the liver tissue of the 4 g group, 2 days after the SARA challenge, Cattle No. 23

source_name: 4 g group_2 days after the SARA challenge

value: Cattle No. 23

value: 4 g group


title: 14-0122

value: Male

tag: strain

value: control

value: poly I:C

value: 1 day


description: Gene expression in the liver tissue of the 0 g group, 2 days after the SARA challenge, Cattle No. 23

value: Holstein

value: 0 g group

value: 2 days after the SARA challenge

value: Liver tissue


description: Gene expression in the liver tissue of the 4 g group, 2 days after the SARA challenge, Cattle No. 24

value: Cattle No. 24


title: iRasDox_1_3'READS

value: mESC

value: Doxycyline


title: iRas_1_3'READS

value: Untreated


title: 14-0118

value: heat

value: saline


description: Gene expression in the liver tissue of the 4 g group, 2 days after the SARA challenge, Cattle No. 20

value: Cattle No. 20


description: Gene expression in the liver tissue of the 0 g group, 2 days after the SARA challenge, Cattle No. 20


title: 14-0176

value: Tcmax