title: DGRP Line 361 Female Rep 1


title: DGRP Line 355 Male Rep 1

status: Public on Feb 28 2020

type: SRA

city: East Lansing

first: Wen

last: Huang

state: MI

address: 474 S Shaw Ln, Anthony Hall 1205F

department: Animal Science

country: USA

institute: Michigan State University

library_source: transcriptomic

data_processing:
Barcoded sequence reads were demultiplexed using the Illumina pipeline v1.9.
Adapter sequences were trimmed using cutadapt v1.642 and trimmed sequences shorter than 50bp were discarded from further analysis.
Trimmed sequences were then aligned to multiple target sequence databases in the following order, using BWA v0.7.10 (MEM algorithm with parameters ‘-v 2 –t 4’):
(1) all trimmed sequences were aligned against a database containing the complete 5S, 18S-5p8S-2S-28S, mt:lrRNA, and mt:srRNA sequences to filter out residual rRNA that escaped depletion during library preparation;
(2) remaining sequences were then aligned against a custom database of potential microbiome component species (see below);
(3) sequences that did not align to either the rRNA or microbiome databases were aligned to all D. melanogaster sequences in RepBase.
The remaining sequences that did not align to any of the databases above were then aligned to the D. melanogaster genome (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e.
Generation of microbiome database: We first performed a preliminary alignment of RNA-seq reads by filtering only rRNA sequences, and then aligning directly to the D. melanogaster genome using the tools and parameters described above. Sequences that did not align to the rRNA database or D. melanogaster reference genome were then analyzed with Trinity v2.1.1 to perform de novo assembly of longer sequences from the short reads. We discarded assembled sequences < 1kb in length, and the remaining sequences were then run through a BLAST search against the refseq_genomic database (downloaded from NCBI on 1/27/16).  We then compiled a list of all refseq genomes that were found as a top BLAST hit for at least two assembled sequences. We compiled all fasta files for each of these refseq genomes into a single database for alignment with BWA.
Genotype validation: To validate the DGRP line assigned to each RNA-seq sample, we identified single nucleotide polymorphisms (SNPs) from the RNA-seq reads that aligned to the D. melanogaster reference genome using STAR as described above. We retained only those SNP calls covered by at least 3 reads and at least 75% of all reads supporting the major genotype (note that DGRP lines are inbred and therefore the majority of SNPs are homozygous). This filtering process produced >400k usable SNPs per sample, primarily located in transcribed regions of the genome. We then performed two validation tests of the DGRP line assigned to each sample X by comparing to the previously published genotype calls for each DGRP line (http://dgrp2.gnets.ncsu.edu/data/website/dgrp2.tgeno).
Inference of novel transcripts: We constructed a de novo transcriptome for each individual sample by inputting the RNA-seq reads aligned to the D. melanogaster reference genome into Cufflinks v2.2.1. We also considered the novel transcribed regions (NTRs) identified in a previous study based on unstranded pooled RNA sequencing of the DGRP lines. However, the previously published data do not provide strand-specific signal, while our current RNA-seq data uses a strand-specific library preparation. Therefore, we reassigned the strand for each of the previously published NTRs that was supported by the greater number of total aligned reads across all samples. We then merged all de novo sample transcriptomes and the previously published NTRs using the cuffmerge tool included with Cufflinks v2.2.1, then removed all merged transcript models with any exon overlapping on the same strand any exon in the known D. melanogaster transcriptome. We defined the known transcriptome here as all gene models in FlyBase v5.57 plus all subsequently added gene models in FlyBase v6.11 to account for recently discovered lncRNA sequences. Thus, the final output of this analysis was a set of NTRs constructed from both our current RNA-seq data and previously published pooled RNA-seq data that do not overlap any known gene exons on the same strand.
Gene expression estimation: Read counts were computed for known and novel gene models using HTSeq-count with the ‘intersection-nonempty’ assignment method. Read counts for each gene were then normalized across all samples using EdgeR as follows. First, genes with low expression overall (<10 aligned reads in >75% of the libraries) were excluded from the analysis by modeling the overall distribution of expression levels as a mixture of background noise and foreground signal to determine an empirical threshold for sufficiently expressed genes. Library sizes were re-computed as the sum of reads assigned to the remaining genes, and further normalized using the Trimmed Mean of M-values (TMM) method. We further adjusted gene expression values by estimating and removing the effect of alignment bias resulting from higher rates of non-reference variants clustering in some lines. We computed the alignment bias score A(g,L) defined as the number of non-reference nucleotides per kb in all exons of gene g in DGRP line L, based on the previous map of genomic variation in the DGRP. We then fit a linear model for each endogenous gene: Y = A + ε, where Y is the normalized expression profile for gene g after the read counting and EdgeR normalization described above. After fitting these linear models, ε represents the alignment bias-corrected expression, and was used as the normalized gene expression in all subsequent analysis.
Genetics of gene expression: For each gene in each sex, we fit mixed-effect models to the gene expression vector across all samples corresponding to: Y = W + L + ε, where Y is the observed log2(normalized read count), W is Wolbachia infection status, L is DGRP line, and ε is the residual error. We identified genetically variable transcripts as those that passed a 5% FDR threshold (based on Benjamini-Hochberg corrected P-values) for the L terms. We computed the broad sense heritabilities (H2) for each gene expression trait separately for males and females as H^2 = V/(V+R), where V and R are, respectively, the among line and within line variance components.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: Tab-delimited text files contain normalized log2 FPKM expression values, variant density correction factors, and within-sex line means for all genes.

molecule: total RNA

organism: Drosophila melanogaster

source_name: DGRP Line 355 Male

growth_protocol: We used 200 inbred, sequenced DGRP lines, established by 20 generations of full sib inbreeding from gravid females collected at the Raleigh, NC USA Farmer’s Market. All lines were reared on cornmeal-molasses-agar medium at 25°C, 60–75% relative humidity and a 12-hr light-dark cycle at equal larval densities. We collected two replicates of 25 females and 30 males per line, for a total of 800 samples. We used a strict randomized experimental design for sample collection. We collected mated 3-5 day old flies between 1-3 pm. We transferred the flies into empty culture vials and froze them over ice supplemented with liquid nitrogen, and sexed the frozen flies. The samples were transferred to 2.0 ml nuclease-free microcentrifuge tubes (Ambion) and stored at -80°C until ready to process.

extract_protocol:
Total RNA was extracted with Trizol using the RNAeasy Mini Kit (Qiagen, Inc.). rRNA was depleted using the Ribo-Zero™ Gold Kit (Epicentre, Inc.) with 5ug total RNA input.
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA. cDNA from each RNA sample was used to produce barcoded cDNA libraries using NEXTflex™ DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TruSeq compatible protocol. Library size was selected using Agencourt Ampure XP Beads (Beckman Coulter, Inc.) and centered around 250 bp with the insert size ~130 bp. Second strand DNA was digested with Uracil-DNA Glycosylase before amplification to produce directional cDNA libraries. Libraries were quantified using Qubit dsDNA HS Kits (Life Technologies, Inc.) and Bioanalyzer (Agilent Technologies, Inc.) to calculate molarity. Libraries were then diluted to equal molarity and re-quantified. A total of 50 pools of 16 libraries were made, again randomly assigning samples to each pool. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM. Pooled library samples were clustered on an Illumina cBot; each pool was sequenced on one lane of Illumina Hiseq2500 using 125 bp single-read v4 chemistry. Libraries with fewer than 5 million reads uniquely aligned to the D. melanogaster reference genome were re-sequenced to achieve sufficient read depth.

treatment_protocol: Not applicable

tag: strain

tag: Sex

value: Male

tag: age

value: 3-5 days old

tag: medium

value: cornmeal-molasses-agar

tag: tissue

value: Whole flies


title: DGRP Line 354 Male Rep 1

source_name: DGRP Line 354 Male


title: DGRP Line 356 Female Rep 1

source_name: DGRP Line 356 Female

value: Female


title: DGRP Line 354 Male Rep 2


title: DGRP Line 360 Female Rep 2

source_name: DGRP Line 360 Female


title: DGRP Line 358 Female Rep 2

source_name: DGRP Line 358 Female


title: DGRP Line 359 Male Rep 2

source_name: DGRP Line 359 Male


title: DGRP Line 354 Female Rep 2

source_name: DGRP Line 354 Female


title: DGRP Line 350 Male Rep 2

source_name: DGRP Line 350 Male


title: DGRP Line 352 Female Rep 2

source_name: DGRP Line 352 Female


title: DGRP Line 356 Female Rep 2


title: DGRP Line 350 Female Rep 2

source_name: DGRP Line 350 Female


title: DGRP Line 350 Female Rep 1


title: DGRP Line 350 Male Rep 1


title: DGRP Line 340 Female Rep 2

source_name: DGRP Line 340 Female


title: DGRP Line 340 Female Rep 1


title: DGRP Line 348 Female Rep 1

source_name: DGRP Line 348 Female


title: DGRP Line 340 Male Rep 1

source_name: DGRP Line 340 Male


title: DGRP Line 348 Male Rep 2

source_name: DGRP Line 348 Male


title: DGRP Line 340 Male Rep 2


title: DGRP Line 348 Male Rep 1


title: DGRP Line 354 Female Rep 1


title: DGRP Line 352 Male Rep 1

source_name: DGRP Line 352 Male


title: DGRP Line 336 Male Rep 1

source_name: DGRP Line 336 Male


title: DGRP Line 348 Female Rep 2


title: DGRP Line 336 Male Rep 2


title: DGRP Line 338 Male Rep 1

source_name: DGRP Line 338 Male


title: DGRP Line 338 Female Rep 1

source_name: DGRP Line 338 Female


title: DGRP Line 338 Male Rep 2


title: DGRP Line 336 Female Rep 1

source_name: DGRP Line 336 Female


title: DGRP Line 338 Female Rep 2


title: DGRP Line 352 Female Rep 1


title: DGRP Line 352 Male Rep 2


title: DGRP Line 335 Male Rep 2

source_name: DGRP Line 335 Male


title: DGRP Line 336 Female Rep 2


title: DGRP Line 335 Female Rep 2

source_name: DGRP Line 335 Female


title: DGRP Line 335 Female Rep 1


title: DGRP Line 332 Male Rep 2

source_name: DGRP Line 332 Male


title: DGRP Line 332 Female Rep 2

source_name: DGRP Line 332 Female


title: DGRP Line 325 Male Rep 2

source_name: DGRP Line 325 Male


title: DGRP Line 332 Female Rep 1


title: DGRP Line 332 Male Rep 1


title: DGRP Line 325 Female Rep 2

source_name: DGRP Line 325 Female


title: DGRP Line 325 Male Rep 1


title: DGRP Line 324 Male Rep 2

source_name: DGRP Line 324 Male


title: DGRP Line 321 Female Rep 1

source_name: DGRP Line 321 Female


title: DGRP Line 324 Female Rep 1

source_name: DGRP Line 324 Female


title: DGRP Line 320 Male Rep 1

source_name: DGRP Line 320 Male


title: DGRP Line 324 Male Rep 1


title: DGRP Line 321 Female Rep 2


title: DGRP Line 319 Male Rep 2

source_name: DGRP Line 319 Male


title: DGRP Line 321 Male Rep 1

source_name: DGRP Line 321 Male


title: DGRP Line 321 Male Rep 2


title: DGRP Line 320 Female Rep 1

source_name: DGRP Line 320 Female


title: DGRP Line 32 Female Rep 2

source_name: DGRP Line 32 Female


title: DGRP Line 32 Male Rep 1

source_name: DGRP Line 32 Male


title: DGRP Line 32 Male Rep 2


title: DGRP Line 319 Male Rep 1


title: DGRP Line 320 Male Rep 2


title: DGRP Line 320 Female Rep 2


title: DGRP Line 32 Female Rep 1


title: DGRP Line 319 Female Rep 2

source_name: DGRP Line 319 Female


title: DGRP Line 319 Female Rep 1


title: DGRP Line 318 Male Rep 2

source_name: DGRP Line 318 Male


title: DGRP Line 324 Female Rep 2


title: DGRP Line 325 Female Rep 1


title: DGRP Line 318 Male Rep 1


title: DGRP Line 318 Female Rep 2

source_name: DGRP Line 318 Female


title: DGRP Line 317 Female Rep 2

source_name: DGRP Line 317 Female


title: DGRP Line 318 Female Rep 1


title: DGRP Line 317 Male Rep 2

source_name: DGRP Line 317 Male


title: DGRP Line 335 Male Rep 1

source_name: DGRP Line 335 Male


title: DGRP Line 317 Male Rep 1


title: DGRP Line 315 Male Rep 2

source_name: DGRP Line 315 Male


title: DGRP Line 315 Female Rep 2

source_name: DGRP Line 315 Female


title: DGRP Line 313 Female Rep 2

source_name: DGRP Line 313 Female


title: DGRP Line 315 Male Rep 1


title: DGRP Line 313 Male Rep 1

source_name: DGRP Line 313 Male


title: DGRP Line 31 Male Rep 1

source_name: DGRP Line 31 Male


title: DGRP Line 31 Male Rep 2


title: DGRP Line 31 Female Rep 1

source_name: DGRP Line 31 Female


title: DGRP Line 313 Male Rep 2


title: DGRP Line 315 Female Rep 1


title: DGRP Line 310 Male Rep 2

source_name: DGRP Line 310 Male


title: DGRP Line 313 Female Rep 1


title: DGRP Line 306 Male Rep 2

source_name: DGRP Line 306 Male


title: DGRP Line 310 Male Rep 1


title: DGRP Line 310 Female Rep 2

source_name: DGRP Line 310 Female


title: DGRP Line 31 Female Rep 2


title: DGRP Line 317 Female Rep 1


title: DGRP Line 310 Female Rep 1


title: DGRP Line 309 Female Rep 2

source_name: DGRP Line 309 Female


title: DGRP Line 309 Male Rep 2

source_name: DGRP Line 309 Male


title: DGRP Line 306 Male Rep 1


title: DGRP Line 304 Female Rep 2

source_name: DGRP Line 304 Female


title: DGRP Line 304 Male Rep 1

source_name: DGRP Line 304 Male


title: DGRP Line 306 Female Rep 1

source_name: DGRP Line 306 Female


title: DGRP Line 303 Male Rep 2

source_name: DGRP Line 303 Male


title: DGRP Line 309 Female Rep 1


title: DGRP Line 303 Male Rep 1


title: DGRP Line 304 Male Rep 2


title: DGRP Line 306 Female Rep 2


title: DGRP Line 303 Female Rep 2

source_name: DGRP Line 303 Female


title: DGRP Line 309 Male Rep 1


title: DGRP Line 303 Female Rep 1


title: DGRP Line 304 Female Rep 1


title: DGRP Line 287 Female Rep 2

source_name: DGRP Line 287 Female


title: DGRP Line 287 Male Rep 1

source_name: DGRP Line 287 Male


title: DGRP Line 301 Female Rep 2

source_name: DGRP Line 301 Female


title: DGRP Line 301 Female Rep 1


title: DGRP Line 301 Male Rep 2

source_name: DGRP Line 301 Male


title: DGRP Line 287 Male Rep 2


title: DGRP Line 287 Female Rep 1


title: DGRP Line 280 Male Rep 2

source_name: DGRP Line 280 Male


title: DGRP Line 280 Female Rep 2

source_name: DGRP Line 280 Female


title: DGRP Line 28 Male Rep 1

source_name: DGRP Line 28 Male


title: DGRP Line 28 Female Rep 2

source_name: DGRP Line 28 Female


title: DGRP Line 28 Male Rep 2


title: DGRP Line 28 Female Rep 1


title: DGRP Line 280 Male Rep 1


title: DGRP Line 280 Female Rep 1


title: DGRP Line 301 Male Rep 1


title: DGRP Line 26 Male Rep 1

source_name: DGRP Line 26 Male


title: DGRP Line 256 Male Rep 2

source_name: DGRP Line 256 Male


title: DGRP Line 26 Male Rep 2


title: DGRP Line 26 Female Rep 2

source_name: DGRP Line 26 Female


title: DGRP Line 26 Female Rep 1


title: DGRP Line 256 Female Rep 2

source_name: DGRP Line 256 Female


title: DGRP Line 239 Male Rep 1

source_name: DGRP Line 239 Male


title: DGRP Line 256 Female Rep 1


title: DGRP Line 239 Female Rep 1

source_name: DGRP Line 239 Female


title: DGRP Line 237 Male Rep 1

source_name: DGRP Line 237 Male


title: DGRP Line 237 Male Rep 2


title: DGRP Line 239 Male Rep 2


title: DGRP Line 239 Female Rep 2


title: DGRP Line 237 Female Rep 1

source_name: DGRP Line 237 Female


title: DGRP Line 235 Male Rep 2

source_name: DGRP Line 235 Male


title: DGRP Line 235 Male Rep 1


title: DGRP Line 235 Female Rep 1

source_name: DGRP Line 235 Female


title: DGRP Line 233 Male Rep 1

source_name: DGRP Line 233 Male


title: DGRP Line 256 Male Rep 1


title: DGRP Line 233 Male Rep 2


title: DGRP Line 233 Female Rep 2

source_name: DGRP Line 233 Female


title: DGRP Line 235 Female Rep 2


title: DGRP Line 229 Male Rep 2

source_name: DGRP Line 229 Male


title: DGRP Line 233 Female Rep 1


title: DGRP Line 229 Male Rep 1


title: DGRP Line 228 Male Rep 1

source_name: DGRP Line 228 Male


title: DGRP Line 229 Female Rep 1

source_name: DGRP Line 229 Female


title: DGRP Line 228 Female Rep 2

source_name: DGRP Line 228 Female


title: DGRP Line 229 Female Rep 2


title: DGRP Line 227 Male Rep 1

source_name: DGRP Line 227 Male


title: DGRP Line 227 Male Rep 2


title: DGRP Line 223 Female Rep 2

source_name: DGRP Line 223 Female


title: DGRP Line 228 Male Rep 2


title: DGRP Line 223 Male Rep 1

source_name: DGRP Line 223 Male


title: DGRP Line 227 Female Rep 2

source_name: DGRP Line 227 Female


title: DGRP Line 228 Female Rep 1


title: DGRP Line 223 Male Rep 2


title: DGRP Line 223 Female Rep 1


title: DGRP Line 217 Male Rep 1

source_name: DGRP Line 217 Male


title: DGRP Line 217 Female Rep 1

source_name: DGRP Line 217 Female


title: DGRP Line 227 Female Rep 1


title: DGRP Line 217 Male Rep 2


title: DGRP Line 21 Male Rep 2

source_name: DGRP Line 21 Male


title: DGRP Line 21 Male Rep 1


title: DGRP Line 237 Female Rep 2


title: DGRP Line 21 Female Rep 1

source_name: DGRP Line 21 Female


title: DGRP Line 21 Female Rep 2


title: DGRP Line 208 Female Rep 1

source_name: DGRP Line 208 Female


title: DGRP Line 195 Male Rep 2

source_name: DGRP Line 195 Male


title: DGRP Line 195 Female Rep 2

source_name: DGRP Line 195 Female


title: DGRP Line 208 Female Rep 2


title: DGRP Line 195 Male Rep 1


title: DGRP Line 217 Female Rep 2


title: DGRP Line 181 Male Rep 2

source_name: DGRP Line 181 Male


title: DGRP Line 189 Female Rep 2

source_name: DGRP Line 189 Female


title: DGRP Line 189 Male Rep 2

source_name: DGRP Line 189 Male


title: DGRP Line 189 Male Rep 1


title: DGRP Line 208 Male Rep 2

source_name: DGRP Line 208 Male


title: DGRP Line 177 Male Rep 2

source_name: DGRP Line 177 Male


title: DGRP Line 181 Male Rep 1


title: DGRP Line 177 Female Rep 2

source_name: DGRP Line 177 Female


title: DGRP Line 181 Female Rep 2

source_name: DGRP Line 181 Female


title: DGRP Line 181 Female Rep 1


title: DGRP Line 177 Male Rep 1


title: DGRP Line 195 Female Rep 1


title: DGRP Line 208 Male Rep 1


title: DGRP Line 176 Male Rep 2

source_name: DGRP Line 176 Male


title: DGRP Line 177 Female Rep 1


title: DGRP Line 176 Male Rep 1


title: DGRP Line 176 Female Rep 1

source_name: DGRP Line 176 Female


title: DGRP Line 161 Male Rep 2

source_name: DGRP Line 161 Male


title: DGRP Line 161 Female Rep 1

source_name: DGRP Line 161 Female


title: DGRP Line 161 Female Rep 2


title: DGRP Line 161 Male Rep 1


title: DGRP Line 158 Male Rep 2

source_name: DGRP Line 158 Male


title: DGRP Line 153 Male Rep 2

source_name: DGRP Line 153 Male


title: DGRP Line 158 Female Rep 1

source_name: DGRP Line 158 Female


title: DGRP Line 153 Male Rep 1


title: DGRP Line 189 Female Rep 1


title: DGRP Line 153 Female Rep 2

source_name: DGRP Line 153 Female


title: DGRP Line 153 Female Rep 1


title: DGRP Line 149 Male Rep 2

source_name: DGRP Line 149 Male


title: DGRP Line 176 Female Rep 2


title: DGRP Line 149 Male Rep 1


title: DGRP Line 149 Female Rep 2

source_name: DGRP Line 149 Female


title: DGRP Line 142 Male Rep 2

source_name: DGRP Line 142 Male


title: DGRP Line 149 Female Rep 1


title: DGRP Line 142 Female Rep 2

source_name: DGRP Line 142 Female


title: DGRP Line 142 Male Rep 1


title: DGRP Line 158 Female Rep 2


title: DGRP Line 138 Female Rep 2

source_name: DGRP Line 138 Female


title: DGRP Line 138 Male Rep 1

source_name: DGRP Line 138 Male


title: DGRP Line 142 Female Rep 1


title: DGRP Line 138 Female Rep 1


title: DGRP Line 136 Male Rep 1

source_name: DGRP Line 136 Male


title: DGRP Line 158 Male Rep 1


title: DGRP Line 136 Female Rep 2

source_name: DGRP Line 136 Female


title: DGRP Line 136 Female Rep 1


title: DGRP Line 129 Female Rep 2

source_name: DGRP Line 129 Female


title: DGRP Line 129 Male Rep 1

source_name: DGRP Line 129 Male


title: DGRP Line 109 Male Rep 1

source_name: DGRP Line 109 Male


title: DGRP Line 129 Male Rep 2


title: DGRP Line 129 Female Rep 1


title: DGRP Line 105 Male Rep 2

source_name: DGRP Line 105 Male


title: DGRP Line 109 Female Rep 1

source_name: DGRP Line 109 Female


title: DGRP Line 109 Female Rep 2


title: DGRP Line 138 Male Rep 2


title: DGRP Line 105 Female Rep 1

source_name: DGRP Line 105 Female


title: DGRP Line 101 Male Rep 1

source_name: DGRP Line 101 Male


title: DGRP Line 105 Male Rep 1


title: DGRP Line 101 Female Rep 2

source_name: DGRP Line 101 Female


title: DGRP Line 101 Male Rep 2


title: DGRP Line 136 Male Rep 2


title: DGRP Line 105 Female Rep 2


title: DGRP Line 100 Male Rep 2

source_name: DGRP Line 100 Male


title: DGRP Line 100 Male Rep 1


title: DGRP Line 109 Male Rep 2


title: DGRP Line 100 Female Rep 1

source_name: DGRP Line 100 Female


title: dsgaf_1

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: nascent RNA

data_processing:
Raw reads were trimmed with cutadapt v 1.10 to remove any adapters and poly-A tails while performing light quality trimming using parameters "--quality-cutoff=20 --minimum-length=25 --overlap=10 -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -a AGATCGGAAGAGC".
Trimmed reads were mapped to the primary chromosomes (2L, 2R, 3L, 3R, 4, X, Y, and mitochondrion_genome) of the FlyBase release 6.11 dm6 assembly with HISAT2 2.0.4 using default parameters.
Reads were counted in annotated genes in FlyBase release 6.11 using featureCounts v1.5.0-p3. Since neuRNA-seq enriches for nascent RNA and the libraries are stranded, we counted reads in full gene bodies using featureCounts parameters "-s 1 -t gene -g gene_id -f".
Counts tables were aggregated across samples into experiment-specific counts matrices.
Genome_build: dm6
Supplementary_files_format_and_content: Counts tables in TSV format, aggregated from featureCounts output, with headers corresponding to the fastq file names. Each counts file containst the set of samples from a single experiment that should be considered together.

source_name: Kc167 cell line

extract_protocol:
neuRNA labeling and capture were performed with Click-iT Nascent RNA Capture Kit (Thermo Fisher Scientific) according to manufacturer’s protocol with the following minor modifications. Cells were incubated with EU at  0.2 mM for 1 h and RNA was extracted with TRizol (Thermo Fisher Scientific). The Click-iT reaction was performed with 0.25 mM biotin azide, and biotinylated RNA was captured with 12 μL T1 beads.
Nascent RNA was used to generate RNA-seq libraries with Ovation RNA-seq Systems 1-16 for Model Organisms (Nugen). All samples were sequenced with HiSeq2500 (Illumina) at the NIDDK Genomics Core Facility by 50 bp single-end sequencing.
neuRNA-seq

tag: treatment

value: dsgaf 1

tag: developmental stage

value: dorsal closure stage

tag: cell type

value: Female Embryonic cell line


title: si5utr_ago2_pwahf_v897e_3

description: nascent RNA

value: si5utr ago2 pwahf v897e 3


title: dscp190_2

description: nascent RNA


title: dssuhw_2

description: nascent RNA

value: dssuhw


title: dssuhw_3

description: nascent RNA


title: dsctcf_2

description: nascent RNA

value: dsctcf


title: si5utr_ago2_pwahf_v897e_1

description: nascent RNA

value: si5utr ago2 pwahf v897e 1


title: dssuhw_1

description: nascent RNA


title: dscp190_1

description: nascent RNA


title: dsctcf_3

description: nascent RNA


title: dscp190_3

description: nascent RNA


title: mock_5

description: nascent RNA

value: mock


title: mock_6

description: nascent RNA


title: DGRP Line 100 Female Rep 2


title: DGRP Line 101 Female Rep 1


title: dsgaf_3

description:
nascent RNA
dsdicer2.counts
dsgaf.counts
dsmi2.counts

value: dsgaf


title: dsmi2_2


title: dsmi2_1


title: dslaminb_h4ac_2

description:
True_seq (Ilumina)
BED File: dslaminb_h4ac.bed

library_source: genomic

data_processing:
Trimming reads for adapters and light quality trimming was performed with cutadapt v1.10 using the parameters "--quality-cutoff 20 -a AGATCGGAAGAGC --minimum-length=25 --overlap=10". Two protocols were used for ChIP-seq library prep. For the libraries using the DNA SMART ChIP-seq kit (Clontech), the additional parameter "-u 3" was used to hard-clip the first three bases, which are added by the kit
Reads were aligned to dm6 using bowtie2 v2.2.8 with default parameters.
Multimapping reads were removed using the "view" program of samtools v1.3.1 with parameter "-q 20"
The Picard tools v2.5.0 program MarkDuplicates was used to remove PCR duplicates from mapped reads.
Peak calling methods depended on whether the binding of the protein is punctate (AGO2) or broad (all others, including histone modifications and all Pol II forms). In both cases we first used the MACS2 v2.1.1.20160309 callpeak program (Zhang et al. 2008 and https://github.com/taoliu/MACS) to call peaks on each replicate independently. For both punctate and broad marks we used the non-default parameters "--gsize dm --bdg --SPMR". Only for broad peaks we included the parameter "--broad". We then ran the same peak-calling steps but on the pooled set of replicates for each target protein, by providing all input and IP replicates to MACS2.
We selected final peaks for broad marks as those peaks in the pooled peak-calling run that were also found in at least one of the individual replicates. Specifically, using BEDTools v2.25.0 and pybedtools v0.7.9 we used "pooled.intersect([replicates], u=True).sort().merge()" where "pooled" points to the pooled peak calls and "[replicates]" is the list of individual peak calls for each replicate.
For the punctate AGO2 peaks, we used the Irreproducible Discovery Rate (IDR) method using IDR v2.0.3 (https://github.com/nboley/idr, and following recommendations from https://sites.google.com/site/anshulkundaje/projects/idr). Initial lenient peaks were called with MACS2 with the lenient parameters "-p 1e-3 --nomodel --to-large" on four versions of the IP data: replicates, pooled pseudoreplicates, self-pseudoreplicates and pooled replicates as recommended by IDR authors. Pooled input was always used as the control for these peak-calling runs. On each pair of replicate, self-pseudoreplicate, and pooled-pseudoreplicate called peaks, we ran IDR with parameters "--use-best-multisummit-IDR --soft-idr-threshold 0.05 --rank p.value --input-file-type narrowPeak --peak-list $POOLED" where "$POOLED" is the peaks called on all replicates pooled together. From the pooled peaks ranked by increasing p-value, we chose the final AGO2 peaks as the top N peaks were N was the number of peaks in the pooled-pseudoreplicate comparison passing an IDR threshold of 0.05, as recommended by the IDR authors.
Genome_build: dm6 (FlyBase r6.11)
Supplementary_files_format_and_content: BED files of called peaks

molecule: genomic DNA

extract_protocol:
Approximately 1-2 X 107 cells were fixed by addition of 1% formaldehyde to cell media for 10 min at RT with gentle agitation. Formaldehyde was quenched by addition of glycine to 0.125 M with gentle agitation for 5 min at RT. Cells were pelleted at 2000xg, washed twice in PBS, and resuspended in 0.8 mL ice–cold cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) supplemented with Complete protease inhibitors (Roche), incubated on ice 10 min pelleted by centrifugation at 2000 xg for 5 min at 4°C. Next, the supernatant was removed and pellets were resuspended in 1 mL nuclear lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA.Na2, 1% SDS) and incubated for 10 min at 4°C. Afterwards, 0.5 mL of IP dilution buffer was added (16.7 mM Tris-HCl pH 8, 1.2 mM EDTA, 167 mM NaCl, 1.1% Triton X-100, 0.01% SDS) and chromatin was fragmented to an average size of 300 bp by using PicoBioruptor (Diagenode) using 10 cycles of 30 s on plus 30 sec off, maximum output. Samples were centrifuged at max speed for 10 min at 4°C, and the supernatant (sheared chromatin) was saved at -80°C. Chromatin was diluted to 1:5 with IP buffer, and the assayed antibody in addition to 50 μL of prewashed protein A/G 50% slurry was added and rotated overnight at 4°C. The next day, beads were washed as follows:
--    3X Low salt IP dilution buffer (20 mM Tris-HCl pH 8, 2 mM EDTA.Na2, 150 mM NaCl, 1% Triton X-100, 0.1% SDS).
--     3X High salt IP dilution buffer (20 mM Tris-HCl pH 8, 2 mM EDTA.Na2, 500 mM NaCl, 1% Triton X-100, 0.1% SDS).
--     2X times  LiCl buffer (10 mM Tris-HCl pH 8, 1 mM EDTA.Na2, 0.25M LiCl, 1% NP-40, 1% DOC).
Chromatin was eluted twice with 200 μL of elution buffer (500 μL of 1M NaHCO3, 250μL of 20% SDS, 4.25 mL dH2O) for 30 min at 65°C each and further incubated overnight at 65°C with 38 μL of decrosslinking solution (20 μL of 5M NaCl, 8 μL of 0.5M EDTA, 10 μL of 1M Tris-HCl pH 8). After de-crosslinking, samples were treated with Proteinase K for 2 h at 50°C and then combined with 1 vol of phenol/chloroform/isoamyl alcohol (25:24:1), vortexed 15 s, and centrifuged for 5 min at 10,000 xg . The top layer was transferred to a new tube, and the procedure was repeated using 1 vol chloroform. The top layer was collected and subsequently precipitated with 0.1 vol of 3M NaOAc pH 5.2 and 2.5 vol of 100% ethanol supplemented with 2 μL of Glycoblue (Ambion). After incubating 30 min at -80°C, samples were centrifuged 20 min at 4°C at 10,000 xg. Pellets were washed with 70% ethanol and centrifuged 5 min at 4°C at 10,000 xg. Pellets were air dried at RT prior to resuspension in 10 μL of dH2O.
Samples for ChIP-seq were prepared according to the manufacturer’s protocol with Clontech or TruSeq adapters (Illumina).

tag: cell line

value: female

value: dslaminb

tag: input sample

tag: antibody

value: H4ac Active Motif 39925


title: si5utr_ago2_pwahf_v897e_2

description: nascent RNA

value: si5utr ago2 pwahf v897e 2


title: dsgaf_2


title: siago2_h4ac_2

description:
True_seq (Ilumina)
BED File: siago2_h4ac.bed


title: dslaminb_h4ac_1


title: mock_h4ac_1

description:
True_seq (Ilumina)
BED File: mock_h4ac.bed


title: dslaminb_h3ac_2

description:
True_seq (Ilumina)
BED File: dslaminb_h3ac.bed

value: H3ac Active Motif61637


title: mock_h4ac_2


title: siago2_h4ac_1


title: dslaminb_h3ac_1


title: dsctcf_1

description: nascent RNA


title: mock_4

description: nascent RNA


title: siago2_h3ac_1

description:
True_seq (Ilumina)
BED File: siago2_h3ac.bed


title: mock_h3ac_2

description:
True_seq (Ilumina)
BED File: mock_h3ac.bed


title: siago2_h3ac_2


title: mock_mi2_2

description:
True_seq (Ilumina)
BED File: mock_mi2.bed

value: Mi-2 (M. Kuroda)


title: siago2_mi2_2

description:
True_seq (Ilumina)
BED File: siago2_mi2.bed


title: mock_h3ac_1


title: dslaminb_input_8

description: True_seq (Ilumina)

value: input


title: dslaminb_mi2_2

description:
True_seq (Ilumina)
BED File: dslaminb_mi2.bed


title: mock_mi2_1


title: siago2_input_8

description: True_seq (Ilumina)


title: dslaminb_mi2_1


title: dslaminb_input_7

description: True_seq (Ilumina)


title: mock_input_9

description: True_seq (Ilumina)


title: mock_input_8

description: True_seq (Ilumina)


title: dslaminb_input_6

description: True_seq (Ilumina)


title: siago2_input_7

description: True_seq (Ilumina)


title: mock_input_10

description: True_seq (Ilumina)


title: siago2_input_6

description: True_seq (Ilumina)


title: siago2_pol2_s5_1

description:
True_seq (Ilumina)
BED File: siago2_pol2_s5.bed

value: RNA Pol II S5 Ab5408


title: dslaminb_pol2_s5_2

description:
True_seq (Ilumina)
BED File: dslaminb_pol2_s5.bed


title: 12-CMVY-1

city: Sendai

first: AINAN

last: TIAN

address: Aramaki

country: Japan

institute: Tohoku University

data_processing:
Illumina Real Time Analysis (version1.13) software used for basecalling.
The raw sequence reads were inputted to the FastQC (version0.10.1) for quality control to ensure the quality value was above Q30. The raw sequence reads were processed with Trimmomatic (version 0.38) to remove reads containing only adaptors.  The trimmed raw sequence reads were performed with STAR (version 2.7) for read mapping and retrieving read counts.
The un-normalized raw read counts were used in DESeq2 Rpackage 3.7 from Bioconductor  for differential expression and statistical analysis according the user manual.
Supplementary_files_format_and_content: COUNT files include raw count data for each sample.
Supplementary_files_format_and_content: CSV files include DESeq2 results.

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Transcriptome analysis of "Necrosis" and HR cell death developed in cucumber mosaic virus-inoculated leaves of Arabidopsis thaliana was performed by RNA-seq, in triplicate, using TruSeq Stranded Total RNA Sample Preparation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: days post inoculation

tag: agent

value: CMV(YYY)

tag: ecotype


title: 12-CMVY-2


title: siago2_pol2_s5_2


title: siago2_mi2_1


title: 12-mock-3


title: 12-mock-2


title: 12-mock-1


title: Col-HYY-3

description: HR cell death (12_mock_CMVY).csv

value: CMV(HYY)


title: Col-HYY-2

description: HR cell death (12_mock_CMVY).csv


title: Col-HYY-1

description: HR cell death (12_mock_CMVY).csv


title: Col-mock-1

description: HR cell death (12_mock_CMVY).csv


title: Col-mock-3

description: HR cell death (12_mock_CMVY).csv


title: Col-mock-2

description: HR cell death (12_mock_CMVY).csv


title: dslaminb_pol2_s5_1


title: dslaminb_pol2_8wg16_1

description:
True_seq (Ilumina)
BED File: dslaminb_pol2_8wg16.bed

value: RNA Pol II 8WG16 Biolegend 920102


title: siago2_pol2_8wg16_2

description:
True_seq (Ilumina)
BED File: siago2_pol2_8wg16.bed


title: siago2_pol2_8wg16_1


title: dslaminb_pol2_8wg16_2


title: 12-CMVY-3


title: dslaminb_pol2_s2_2

description:
True_seq (Ilumina)
BED File: dslaminb_pol2_s2.bed

value: RNA Pol II S2 Ab5095


title: siago2_pol2_s2_2

description:
True_seq (Ilumina)
BED File: siago2_pol2_s2.bed


title: mock_pol2_s5_2

description:
True_seq (Ilumina)
BED File: mock_pol2_s5.bed


title: mock_pol2_s5_1


title: mock_pol2_s2_1

description:
True_seq (Ilumina)
BED File: mock_pol2_s2.bed


title: mock_pol2_s2_2


title: siago2_h3k9me3_2

description:
SMART Kit (Clontech)
BED File: siago2_h3k9me3.bed


title: dslaminb_h3k9me3_1

description:
SMART Kit (Clontech)
BED File: dslaminb_h3k9me3.bed


title: siago2_h3k9me3_1


title: mock_h3k9me3_2

description:
SMART Kit (Clontech)
BED File: mock_h3k9me3.bed


title: mock_h3k9me3_1


title: dslaminb_h4k16ac_1

description:
SMART Kit (Clontech)
BED File: dslaminb_h4k16ac.bed

value: H4K16ac Millipore 07-329


title: dslaminb_h4k16ac_2


title: siago2_h4k16ac_1

description:
SMART Kit (Clontech)
BED File: siago2_h4k16ac.bed


title: dslaminb_pol2_s2_1


title: siago2_h4k16ac_2


title: siago2_pol2_s2_1


title: mock_h4k16ac_2

description:
SMART Kit (Clontech)
BED File: mock_h4k16ac.bed


title: dslaminb_h3k9me3_2


title: mock_h4k16ac_1


title: dslaminb_input_5


title: siago2_input_5


title: dslaminb_input_4


title: siago2_input_4


title: Me3_3-25_R1: H3K4me3-1 ChIP-Seq

city: Rochester

first: Michael

last: Bulger

state: NY

address: 601 Elmwood Ave.

department: Pediatrics

institute: University of Rochester

data_processing:
Illumina to fastq and demultiplexing - bcltofastq 1.8.4
quality control trimmomatic 0.32 SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15
alignment bowtie 1.0.1 -m 1 -S
ChIP-Seq enrichments were determined by MACS2 using the following parameters: --broad -g hs --broad-cutoff 0.1
for ATAC data, black list (JDB_blacklist.mm9.bed) and chrM regions were removed using samtools
ATAC-Seq enrichements were determined by MACS2 using the following parameters: --nomodel --shift -100 --extsize 200 -f BAM
Genome_build: mm9
Supplementary_files_format_and_content: broadPeak/narrowPeak

organism: Mus musculus

source_name: Fetal liver

extract_protocol:
2x107 cells were washed with PBS once, then cross-linked with 1% formaldehyde for 10 minutes at room temperature. Cross-linking was quenched with 5M glycine for 1 minute at room temperature, and cells were washed with PBS once. Cells were incubated in swelling buffer for 20 minutes on ice, followed by dounce homogenization to isolate cross-linked nuclei. Nuclei were placed in lysis buffer for 30 minutes and then sonicated into ~200 bp fragments using a Diagenode Bioruptor. Samples were diluted and immunoprecipitated with an antibody to H3K4Me1 (Abcam #ab8895), H3K4Me3 (Active Motif # 39916), H3K27Ac (Active Motif # 39134), H3K4Me2 (Millipore # 07-030), or nonspecific rabbit immunogloblulin G (Millipore # 12-370) on a rotator for 18h at 4C. DNA-protein complexes were recovered with protein G magnetic beads (Invitrogen).  Samples were cleaned with QIAquick PCR purification kit (QIAGEN) following manufacture’s protocol.
Libraries were prepared as previously described (Su, M.Y., Steiner, L.A., Bogardus, H., Mishra, T., Schulz, V.P., Hardison, R.C., & Gallagher, P.G.) Approximately 500ng of ChIP DNA was run on a 1.5% agarose gel to size select ChIP DNA in the 200-300-bp range. The size-selected ChIP DNA was purified using a gel extraction kit (Qiagen) and processed for sequencing as per manufacturer's protocol. Briefly, size-selected ChIP DNA was end repaired using an End-IT DNA end repair kit (ER0720; Epicenter), followed by addition of an adenine base at the 3′ end by Klenow reaction and Solexa adaptor ligation. The modified DNA was then PCR amplified with one initial heating step of 98°C for 30 s, followed by 15 cycles of amplification with a melting temperature of 98°C for 30 s, an annealing temperature of 65°C for 30 s, and a product extension at 72°C for 30 s. At the end of the amplification, a final extension at 72°C for 5 min was performed. Amplified ChIP DNA was then size selected on a 1.5% agarose gel, purified by using a gel extraction kit (Qiagen), and subjected to deep sequencing.

tag: embryonic day

value: Fetal liver

tag: chip antibody


title: Me2_3-25_R1: H3K4me2-2 ChIP-Seq


title: Me3_3-18_R1: H3K4me3-2 ChIP-Seq


title: Me2_3-18_R1: H3K4me2-1 ChIP-Seq


title: Input_March_R1: Input DNA


title: mock_input_7


title: mock_input_6


title: dslaminb_h3k27me3_2

description:
SMART Kit (Clontech)
BED File: dslaminb_h3k27me3.bed

value: H3K27m3 Millipore 07-449


title: Me1_4-8_R1: H3K4me1-2 ChIP-Seq

value: Abcam ab8895


title: ProE-2_R1: ProE-2 ATAC-Seq

source_name: Proerythroblasts

value: Proerythroblasts


title: Me1_4-1_R1: H3K4me1-3 ChIP-Seq


title: siago2_h3k27me3_3

description:
SMART Kit (Clontech)
BED File: siago2_h3k27me3.bed

value: female


title: dslaminb_h3k27me3_1

value: dslaminb


title: mock_h3k27me3_3

description:
SMART Kit (Clontech)
BED File: mock_h3k27me3.bed

value: mock


title: siago2_h3k27me3_2


title: 27Ac_3-18_R1: H3K27ac-1 ChIP-Seq


title: mock_h3k27me3_2


title: dslaminb_h3k36m3_2

description:
SMART Kit (Clontech)
BED File: dslaminb_h3k36m3.bed


title: 27Ac_3-23_R1: H3K27ac-2 ChIP-Seq


title: siago2_h3k36m3_2

description:
SMART Kit (Clontech)
BED File: siago2_h3k36m3.bed


title: dslaminb_h3k36m3_1


title: siago2_h3k36m3_1


title: ProE-1_R1: ProE-1 ATAC-Seq


title: mock_h3k36m3_1

description:
SMART Kit (Clontech)
BED File: mock_h3k36m3.bed


title: dslaminb_h3_3

description:
SMART Kit (Clontech)
BED File: dslaminb_h3.bed


title: mock_h3k36m3_2


title: Me1_4-20_R1: H3K4me1-1 ChIP-Seq


title: siago2_h3_3

description:
SMART Kit (Clontech)
BED File: siago2_h3.bed


title: dslaminb_h3_2


title: siago2_h3_2


title: mock_h3_3

description:
SMART Kit (Clontech)
BED File: mock_h3.bed


title: mock_h3_2


title: dslaminb_h3k27ac_3

description:
SMART Kit (Clontech)
BED File: dslaminb_h3k27ac.bed


title: OB_siRNA-NFIB_ChIP_2

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC. Reads were mapped to the mouse genome (mm10) using bowtie2 (2.2.6).
Alignment files were used to build tag directories using makeTagDirectory from HOMER (v4.10).
Peaks were called using findPeaks from HOMER with the -style factor setting and annotated using annotatePeaks.pl with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage from the deepTools package suit. Scores represent the number of reads per bin with a default bin size of 50bp.

source_name: Olfactory bulb

extract_protocol:
Lysates from 20-week old wild type hippocampus and olfactory bulb were sonicated, and NFIA-DNA complexes were purified with antibody in triplicates. NFIA-DNA complexes were isolated from siRNA-NFIB and siRNA-scramble olfactory bulb in duplicate.
DNA libraries were constructed from 5-10ng of chromatin immunoprecipitated DNA using the TruSeq ChIP library preparation kit (Cat# IP-202-1012) following the manufactures instructions. Libraries were validated on a fragment analyzer to verify successful gel extraction.

value: Olfactory bulb

value: NFIA

tag: transfection

value: siRNA-NFIB


title: OB_siRNA-scramble_Input_2

tag: strain

value: siRNA-scramble


title: OB_siRNA-scramble_ChIP_2


title: OB_siRNA-scramble_ChIP_1


title: OB_siRNA-scramble_Input_1


title: OB_siRNA-NFIB_Input_2


title: dslaminb_h3k27ac_2

tag: Sex


title: OB_siRNA-NFIB_ChIP_1

tag: age


title: MDSCs_DMSO_control_6h_rep2

type: RNA

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 100 Mason Center, Building GALVIN Department of Biological Sciences

department: Biological Sciences

institute: University of Notre Dame

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: MDSCs, DMSO control ex vivo, 6h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Gr-MDSCs were cultured in RPMI-1640 supplemented with 10% FBS and antibiotics

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

treatment_protocol: Gr-MDSCs were immediately treated with 0.1uM Dactolisib or 0.1uM Dasatinib or DMSO after isolation and incubate for 6h

value: myeloid derived suppressor cells (MDSC)

tag: genotype

value: PB-Cre+ PtenL/L p53L/L Smad4L/L mTmGL/+ LSL-LucL/+ (CPPSML)

value: 12-16 weeks

value: DMSO


title: MDSCs_DMSO_control_6h_rep5

tag: tissue


title: siago2_h3k27ac_3

description:
SMART Kit (Clontech)
BED File: siago2_h3k27ac.bed

tag: treatment


title: MDSCs_Dasatinib_treated_6h_rep2

source_name: MDSCs, Dasatinib treated ex vivo, 6h

value: Dactolisib


title: MDSCs_Dactolisib_treated_6h_rep1

source_name: MDSCs, Dactolisib treated ex vivo, 6h


title: MDSCs_DMSO_control_6h_rep3


title: MDSCs_DMSO_control_6h_rep4


title: OB_siRNA-NFIB_Input_1


title: MDSCs_Dactolisib_treated_6h_rep2


title: OB_ChIP_3

value: WT


title: mock_h3k27ac_3

description:
SMART Kit (Clontech)
BED File: mock_h3k27ac.bed


title: mock_h3k27ac_2


title: siago2_h3k27ac_2


title: OB_Input_3


title: dslaminb_h3k4me1_3

description:
SMART Kit (Clontech)
BED File: dslaminb_h3k4me1.bed


title: OB_ChIP_2


title: dslaminb_h3k4me1_2


title: OB_Input_2


title: OB_ChIP_1


title: siago2_h3k4me1_3

description:
SMART Kit (Clontech)
BED File: siago2_h3k4me1.bed


title: HP_Input_3

source_name: Hippocampus

value: Hippocampus


title: siago2_h3k4me1_2


title: HeLa-U1A iCLIP-seq-GGTT

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

country: China

institute: sysu

description: total protein-RNAs were recovered by U1A antibodies

data_processing:
Sequenced reads were trimmed for adaptor sequence, and remove low-complexity or low-quality sequence.Surviving reads were mapped to the hg19  using hisat2 with default settings.
Extract the 5' mapping position of read and align it to upstream or downstream of polyA sites.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage; Scores represent number of reads per bin.

organism: Homo sapiens

source_name: HeLa cell line

growth_protocol: Hela cells were grown using standard DEME medium plus 10% FBS under 5% CO2 condition

extract_protocol:
RNAs were recovered by U1A antibodies
Recovered RNAs were ligated onto an 3' adaptor, RT reactions were carried out for converting RNAs to cDNA, cDNAs were further circularized, digested, and PCR amplified. PCR product were sent for sequencing.Single-end sequencing (SE50) was performed on an Illumina platform

treatment_protocol: Hela cells were harvest when they were grown in the periods of logarithmic phase without treatment

value: HeLa


title: HeLa-U1A iCLIP-seq-TTGT


title: HP_ChIP_3


title: mock_h3k4me1_3

description:
SMART Kit (Clontech)
BED File: mock_h3k4me1.bed


title: dslaminb_input_3

value: input


title: mock_h3k4me1_2


title: HP_ChIP_2


title: HP_ChIP_1


title: siago2_input_2


title: siago2_input_3


title: dslaminb_input_2


title: HP_Input_1


title: MDSCs_Dasatinib_treated_6h_rep1


title: mock_input_5


title: OB_Input_1


title: dslaminb_h3k4me3_3

description:
SMART Kit (Clontech)
BED File: dslaminb_h3k4me3.bed


title: mock_h3k4me3_2

description:
SMART Kit (Clontech)
BED File: mock_h3k4me3.bed


title: dslaminb_h3k4me3_2


title: mock_h3k4me3_3


title: siago2_h3k4me3_2

description:
SMART Kit (Clontech)
BED File: siago2_h3k4me3.bed


title: mock_input_1


title: siago2_input_1


title: siago2_h3k27ac_1


title: dslaminb_input_1


title: mock_h3k27ac_1


title: mock_h3k4me1_1


title: siago2_h3k4me1_1


title: RARRXR1_SLOTv4_mEND_rep1A_DpnII

city: Cambrdige

first: Jennifer

last: Hammelman

state: MA

address: 32 Vassar Street

institute: MIT

description: To induce differentiation, cells were grown for 48 hours in mESC media without GSK3 inhibitor XV and UO126 and then seeded at 10^4 cells/cm2 in mESC media without GSK3 inhibitor XV and UO126. After 24 hours, media was replaced with serum-free differentiation media: Advanced DMEM supplemented with N-2, B27 Supplement without vitamin A, and Glutamax (Thermo Fisher). After 24 hours, media was replaced with differentiation media: Advanced DMEM with 2% ES-tested FBS and Glutamax. To induce endoderm differentiation, cells were treated for 24 hours in differentiation media with 50 ng/mL E. coli-derived Activin A (Peprotech) for 24 hours to produce mesendoderm, then cells were fed with Advanced DMEM with 2% FBS, Glutamax, 50 ng/mL Activin A and 1 µM Dorsomorphin (Sigma) for 48 hours.

data_processing:
Reads were mapped to library phrases by taking the reverse complement to the raw read, where the first N nucleotides (between 70 and 100 based on the size of the designed phrase) are the designed variable phrase. Perfect matches were counted using a custom R script.
Supplementary_files_format_and_content: Raw read counts provided in file phrase_libraries_raw_counts.xlsx

source_name: mEND

growth_protocol: mESCs were maintained on gelatin-coated plates feeder-free in mESC media composed of Knockout DMEM (Life Technologies) supplemented with 15% defined fetal bovine serum (FBS) (HyClone), 0.1mM nonessential amino acids (NEAA) (Life Technologies), Glutamax (GM) (Life Technologies), 0.55mM 2 -mercaptoethanol (Sigma), 1X ESGRO LIF (Millipore), 5 nM GSK-3 inhibitor XV and 500 nM UO126.

extract_protocol:
DPNI: 10ug genomic DNA DPNII: 20ug genomic DNA
Library prep was performed by 3 successive PCRs. In the first PCR, the entire DpnI-digested genomic DNA was used in a 400 uL PCR rxn, and the entire DpnII-digested genomic DNA was used in a 800 uL PCR rxn. 13 cycles of PCR1 (Q5 UltraII mastermix, Ta=66, 60 second 72 deg extension per cycle) was performed. PCR 1 was purified using PCR purification in a single column, eluting in 50 uL. PCR2 was performed for 7 cycles (Q5 UltraII mastermix, Ta=66, 60 second 72 deg extension per cycle) using 22.5 uL of PCR1 product in a 100 uL reaction. PCR 2 was purified in a single column, eluting in 50 uL.  qPCR (Q5 UltraII mastermix with EvaGreen (Biotium), Ta=66, 60 second 72 deg extension per cycle) was used to determine PCR3 cycle counts. PCR3 was performed by subtracting 2-3 cycles from the Ct and using 2.5 uL of a mix of distinct indexed primers from the NEBNext Dual Index Kit for Illumina (New England Biolabs) using 22.5 uL PCR2 product in a 50 uL reaction volume (Q5 UltraII mastermix with EvaGreen (Biotium), Ta=66, 60 second 72 deg extension per cycle). PCR3 products were PCR-purified and Tapestation (Agilent) was used to quantify and pool samples for NGS.

treatment_protocol: Induction of Rarg-DamN126A expression was performed by treatment of mESCs or mESC-derived endoderm with 2 ug/mL Doxycycline (Sigma) for 24 hours prior to genomic DNA collection using the Purelink Genomic DNA miniprep kit (Life Technologies).

value: LoxP site-containing rtTA-expressing 129P2/OlaHsd mouse embryonic stem cells


title: RARRXR1_SLOTv4_mEND_rep1B_DpnII


title: RARRXR1_SLOTv4_mEND_rep2A_DpnI


title: RARRXR_SLOTv3_TRE FoxA2 + 24h Dox rep2 DpnI

description: To generate sublines with inducible expression of FoxA2 or Brachyury, full-length mouse cDNAs for these genes were cloned into a Tol2 expression plasmid containing a 7X TRE promoter and Blasticidin resistance1. Co-transfection of Tol2 transposase with TRE-Foxa2/Brachyury plasmids was performed followed by selection with 10 ug/mL Blasticidin for one week.


title: RARRXR_SLOTv3_TRE FoxA2 + 24h Dox rep2 DpnII


title: RARRXR_SLOTv3_TRE Brachyury + 24h Dox rep2 DpnII

source_name: mESC+Brachyury


title: RARRXR1_SLOTv4_mESC_repB_DpnII

source_name: mESC


title: RARRXR_SLOTv3_TRE Brachyury + 24h Dox rep2 DpnI


title: RARRXR1_SLOTv4_mEND_rep2B_DpnI


title: RARRXR1_SLOTv4_mEND_rep2A_DpnII


title: RARRXR1_SLOTv4_mESC_rep1A_DpnI


title: RARRXR1_SLOTv4_mEND_rep1A_DpnI


title: RARRXR1_SLOTv4_mEND_rep1B_DpnI


title: RARRXR1_SLOTv4_mESC_repB_DpnI


title: RARRXR1_SLOTv4_mESC_rep1A_DpnII


title: RARRXR1_SLOTv4_mEND_rep2B_DpnII


title: dslaminb_h3k27ac_1

value: female


title: RARRXR_SLOTv3_TRE FoxA2 + 24h Dox rep1 DpnII


title: siago2_h3k4me3_3


title: dslaminb_h3k4me3_1

value: dslaminb


title: RARRXR_SLOTv3_TRE FoxA2 + 24h Dox rep1 DpnI


title: RARRXR_SLOTv3_TRE Brachyury + 24h Dox rep1 DpnII


title: siago2_h3k4me3_1


title: RARRXR_SLOTv3_TRE Brachyury + 24h Dox rep1 DpnI


title: mock_h3k4me3_1

value: mock


title: RARRXR_SLOTv3_mEND_2.2_DpnII


title: RARRXR_SLOTv3_mEND_2.2_DpnI


title: RARRXR_SLOTv3_mEND_2.1_DpnI


title: RARRXR_SLOTv3_mEND_2.1_DpnII


title: GM12878 Hi-C

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

data_processing:
In situ Hi-C data: Hi-C reads were mapped to reference genome (hg38) by BWA-MEM (version 0.7.7) in single end mode after ligation junction removal using Cutadapt (version 1.8.1). Uniquely mapped reads were paired up and filtered (e.g. duplicates, self-ligations, continuous genomic fragments or re-ligation events, regions with abnormally high concentrations in reads) using HOMER (version 4.8). Raw contact maps were constructed using HOMER 59 and corrected by total number of contacts for each sample.
Genome_build: hg38
Supplementary_files_format_and_content:  [In situ Hi-C data]  chromosome of read 1, position of read 1,strand of read 1, number of contacts, length of the read 1, chromosome of read 2, position of read 2,strand of read 2, length of the read 2.  For "position of read", 0 is pos strand and 1 = neg strand.

source_name: lymphoblastoid cell

extract_protocol:
Lymphocytes were isolated from whole blood samples by centrifugation after dilution with PBS and underlaying Sigma Histopaque-1077 to the bottom. Genomic DNA and total RNA were extracted simultaneously from lymphocytes using QIAGEN's AllPrep DNA/RNA Mini Kit.
Five million cells were crosslinked with formaldehyde and lysed with protease inhibitors (Sigma, P8340). Chromatins were subsequently digested by MboI restriction enzyme (NEB, R0147). Restriction fragment overhangs were filled and the DNA ends were marked with biotin. Next, biotinylated DNA were sheared to a size of 300-500 bp, whose ends were repaired subsequently. dATP were attached and Illumina indexed adapter (TrueSeq nano) were ligated. The DNA fragments were then amplified and purified.

tag: chromosomes

value: XX

value: lymphoblastoid cell


title: ID00016 Hi-C

value: XY

tag: cell type


title: RARRXR_SLOTv3_mEND_1.2_DpnII

tag: cell line


title: Tho_a_CD3_HDAC1_KO_b3

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

description: processed data file: LG_HDAC1cKO_TH0_Daten.xls

data_processing:
The quality of the sequenced reads was checked using FastQC tool.
STAR 2.5.2b was used to align the reads to the mouse reference genome mm10 (UCSC; downloaded from Illumina iGenomes website). The number of uniquely mapped reads associated with each gene according to Ensembl gene annotation was counted using subread v1.5.1 package.
The downstream data analysis was performed using R version 3.4 and its corresponding Bioconductor module. The count data were normalized for library size using the Trimmed Mean of M-values (TMM) method implemented in edgeR R package. Genes that did not have at least one count per million (CPM) in at least three samples among the compared sample groups were filtered out as lowly expressed.
Prior to statistical testing, an offset of 1 was added to the normalized expression values and the data were log2 transformed. R package ROTS was used for performing the statistical testing and p-value < 0.05 and absolute fold change > 1.5 were required for detecting the differentially expressed genes. The Gh gene was removed from the final DE gene list as the inspection of the aligned reads revealed that the alignments for Gh had almost identical positions on a narrow region and contained many mismatches
Genome_build: mm10

source_name: HDAC1f/f x CD4cre

extract_protocol:
Total RNA was prepared from approximately 1 - 2 x 106 viable FACS-purified activated CD4+ T cells from WT and HDAC1f/f x CD4cre mice with the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina).

tag: strain backgound

tag: genotype/variation

value: HDAC1f/f CD4-cre+

value: Spleen

value: activated CD4+ T cells


title: GM17879 Hi-C

value: XXY


title: mock_h3_1

tag: input sample

tag: antibody


title: siago2_h3_1


title: dslaminb_h3_1


title: Tho_a_CD3_HDAC1_KO_b1


title: GM23916 Hi-C

value: XO


title: Tho_a_CD3_HDAC1_KO_b2


title: siago2_h3k27me3_1

description:
SMART Kit (Clontech)
BED File: siago2_h3k27me3.bed

value: H3K27m3 Millipore 07-449


title: RARRXR_SLOTv3_mESC_4.2_DpnII


title: Th0_a_CD3_HDAC1_WT_b2

source_name: WT

value: wild type


title: Th0_a_CD3_HDAC1_WT_b3


title: RARRXR_SLOTv3_mEND_1.2_DpnI


title: RARRXR_SLOTv3_mEND_1.1_DpnII


title: Th0_a_CD3_HDAC1_WT_b1


title: chicken_HL_HH29_rep4

city: SLC

first: Elena

last: Boer

state: UT

department: School of Biological Sciences

institute: University of Utah

data_processing:
Sequencing read quality was assessed with FastQC.
Illumina adapters were trimmed with STAR.
Reads were aligned to the pigeon Cliv_2.1 reference assembly or chicken Gallus_gallus-5.0 genome assembly with STAR using the 2-pass mode.
Mapped reads were assigned to genes using FeatureCounts.
Principal component and differential expression analyses were performed with the R package DESeq2.
Genome_build: Cliv_2.1
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: Tab-delimited text (.txt) files include read count files (FeatureCounts output) for each sample.
Supplementary_files_format_and_content: Comma-separated value (.csv) files include differential expression results (DESeq2 output) for each phenotypic comparison at each developmental stage.

organism: Gallus gallus

source_name: limb bud

extract_protocol:
Pairs of forelimb (FL) and hindlimb (HL) buds were dissected from scaled, grouse and muff pigeon embryos or chicken embryos at HH21 (embryonic day E3.5), HH25 (E4.5), and HH29 (E6) and stored in RNAlater (ThermoFisher Scientific) at -80°C. Total RNA was extracted from FL and HL bud samples using the RNeasy Mini Kit with RNase-Free DNAse Set and a TissueLyser LT (Qiagen).
RNA-sequencing libraries were prepared and sequenced by the High-Throughput Genomics and Bioinformatic Analysis Shared Resource at the University of Utah. RNA sample quality was assessed using the RNA ScreenTape Assay (Agilent) and a sequencing library was prepared using the TruSeq Stranded mRNA Sample Prep Kit with oligo(dT) selection (Illumina). 125-cycle paired-end sequencing was performed on an Illumina HiSeq 2500 instrument (12 libraries/lane).

tag: developmental stage

tag: limb type

value: HL

tag: phenotype

value: scale


title: RARRXR_SLOTv3_mESC_4.2_DpnI


title: RARRXR_SLOTv3_mESC_4.1_DpnII


title: chicken_FL_HH29_rep4

value: FL


title: 514a1_cleaved_product

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The 3'-adapter in raw reads was trimmed using cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG), after which fastq_quality_filter (-q 20 -p 90) was used to filter low-quality reads. We then used fastx_collapser (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13) to remove the duplicated reads. We cut out the random barcode sequences for different samples as follows. We removed the 6-nt random barcode sequences at 3'-end of the pri-mir-106a original substrates, the 6-nt random barcode sequences at 5'-end and the 4-nt random barcode sequences at 3'-end of the pri-mir-342 and pri-mir-514a-1 original substrates, the 4-nt random barcode sequences at either end of the cleaved products for three pri-miRNAs. The processed reads were then mapped to the reference sequences using BWA. The reference sequences contain 53920, 39472, and 57856 variants generated from pri-mir-342, pri-mir-514a-1, and pri-mir-106a backbones, respectively. The perfectly mapped reads were selected for further analysis. The read cutoff of 30 and 15 were used for the original substrate and cleaved product samples, respectively. In each sample, the raw read counts were normalized as the counts per million.
Supplementary_files_format_and_content: primiRNA_variant_sequence.txt.gz: pri-miRNA variant sequences of three backbones
Supplementary_files_format_and_content: 106a_raw_count.txt.gz: raw read counts of the original substrates and cleaved products samples for pri-mir-106a variants
Supplementary_files_format_and_content: 342_raw_count.txt.gz: raw read counts of the original substrates and cleaved products samples for pri-mir-342 variants
Supplementary_files_format_and_content: 514a1_raw_count.txt.gz: raw read counts of the original substrates and cleaved products samples for pri-mir-514a1 variants

organism: synthetic construct

source_name: synthetic

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
To synthesize each group of pri-mir-106a, pri-mir-342 or pri-mir-514a-1, two oligos each containing 3-nt randomized sequence were annealed using the complementary region of 20 base pairs and then annealed DNA was extended using Klenow (Thermo Scientific, EP0421). Subsequently, the Klenow-extended DNA duplexes were amplified by two PCR primers in which the forward primers contain the T7 promoter sequence. 200 ng of each dsDNA group was used in a 20 µl in vitro transcription reaction using the MEGAscript T7 transcription kit (Invitrogen, AM13345).  In the high-throughput pri-mir-106a processing assays, 5 pmol of each pri-mir-106a group was incubated with 10 pmol of the D3-G2 complex in 10 µl standard reaction buffer at 37°C for 120 min. The original substrate from the control samples and the cleaved product were the gel-purified. The control sample was reverse transcribed using the R-RA3-6N-106a primer and Superscript IV reverse transcriptase. The synthesized cDNAs were first amplified using F-RA5-106a and RPI4 (index:TGGTCA) primers. Then the first PCR product was further amplified using RP1 and RPI4 primers to get the final PCR product for NGS. The cleaved samples (i.e., F2 fragment) were first ligated to the 3'-adapter (4N-RA3) using T4 RNA ligase 2, truncated KQ(NEB, M0373L).The RA3-ligated cleaved samples were separated from the unligated RNAs and 4N-RA3 by 10% Urea-PAGE and then gel-purified. The RA3-ligated RNAs were further ligated to the 5'-adapter (RA5-4N) using T4 RNA ligase I (NEB, M0204L). These two-adapter ligated RNAs were then reverse transcribed using the R-RA3 primer and Superscript IV reverse transcriptase and the synthesized cDNAs were amplified using RP1 and RPIx primers. The high-throughput pri-miRNA processing assays were carried out similarly for pri-mir-514a-1 and pri-mir-342 variants using the D3TN1-G2 complex. The pooled control and cleaved RNAs were first ligated to the 3'-adapter (4N-RA3) using T4 RNA ligase 2, truncated KQ. After that, the 4N-RA3-ligated control RNAs were further processed similarly as what described for arti1. The 4N-RA3-ligated cleaved RNAs were subsequently cloned similarly as what described for the pri-mir-106a library. The final PCR products were subjected to Illumina Nextseq 500 sequencer using NSQ 500/550 High Output KT v2.5 (150 CYS) (Illumina, 20024907) in single-end running mode.

tag: backbone

tag: enzyme complex

tag: barcode

value: ACTTGA


title: 514a1_original_substrate

value: TGACCA


title: chicken_FL_HH29_rep3


title: chicken_HL_HH29_rep3


title: 342_cleaved_product

value: CTTGTA


title: chicken_HL_HH25_rep4


title: RARRXR_SLOTv3_mESC_4.1_DpnI

value: LoxP site-containing rtTA-expressing 129P2/OlaHsd mouse embryonic stem cells


title: RARRXR_SLOTv3_mESC_3.2_DpnII


title: chicken_HL_HH25_rep3


title: 342_original_substrate

value: GCCAAT


title: 106a_cleaved_product


title: chicken_FL_HH25_rep3


title: chicken_FL_HH21_rep4


title: chicken_HL_HH21_rep3


title: mock_h3k27me3_1

description:
SMART Kit (Clontech)
BED File: mock_h3k27me3.bed

source_name: Kc167 cell line

tag: Sex

value: female

value: mock


title: chicken_HL_HH29_rep2


title: 106a_original_substrate


title: chicken_HL_HH21_rep4


title: chicken_FL_HH21_rep3


title: RARRXR_SLOTv3_mESC_3.1_DpnI


title: chicken_FL_HH29_rep2


title: RARRXR_SLOTv3_mESC_3.1_DpnII


title: RARRXR_SLOTv3_mESC_3.2_DpnI


title: HDAC1f/f HDAC2f/+ x CD4cre 4

description:
Sample 8 (TP101_188_plus)
processed data file: TP_Hdac1Hdac2_2fold.xlsx

data_processing:
The quality of the sequenced reads was checked using FastQC tool.
STAR 2.5.2b was used to align the reads to the mouse reference genome mm10 (UCSC; downloaded from Illumina iGenomes website). The number of uniquely mapped reads associated with each gene according to Ensembl gene annotation was counted using subread v1.5.1 package.
The downstream data analysis was performed using R version 3.4 and its corresponding Bioconductor module. The count data were normalized for library size using the Trimmed Mean of M-values (TMM) method implemented in edgeR R package. Genes that did not have at least one count per million (CPM) in at least three samples among the compared sample groups were filtered out as lowly expressed.
Prior to statistical testing, an offset of 1 was added to the normalized expression values and the data were log2 transformed. R package ROTS was used for performing the statistical testing and p-value < 0.05 and absolute fold change > 1.5 were required for detecting the differentially expressed genes. The Gh gene was removed from the final DE gene list as the inspection of the aligned reads revealed that the alignments for Gh had almost identical positions on a narrow region and contained many mismatches.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_genes_fpkm.tsv: Tab-separated text files include FPKM values.
Supplementary_files_format_and_content: TP_Hdac1Hdac2_2fold.xls

source_name: Spleen

extract_protocol:
Total RNA was prepared from approximately 1-2 x 10e6 viable FACS-purified activated CD4+ T cells from WT and HDAC1f/f HDAC2f/+ x CD4cre mice with the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina).

tag: strain/background

value: HDAC1f/f HDAC2f/+ CD4-cre+

value: Activated CD4+ T cells


title: RARRXR_SLOTv3_mESC_2.2_DpnII


title: chicken_FL_HH25_rep4


title: E.coli 3h

city: Fukuoka

first: Tun

last: Xin

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku,

department: Medical Institute of Bioregulation

institute: Kyushu University

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

source_name: PEC,Vγ6+ γδT cells, 3hr,

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

value: C57BL/6 mice

tag: tissue

value: PEC

tag: gender

value: male

tag: age


title: WT

source_name: PEC,Vγ6+ γδT cells, 0hr,


title: HDAC1f/f HDAC2f/+ x CD4cre 3

description:
Sample 7 (TP101_186_plus)
processed data file: TP_Hdac1Hdac2_2fold.xlsx

tag: cell type


title: HDAC1f/f HDAC2f/+ x CD4cre 2

description:
Sample 6 (TP101_185_plus)
processed data file: TP_Hdac1Hdac2_2fold.xlsx


title: chicken_FL_HH25_rep2


title: chicken_HL_HH25_rep1


title: chicken_HL_HH25_rep2


title: chicken_FL_HH29_rep1


title: RARRXR_SLOTv3_mESC_2.1_DpnII

tag: cell line


title: RARRXR_SLOTv3_mEND_1.1_DpnI


title: RARRXR_SLOTv3_mESC_2.1_DpnI


title: chicken_FL_HH25_rep1


title: dslaminb_h3k4me1_1

tag: treatment

value: dslaminb


title: HDAC1f/f HDAC2f/+ x CD4cre 1

description:
Sample 5 (TP101_182_plus)
processed data file: TP_Hdac1Hdac2_2fold.xlsx

tag: genotype/variation


title: RARRXR_SLOTv3_mESC_1.2_DpnII


title: chicken_HL_HH21_rep2


title: chicken_FL_HH21_rep2


title: WT 4

description:
Sample 4 (TP101_190)
processed data file: TP_Hdac1Hdac2_2fold.xlsx

value: Wild type


title: chicken_HL_HH21_rep1

value: HL


title: WT 3

description:
Sample 3 (TP101_189)
processed data file: TP_Hdac1Hdac2_2fold.xlsx


title: Healthy 1083

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Healthy

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment with TopHat2 v2.0.11 and SAMtools version 1.4 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq hg19 annotation download on May 2015
Normalization using DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 rlog counts for each Sample.

source_name: circulating CD14+ monocytes

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated using a Ficoll-based density gradient. Blood and cells were kept at 4 °C during the procedure to care for minimal cell activation. Whole blood was mixed with an equal amount of phosphate-buffered saline (PBS, PAN Biotech, Aidenbach, Germany), and was subsequently carefully manually layered over 1077 Lymphocyte Separation Medium (PAA, Pasching, Austria), followed by a centrifugation at 1600 rpm for 40 min without the use of a brake at room temperature. The intermediate layer containing the PBMC was then carefully harvested, washed with PBS, and centrifuged at 1300 rpm for 10 min three times. In the last step, the cells were resuspended in PBS and counted using a Neubauer chamber as a preparation for antibody staining and MACS. At least 10000000 cells were resupsended in MACS buffer (PBS, 2mM EDTA, 0.5% BSA), incubated with CD14-Microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and CD14+ cells were isolated according to standard protocols provided by the manufacturer. Cells were stored in PeqGOLD Trifast (peqlab, Erlangen, Germany) at -80°C until further analysis.
According to the manufacturer´s instructions in the Tru-Seq RNA library preparation kit v2, 10 ng of RNA was converted into cDNA libraries
75 bp single-end run was performed on a HiSeq1500

tag: genetic background

value: Healthy volunteer

tag: patientid


title: Healthy 1084

description: Healthy


title: chicken_HL_HH29_rep1

tag: developmental stage

tag: limb type

value: scale


title: WT 2

description:
Sample 2 (TP101_184)
processed data file: TP_Hdac1Hdac2_2fold.xlsx


title: RARRXR_SLOTv3_mESC_1.2_DpnI


title: RARRXR_SLOTv3_mESC_1.1_DpnI


title: Healthy 1081

description: Healthy


title: uCd8_SLOTv3_mEND_repB_DpnII


title: RARRXR_SLOTv3_mESC_1.1_DpnII


title: Healthy 1080

description: Healthy


title: Non-Sepsis 1077

description: Non-Sepsis

value: Non-Sepsit ICU patient


title: Non-Sepsis 1076

description: Non-Sepsis


title: Non-Sepsis 1075

description: Non-Sepsis


title: uCd8_SLOTv3_mEND_repB_DpnI


title: uCd8_SLOTv3_mEND_repA_DpnII


title: EpiSC-IwSB-noAct_REP3

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

data_processing:
Extraction and alignment: Raw reads from published dataset and from newly generated data were extracted and aligned using Salmon program (Patro et al 2017) using reference transcriptome M17 (05/04/2018) from Gencode (Website) which converts the raw reads into Transcripts Per Million (TPM).
Filtering: Transcripts which had a count value of 0 across all conditions were removed from the analysis.
Normalisation: We performed normalisation of the TPM across the different samples by using DESEq2 and negative binomial transformation of the data per sample was performed by using the EdgeR package.
Genome_build: Gencode M17

source_name: Epiblast Stem Cell

growth_protocol: Dissected epiblast were maintained on gelatin 0.1%  inactivated mouse embryonic fibroblasts (MEF) in EpiSC culture medium consisting of Knockout-DMEM , Knockout Serum Replacement (20%), Non-Essential Amino Acid , GlutaMAX-TM , Penicillin-Streptomycinand β-Mercaptoethanol .

extract_protocol:
RNA was extracted from cell samples with the ISOLATE II RNA Mini Kit (Bioline, Cat# BIO-52075)
TruSeq Stranded mRNA Sample preparation protocol

treatment_protocol: Media were supplemented with recombinant human Fgf2 (10ng/mL) and recombinant Human/Mouse/Rat Activin A (20ng/mL), IWP2 (5µM) and SB431542 (2 µM).

value: Epiblast Stem Cell

value: Wnt and TGFb inhibited no Activin A

tag: growth factor

tag: inhibitor

value: IWP2 +SB43


title: EpiSC-IwSB-noAct_REP2


title: Sepsis 1072

description: Sepsis

value: Sepsit ICU patient


title: Sepsis 1074

description: Sepsis


title: EpiSC-IwSB-noAct_REP1

value: Activin A + FGF2


title: Sepsis 1071

description: Sepsis


title: EpiSC-IwSB_REP3

value: Wnt and TGFb inhibited


title: uCd8_SLOTv3_mEND_repA_DpnI

value: LoxP site-containing rtTA-expressing 129P2/OlaHsd mouse embryonic stem cells


title: Healthy 1082

description: Healthy


title: chicken_FL_HH21_rep1

value: FL

tag: phenotype


title: uCd8_SLOTv3_mESC_repB_DpnII


title: WT 1

description:
Sample 1 (TP101_183)
processed data file: TP_Hdac1Hdac2_2fold.xlsx

value: Activated CD4+ T cells


title: m378_5KO_ADC

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Gprc5a KO tumors transcripts 12_04_2017.txt

data_processing:
Adaptors were trimmed
Alignment was performed using the STAR algorithm v2.4.1d
Unaligned reads were then aligned using Bowtie 2 v 2.1.0
Aligned reads from both alignment steps were then combined
Transcripts were then quantified using a modified version of the expectation-maximization (E/M) algorithm in the Partek Flow software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample. Data from all 11 samples are in one file

source_name: Mouse lung

extract_protocol:
RNA was isolated using the miRNeasy kit from Qiagen according to the manufacturer's protocol. Purified RNA samples were then cleaned and resuspended in nuclease-free water using the RNeasy MinElute Cleanup kit from Qiagen according to the manufacturer’s protocol. RNA quantity was measured using the Nanodrop 1000. Quality of RNA samples was quantitatively assessed by computation of RNA integrity numbers (RINs) using the Agilent RNA 6000 Pico kit (Agilent) following the manufacturer’s protocol.
RNA samples with RINs ≥ 7 were selected for RNA-sequencing (RNA-Seq). Libraries were then prepared from poly-A RNAs using the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s protocol for barcoded whole-transcriptome libraries. Size distribution of samples was assessed using the Agilent 2100 Bioanalyzer and 6000 RNA Pico kit. Library concentrations were quantified using the Agilent DNA 1000 assay and the 2100 Bioanalyzer according to the manufacturer’s instructions. Reactions were loaded onto Ion PI Chips v3 (Thermofisher) for sequencing on an Ion Proton sequencer according to the manufacturer’s protocol.

tag: mouse id

tag: time point after nnk (in months)

value: Seven

tag: tumor

value: Tumor


title: m372_5KO_ADC


title: EpiSC-IwSB_REP2

tag: tissue


title: m335_3KO_ADC

value: Four


title: Non-Sepsis 1079

description: Non-Sepsis


title: EpiSC-IwSB_REP1


title: m335_3KO_ADN


title: m368_4KO_ADN

value: Six


title: m350_5KO_ADN


title: uCd8_SLOTv3_mESC_repA_DpnII


title: uCd8_SLOTv3_mESC_repA_DpnI


title: AdIl17rc KO3

city: Boston

first: Spiegelman

last: Lab

address: 360 Longwood Avenue, Longwood Center

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
Sequenced reads were aligned to the UCSC mm9 reference genome assembly and gene counts were quantified using STAR (v2.5.1b). Differential gene expression testing was performed by DESeq2 (v1.10.1) and normalized read counts (FPKM) were calculated using cufflinks (v2.2.1). RNAseq analysis was performed using the VIPER snakemake pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: XLSX file, Cuff_Gene_Counts

molecule: polyA RNA

source_name: brown adipose tissue

extract_protocol:
Brown fat were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brown adipose tissue

tag: strain

tag: genotype

value: AdIl17rc KO


title: m378_5KO_N

value: Adjacent normal lung tissue


title: m368_4KO_N


title: RARRXR_SLOTv3_mESC_2.2_DpnI


title: uCd8_SLOTv3_mESC_repB_DpnI


title: m350_5KO_N


title: Huh7.5 lentivirally transduced with empty pWPI vector

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

data_processing:
Sequencing of libraries was performed on Hiseq 2500 (SR50).
bcl files were converted to fastq files with bcl2fastq v2.20.0.422
Quality check and  mapping of fastq files to homo sapiens (hg 19) sequence and calculation of Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed using CLC Genomics Workbench 11.0.1 (Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.8; Similarity fraction = 0.8)
Raw data were mapped against the hg19 human reference genome.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: CSV sheets of expression values (RPKM, TPM, total reads and unique reads) of human genes (Name, GeneID, ENSEMBL)

source_name: human hepatoma cell line Huh7.5

growth_protocol: Huh-7.5 cell lines were cultured in Dulbecco’s modified Eagle medium (Invitrogen) containing 10% fetal calf serum (FCS), 2 mM L-glutamine (Invitrogen), 0.1 mM non-essential amino acids (Invitrogen), 10 U/mL Penicillin (Invitrogen) and 10 μg/mL Streptomycin (Invitrogen) at 37°C, 5% CO2

extract_protocol:
Total RNA from cell cultures was extracted using the Nucleospin RNA II kit (Machery Nagel), following the manufacturer’s instructions. RNA quality checking was performed using an Agilent Bioanalyzer and sequencing libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.
Sequencing libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Sequencing of libraries was performed on Hiseq 2500 (SR50).

treatment_protocol: Cell cultures of non-treated Huh-7.5 cells stably expressing empty vector or 3xFLAG-C19orf66 were used.

tag: modification

value: empty vector control


title: 368_4KO

data_processing:
Adaptors were trimmed
Alignment was performed using the STAR algorithm v2.4.1d
Unaligned reads were then aligned using Bowtie 2 v 2.1.0
Aligned reads from both alignment steps were then combined
Transcripts were then quantified using a modified version of the expectation-maximization (E/M) algorithm in the Partek Flow software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample. Data from all 28 samples are in one file

tag: age

value: 6 - 8 weeks

tag: exposed to

value: 50 mg/kg body weight NNK 3 times/wk for 8 wks

tag: timepoint

value: 6 months following completion of NNK treatment (t=6)

value: Mouse airway epithelia


title: m372_5KO_N


title: 366_4KO

tag: genotype/variation


title: WT3

value: WT


title: AdIl17rc KO1


title: Huh7.5 lentivirally transduced with C19ORF66 encoding pWPI vector

value: hC19ORF66 overexpressing


title: sample02_20170512

city: Wuhan

first: Zili

last: Li

state: Hubei

institute: HuaZhong Science and Technology University

data_processing:
Illumina Casava 1.7 software was used for basecalling.
After sequencing, the adaptor sequences were trimmed using fastx_toolkit (0.0.14) and the quality-filtered reads were harvested as clean reads.
The clean reads were clustered to unique sequences and mapped to databases of human genome, RFam, RepBase, mRNA database, miRBase using bowtie(1.0.0) software,
Based on miRNA biogenesis model, we used miRDeep2 software to predict novel miRNAs
The clean reads of each sample were aligned to merged miRNA databases (known miRNAs from miRBase plus the newly predicted miRNAs) to calculate the miRNA expression levels. The numbers of mapped tags were defined as the raw expression levels of that miRNAs. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tags aligned
Genome_build: hg19, RFam12, RepBase19.07, miRBase Release 21
Supplementary_files_format_and_content: CSV files include TPM values for each Sample ...

source_name: embryo culture media

extract_protocol:
RNA was extracted using miRNeasy Serum/Plasma Kit.
The miRNA sequencing library was constructed using the TruSeq® miRNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA). Briefly, total RNA of each sample was used to prepare the miRNA sequencing library as the following steps, 3′-adaptor ligation, 5′-adaptor ligation, cDNA synthesis, PCR amplification, and gel purification for 145–160bp PCR-amplified fragments. After quantification with Qubit (Thermo Fisher, Waltham, MA, USA), the libraries were captured on cBOT (Illumina, San Diego, CA, USA) to be amplified in situ as clusters, and finally sequenced on the HiSeq™ 2500 System (Illumina, San Diego, CA, USA) as per the manufacturer’s instructions

tag: sample type

value: embryo culture media

tag: embryo stage

value: cleavage stage


title: sample02_20170324

value: blastocyst stage


title: sample01_20170512


title: 349_4KO


title: 341_4KO


title: 365_4KO


title: WT2


title: sample01_20170324


title: 377_3KO

value: 4 months following completion of NNK treatment (t=4)


title: 371_3KO


title: m335_3KO_N


title: HCT116 cells transfected with pCDNA3 mutant 1 pri-miRNAs plasmids

data_processing:
We trimmed the 3' adapter using cutadapt (-a TGGAATTCTCGGGTGCCAAGG -m 18 -M 26) and removed low-quality reads using fastq_quality_filter (-q 20 -p 90). The surviving reads were then mapped to the human genome (hg38) using Bowtie2. Unambiguously aligned reads with only mismatches at their 3′ end allowed were collected. Next, we selected the unambiguous reads that mapped to the miRNA loci using the miRNA annotation obtained from miRBase v22 (miRbase.org). The unmapped reads from the previous step were aligned with the transfected mutant pri-miRNA sequences using Bowtie2 and the resulting unambiguous reads as defined above from this alignment were collected. We calculated the relative abundance of miRNA using hsa-mir-16-5p as a  normalization factor.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_count.txt.gz contains the raw read counts
Supplementary_files_format_and_content: transfected_miRNA_annotation.txt.gz contains transfected miRNA annotation

source_name: HCT116 cells

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
Small RNA-seq libraries were generated with TruSeq Small RNA Sample Prep Kit (Illumina).

tag: disease state

value: colon carcinoma

tag: cell line

tag: transfect

value: pCDNA3 mutant 1 pri-miRNAs plamsids


title: AdIl17rc KO2


title: 348_3KO


title: 340_3KO


title: Sepsis 1070

description: Sepsis

tag: genetic background

value: Sepsit ICU patient

tag: patientid


title: 335_3KO


title: HCT116 cells transfected with pCDNA3 empty plasmid

value: pCDNA3 empty plasmid


title: NRN1 WT eTreg

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description:
A
mRNA

data_processing:
Sequencing was performed on Illumina NextSeq500 with the type of paired-end, 76bp.
The quality of sequencing data were assessed by the software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The mapping to mouse reference genome of mm10 was conducted by TopHat.
Differentially-Expressed genes were called by Cuffdiff, and the normalized FPKM values were called by Cuffnorm.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_eTreg.txt: Tab-delimited text files include FPKM values.

growth_protocol: Nrn1-/- and Nrn1+/- CD4+CD25+Cd62LlowCD44highFoxp3gfp+ were sorted from Nrn1-/- and Nrn1+/- mice on Foxp3DTRgfp background and subjected to RNASeq analysis

extract_protocol:
Cells stored in RNA protect before subject to RNA extraction.
Samples were sent to Admera Health for RNA extraction (RNeasy Mini Kit (QIAGEN)) and to process library construction and data analysis. Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used.

treatment_protocol: Sorting with FACSAria Fusion.

tag: strain/background

tag: cell type

value: eTreg cells


title: 358_2KO

value: 2 months following completion of NNK treatment (t=2)

tag: tissue


title: 347_2KO


title: VAT-Treg-male-2-Primer-Ad2-4_S4: VAT-Treg-male-Rep2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

data_processing:
The paired-end libraries were mapped to the GRCm38/mm10 reference genome by using Subread-1.6.2. Only uniquely mapped read-pairs were allowed in mapping. Peaks were then called from the mapping results by using Homer (v4.9) at an FDR cutoff of 1E-5.
The peaks from all the samples were merged by taking the union of the peaks; the merged peaks were then assigned to the nearest genes in the NCBI RefSeq gene annotation for mm10 (build 38.1). The mapped read-pairs were assigned to the merged peak regions by using featureCounts.
Merged peaks were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.7 in at least 2 libraries. Counts were converted to log2 CPM values, library normalized and precision weighted with the “voom” function of the limma package.
A linear model was fitted to each merged peak, and empirical Bayes moderated t-statistics were used to assess differences of accessibility of the chromatin. Merged peaks were called differential if they achieved a false discovery rate of 0.2 or less, and have a fold change greater than 2 between the two compared cell types.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files consisting of log2 CPM (counts per million mapped reads) values of peaks and their corresponding genes

source_name: Treg cells were flow cytometry sorted from the VAT of Foxp3RFP (RFP+) mice (n=3 mice, pooled)

extract_protocol:
DNA was extracted using cell lysis buffer as described previously (Buenrostro, et al 2013)
Libraries were generated following the protocol as described previously (Buenrostro, et al 2013)

tag: strain

value: visceral adipose tissue

value: Treg cells

tag: Sex

value: Male


title: HCT116 cells transfected with pCDNA3 wild-type pri-miRNAs plasmids

value: pCDNA3 wild-type pri-miRNAs plamsids


title: 375_1KO

value: 6 - 8 weeks

value: 50 mg/kg body weight NNK 3 times/wk for 8 wks

value: immediately following the eight-week exposure (t=0)

value: Mouse airway epithelia


title: MDA-MB-231_rep3_smallRNAseq

city: Barcelona

first: Luis

last: Serrano

address: C/ Dr. Aiguader, 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation (CRG)

description: No fractionation

data_processing:
Sequencing adapters were trimmed using BBDuk from the BBMap toolkit [v38.22] (https://sourceforge.net/projects/bbmap): k-mer=10 (allowing 8 at the end of the read), Hamming distance=1, length=10-50bp, Phred>25.
A total of 856 nuclear tRNAs and 21 mitochondrial tRNAs were annotated with tRNAscan-SE [v2.0]
Trimmed fastq files were then mapped using a specific pipeline for tRNAs (Hoffmann et al., Bioinformatics, 2018). Summarizing, an artificial genome is first generated by masking all annotated tRNA genes and adding pre-tRNAs (i.e. tRNA genes with 3' and 5' genomic flanking regions) as extra chromosomes. Upon mapping to this artificial genome with Segemehl [v0.3.1], reads that map to the tRNA-masked chromosomes or to the tRNA flanking regions are filtered out in order to remove non-tRNA reads and unmature-tRNA reads respectively. After this first mapping step, a second library is generated by adding 3' CCA tails and removing introns from tRNA genes. All 100% identical sequences of this so-called mature tRNAs are clustered to avoid redundancy. Next, the subset of filtered reads from the first mapping is aligned against the clustered mature tRNAs using Segemehl [v0.3.1]. Mapped reads are then realigned with GATK IndelRealigner [v3.8] to reduce the number of mismatching bases across all reads.
For quantification, isoacceptors were quantified as reads per million (RPM). In order to increase the coverage for anticodon-level quantification, we consider all reads that map unambiguously to a certain isoacceptor, even though they ambiguously map to different isodecoders (i.e. tRNA genes that differ in their sequence but share the same anticodon). Ambiguous reads mapping to genes of different isoacceptors were discarded.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-separated file that, for each sample, includes the RPM values for each isoacceptor, as well as the total number of mature tRNA mapped reads.

growth_protocol: Cells were maintained at 37 °C in a humidified atmosphere at 5% CO2 in DMEM 4.5g/L Glucose with UltraGlutamine media supplemented with 10% of FBS and 1% penicillin/streptomycin.

extract_protocol:
Small RNA-seq: Total RNA was directly adaptor-ligated, reverse-transcribed and PCR-amplified for 12 cycles.
Cells were grown in 60mm dishes for 48h. Total RNA from HeLa, HEK293, HCT116, MDA-MB-231 and fibroblast BJ/hTERT was extracted using the miRNeasy Mini kit. Independent replicates where grown and RNA was extracted on different days.
Upon applying either the hydro-tRNAseq or small RNA-seq protocol, the resulting cDNA was purified using a QIAQuick PCR Purification Kit. The adaptor ligated to the 3' end of the RNA is the standard TruSeq adaptor: 5’-AGATCGGAAGAGCACACGTCT-3’. The adaptor ligated to the 5' end is the TruSeq smallRNA adaptor: 5’-GTTCAGAGTTCTACAGTCCGACGATC-3’.

value: breast

tag: fraction

value: No fractionation


title: 334_2KO

city: Houston

tag: age


title: 339_2KO

tag: exposed to


title: MDA-MB-231_rep1_smallRNAseq

description: No fractionation


title: WT1

value: brown adipose tissue

tag: genotype

value: WT


title: 374_1KO

tag: genotype/variation

tag: timepoint


title: 367_1KO


title: VAT-Treg-female-2-Primer-Ad2-6_S6: VAT-Treg-female-Rep2

value: Female


title: HCT116 cells transfected with pCDNA3 mutant 2 pri-miRNAs plasmids

value: colon carcinoma

value: pCDNA3 mutant 2 pri-miRNAs plamsids


title: NRN1 KO eTreg

description:
B
mRNA

value: eTreg cells


title: VAT-Treg-female-1-Primer-Ad2-5_S5: VAT-Treg-female-Rep1


title: BJ_rep3_smallRNAseq

description: No fractionation

value: BJ fibroblasts

value: fibroblasts


title: 357_1KO


title: 336_3KO

value: 4 months following completion of NNK treatment (t=4)


title: VAT-CD4-male-2-Primer-Ad2-8_S8: VAT-CD4-male-Rep2

source_name: CD4+ T cells were flow cytometry sorted from the VAT of Foxp3RFP (RFP-) mice (n=3 mice, pooled)

value: visceral adipose tissue

value: CD4+ T cells

value: Male


title: 360_2KO

value: 6 - 8 weeks

value: 50 mg/kg body weight NNK 3 times/wk for 8 wks

value: 2 months following completion of NNK treatment (t=2)


title: 332_1KO

value: immediately following the eight-week exposure (t=0)

value: Mouse airway epithelia


title: 359_1KO


title: MDA-MB-231_rep2_smallRNAseq

description: No fractionation

value: breast

value: No fractionation


title: BJ_rep2_smallRNAseq

description: No fractionation


title: VAT-CD4-male-1-Primer-Ad2-7_S7: VAT-CD4-male-Rep1

value: Visceral adipose tissue


title: 355_0KO

value: prior to NNK exposure


title: 352_0KO


title: VAT-Treg-male-1-Primer-Ad2-3_S3: VAT-Treg-male-Rep1

value: Treg cells


title: 344_0KO


title: 345_0KO


title: HCT116_rep3_smallRNAseq

description: No fractionation

value: colon


title: 343_0KO


title: Spleen-Treg-1-Primer-Ad2-1_S1: Spleen-Treg-Rep1

source_name: Treg cells were flow cytometry sorted from the spleen of Foxp3RFP (RFP+) mice (n=3 mice, pooled)

value: Spleen


title: HCT116_rep2_smallRNAseq

description: No fractionation


title: 18-VAT-Treg-M2_S2: VAT-Treg-Male-Rep2

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Subread-1.6.2; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in 2 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.10 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in all the libraries.

source_name: Treg cells were Flow cytometry sorted from 25 week old male Foxp3RFP mice (RFP+) n=4 mice, pooled

extract_protocol:
RNA purification was performed following the manufacturer's protocol using the RNAeasy Plus Mini or Micro Kit (Qiagen). For VAT and adipocyte samples RNA was extracted using Qiagen Rneasy lipid tissue mini kit as per the manufacterurs protocol.  tissue RNA kit was used
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA). Library for Stroma-GP38+ Male/female, Stroma-GP38- Male/Female and VAT ILC2 Male/Female RNA libraries were made using Clontech kit as per the manufacterurs protocol.


title: HCT116_rep1_smallRNAseq

description: No fractionation


title: 356_0KO


title: 17-VAT-Treg-M1_S1: VAT-Treg-Male-Rep1


title: HELA_rep3_smallRNAseq

description: No fractionation

value: HELA

value: cervix


title: 20-VAT-Treg-F2_S4: VAT-Treg-Female-Rep2

source_name: Treg cells were Flow cytometry sorted from 25 week old female Foxp3RFP mice (RFP+) n=4 mice, pooled

value: visceral adipose tissue

value: Female


title: Total_liver_rep3

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

institute: Takeda pharmaceuticals

description: Sample 27

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer ( Torrent suite ver.5.10.1 ) .
Sequenced reads were trimmed for adaptor sequence low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using a combination of using software provided with the Ion Torrent Proton sequencer ( AmpliSeqRNA v5.10.1  )
RPM were calculated using software provided with the Ion Torrent Proton sequencer ( AmpliSeqRNA v5.0.4.0  )
Genome_build: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary_files_format_and_content: Tab-delimited text file includes gene symbol and gene expression (RPM) for each sample.

source_name: total Liver RNA #3

extract_protocol:
RNAs were extracted using RNAeasy mini Kit (Qiagen) following manufacturer's instructions.
Libraries were prepared according to the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). Briefly, cDNA was generated from 10ng of total RNA. The resulted cDNA was amplified and barcoded using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Barcoded cDNA Libraries were quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific). Libraries were then diluted to 45 pM and pooled  by combining an equal volume of each.

value: wild type

value: liver


title: HepG2_cells_rep1

description: Sample 22

source_name: HepG2 #1


title: HepG2_cells_rep3

description: Sample 24

source_name: HepG2 #3


title: HepG2_cells_rep2

description: Sample 23

source_name: HepG2 #2


title: Total_liver_rep2

description: Sample 26

source_name: total Liver RNA #2


title: HepaRG_cells_rep2

description: Sample 20

source_name: HepaRG at day7 #2

value: HepaRG


title: HELA_rep2_smallRNAseq

description: No fractionation


title: BJ_rep1_smallRNAseq

description: No fractionation

value: BJ fibroblasts

value: fibroblasts


title: HepaRG_cells_rep1

description: Sample 19

source_name: HepaRG at day7 #1


title: 26-VAT-CD4-M2_S10: VAT-CD4-Male-Rep2

source_name: CD4+ T cells were Flow cytometry sorted from 25 week old male Foxp3RFP mice (RFP-) n=4 mice, pooled

value: CD4 T cells

value: Male


title: PHH_day4_rep3

description: Sample 18

source_name: PHH at day4 #3

value: primary hepatocytes

value: day 4 in culture


title: PHH_day4_rep2

description: Sample 17

source_name: PHH at day4 #2


title: Spleen-Treg-2-Primer-Ad2-2_S2: Spleen-Treg-Rep2


title: HELA_rep1_smallRNAseq

description: No fractionation

value: No fractionation


title: Total_liver_rep1

description: Sample 25

source_name: total Liver RNA #1


title: HEK293_rep2_smallRNAseq

description: No fractionation

value: kidney


title: PHH_day1_rep3

description: Sample 15

source_name: PHH at day1 #3

value: day 1 in culture


title: PHH_day4_rep1

description: Sample 16

source_name: PHH at day4 #1


title: 35-VAT-CD4-F2_S12: VAT-CD4-Female-Rep2

source_name: CD4+ T cells were Flow cytometry sorted from 25 week old female Foxp3RFP mice (RFP-) n=4 mice, pooled


title: HepaRG_cells_rep3

description: Sample 21

source_name: HepaRG at day7 #3


title: HEK293_rep1_smallRNAseq

description: No fractionation


title: PHH_day1_rep1

description: Sample 13

source_name: PHH at day1 #1