title: PBS_Lung

city: Chiba

first: Takashi

last: Ito

state: Chiba

address: Inohana

country: Japan

institute: Chiba university

data_processing:
CASAVA 1.8.2 software used for base-calling
Default parameters of Tophat2 use for alignment
Cufflinks 2.2.1 used for FPKM normalization
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Lung

extract_protocol:
Total RNA was extracted from frozen lungs using PureLink RNA Mini Kit (invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: [WT_asthma and IL22KO_asthma] WT and IL22KO mice were sensitized and challenged with HDM. Forty-eight hours after the last HDM administration, total RNAs were prepared from the lung. [PBS_Lung and IL22_Lung] PBS and recombinant IL-22 was intratracheally administered to WT mice. Twenty-four hours after the administration, total RNAs were prepared from the lung.

value: Lung

value: wild type


title: IL22KO_asthma

status: Public on Aug 10 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype


title: rB_wt_p300

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

country: USA

institute: NIH

library_source: genomic

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
MNaseI-Seq_density: quality and adapter trimming: fqtrim-v0.94/fqtrim -A 125 -q 20  -f adapters -p22 -P33
MNaseI-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --local --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 22
MNaseI-Seq_density: filtering and sorting(uniquely aligned reads): samtools-0.1.19/samtools view -Sb | samtools sort -@ 20 -m 1G
MNaseI-Seq_density: merging: samtools-1.1/samtools merge
MNaseI-Seq_density: raw tag density: custom program, density estimate of nucleosome dyads genome wide, wigToBigWig -fixedSummaries -keepAllChromosomes
MNaseI-Seq_density: tag ratio between input and control: ucsc-314/wiggletools ratio input.bw control.bw | wigToBigWig
MNaseI-Seq_density: aB_minus_rB density: ucsc-314/wiggletools diff aB_ratio.bw rb_ratio.bw | wigToBigWig
ATAC-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --end-to-end --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 16
ATAC-Seq_density: filtering (remove random contigs): sed '/random/d;/chrUn/d'
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19/samtools view -S -b -F4
ATAC-Seq_density: merging: samtools-0.1.19/samtools merge && samtools sort -m 10G
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: contact_matrix: 5kb contact matrix was generated from the filtered alignment
HiC-Seq: loop call: juicebox hiccups -m 500 -r 5000 -k KR -f 0.1 -p 4 -i 10 -t 0.01,1.5,1.75,2 -d 20000
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: Gro-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: MNaseI-Seq: .wig files tag density ratio difference between activated and resting B cells (ratio)
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: HiC-Seq: tab seperated loop coordinates with other information

molecule: genomic DNA

source_name: resting B cell

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing.  Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).                                                                                HiC-Seq:  we used the same protocol for situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)                                                                                ATAC-Seq: we followed the protocol at Buenrostri J.D. et al. (Nat Methods, 2013 Dec; 10(12):1213-8)                 Gro-seq:  Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the  RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated  with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and  purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was  dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation.  Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz  Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis  was performed the next day as described in (Wang et al., 2011). However, for reverse  transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT  GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA  TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England  Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and  RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA  fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel  (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The  final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA  clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                                                                MNase-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina)                                                        ATAC-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                   HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                    Gro-seq: 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).

treatment_protocol: Gro-seq: Myc floxed allele was obtained from Douglas Green (St. Jude Children’s research hospital). Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice). The deletion of floxed allele was checked by PCR or intracellular staining of Myc protein.

value: WT

value: spleen

tag: chip antibody

value: Santa Cruz, sc-585

tag: activation time


title: rB_wt_Rad21_rep2

value: abcam, ab992


title: rB_wt_Wdr5

value: Bethy Laboratories, A302-429A


title: WT_asthma


title: Pool_1002_AD010_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
genome build: hg19
For multiplexed single nucleus methylome samples, reads were first trimmed to remove sequencing adaptors using Cutadapt 1.11 with the following parameters in paired ends mode: -f fastq -q 20 -m 62 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. For singleplex samples, -m parameter was set to 40. For multiplexed samples, 16bp was further trimmed from both 5’- and 3’- ends of R1 and R2 reads to remove random primer index sequence and C/T tail introduced by Adaptase, with the following parameters: -f fastq -u 16 -u -16 -m 30. For singleplex samples, 10bp was trimmed from both 5’- and 3’- ends of R1 and R2 reads with the following parameters: -f fastq -u 10 -u -10 -m 30. Trimmed reads for mouse and human single nuclei were mapped to mm10 and hg19 reference genome, respectively. R1 and R2 reads were mapped separately as single-ended reads using Bismark v0.15.0 with parameter --bowtie2. --pbat option was activated for mapping R1 reads. Resulted bam files were sorted using samtools 1.3 sort, followed by removal of duplicate reads using Picard 1.141 MarkDuplicates with the option REMOVE_DUPLICATES=true. Non-clonal reads were further filtered for minimal MAPQ = 30 using samtools view with option -q30. To prevent regional mCH level estimation from being skewed by rare reads failed to be bisulfite converted, reads with read-level mCH level greater than 0.7 were excluded. The calling of unmethylated and methylated base calls were performed by call_methylated_sites of Methylpy (https://github.com/yupenghe/methylpy/) (1–3).
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

organism: Homo sapiens

source_name: Human frontal cortex

growth_protocol: For the production of single neuron methylomes from layer dissected mouse frontal cortex tissue, eight week old C57BL/6J male mice were purchased from Jackson Laboratories, Bar Harbor ME, and allowed a week of acclimation in our animal facility with 12 h light/dark cycles and food ad libitum, before dissections. The human brain specimen was obtained from the NICHD Brain and Tissue Bank for Developmental disorders at the University of Maryland, Baltimore, MD. The frozen middle frontal gyrus tissue belonged to a 25-year-old Caucasian male (UMB#4540) with a PMI of 23 h.

extract_protocol:
A detailed protocol for MethylC-seq libraries preparation can be found in Urich et al., (2015). MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10, 475-483.
Nuclei isolation from mouse and human cortical tissues was performed as described in (Lister et al., 2013) with the following modifications: Proteinase inhibitor (11836153001, Roche) and RNAse Inhibitor (30 U/ml, PRN2611 from Promega) was added to the lysis buffer and sucrose gradients. After centrifugation, nuclei were resupended in 0.5% BSA (AM2616, Ambion) PBS (Ca2+ and Mg2+ free, 14190-144 from Life Technologies,) with protein and RNAse inhibitors. Isolated nuclei from mouse and human tissues were labeled by incubation with 1:1000 dilution of AlexaFluor488 conjugated anti-NeuN antibody (MAB377X, Millipore) at 4°C for 1 hour. Nuclei isolated from CLSun1-G35-Cre line were incubated with AlexaFluor647 conjugated anti-NeuN antibody (anti-NeuN antibody MAB377 labeled using Apex Alexa Fluor 647. A10475, Life Technologies) and AlexaFluor488 conjugated anti-GFP antibody (A21311, Life Technologies). Fluorescence activated sorting of single nuclei was performed using a BD Influx sorter with an 85 µm nozzle at 22.5 PSI sheath pressure. Single nuclei were sorted into each well of a 384-well plate preloaded with 2 µl of Proteinase K digestion buffer (1 µl M-Digestion Buffer, 0.1 µl 20 µg/µl Proteinase K and 0.9 µl H2O). The alignment of receiving 384-well plate was performed by sorting sheath flow into wells of an empty plate and making adjustment based on the liquid drop position. Single cell (1 drop single) mode was selected to ensure the stringency of sorting.
Steps of library preparation prior to SPRI purification were performed in a horizontal laminar flow hood to minimize environmental DNA contamination. Bisulfite conversion of single nuclei was carried out using Zymo EZ-96 DNA Methylation-DirectTM Kit (Deep Well Format, cat. #D5023) following the product’s manual with reduced reaction volume. 384-well plate (ThermoFisher Armadillo PCR Plate cat. # AB2384) containing FACS isolated single nuclei were heated at 50°C for 20 min. 25 µl CT Conversion Reagent was added to each well followed by pipetting up-and-down to mix. Plates were treated with a following program using a thermocycler: 98°C for 8 min, 64°C for 3.5 hours and 4°C. Each well of Zymo-Spin™ I-96 Binding Plates was preloaded with 150 µl M-binding buffer. Bisulfite conversion reactions were transferred from 384-well plates to I-96 Binding Plates followed by pipetting up-and-down to mix. I-96 Binding Plates were centrifuged at 5,000g for 5 min. Wells were washed with 400 µl of M-Wash Buffer followed by centrifugation at 5,000g for 5 min. 200 µl of M-Desulphonation Buffer was added to each well and was incubated for 15 min at room temperature before removed by centrifugation at 5,000g for 5 min. Each well was then washed with 400 µl of M-Wash Buffer for two rounds. 12 µl of M-Elution Buffer was added to each well and was incubated for 5 min at room temperature. I-96 Binding Plate was placed above a 96-well PCR plate (Applied Biosystems MicroAmp® EnduraPlateTM cat. # 4483348) and was centrifuged at 5,000g for 3min. 9 µl of eluted DNA was commonly collected in each well of the PCR plate. 1 µl of 5 µM P5L-AD002-N9, P5L-AD006-N9, P5L-AD008-N9 or P5L-AD010-N9 indexed random primer was added to each well of 96-well plate followed by mixing with vortexing. All DNA oligos were purchased from Integrated DNA Technologies (IDT). Plate was heated at 95°C for 3 min to denature the sample and was immediately chilled on ice for more than 2 min. 10 µl enzyme mix containing 2 µl of Blue Buffer (Enzymatics cat. # B0110), 1 µl of  10mM dNTP (NEB cat. # N0447L), 1 µl of Klenow exo- (50U/µl, Enzymatics cat. # P7010-HC-L) and 6 µl H2O. After mixing with vortexing, plate was treated with a following program: 4°C for 5 min, ramp up to 25°C at 0.1°C/sec, 25°C for 5 min, ramp up to 37°C at 0.1°C/sec, 37°C for 60 min, 4°C. 2 µl of Exonuclease 1 (20U/µl, Enzymatics cat. # X8010L) was added to each well followed by mixing with vortexing. Plate was incubated at 37°C for 30 min and then 4°C. 17.6 µl of home-made SPRI beads was added to each well. Sample/bead mixture from four plates indexed using distinct indexed random primers were combined followed by pipetting up-and-down to mix. Sample/bead mixture was incubated at room temperature for 5 min before placed on a 96-well magnetic separator. Supernatant was removed from each well followed by three rounds of washing with 180 µl of 80% ethanol. After air drying beads at room temperature, 10 µl M-Elution buffer was added to each well to fully resuspend the beads. Eluted sample was transferred to a new 96-well PCR plate. PCR plate was heated at 95°C for 3 min to denature the sample and was immediately chilled on ice for more than 2 min. 10.5 µl Adaptase (Swift Biosciences) mix (2 µl Buffer G1, 2 µl Reagent G2, 1.25 µl Reagent G3, 0.5 µl Enzyme G5, 0.5 µl Enzyme G6 and 4.25 µl M-Elution buffer) was added into each well followed by mixing with vortexing. Plates was incubated at 37°C at 30 min and then 4°C. 30 µl PCR mix (25 µl KAPA HiFi HotStart ReadyMix, KAPA BIOSYSTEMS, cat. # KK2602, 1 µl 30 µM P5 indexing primer and 5 µl 10 µM P7 indexing primer) was added into each well followed by mixing with vortexing. PCR plate was treated with the following program: 95 °C for 2 min, 98°C for 30 sec, 17 cycles of (98°C for 15 sec, 64°C for 30 sec, 72°C for 2min), 72°C for 5 min then 4°C. PCR products were cleaned up using 0.8x SPRI beads and was combined into one tube for each 96–well plate. Pooled PCR product was resolved on 2% agarose gel, smear between 400 bp and 2 Kb were excised and purified using QIAquick Gel Extraction Kit (Qiagen cat. # 28706). Library concentration was determined using Qubit® dsDNA HS (High Sensitivity) Assay Kit (Invitrogen cat. # Q32851).

value: frontal cortex

tag: Sex

value: Male

tag: age

value: 25 yr


title: rB_wt_Mll1

value: Bethy Laboratories, A300-086A


title: Pool_1001_AD010_indexed


title: Pool_1001_AD008_indexed


title: rB_wt_HDAC2

value: Bethy Laboratories, A300-705A


title: Pool_1000_AD010_indexed


title: IL22_Lung


title: Pool_1000_AD008_indexed


title: rB_wt_Chd4

value: abcam, ab72418


title: Pre-immune

city: University Park

first: David

middle: S

last: Gilmour

state: Pennsylvania

address: 465 North Frear

institute: Penn State University

description: ChIP-exo

data_processing:
Basecalls performed using Bcl2FastQ version 2.16.0
Sequenced reads were masked for low-quality sequence, then mapped to dm3 whole genome using bwa mem 0.7.9a,0.7.12 with the default parameters.
Replicates were megred and  and only the 5' end of read1 was kept.
Tag directories were created in homer with a fragment length of 1.
BedGraph files were generated using the Homer makeUCSCfile command with reads normalized to 1E7
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files for each sample were generated using homer's makeUCSCfile function by normalizing to 1E7 and keeping strand information.

organism: Drosophila melanogaster

source_name: S2R+ cell line

growth_protocol: M3+BPYE media at 25°C

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with rabbit IgG antibody.
ChIP-exo

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 250mM glycine

tag: sample type

value: Protein-DNA complex

tag: antibody

value: sera from Preimmune rabbit

tag: protocol

value: ChIP-exo


title: rB_wt_HDAC1_rep

description: replicate

value: abcam, ab7028


title: rB_wt_HDAC1


title: M1BP ChIP-exo

description: ChIP-exo


title: TAF1

description: ChIP-exo

value: TAF1 (TAF250)


title: rB_wt_0nMTSA_H3K27Ac

value: abcam, ab4729


title: rB_wt_25nMTSA_H3K27Ac

description: TSA treatment

value: WT


title: rB_wt_75nMTSA_H3K27Ac

description: TSA treatment

value: spleen


title: XL22-138-D

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: RGAP 7.0
Supplementary_files_format_and_content: The processed data is presented in Microsoft Excel file format (.xls), which involves "GeneID",  "Length", "FPKM", "Locus", "Strand", "Count", "Normalized".

organism: Oryza sativa Japonica Group

source_name: Rice plants at reproductive stage

growth_protocol: plants were grown in a paddy field facilitated with a movable rain-off shelter during the summer of 2016 in Wuhan, Hubei Province, China. Ten plants for each family were planted in two rows (one plot) with a planting density similar to real agricultural fields.

extract_protocol:
RNA for the RNA-Seq analysis was extracted using TRIzol® reagent (AmbionTM, Lot No. 15596018) according to the manufacturer’s protocol.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Drought stress was applied by stopping watering at the booting stage (about 2 weeks before flowering) in the field, and drought stress was considered to take place when the mean TDR (Time Domain Reflectometry) value of a block was less than 25

value: The second upper leaves

value: OsbZIP46CA1 and SAPK6 Co-overexpressing line -138

tag: treatment

value: Drought


title: XL22-138-N

value: Normal


title: XL22-125-N

value: OsbZIP46CA1 and SAPK6 Co-overexpressing line -125


title: Pool_1003_AD008_indexed

value: frontal cortex

value: Male

value: 25 yr


title: aB_wt_p300

source_name: activated B cell

value: Santa Cruz, sc-585


title: aB_wt_Wdr5

value: Bethy Laboratories, A302-429A


title: SAPK6-OE-33-D

value: SAPK6 Overexpressing line -33


title: SAPK6-OE-19-N

value: SAPK6 Overexpressing line -19


title: aB_wt_DMSO_H3K27Ac


title: aB_wt_Mll1

value: Bethy Laboratories, A300-086A


title: TRF2

description: ChIP-exo

value: Protein-DNA complex

value: ChIP-exo


title: SAPK6-OE-19-D


title: SAPK6-OE-33-N


title: aB_wt_HDAC2

value: WT

value: Bethy Laboratories, A300-705A


title: CA1-OE-19-N

value: The second upper leaves

value: OsbZIP46CA1 Overexpressing line -19


title: aB_wt_HDAC1

value: spleen

value: abcam, ab7028


title: CA1-OE-19-D

value: Drought


title: aB_wt_CTCF_rep2

value: abcam, ab70303


title: CA1-OE-4-N

value: OsbZIP46CA1 Overexpressing line -4

value: Normal


title: CA1-OE-4-D


title: rB_wt_H4K91Ac

value: abcam, ab4627


title: XL22-125-D

value: OsbZIP46CA1 and SAPK6 Co-overexpressing line -125


title: 393PZeb1-3

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: tranfected with ZEB1 expression vector

data_processing:
LifeScope Genomic Analysis Software v2.5.1 was used to process the .xsq files, and generate raw counts and RPKM for the genes.
XSQ Tools was used to convert .xsq files to CSFASTA/QUAL files.
Supplementary_files_format_and_content: tab-delimited text files containing the raw counts of sequencing reads and RPKM for the genes.

source_name: KP lung cancer cells

growth_protocol: Cell transfectants were cultured in RPMI-1640 medium supplemented with 10% FCS.

extract_protocol:
Cells were lysated and totall RNA was purified using RNeasy Mini Kit (Qiagen).SOLiD™ total RNAseq kit with protocol guidelines (PN 4445374, Life Technologies) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard SOLiD protocols

tag: cell type

value: mouse lung cancer cell transfectant

value: lung


title: 393PZeb1-2

description: tranfected with ZEB1 expression vector


title: rB_wt_H4K8Ac

value: Millipore, 07-328


title: aB_wt_Chd4

value: abcam, ab72418


title: rB_wt_H4K5Ac

value: Millipore, 07-327


title: rB_wt_H4K20me3

value: WT

value: Diagenode, C15410207


title: 393PVec-2

description: tranfected with empty vector


title: aB_wt_HDAC1_rep

description: replicate


title: rB_wt_H4K20me1


title: 393PVec-3

description: tranfected with empty vector


title: 393PVec-1

description: tranfected with empty vector


title: rB_wt_H3K79me3

value: abcam, ab2621


title: rB_wt_H3K9me2

value: abcam, ab1220


title: rB_wt_H3K9me1

value: spleen

value: abcam, ab9045


title: rB_wt_H3K79me2

value: abcam, ab3594


title: rB_wt_H3K9me3

value: abcam, ab8898


title: rB_wt_H3K9Ac

value: abcam, ab4441


title: rB_wt_H4K12Ac

value: Millipore, 07-595


title: rB_wt_H3K4me3

value: Millipore, 04-745


title: rB_wt_H3K36me3

value: abcam, ab9050


title: rB_wt_H3K4Ac

value: Millipore, 07-539


title: rB_wt_H3K4me2

value: Millipore, 07-030


title: rB_wt_H3K36me2

value: abcam, ab9049


title: rB_wt_H3K36me1

value: abcam, ab9048


title: rB_wt_H3K36Ac

value: Millipore, 07-540


title: 393PZeb1-1

description: tranfected with ZEB1 expression vector

value: mouse lung cancer cell transfectant

value: lung


title: rB_wt_H3K27me2

value: WT


title: rB_wt_H3K27me1

value: Millipore, 07-448


title: rB_wt_H3K18Ac

value: spleen

value: Diagenode, C15410139


title: rB_wt_H3K23Ac

value: Millipore, 07-355


title: rB_wt_H2BK20Ac

value: Millipore, MABE351


title: rB_wt_H3K14Ac

value: Millipore, 07-347


title: rB_wt_H2BK5Ac

value: Active motif, 39123


title: rB_wt_H2BK5me1


title: rB_wt_H2BK120Ac

value: active motif, 39119


title: rB_wt_H2AZ

value: abcam, ab4174


title: newmag1 1hr

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description:
mag1∆
mag1∆ 1hr repair.

data_processing:
Library strategy: NMP-seq
Base calling by Torrent_Suite 5.0.4.
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, using a custom perl script.
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files.
SAM files were converted to BAM files using samtools.
BAM files were converted to BED files using BEDTOOLS2 bamtoBed.
Damage coordinates were mapped using custom perl script.
Only reads mapping to A or G nucleotides, corresponding to 3meA or 7meG lesions, were retained in BED file using custom perl script. A different BED file (and resulting wig file) was generated for A nucleotide lesions and G nucleotide lesions.
BED files were converted to WIG file using COUNT function of IGVTools.
Background values at A or G nucleotides were generated in WIG file using custom perl script.
Genome_build: SacCer3 (R64)
Supplementary_files_format_and_content: WIG files containing counts of DNA alkylation damage reads filtered for only A (3-methyladenine) or G (7-methylguanine) mapping sequences and including background value of 0.0 for A or G nucleotides with no mapped sequencing reads. Note, WT1 DNA samples (No_MMS, wt1_0hr, and wt1_30min) were also digested with NotI as a control, so NotI sites in the yeast genome were removed from further analysis.

organism: Saccharomyces cerevisiae

source_name: Yeast cells, mag1∆, 0.4% MMS for 10 min, 1 hr repair

growth_protocol: Yeast cultures (BY4741 and MP059) were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI, (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 12 μg of DNA was used for each sequencing library preparation.
N-methylpurine (NMP)-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433-1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP. CPD lesions were cleaved with Alkyladenine DNA glycosylase (AAG) and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for 5-6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: For repair time points experiments, MMS was added to the yeast cultures to the final concentrations of 0.2% or 0.4% as indicated, and incubated for 10 minutes. Cells were collected and washed with sterile deionized H2O twice to remove MMS. Cells were resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) for repair. Aliquots (10 ml of yeast culture) were taken before MMS treatment (No MMS), immediately after MMS treatment (0hr), and at different repair time points as indicated. Cells were spun down and kept at -80˚C until genomic DNA isolation. For chronic MMS treatment, yeast cells were incubated in YPD containing 0.02% MMS for 3hr. Cells were collected and washed with sterile deionized H20 to remove residual MMS. Cell pellets were stored at -80˚C for DNA isolation.

tag: genotype/variation

value: 0.4% MMS for 10 min

tag: repair time

value: 1 hr


title: newmag1 2hr

description:
mag1∆
mag1∆ 2hr repair.

source_name: Yeast cells, mag1∆, 0.4% MMS for 10 min, 2 hr repair

value: 2 hr


title: rB_wt_H3K79me1

value: Diagenode, C15410082


title: rB_wt_H2AK9Ac

value: Millipore, 07-289


title: mag1 3hr chronic

source_name: Yeast cells, mag1∆, 0.02% MMS for 3 hr, chronic repair

value: 0.02% MMS for 3 hr

value: chronic


title: aB_wt_H4K91Ac

value: WT

value: abcam, ab4627


title: newmag1 0hr

description:
mag1∆
Control for mag1∆ 1hr and 2hr repair time points.

source_name: Yeast cells, mag1∆, 0.4% MMS for 10 min, 0 hr repair

value: 0 hr


title: aB_wt_H4K8Ac

value: spleen

value: Millipore, 07-328


title: 2hr wt

description: 2hr wt repair.

source_name: Yeast cells, wild-type, 0.4% MMS for 10 min, 2 hr repair

value: Wild-type


title: aB_wt_H4K20me1


title: aB_wt_H4K5Ac

value: Millipore, 07-327


title: 0hr mag1 rep 2

description:
mag1∆
Control for 2hr wt repair time point.


title: aB_wt_H4K20me3

value: Diagenode, C15410207


title: wt 1hr

description: wt 1hr repair.

source_name: Yeast cells, wild-type, 0.4% MMS for 10 min, 1 hr repair


title: mag1 0hr

description:
mag1∆
Control for wt 1hr repair time point.


title: aB_wt_H4K12Ac

value: Millipore, 07-595


title: wt 0hr rep 2

source_name: Yeast cells, wild-type, 0.4% MMS for 10 min, 0 hr repair


title: wt1_30min

description: wt1 30 min repair.

source_name: Yeast cells, wild-type, 0.2% MMS for 10 min, 30 min repair

value: 0.2% MMS for 10 min

value: 30 min


title: rB_wt_H2BK12Ac

value: Diagenode, C15410212


title: wt1 0hr

description: Control for wt1 30min repair time point.

source_name: Yeast cells, wild-type, 0.2% MMS for 10 min, 0 hr repair


title: aB_wt_H3K9me3

value: abcam, ab8898


title: aB_wt_H3K9me2

value: abcam, ab1220


title: aB_wt_H3K9me1

value: abcam, ab9045


title: AB-P3_S21_R1

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

description: strand-specific RNAseq

data_processing:
Data was pre-processed using FastQC. Mapping quality was checked using RSeQC pipeline.
Pre-processed data was mapped to the zebrafish genome using STAR aligner
Htseq-count was used to get the read counts mapped.
EdgeR was used for statistical analysis
Genome_build: ensembl version 84 (GRCz10)
Supplementary_files_format_and_content: text format; count data files include identifier and the raw counts.

organism: Danio rerio

source_name: Brain

growth_protocol: Embryos were raised in 0.3x Danieu's solution during embryonic development and subsequently raised in system water (pH 7.2-7.5) in 2 gallon aquarium tanks with continuous aeration and 12:12 dark/light photoperiod. Larva were fed with rotifers. Juveniles and adults were fed brine shrimp and a commerical microencapsulated diet (300 microns; skettring Inc) daily.

extract_protocol:
Total RNA from embryoand larval samples was isolated using BioRad aurum kit.  Brain samples ware isolated following the method of Peña-Llopis and Brugarolas (2013).
Library construction was done using Illumina TruSeq with Ribozero and 50 bp single end strand-specific sequencing was done at Tufts Molecular core facility.

treatment_protocol: Embryos were exposed to DMSO or PCB126 in 0.3x Danieu's solution and subsequently raised in clean system water until adulthood.

tag: developmental stage

value: 4 month old adult

tag: agent


title: AB-1-2-P3_S24_R1

description: strand-specific RNAseq


title: aB_wt_H3K79me2

value: abcam, ab3594


title: aB_wt_H3K79me3

value: WT

value: abcam, ab2621


title: AB-1-2-P1_S22_R1

description: strand-specific RNAseq


title: AB-P2_S20_R1

description: strand-specific RNAseq


title: aB_wt_H3K79me1

value: Diagenode, C15410082


title: aB_wt_H4K16Ac

value: spleen

value: Millipore, 07-329


title: aB_wt_H3K4me3

value: Millipore, 04-745


title: AB-P1_S19_R1

description: strand-specific RNAseq


title: AB-D3_S18_R1

description: strand-specific RNAseq

value: DMSO treated


title: aB_wt_H3K36me3

value: abcam, ab9050


title: 5d-1-2-P2_S14_R1

description: strand-specific RNAseq

source_name: Larvae

value: 5 days post-fertilization


title: AB-D2_S17_R1

description: strand-specific RNAseq


title: 5d-1-2-P3_S15_R1

description: strand-specific RNAseq


title: aB_wt_H3K4me2

value: Millipore, 07-030


title: AB-D1_S16_R1

description: strand-specific RNAseq


title: aB_wt_H3K36me2

value: abcam, ab9049


title: aB_wt_H3K4Ac

value: Millipore, 07-539


title: 5d-1-2-P1_S13_R1

description: strand-specific RNAseq


title: 5d-P3_S12_R1

description: strand-specific RNAseq


title: No MMS

source_name: Yeast cells, wild-type, untreated

value: Wild-type


title: AB-1-2-P2_S23_R1

description: strand-specific RNAseq


title: aB_wt_H3K9Ac

value: abcam, ab4441


title: aB_wt_H3K27me3

value: Millipore, 07-449


title: aB_wt_H3K36me1

value: abcam, ab9048


title: 5d-P2_S11_R1

description: strand-specific RNAseq


title: aB_wt_H3K36Ac

value: Millipore, 07-540


title: 5d-D2_S8_R1

description: strand-specific RNAseq


title: aB_wt_H3K23Ac

value: WT

value: Millipore, 07-355


title: aB_wt_H3K18Ac

value: Diagenode, C15410139


title: 5d-P1_S10_R1

description: strand-specific RNAseq


title: 5d-D3_S9_R1

description: strand-specific RNAseq


title: 48-P3_S6_R1

description: strand-specific RNAseq

source_name: Embryos

value: 48 hours post-fertilzation


title: 48-P2_S5_R1

description: strand-specific RNAseq


title: aB_wt_H2BK5me1

value: spleen


title: aB_wt_H3K27me2


title: aB_wt_H2BK5Ac

value: Active motif, 39123


title: 48-D3_S3_R1

description: strand-specific RNAseq

value: DMSO treated


title: aB_wt_H2BK20Ac

value: Millipore, MABE351


title: 48-P1_S4_R1

description: strand-specific RNAseq


title: aB_wt_H2BK120Ac

value: active motif, 39119


title: aB_wt_H2BK12Ac

value: Diagenode, C15410212


title: 48-D2_S2_R1

description: strand-specific RNAseq


title: 48-D1_S1_R1

description: strand-specific RNAseq


title: aB_wt_H3K27me1

value: Millipore, 07-448


title: HSV1_3

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

description: small RNA

data_processing:
Briefly, the sequences were blasted to human reference genome hg38 (GRCh38.p7), the RFam and Repbase to identify possible mRNA, rRNA, tRNA, snRNA, snoRNA and other ncRNAs.
To identify the known miRNAs, the remaining sequences were aligned to the miRBase (release 21.0) by using Bowtie. Matched sequences with no more than one mismatch were considered as known miRNAs.
Besides, the unmatched sequences were used to predict candidate novel miRNAs using miRDeep2. The hairpin RNA structures containing the unmatched sequences were predicated complying with criteria of the pre-miRNAs to identify potentially novel miRNAs.
Expression level of miRNAs was determined by normalizing reads to tags per million (TPM) counts. The TPM was calculated as follows: normalized expression, TPM = (actual miRNA count/number of total clean read) × 106.
Genome_build: human reference genome hg38 (GRCh38.p7)
Supplementary_files_format_and_content: sequence, count and TPM expression value of novel and known miRNAs

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: HSV1-infected human fibroblast KMB17 cells

growth_protocol: Human fibroblast KMB17 strain (Institute of Medical Biology, CAMS), a normal diploid cell line that was originated from fetal lung tissue, was cultured in Minimum Essential Medium (MEM) supplemented with 10% bovine serum (Minhai Biotech, Beijing, China) at 37°C in 5% CO2.

extract_protocol:
At 48 h postinfection, total RNA from HSV-1 infected and uninfected KMB17 cells was isolated with Trizol regeant (Invitrogen) followed by digestion with DNase I (Epicentre) for 15 min at 37°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KMB17 cells were mock- infected or infected with HSV-1 at a multiplicity of infection (m.o.i) of 1.

tag: cell line

value: Human fetal lung tissue-derived fibroblast cells

tag: infected with

value: herpes simplex virus type 1

tag: passages

tag: virus strain

value: HSV-1 strain 17 (GenBank:NC_001806.2)


title: HSV1_2

description: small RNA


title: aB_wt_H2AK9Ac

tag: genotype

tag: tissue

tag: chip antibody

value: Millipore, 07-289


title: aB_wt_H2AZ

value: abcam, ab4174

tag: activation time


title: HSV1_1

description: small RNA


title: aB_wt_H3K14Ac

value: Millipore, 07-347


title: 5d-D1_S7_R1

description: strand-specific RNAseq

value: 5 days post-fertilization


title: Fr-iCLIP_mSRSF7Nu-Replicate2

city: New Haven

first: Mattia

last: Brugiolo

state: Connecticut

address: 333 Cedar Street

department: Molecular biophysics and biochemistry

institute: Yale University

description: Processed_peaks_P19_mSRSF7_Nu-3Repl_mm9--ensembl59_lowFDR.bed

data_processing:
Data processing was done as published in: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Barcodes are given in the name of the raw file, for each replicate
Genome_build: mm9
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tags for combined replicates (3-4 replicates)

source_name: P19 cell line

growth_protocol: P19 cells were grown to confluency in DMEM medium supplemented with 10% FBS and 100 U/ml Pen and 100 µg/ml Strep

extract_protocol:
Cell pellet was subjected to subcellular fractionation and iCLIP (Fr-iCLIP)
Library and barcodes were prepared according to iCLIP protocol as published in Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, Konig J, Ule J: iCLIP: protein-RNA interactions at nucleotide resolution. Methods 2014, 65(3):274-287.

treatment_protocol: Cells were wased with ice cold PBS and then crosslinked at wavelength of 254nm with an energy of 100mJ/cm2

value: P19 embryonal carcinoma cell line fusion protein expression:SRSF7-GFP

tag: subcellular fraction

value: Nucleoplasm

tag: barcode

value: NNNCCGGNN


title: Fr-iCLIP_mSRSF7Nu-Replicate3

value: NNNTTGTNN


title: Fr-iCLIP_mSRSF7Nu-Replicate1


title: Fr-iCLIP_mSRSF7Cy-Replicate3

description: Processed_peaks_P19_mSRSF7_Cy-3Repl_mm9--ensembl59_lowFDR.bed

value: Cytoplasm

value: NNNGGTTNN


title: Fr-iCLIP_mSRSF7Cy-Replicate1


title: Fr-iCLIP_mSRSF7Cy-Replicate2

value: NNNGGCGNN


title: Fr-iCLIP_P19_mSRSF3Nu-Replicate4

description: Processed_peaks_P19_mSRSF3_Np_4Repl_mm9--ensembl59_lowFDR.bed

value: P19 embryonal carcinoma cell line fusion protein expression:SRSF3-GFP

value: NNNCAATNN


title: Fr-iCLIP_P19_mSRSF3Nu-Replicate3

value: NNNCCACNN


title: Fr-iCLIP_P19_mSRSF3Cy-Replicate2

description: Processed_peaks_P19_mSRSF3_Cy_4Repl_mm9--ensembl59_lowFDR.bed

value: NNNTGGCNN


title: Fr-iCLIP_P19_mSRSF3Nu-Replicate2


title: Fr-iCLIP_P19_mSRSF3Cy-Replicate3


title: Fr-iCLIP_P19_mSRSF3Cy-Replicate1


title: Fr-iCLIP_P19_mSRSF3Nu-Replicate1


title: Fr-iCLIP_P19_mSRSF3Ch-Replicate3

description: Processed_peaks_P19_mSRSF3_Ch_4Repl_mm9--ensembl59_lowFDR.bed

value: Chromatin


title: Fr-iCLIP_mSRSF7Ch-Replicate1

description: Processed_peaks_P19_mSRSF7_Ch-3Repl_mm9--ensembl59_lowFDR.bed


title: Fr-iCLIP_P19_mSRSF3Cy-Replicate4


title: Fr-iCLIP_P19_mSRSF3Ch-Replicate4


title: Shoot without salt treatment 3

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
The tagged libraries were sequenced using a HiSeq 2500 (Illumina Inc.).
Trimmomatic (Bolger et al., 2014) was used to discard low-quality reads, trim adaptor sequences, trim low quality nucleotides at the beginning or end of the read (PHRED33 quality score of less than 3), and discard short reads (under 21 nt).
The retained high-quality reads were mapped to the C. sativa reference genome and transcripts available in the NCBI C. sativa release 100 (JFZQ00000000.1, Kagale et al., 2014) using STAR (Dobin et al, 2012)
For each gene, normailization for library size was performed by dividing the counts by the library size following the method described by Anders and Huber, 2010 to yield CPM
Further normalization was performed using DESeq to approximate a negative binomial distribution.
The differential expression analysis of digital gene expression data software (edgeR) was used to calculate expression changes between libraries (Chen et al., 2014).  The Biological Coefficient of Variation (BCV) value was set to 2 according to the software's instructions.  Expression changes were said to be significant if the multiple test corrected p-value and the false discovery rate (FDR) were ≤ 0.05 and the absolute value of  log 2 CPM was higher than 1.
Genome_build: C. sativa release 100 (JFZQ00000000.1)
Supplementary_files_format_and_content: MS Excel spreadsheet with the genes as rows and the samples as columns.  Each replicate is it's own column.

molecule: polyA RNA

organism: Camelina sativa

source_name: Whole Shoot

growth_protocol: Camelina sativa cv. DH55 seeds were sown in soil-less potting mixture (Stringham, 1971) in 10 x 10 x 8 cm square pots.  Plants were grown in a controlled growth chamber (16 h light/8 h dark, 20/17°C) supplemented with halogen lights.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen Inc.)
cDNA libraries were prepared using the TruSeq Stranded mRNA and Total RNA Library Prep kits with TruSeq LT indexed adaptors (Illumina Inc.).

treatment_protocol: NaCl solutions at 192 mM were prepared to obtain a solution with an electrical conductivitie (EC) of 15 dSm-1 at 20°C. 50 ml of tap water (EC 1,248 µSm-1) was applied daily to each pot and replaced with 50 ml of saline solution (EC 15 dSm-1) 7 days after sowing.  The accumulation of salt in the pots was controlled by draining and the EC of the drained water was measured weekly.  Shoot and root matter was harvested 21 days after the initial salt treatment just before the plants began to bolt.

tag: infraspecific name

value: 28 days after planting

value: Whole Shoot


title: Shoot without salt treatment 2


title: Fr-iCLIP_P19_mSRSF3Ch-Replicate2


title: Root without salt treatment 3

source_name: Root

value: Root


title: Fr-iCLIP_P19_mSRSF3Ch-Replicate1


title: Root without salt treatment 2


title: Root without salt treatment 1


title: Shoot without salt treatment 1


title: Root after salt treatment 3


title: Root after salt treatment 2


title: Fr-iCLIP_mSRSF7Ch-Replicate3


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 52

status: Public on Aug 09 2017

city: Boston

middle: N

last: Campbell

state: Massachusetts

address: Center for Life Science, room 7-717

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
Base calls performed with bcl2fastq2.17.1.14
Alignment by HISAT2 v2.0.5 (with option "-k 2")
Removal of duplicates and low quality reads, indexing, and sorting: Picard 2.5.0 and samtools 0.1.19.
Assigned reads to features: featureCounts-1.4.6. [Using recommended setting and a custom meta-annotation that merges overlapping isoforms.]

Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CSV file containing expression values in log2 (counts per million +1) with columns of single-neuron samples and rows of genes

source_name: NTS HSD2 Neuron

extract_protocol:
tdTomato+ cells were manually isolated from a cell suspension prepared by triturating and washing papain-digested Arc-ME
Single cells were frozen at -80degC and then processed into RNA-seq libraries using Smart-Seq2 (Picelli et al., 2015) and Nextera XT

tag: strain

value: Mixed

value: Nucleus of the solitary tract

tag: Sex

value: M

tag: diet

value: low sodium


title: Fr-iCLIP_mSRSF7Ch-Replicate2

value: P19 embryonal carcinoma cell line fusion protein expression:SRSF7-GFP


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 51


title: Root after salt treatment 1


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 50


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 49


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 47


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 46


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 48


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 45


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 31


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 30


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 42


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 25


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 28


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 32


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 18


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 17


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 57


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 16


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 15


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 10


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 7


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 9


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 14


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 13


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 5


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 12


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 6


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 4


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 3


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 34


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 65

value: standard chow


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 63


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 35


title: rB_wt_H4K16Ac

source_name: resting B cell

value: WT

value: spleen

value: Millipore, 07-329


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 59


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 62


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 60


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 55


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 35


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 39


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 36


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 32


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 33


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 21


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 27


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 66


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 20


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 68


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 12


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 19


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 8


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 7


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 23


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 9


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS LSD Neuron 8


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 4


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 18


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 3


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 38


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 49


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 17


title: Tn5_seq_WT_parS_plus

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
Library strategy: Tn5-Seq
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. For analysis of E. coli ChIP-seq data, reference genomes were first reconstructed in silico by inserting the nucleotide sequence of parS and apramycin antibiotic resistance cassette to the ybbD locus of E. coli MG1655 genome. Afterwards, Hiseq 2500 Illumina short reads were mapped back to these reconstructed reference genomes using Bowtie 1. Sequence coverage at each nucleotide position was also computed using BEDTools. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
For analysis of IDAP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, sequencing reads were sorted to either being mapped to the upper DNA strand or to the lower strand of the reference genome, as suggested in the original IDAP-seq publication (Belitsky and Sonenshein, 2013). The number of 5’ end of reads that were mapped to the upper strand was counted for each nucleotide position along the Caulobacter genome using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -5 -strand + -ibam output.sorted.bam -g NA1000.fna > upper_strand_output.txt. To count the number of 5’ end of reads that were mapped to the lower strand, the following command was used instead: bedtools genomecov -d -5 -strand - -ibam output.sorted.bam -g NA1000.fna > lower_strand_output.txt. The IDAP-seq profile was then plotted using R. The sequence in between the summit of upper strand profile and that of the lower strand profile defines the minimal parS sequence required for binding to ParB.
Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage for each nucleotide position was computed using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, the ratio between the number of reads of libraries generated from pMCS1-Tn5-ME-R6Kγ-kanR-ME or pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME were calculated. Results were binned over 1 kb and represented as a log10 scale.
Genome_build: NC_000913.3
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from RNA-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides

source_name: Caulobacter crecentus CB15N

growth_protocol: Cultures of Caulobacter (TLS1631-TLS1633) were grown at 30oC in PYE and supplemented with antibiotics, as necessary, at appropriate concentrations. To deplete wild-type non-tagged ParB, exponential-phase cells were washed off xylose and re-introduced to PYE+0.2% glucose for an additional 5 hours. After 4 hours, vanillate was added to induce the expression of flag-parB (WT) or flag-parB (G101S/R104A) for an hour. Cultures of Escherichia coli (TLS1637-TLS1650) were grown at 30oC in LB and supplemented with antibiotics, as necessary, at appropriate concentrations. IPTG (0.5mM) was added to induce the production of T18-ParB (WT) or T18-ParB (G101S). After an hour, formadehyde (1% final concentration) were added to fix cells for ChIP-seq.

extract_protocol:
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 sequencing platform

treatment_protocol:
no treatment
None

value: mixed population, exponential phase

value: wild-type CB15N


title: Tn5_seq_Flip25_parS_plus

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. For analysis of E. coli ChIP-seq data, reference genomes were first reconstructed in silico by inserting the nucleotide sequence of parS and apramycin antibiotic resistance cassette to the ybbD locus of E. coli MG1655 genome. Afterwards, Hiseq 2500 Illumina short reads were mapped back to these reconstructed reference genomes using Bowtie 1. Sequence coverage at each nucleotide position was also computed using BEDTools. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
For analysis of IDAP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, sequencing reads were sorted to either being mapped to the upper DNA strand or to the lower strand of the reference genome, as suggested in the original IDAP-seq publication (Belitsky and Sonenshein, 2013). The number of 5’ end of reads that were mapped to the upper strand was counted for each nucleotide position along the Caulobacter genome using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -5 -strand + -ibam output.sorted.bam -g NA1000.fna > upper_strand_output.txt. To count the number of 5’ end of reads that were mapped to the lower strand, the following command was used instead: bedtools genomecov -d -5 -strand - -ibam output.sorted.bam -g NA1000.fna > lower_strand_output.txt. The IDAP-seq profile was then plotted using R. The sequence in between the summit of upper strand profile and that of the lower strand profile defines the minimal parS sequence required for binding to ParB.
Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage for each nucleotide position was computed using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, the ratio between the number of reads of libraries generated from pMCS1-Tn5-ME-R6Kγ-kanR-ME or pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME were calculated. Results were binned over 1 kb and represented as a log10 scale.
Genome_build: NC_000913.3
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from RNA-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

treatment_protocol: no treatment

value: Flip2_5 CB15N


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 5


title: Tn5_seq_Flip15_parS_plus

value: Flip1_5 CB15N


title: Tn5_seq_Flip15_parS_minus


title: Tn5_seq_WT_parS_minus


title: IDAP_seq_ParB_His6

data_processing:
Library strategy: IDAP-Seq
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. For analysis of E. coli ChIP-seq data, reference genomes were first reconstructed in silico by inserting the nucleotide sequence of parS and apramycin antibiotic resistance cassette to the ybbD locus of E. coli MG1655 genome. Afterwards, Hiseq 2500 Illumina short reads were mapped back to these reconstructed reference genomes using Bowtie 1. Sequence coverage at each nucleotide position was also computed using BEDTools. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
For analysis of IDAP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, sequencing reads were sorted to either being mapped to the upper DNA strand or to the lower strand of the reference genome, as suggested in the original IDAP-seq publication (Belitsky and Sonenshein, 2013). The number of 5’ end of reads that were mapped to the upper strand was counted for each nucleotide position along the Caulobacter genome using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -5 -strand + -ibam output.sorted.bam -g NA1000.fna > upper_strand_output.txt. To count the number of 5’ end of reads that were mapped to the lower strand, the following command was used instead: bedtools genomecov -d -5 -strand - -ibam output.sorted.bam -g NA1000.fna > lower_strand_output.txt. The IDAP-seq profile was then plotted using R. The sequence in between the summit of upper strand profile and that of the lower strand profile defines the minimal parS sequence required for binding to ParB.
Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage for each nucleotide position was computed using BEDTools (Quinlan & Hall, 2010) and the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, the ratio between the number of reads of libraries generated from pMCS1-Tn5-ME-R6Kγ-kanR-ME or pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME were calculated. Results were binned over 1 kb and represented as a log10 scale.
Genome_build: NC_000913.3
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from RNA-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

treatment_protocol:
sonication-fragmented genomic DNA from wild-type Caulobacter was used. ParB-His6 was added duing in vitro affinity purification.
None


title: Tn5_seq_delta_smc_parS_minus

value: CB15N delta smc


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 29


title: Tn5_seq_delta_smc_parS_plus


title: IDAP_seq_no_protein_control

treatment_protocol:
sonication-fragmented genomic DNA from wild-type Caulobacter was used. No protein was added duing in vitro affinity purification.
None


title: LELab_ChIP_seq_TLS1633_anti_FLAG

treatment_protocol:
cells were depleted of wild-type non-tagged ParB for 5 hours, then FLAG-ParB (R104A) were produced for an hour before formadehyde were added to 1% (final concentration) to fix cells for ChIP-seq.
None

value: CB15N parB::Pxyl-parB van::Pvan-1xflag-parB (R104A)

tag: antibody

value: Flag


title: LELab_ChIP_seq_TLS1632_anti_FLAG

treatment_protocol:
cells were depleted of wild-type non-tagged ParB for 5 hours, then FLAG-ParB (G101S) were produced for an hour before formadehyde were added to 1% (final concentration) to fix cells for ChIP-seq.
None

tag: developmental stage

value: CB15N parB::Pxyl-parB van::Pvan-1xflag-parB (G101S)


title: LELab_ChIP_seq_WT_anti_ParB

treatment_protocol:
formadehyde was added to 1% (final concentration) to fix cells for ChIP-seq
None

value: ParB


title: Col-S ozone rep2

city: Helsinki

first: Mikael

last: Brosché

address: Viikinkaari 1

department: Department of Biosciences

country: Finland

institute: University of Helsinki

data_processing:
RNA-seq data analysis was performed with the JAVA-based client-server system Chipster
Quality of sequences was checked with FastQC package
First 13 reads were trimmed FRINSEQ package, then mapped to wild type Col-0 whole genome using TopHat2 with following settings:Do not ignore novel junctions, hits allowed=2, allowing 2 nucleotide mismatches, minimum anchor length=8, Maximum number of mismatches allowed in the anchor=0, minimum intron length=20, Maximu intron length=2000
Generated BAM files were sorted and indexed with SAMtools package
Number of Reads of each gene was counted and calculated with HTSeq package
Genome_build: Col-0 TAIR10.23
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromsomes, start, end, length and reads per gene values for each sample

organism: Arabidopsis thaliana

source_name: whole rosette

growth_protocol: Seeds were sown on 1:1 peat: vermiculite, stratified for three days, and then grown at 22°C/19°C for a week. Subsequently the geminated seedlings were transplanted into new 1:1 peat: vermiculite mixture, one plants per pot (6cm x 6cm), and eight plants per genotype. All plants were randomly placed, grown in controlled chamber (Weiss Bio1300; Weiss Gallenkamp), at 22°C/19°C, and relative humidity of 70%/90%, under a 12-h light/12-h dark cycle for two weeks.

extract_protocol:
Ten to 15 rosettes per genotype from control and ozone treatment were pooled and frozen into liquid nitrogen. Three biological replicates of RNA were isolated with GeneJet Plant RNA purification Mini Kit (Fermentas, now part of Thermo Scientific). Quality and quantity of RNA was assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared from 100 ng of total RNA with Illumina TruSeq RNA Sample Prep Kit v2 according to the kit manual.

treatment_protocol: Plants were exposed with 350 nL L-1 ozone for two hours.

value: Col-S

value: 3 weeks old plants

value: whole rosette

tag: treatment

value: 350 ppb ozone exposure for 2hr


title: LELab_ChIP_seq_MT190_anti_GFP

value: CB15N parB::cfp-parB

value: GFP


title: LELab_ChIP_seq_TLS1634_anti_FLAG

treatment_protocol:
exponential-phase cells in PYE + 0.3% xylose, 1% formadehyde was added to fix cells for ChIP-seq
None

value: CB15N pML477::1xflag-yfp


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 1

value: Mixed

value: Nucleus of the solitary tract

value: M

value: standard chow


title: Col-S ozone rep1


title: Col-S ctrl rep2

value: control


title: Tn5_seq_Flip25_parS_minus

value: mixed population, exponential phase

value: Flip2_5 CB15N


title: Col-S ctrl rep3


title: LELab_ChIP_seq_TLS1631_anti_FLAG

treatment_protocol:
cells were depleted of wild-type non-tagged ParB for 5 hours, then FLAG-ParB (WT) were produced for an hour before formadehyde were added to 1% (final concentraation) to fix cells for ChIP-seq.
None

value: CB15N parB::Pxyl-parB van::Pvan-1xflag-parB (WT)

value: Flag


title: Col-S ozone rep3


title: Cvi-0 ctrl rep3


title: Cvi-0 ozone rep3


title: Col-S ctrl rep1


title: Cvi-0 ctrl rep1


title: Cvi-0 ctrl rep2


title: Col-0 ozone rep3


title: Col-0 ozone rep1


title: Col-0 ctrl rep3


title: Col-0 ctrl rep2


title: Col-0 ctrl rep1


title: J1-F

city: Manassas

first: Fatah

last: Kashanchi

state: VA

address: 10900 University Blvd

institute: George Mason University

description: Novel viral noncoding RNA

data_processing:
Base calling: bcl2fastq 2.17.1.14, Output: FastQ file
Read Alignment: bowtie 2.2.9, Output: Bam file
Peak-calling: Samtools 1.3.1 and perl scripts, Output: wig file
Genome_build: HIV_genome
Supplementary_files_format_and_content: WIG format; read depth at each genomic location

source_name: J1.1-derived exosomes

growth_protocol: Cells were grown in RPMI 1640 complete media at 37 degrees Celsius and 5.0% carbon dioxide for five days.

extract_protocol:
Fragmented by Fragmentase
Exosomes were isolated from culture media using nanotrap particles NT80 and NT82 (Ceres Nanosciences).  The samples were rotated with the nanotraps overnight at 4 degrees Celsius.  The RNA was then isolated from the exosomes using TRI Reagent-LS (MRC) according to the manufacturer's protocol.
The extracted RNA was converted to cDNA using miRNA cDNA Synthesis Kit (Applied Biological Materials Inc.) with two sequence specific primers. Three sequencing libraries were made from the same cDNA library: 1) Nextera XT method, 2) Fragmentase method, and 3) unfragmented.

tag: cell type

value: HIV-1 LAV

tag: molecule subtype

value: HIV TAR-gag RNA


title: OM10-F

description: Novel viral noncoding RNA

source_name: OM10.1-derived exosomes


title: OM10-U

description: Novel viral noncoding RNA

extract_protocol:
Unfragmented
Exosomes were isolated from culture media using nanotrap particles NT80 and NT82 (Ceres Nanosciences).  The samples were rotated with the nanotraps overnight at 4 degrees Celsius.  The RNA was then isolated from the exosomes using TRI Reagent-LS (MRC) according to the manufacturer's protocol.
The extracted RNA was converted to cDNA using miRNA cDNA Synthesis Kit (Applied Biological Materials Inc.) with two sequence specific primers. Three sequencing libraries were made from the same cDNA library: 1) Nextera XT method, 2) Fragmentase method, and 3) unfragmented.


title: Cvi-0 ozone rep1

value: 3 weeks old plants


title: J1-XT

description: Novel viral noncoding RNA

extract_protocol:
Nextera XT method
Exosomes were isolated from culture media using nanotrap particles NT80 and NT82 (Ceres Nanosciences).  The samples were rotated with the nanotraps overnight at 4 degrees Celsius.  The RNA was then isolated from the exosomes using TRI Reagent-LS (MRC) according to the manufacturer's protocol.
The extracted RNA was converted to cDNA using miRNA cDNA Synthesis Kit (Applied Biological Materials Inc.) with two sequence specific primers. Three sequencing libraries were made from the same cDNA library: 1) Nextera XT method, 2) Fragmentase method, and 3) unfragmented.


title: J1-U

description: Novel viral noncoding RNA


title: Chip3-H9_S96

city: London

first: Deena

middle: L.

last: Gibbons

address: Great Maze Pond

department: Dept. Immunology

institute: Kings College London

data_processing:
Paired-end RNASeq reads from these samples were simultaneously aligned to the human genome (GRCh37/hg19) and ERCC92 spike-in control sequence using Tophat (v2.0.4) and Bowtie2 v2.0.0.beta6 with default settings.
Raw sequence counts mapped to genes or ERCC spike-in controls were obtained using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: consolidated_raw_counts_final - tab-delimited matrix of htseq-count results - gene name (rows) by sample names (columns)

source_name: CD4 T cell

growth_protocol: CD4 T cells from cord blood samples (n=2) were isolated by cell sorting on a FACS Aria (BD) after staining with antibodies for CD4 negative selection (Miltenyi). Samples were then activated for 2.5hrs with PMA and ionomycin (P/I) before washing and collection.

extract_protocol:
The SMARTer kit (Clontech, Mountain View, CA, USA) was used for cDNA generation. 1µL of the ERCC spike-in mix (Life Technologies, Carlsbad, CA, USA) was included in the cell lysis mix at a dilution of 1:1000.  cDNA quantity was measured using the Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and a subset of cDNAs were checked for quality using the Agilent 2200 Tapestation (Agilent Technologies, Waldbronn, Germany).
IL-8 qPCR: To determine expression levels of IL-8, real-time PCR was performed on all 104 single-cell cDNA samples using a sybr-green labelled primer/probe set Hs_CXCL8_1_SG QuantiTect Primer (Qiagen, Germantown, MD, USA). Two Taqman® endogenous control assays were used for normalisation purposes: GAPDH Hs99999905_m1 and EIF4A2 Hs00756996_g1 (Life Technologies). A standard curve of control cDNA from a sample known to express IL8 was run alongside the single-cell DNAs, and all samples were run in triplicate. Data was analysed using the ΔΔCt method.  Library preparation and sequencing: A total of 96 single cells were taken forward for RNA-seq. Libraries were prepared using the Illumina Nextera XT Sample Preparation Kit (Illumina Inc., Cambridge, UK) with an input of 150pg of cDNA per sample. 75bp paired-end reads were generated for each library using the Illumina NextSeq®500.

treatment_protocol: Single-cell capture: Single-cells were captured using the C1™ Single-Cell Auto Prep System (Fluidigm, San Francisco, CA, USA).  Two C1 arrays for mRNA sequencing (5-10µM) were used to isolate single cells. Briefly, 1000 cells were loaded onto each array after confirming cell suspension concentration using a disposable haemocytometer (C-Chip, InCyto, Chungcheongnam-do, Korea). The first array yielded 43 single cells, and the second 61 single cells. Excluded capture sites contained no cell, single cells with obvious cell debris or multiple cells.

value: cord blood

value: CD4 T cell


title: Chip3-H12_S36


title: Chip3-H2_S48


title: Cvi-0 ozone rep2

value: whole rosette

value: 350 ppb ozone exposure for 2hr


title: Chip3-G6_S95


title: Chip3-G8_S24


title: Chip3-H7_S84


title: Chip3-G7_S12


title: Chip3-H3_S60


title: Chip3-H6_S72


title: Col-0 ozone rep2


title: Chip3-G12_S71


title: Chip3-F9_S47


title: Chip3-G3_S83


title: Chip3-F8_S35


title: Chip3-F6_S23


title: Chip3-F12_S11


title: OM10-XT

description: Novel viral noncoding RNA


title: Chip3-F1_S82


title: Chip3-F10_S94


title: Chip3-E9_S70


title: Chip3-E8_S58


title: Chip3-E5_S22


title: Chip3-E6_S34


title: Chip3-E4_S10


title: Chip3-G10_S59


title: Chip3-E7_S46


title: Chip3-E2_S93


title: Chip3-D6_S33


title: Chip3-D9_S57


title: Chip3-C3_S56


title: Chip3-C4_S68


title: Chip3-C5_S80


title: Chip3-D12_S9


title: Chip3-D2_S21


title: Chip3-E10_S81


title: Chip3-D7_S45


title: Chip3-C11_S20


title: Chip3-C12_S32


title: Chip3-C10_S8


title: Chip3-C1_S91


title: Chip3-C2_S44


title: Chip3-B8_S67


title: Chip3-B2_S31


title: Chip3-B9_S79


title: Chip3-B4_S55


title: Chip3-E1_S69


title: Chip3-B3_S43


title: Chip3-D10_S92


title: Chip3-A6_S66


title: Chip3-A9_S90


title: Chip3-A3_S54


title: Chip3-A1_S18


title: Chip3-B1_S7


title: Chip3-A7_S78


title: Chip3-A10_S30


title: Chip3-B11_S19


title: Chip2-G3_S29


title: Chip2-H9_S6


title: Chip2-H1_S65


title: Chip2-F8_S5


title: Chip2-F5_S64


title: Chip2-H2_S77


title: Chip2-G8_S53


title: Chip2-H6_S89


title: Chip2-G4_S41


title: Chip2-F6_S76


title: Chip2-F7_S88


title: Chip2-G12_S17


title: Chip2-F3_S52


title: Chip2-F10_S28


title: Chip3-A11_S42


title: Chip2-D5_S27


title: Chip2-D11_S15


title: Chip2-C2_S3


title: Chip2-D7_S39


title: Chip2-C11_S86


title: Chip2-E8_S16


title: Chip2-E5_S4


title: Chip2-B9_S50


title: Chip2-B5_S14


title: Chip2-B7_S26


title: Chip2-A8_S73


title: Chip2-A3_S49


title: Chip2-B4_S2


title: Chip2-E12_S87


title: Chip2-A7_S61


title: Chip2-E1_S63


title: Patient 221

first: Kenzie

last: MacIsaac

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck Research Labs

data_processing:
Transcriptome sequencing was performed at WuXi AppTec Genome Center on Illumina HiSeq2000 platform (50M cluster, PE100 sequencing).
RNA-Seq data were analyzed using Omicsoft ArraySuite® software
Reads were aligned to the genome using the OSA aligner
The ArraySuite software was used to quantitate transcripts using UCSC gene models
Genome_build: NCBI build 37.1
Supplementary_files_format_and_content: A gene level matrix of FPKM values for each sample is provided in NPC_mRNA_processed.txt

source_name: NPC tumor

extract_protocol:
RNA was prepared from snap-frozen NPC biopsies using Qiagen Allprep DNA/RNA kit (Cat#80204) according to the manufacturer's protocols
Illumina TruSeq RNA Sample Preparation kit was used to construct libraries.

tag: expression-based subtype

value: I

tag: time to event

tag: event

value: Disease progression

tag: clinical stage

value: III

tag: % stromal tils

tag: % intratumoral tils

tag: morphology

value: mixed (round & spindle)

tag: non-synonymous mutation burden

tag: cohort

value: Unpaired


title: Patient 39

value: II

value: Last follow-up

value: Not evaluated


title: Chip2-E10_S75

tag: tissue


title: Patient 369

value: Paired


title: Patient 178

value: IV

value: undifferentiated, round


title: Patient 346

value: differentiated


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 47

tag: strain

value: Mixed

value: Nucleus of the solitary tract

tag: Sex

value: M

value: standard chow


title: Hsd11b2-Cre::Ai9(lox)tdTomato+ NTS CHOW Neuron 45

tag: diet


title: Chip2-F2_S40

value: cord blood

value: CD4 T cell


title: Chip2-C1_S62


title: Patient 56

value: I

value: Disease progression


title: Patient 298

value: III


title: Chip2-B8_S38


title: Patient 443

value: Unpaired


title: Chip2-A2_S37


title: Chip2-A1_S1


title: Patient 260

value: mixed (round & spindle)


title: Chip2-D9_S51


title: Patient 151

value: II

value: Unknown


title: Patient 237

value: Last follow-up


title: Patient 293

value: undifferentiated, spindle


title: Patient 71

value: Paired


title: Chip2-A10_S13


title: Patient 357

value: undifferentiated, round


title: Patient 173


title: Patient 296


title: Patient 27

value: IV

value: Not evaluated


title: Patient 1


title: Chip2-A12_S25


title: Chip2-C10_S74


title: Patient 426


title: Patient 383


title: Chip2-B2_S85


title: Patient 336


title: Patient 421


title: Patient 207


title: Patient 5


title: Patient 337


title: Patient 431


title: Patient 341

value: differentiated


title: Patient 40


title: Patient 391


title: Patient 439


title: Patient 290


title: Patient 305


title: Patient 320


title: Patient 332


title: Patient 322


title: Patient 388


title: Patient 14


title: Patient 258


title: Patient 54


title: Patient 97


title: Patient 144


title: Patient 69


title: Patient 15


title: Patient 407


title: Patient 41


title: Patient 20


title: Patient 355


title: Patient 406


title: Patient 192


title: Patient 278


title: Patient 306


title: Patient 229


title: Patient 329


title: Patient 338


title: Patient 392


title: Patient 243


title: Patient 233


title: Patient 235


title: Patient 240


title: Patient 389


title: Patient 55


title: Patient 302


title: Patient 65


title: Patient 445


title: Patient 209


title: Patient 286


title: Patient 70


title: Patient 36


title: Patient 204


title: Patient 13


title: Patient 34


title: Patient 37


title: Patient 38


title: Patient 294


title: Patient 396


title: Patient 452


title: Patient 414


title: Patient 99


title: Patient 19


title: Patient 46


title: Patient 226


title: Patient 354


title: Patient 96


title: Patient 438


title: Patient 44


title: Patient 450


title: Patient 79


title: Patient 12


title: Patient 422


title: Patient 18


title: Patient 177


title: Patient 16


title: Patient 75


title: Patient 263


title: Patient 48


title: CBP80_rep3

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT against hg19.
Uniquely mapped and properly paired reads were used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

source_name: CBP80 total RNA replicate 3

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNA was extracted with Trizol and PureLink RNA Mini Kits (Thermo Scientific) and using on-column DNase I (PureLink DNase; Thermo Scientific) digestion according to the manufacturer’s manual.
Libraries were prepared, after rRNA-depletion using Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat; Illumina), using Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: siRNA transfections were performed targeting EGFP(control), ARS2, ZC3H18 and CBP80

value: HeLa Kyoto

tag: transfected with

value: siRNA targeting CBP80


title: Patient 100


title: CBP80_rep2

source_name: CBP80 total RNA replicate 2


title: CBP80_rep1

source_name: CBP80 total RNA replicate 1


title: Patient 437


title: Patient 331


title: Patient 196


title: Patient 152


title: DNA Input KO

city: Portsmouth

first: Samuel

last: Robson

address: St Michael's Building

department: School of Pharmacy & Biomedical Science

institute: University of Portsmouth

data_processing:
Library strategy: ChIRP-Seq
ChIRP-seq: Multiplexed reads were split based on their TRUseq barcodes using Illumina Basespace. Reads were tirmmed to remove the TRUseq adapter using trim_galore with parameters "-q 0 -a AGATCGGAAGAGCACACGTCTGAA --phred33 --fastqc". Read quality was assessed using FastQC. Ribosomal contamination was removed by first mapping the reads to mm10 rDNA sequences using bwa, and removing all reads that map. Trimmed non-ribosomal reads were mapped to the mm10 genome using bwa with default parameters. Multiple reads mapping to a single genomic locus were treated as PCR duplicates, and were removed using samtools rmdup. Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag XT:A:U in the output bam file from bwa. Reads were further filtered to remove reads with mapping quality less than 20 using samtools. Genome coverage bedgraph files were generated using genomeCoverageBed from the bedtools suite of tools. Coverage files were converted to bigwig format using bedGraphToBigWig. Peaks were called against either the WT or KO input sample using MACS1.4 using parameters "-f BAM -g mm -p 0.01 --bw=300 -m 10,30".
RNA-seq: Single end sequencing was performed and the reads were mapped using NCBI38/mm10 with Ensembl version 75 annotations. RNA-seq reads were aligned to the reference genome using tophat2. Only uniquely mapped reads were used for further analysis. Gene counts from SAM files were obtained using htseq-count with mode intersection non-empty, -s reverse. Differential gene expression analysis was conducted using Bioconductor R package DESeq2 version 1.4.5. DESeq2 provides two P-values, a raw P-value and a Benjamini-Hochberg P-value (adjusted p value). An adjusted p-Value threshold of 0.05 was used to determine differential gene expression (95% of the results are not false discoveries, error rate 0.05 =5%).
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files give coverage scores across the whole mm10 genome at each base position for the ChIRP seq reads. Normalised and non-normalised coverage files are provided for each sample. Peak bed files give the enriched peak regions called against input for the ChIRP-Seq data. htseq files give read counts of uniquely mapping RNA seq data across all transcripts in Ensembl 75 database using "-m intersection-nonempty" and either "-s reverse" ("[filename].uniq.rsorted.sr.counts.intersection.nonempty" or  "-s yes" ("[filename].uniq.rsorted.ss.counts.intersection.nonempty".

source_name: Whole cell

growth_protocol: ESCs were cultured on 0.1% gelatin in PDL/LIF medium (NDiff B27 base medium, Stem Cell Sciences, cat. SCS‐SF‐ NB‐02, supplemented with 1 μM PD0325901 and 20 ng/ml LIF).

extract_protocol:
Probe bound DNA was eluted and the DNA was purified using phenol:chloroform:isoamyl (Invitrogen) and precipitated with ethanol at −80°C overnight.
The sequencing library was prepared and barcoded using ThruPLEX DNA-seq protocol (Rubicon Genomics).Barcoded samples were combined together at uniform molarity to create a single pool, which was sequenced in a single end 50 bp run on an Illumina HiSeq 4000 machine.

treatment_protocol: The antisense oligo probes were selected with GC content in the range of 40%-50% in regions of the Ephemeron exons without repetitive sequences. CHIRP was conducted following published protocol (Chu et al., 2011).

value: mouse embryonic stem (mES) cells

tag: background strain

tag: genotype/variation

value: knockout of the lncRNA ephemeron (KO)

tag: concentration

tag: truseq barcode

value: TTCAGCTC


title: Patient 61

tag: expression-based subtype

value: I

tag: time to event


title: Ephemeron KO Rep2

tag: cell type

value: TCAGATTC


title: Patient 236

tag: event

tag: clinical stage

tag: % stromal tils

value: mixed (round & spindle)

value: Unpaired


title: DNA Input WT

value: wild-type

value: TACTAGTC


title: Patient 349

value: Last follow-up

value: II

tag: % intratumoral tils

tag: morphology

tag: non-synonymous mutation burden


title: Patient 289

value: III

value: Unknown

tag: cohort

value: Paired


title: 7SK WT

value: TGGCTCAG


title: Ephemeron WT Rep2

value: TCATTGAG


title: Ephemeron KO Rep1

value: TATGCCAG


title: Ephemeron WT Rep1

value: mouse embryonic stem (mES) cells

value: CTTGTACT


title: Patient 344

value: undifferentiated, round


title: Patient 300

value: I


title: Patient 29

value: differentiated

value: Not evaluated


title: RNAseq_08hpi_cytoplasmic

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: Directional RNA sequencing

data_processing:
Due to the design of our 5’ RNA adapter, each capsnatch-Seq read starts with 12 adapter-derived nucleotides, consisting of 3 random nt, followed by a 6-nt unique barcode sequence, and another 3 random nts. Demultiplexing and removal of these 5’ adapter sequences was done using custom scripts, allowing up to two barcode base mismatches and no insertions/deletions. Remaining sequences were additionally trimmed at the 3’-end after reaching a base with a phred quality score lower than 10, or after encountering 15 bases with a phred score lower than 28. Finally, 3' Illumina adapter sequences were removed using cutadapt with a minimal overlap of 6bp and allowing for an adapter error rate of 15%. Reads less than 50nt in length after quality and adapter trimming were removed from further analysis.
To identify uniformly host- and virus-derived 5’ RNA sequences, full-length adapter-trimmed reads were mapped to the human (hg19) and viral (IAV, IBV or LCMV) reference genomes using TopHat 2.0.12 and Bowtie 1.0.1 with the corresponding gene annotations (Gencode GRCh37/V19-Ensembl74 for the human genome), requiring a minimal anchor size of 10 nucleotides and using default settings for all other arguments. To identify hybrid viral mRNA sequences, the first 20 nucleotides of each read were first masked prior to mapping to viral reference genomes using the same strategy. Hybrid reads were then identified as those masked reads mapping to the positive strand of a viral genome segment, with a start coordinate less than 20bp from the segment start. In the case of the LCMV virus, which produces both positive- and negative-strand mRNAs, a custom reference genome sequence was used during this step. To prepare the custom LCMV reference, the ‘S’ segment was cut at position 1610, maintaining the 5’ part as the reference for the “envelope glycoprotein” (EGP) gene, while the remainder of the segment was reverse-complemented and used as the reference for the “nucleoprotein” (NP) gene. Likewise, the ‘L’ reference sequence was cut at position 6300 to produce a 5’ sequence encoding the “L protein” and a reverse-complemented 3’ sequence encoding a putative “hypothetical protein”. Finally, the host- and virus-derived segments of each hybrid read were identified by comparing the unmasked reads to the consensus viral genome segment sequence.
For comparison of capsnatched sequences to human 5' RNA sequences and attribution of capsnatch origin, a dictionary of unique human RNA 5' ends (9-16bp) and their genes of origin was first built based on full-length reads mapped to the human genome. Each mapped read was associated to the closest gene transcription start site (TSS) up to a maximum distance of 500bp. Host-derived capsnatch sequences were then matched to the host 5’ end sequence dictionary and assigned a gene and TSS of origin. In case capsnatch sequences mapped to multiple origins, capsnatch sequence counts were proportionally distributed among matching host genes according to the 5’-end read abundance of the host genes.
For directional RNA-seq, reads were aligned against the human reference genome using STAR. Number of reads matching refseq annotations were counted using htseq-count (mode intersection-strict).
Genome_build: Human: Gencode GRCh37/V19-Ensembl74
Genome_build: IAV: A/Puerto Rico/8/1934 H1N1, assembly ViralMultiSegProj15521
Genome_build: IBV: B/Wisconsin/01/2010 (https://www.fludb.org/brc/fluStrainDetails.spg?strainName=B/Wisconsin/01/2010&decorator=influenza Sequences from IRD submission "NIGSP_BUCB_00032" were used as reference)
Genome_build: LCMV: Armstrong 53b (Segment S: NCBI NC_004294.1 – LCMV Segment L: NCBI NC_004291.1), assembly ViralMultiSegProj14862
Supplementary_files_format_and_content: Tab-separated text files summarizing for each gencode transcript the number of host-mapped reads as well as the count of capsnatch events after proportional reattribution

molecule: cytoplasmic RNA

source_name: Infected adenocarcinomic human alveolar basal epithelial cells

growth_protocol: A549 cells were originally obtained from the American Type Culture Collection and maintained at 37 °C with 5% CO2 in F-12K Media (Gibco) supplemented with 10% Fetal Bovine Serum (Corning) and 1%Penicillin Streptomycin Solution (Corning cellgro). Cells were infected with either Influenza A/Puerto Rico/8/1934(H1N1), Influenza B/Wisconsin/01/2010, or Lymphocytic Choriomeningitis (ARM 53b) virus at a multiplicity of infection (MOI) of 2 with a viral media consisting of 1X PBS + 0.3% BSA.  Virus was removed 1hr post infection and cells were allowed to grow in complete F-12K media (as described above) at 37°C. Cell pellets were collected from uninfected controls (0hrs), as well as 2hrs, 4hrs, 6hrs, 8hrs, and 10hrs post-infection for IAV or 4hrs and 8hrs post infection for IBV and LCMV. Cell pellets were washed with 1X PBS twice and stored at -80°C until RNA extraction.

extract_protocol:
Directional RNA sequencing : 1 µg  of DNase-treated RNA was depleted of rRNAs using the Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina) according to the manufacturer’s instructions, and purified post-depletion with 1.6X volume AMPureXP beads. Barcoded directional RNA-Seq libraries were then prepared using the NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs), per kit instructions. PCR products were purified with 1.8X volume AMPure XP beads and fragments of 300-500bp were size-selected using BluePippin 2% M1 gels (Sage Scientific). Afterwards, libraries were sequenced on the Illumina HiSeq 2500 platform in a 100 bp single-end read run format.
Cytosolic/Nucleic fractionation: Cell pellets were re-suspended in 1.2 mL of solubilization buffer (50mM 1M HEPES-KOH, pH 7.5; 140mM 5M NaCl; 1mM 0.5M EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; water to 100ml) containing 1X proteinase inhibitor cocktail mix, and rotated at 4°C for 10 minutes. Samples were centrifuged at 1350g for 5 minutes at 4°C. The cytosolic supernatant was transferred to a clean tube, leaving behind the nuclear pellet. RNA extraction : RNA was extracted from cytosolic, nucleic or total fractions using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions, adding 600 µls RLT Buffer and 6 µls of B-Mercaptoethanol to each sample. The RNA was eluted in 30 µl of nuclease-free water. Samples were DNase treated with 1U Baseline Zero DNase (Epicentre) at 37°C for 30 minutes according to the manufacturer’s instructions, cleaned up with 1.8X volume of AMPureXP beads (Beckman-Coulter) and eluted in nuclease free water. RNA quality (RIN>9) was assessed using the Agilent Bioanalyzer and quantified using the Qubit RNA Broad Range Assay kit (ThermoFisher). An aliquot of each sample was tested for mycoplasma contamination using the eMyco Plus Mycoplasm PCR Detection Kit (Intron Biotechnology). Additional testing was done during capsnatch-seq data analysis by determining if any next-generation sequencing reads mapped exclusively to mycoplasma reference genomes available in the NIH Genbank database.

tag: cell line

tag: viral strain

value: A/Puerto Rico/8/1934 H1N1

tag: treatment

tag: timepoint

value: 08 hours post-infection


title: Patient 234

value: mixed (round & spindle)


title: Patient 78

value: Disease progression


title: RNAseq_04hpi_nucleic

description: Directional RNA sequencing

molecule: nuclear RNA

value: 04 hours post-infection


title: RNAseq_08hpi_nucleic

description: Directional RNA sequencing


title: RNAseq_04hpi_cytoplasmic

description: Directional RNA sequencing


title: Patient 264

value: Last follow-up

value: Unpaired


title: ZR-75B

city: Suwon-si,

first: Seong-Jin

last: Kim

address: 145 Gwanggyo-ro, Yeongtong-gu,

country: South Korea

institute: Nano-Bio Medicine Research Center

data_processing:
An Illumina platform (Illumina) was used to analyze transcriptomes with 90 bp paired-end library.
Illumina Hiseq software used for basecalling.
Samples were paired-end sequenced with the Illumina HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: text files include FPKM values for each Sample.

source_name: Breast cancer cell lines

extract_protocol:
Total RNAs of each cell were isolated using the TRIzol reagent for RNA sequencing following manufacturer’s instructions. The total RNAs were treated with DNase I, purified with miRNeasy Mini Kit and subsequently quality checked using an Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subtype

value: Luminal

tag: species

value: Human


title: RNAseq_00hpi_cytoplasmic

description: Directional RNA sequencing

source_name: adenocarcinomic human alveolar basal epithelial cells

value: 00 hours post-infection


title: MDA-MB-435

value: Basal-like