title: micro-g rep. 3

city: Gainesville

first: Kelly

middle: C

last: Rice

state: FL

address: 1355 Museum Dr

department: Microbiology and Cell Science

institute: University of Florida

data_processing:
Illumina CASAVA software was used to create genomic builds and count reads
TopHat-2.0.8b was used to align reads to the S. mutans UA159 genome
Cufflinks-2.0.1 was used to perform DE analysis using FPKM (fragments per kilobase per million mapped reads) values and fold-change was expressed as log2 (FPKM normal gravity / FPKM simulated microgravity)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: text file with cuffdiff output

organism: Streptococcus mutans

source_name: simulated microgravity HARV culture

growth_protocol: All S. mutans cultures (including HARV vessels) were grown at 37°C in a 5% CO2 incubator. For each experiment, S. mutans was freshly streaked from a frozen 30% (vol vol-1) glycerol stock onto Brain Heart Infusion (BHI) agar and grown for 48 hours. A single colony was then inoculated into 30 ml BHI broth, and grown as a static culture for 16-18 hours prior to inoculation of HARVs. Disposable Vessel Rotary Cell Culture Systems (Synthecon) with vertical and horizontal 4-station rotator bases were used to simulate microgravity (HARV rotated on axis perpendicular to gravitational vector) and “normal” (1 xg) gravity (HARV rotated on axis parallel to gravitational vector), respectively. HARV vessels were filled with sterile media according to manufacturer’s recommendations, and incubated at room temperature for 18 hours prior to each experiment. This media was then aseptically removed, and 20x dilute S. mutans overnight culture (approximate OD600 = 0.06/ml) in room-temperature semi-defined biofilm media containing 11 mM glucose and 10 mM sucrose, was used to fill each HARV. For each experiment (n=3 independent experiments total), 3 simulated microgravity and 3 normal gravity HARV cultures were grown in parallel at 37°C, 5% CO2, and 30 RPM for 8 hours.

extract_protocol:
A 10-ml aliquot of each HARV culture was centrifuged at 3,000 RPM, 4°C for 20 minutes and immediately placed on ice. Culture supernatants were decanted and 1 ml RNAlater (Ambion) was added to each cell pellet prior to immediate storage at -80°C. RNA was isolated with the RNeasy Kit (Qiagen) and FASTPREP lysing matrix B tubes (MP Biomedical) using previously-described methods. Each RNA sample was then subjected to a second DNAse treatment using the TURBO DNA-free™ Kit (Thermo Fisher Scientific) per the manufacturer’s protocols. Lack of contaminating genomic DNA in each RNA sample was determined using quantitative real-time PCR prior to sending ≥ 5 µg of each RNA sample to Seqwright Genomic Services (Houston, TX), who performed all steps of the RNA-seq workflow, data curation, differential expression and corresponding statistical analysis.
Each RNA sample was subjected to an mRNA enrichment step and generation of a library of cDNA template molecules of known strand origin using the TruSeq Total mRNA Sample Preparation Kit (Illumina). Sequencing was performed using the Illumina HiSeq 2500 platform, generating 2 x 100bp read lengths for a total of 2 x 10M reads per sample.

tag: time point

value: 8 hours growth

tag: gravity level

value: simulated microgravity


title: flg22 9 hrs; dde2-2; rep1

status: Public on Mar 01 2017

type: SRA

city: St Paul

first: Fumiaki

last: Katagiri

state: Minnesota

address: 1500 Gortner Ave

department: Dept of Plant and Microbial Biology

country: USA

institute: Univ of Minnesota

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 87

library_source: transcriptomic

data_processing:
quality filter (during lane de-multiplexing): reads with any undetermined bases (N) in the barcode were removed
barcode trimming: internal barcodes were trimmed off of sequence reads
artifacts filtering: reads that resemble seqeuncing artifacts were removed using the artifacts filter in the fastx toolkit
read mapping: reads were mapped to TAIR10 transcripts using bowtie version bowtie-0.12.8
counting mapped reads: reads mapping to the forward strand of transcript(s) from a single gene were tallied (raw counts)
sample scaling: A scaling percentile normalization was applied to the raw counts of each sample: raw transcript counts at the 90th percentile of sample count values were scaled to match to the largest 90th percentile value, 300 counts, across all samples.
data transformation: The data were transformed to produce approximately homoscedastic data values, using the transformation log2 (scaled counts+79) - log2 (79). These transformed, scaled data with are referred to as normalized data in the following.
data correction: Normalized data were corrected for statistical artifacts using a mixed linear model for each gene individually: normalized data ~ genotype:time+(1|machine/lane)+(1│barcode)+(1|replicate). The normalized and corrected data are called transcript expression levels here.
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts for reads mapped to TAIR10 genes

molecule: total RNA

organism: Arabidopsis thaliana

source_name: flg22 9 hrs; dde2-2

growth_protocol: Plants were grown under a 12hr photoperiod in a controlled environment at 22°C and 75% relative humidity.

extract_protocol:
Total RNA extraction
Stranded mRNA Tag-Seq libraries were prepared as previously described, BMC Genomics. 2014 May 6;15:341. doi: 10.1186/1471-2164-15-341.

treatment_protocol: 3 leaves (leaf stages 7-9) of a single plant of each genotype from 31-32 days-old plants were syringe-inoculated with a 1 μM solution of flg22, and harvested at the indicated time after treatment. Leaves of plants from the same genotype and time point sampling in four independent experiments were pooled into a single biological replicate.

tag: genotype/variation

tag: concise genotype name

value: jEPS

tag: hrs after flg22 infiltration

value: 9 hrs

tag: tissue

value: leaf

tag: barcode

value: ACTGT

tag: gaiix lane

tag: machine location

value: umn


title: flg22 9 hrs; ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 88

source_name: flg22 9 hrs; ein2-1

value: JePS

value: ATCCT


title: flg22 9 hrs; Col-0; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 86

source_name: flg22 9 hrs; Col-0

value: JEPS

value: GTACT


title: normal-g rep. 3

source_name: normal-gravity HARV culture

tag: strain

value: normal


title: flg22 5 hrs; fls2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 85

source_name: flg22 5 hrs; fls2

value: 5 hrs

value: GCTCT


title: micro-g rep. 1


title: normal-g rep. 2


title: flg22 5 hrs; dde2-2 ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 84

value: dde2-2 ein2-1 pad4-1 sid2-2

value: jeps

value: GCAT


title: flg22 9 hrs; dde2-2 ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 97

source_name: flg22 9 hrs; dde2-2 ein2-1 pad4-1

value: dde2-2 ein2-1 pad4-1

value: jepS

value: AGCT


title: flg22 5 hrs; ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 83

source_name: flg22 5 hrs; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps

value: CGGT


title: flg22 5 hrs; dde2-2 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 82

source_name: flg22 5 hrs; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: jEps

value: leaf

value: TCGT

value: umn


title: flg22 5 hrs; dde2-2 ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 80

source_name: flg22 5 hrs; dde2-2 ein2-1 pad4-1

value: ATCCT


title: flg22 9 hrs; dde2-2 ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 91

source_name: flg22 9 hrs; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS

value: 9 hrs

value: GACACT


title: flg22 5 hrs; ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 78

source_name: flg22 5 hrs; ein2-1 sid2-2

value: ein2-1 sid2-2

value: JePs

value: 5 hrs

value: GTACT


title: flg22 5 hrs; ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 77

source_name: flg22 5 hrs; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

value: GCTCT


title: flg22 5 hrs; pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 79

source_name: flg22 5 hrs; pad4-1 sid2-2

value: pad4-1 sid2-2

value: JEps

value: ACTGT


title: flg22 5 hrs; dde2-2 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 76

source_name: flg22 5 hrs; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs

value: leaf

value: GCAT


title: flg22 9 hrs; pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 89

source_name: flg22 9 hrs; pad4-1

value: JEpS

value: TTGGAT

value: umn


title: flg22 5 hrs; dde2-2 ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 74

source_name: flg22 5 hrs; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS

value: TCGT


title: RNA-seq 15min

city: Göttingen

first: Carina

last: Demel

address: Am Fassberg 11

country: Germany

institute: Max-Planck Institute for biophysical Chemistry

data_processing:
TT-seq and RNA-seq samples were mapped using STAR (version 2.3.0)
ChIP-seq reads were mapped with Bowtie (version 2.1.0) and duplicates were removed using PicardTools (version 1.118) MarkDuplicates.
Samtools was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected
PicardTools (version 1.118) CollectInsertSizeMetrics was used to determine average insert size and standard deviation with default settings: Deviations: 10.0; Minimum percentage: 0.05, Metric Accumulation Level: All reads
Genome_build: hg38 + Spikeins ERCC-00043, ERCC-00170, ERCC-00136, ERCC-00145, ERCC-00092 and ERCC-00002
Supplementary_files_format_and_content: gtf file contains the annotation used by us (available on the series record); bigwig files contain Coverage Files per sample (in case of RNAseq strand-specific antisense-corrected read coverage, in case of ChIP-seq not strand-specific, fragment coverage after duplicate removal)

organism: Homo sapiens

source_name: T cells

growth_protocol: Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (Gibco) and 1% Penicillin/Streptomycin (100x, PAA) at 37°C under 5% CO2

extract_protocol:
RNA was extracted using TRIzol (Life Technologies)
fragmentation: yes; BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF
sequencing libraries were prepared with the Ovation Human Blood RNA-seq library kit (NuGEN) following the manufacturer's’ instructions.

treatment_protocol: Cells  were labeled in media for 5 min with 500 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 2 min at 3,000 rpm.

tag: cell line

value: Jurkat cells

tag: passage

tag: treatment

value: PMA + ionomycin

tag: treatment duration


title: flg22 5 hrs; pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 72

source_name: flg22 5 hrs; pad4-1

value: 5 hrs

value: TGTGCGAT


title: flg22 5 hrs; sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 73

source_name: flg22 5 hrs; sid2-2

value: JEPs

value: AGCT


title: RNA-seq 10min


title: flg22 5 hrs; dde2-2 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 75

source_name: flg22 5 hrs; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: CGGT


title: flg22 5 hrs; ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 71

source_name: flg22 5 hrs; ein2-1

value: JePS

value: leaf

value: AACAGAGT


title: flg22 5 hrs; dde2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 70

source_name: flg22 5 hrs; dde2-2

value: jEPS

value: TTGCGCT


title: normal-g rep. 1

source_name: normal-gravity HARV culture

value: 8 hours growth

value: normal


title: flg22 5 hrs; Col-0; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 69

source_name: flg22 5 hrs; Col-0

value: JEPS

value: CATACGT

value: umn


title: micro-g rep. 2

source_name: simulated microgravity HARV culture

value: simulated microgravity


title: flg22 3 hrs; ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 66

source_name: flg22 3 hrs; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps

value: 3 hrs

value: CGAGAT


title: cnc1jhd2_H3_biorep1_techrep2

city: Stratford

first: Michael

middle: J

last: Law

state: NJ

address: 2 Medical Center Dr., #122

department: Molecular Biology

institute: Rowan University

library_source: genomic

data_processing:
FastQC-.fastq.gz file quality control metrics
BWA-ChIP-seq read alignments using default parameters and SK1 reference genome.
Qualimap- mapping quality assessment
MACS2- peak calling using the following parameters: “callpeak -g 1.2E7 -p 0.01 --nomodel --extsize147 --tolarge” with histone H3 immunoprecipitations serving as the input control
DiffBind- differential peak analyses using default edgeR parameters
Genome_build: SK1
Supplementary_files_format_and_content: bdg are bedgraph files with peak intensities generated from MACS2

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown to mid-logarithmic phase in non-fermentable carbon using YEPA.

extract_protocol:
Yeast were spheroplasted and 50 ug of chromatin solution was used per immunoprecipitation. Chromatin solutions were pre-cleared using protein G agarose for 1 hr. at 4 degrees. Immunoprecipitations were performed overnight using Abcam ab1791 (histone H3) or ab8580 (H3Lys4 3me).
Illumina barcodes were ligated, low cycle PCR was performed, and library quality was assessed using the Bioanalyzer.

treatment_protocol: Cultures were crosslinked for 15 minutes using 1% formaldehyde.

tag: strain background

tag: ip antibody

value: Anti-Histone H3 antibody; Abcam ab1791


title: cnc1jhd2_H3_biorep2_techrep1


title: TT-seq 15min Rep2

description: TT-seq

extract_protocol:
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Dolken et al., RNA, 2008.
fragmentation: yes; BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF
sequencing libraries were prepared with the Ovation Human Blood RNA-seq library kit (NuGEN) following the manufacturer's’ instructions.

value: Jurkat cells

value: PMA + ionomycin


title: cnc1jhd2_H3_biorep2_techrep2


title: TT-seq 15min Rep1

description: TT-seq


title: flg22 5 hrs; dde2-2 ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 81

source_name: flg22 5 hrs; dde2-2 ein2-1 sid2-2

value: dde2-2 ein2-1 sid2-2

value: jePs

value: 5 hrs

value: leaf

value: AGCT


title: flg22 3 hrs; dde2-2 ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 64

source_name: flg22 3 hrs; dde2-2 ein2-1 sid2-2

value: TGTGCGAT


title: flg22 3 hrs; fls2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 68

source_name: flg22 3 hrs; fls2

value: CAGAGT


title: flg22 3 hrs; dde2-2 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 65

source_name: flg22 3 hrs; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: jEps

value: TTGGAT


title: TT-seq 10min Rep2

description: TT-seq


title: cnc1jhd2_H3_biorep1_techrep1


title: wild_type_H3_biorep2_techrep2

value: wild type


title: wild_type_H3_biorep1_techrep2


title: TT-seq 10min Rep1

description: TT-seq


title: TT-seq 5min Rep2

description: TT-seq


title: flg22 3 hrs; dde2-2 ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 67

value: dde2-2 ein2-1 pad4-1 sid2-2

value: jeps

value: GACACT

value: umn


title: wild_type_H3_biorep2_techrep1

value: Anti-Histone H3 antibody; Abcam ab1791


title: TT-seq 5min Rep1

description: TT-seq

value: Jurkat cells

value: PMA + ionomycin


title: wild_type_H3_biorep1_techrep1


title: RNA-seq 5min


title: flg22 3 hrs; ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 60

source_name: flg22 3 hrs; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

value: 3 hrs


title: CLIP_AGO2_2

city: Nice

first: Silvia

last: Bottini

address: 299, chemin de la ginestiere

country: France

description: HITS-CLIP

data_processing:
Reads were trimmed with the program cutadapt
Reads were mapped onto mm10 genome using the program Novoalign
Peaks were called with four different peak calling tools, namely: CIMS, PIPE-CLIP, Piranha and Pyicoclip
Genome_build: mm10
Supplementary_files_format_and_content: [.bed] peaks files (pvalue threshold: 0.001, reads threshold: 10)

organism: Mus musculus

extract_protocol:
RNA was recovered from the nitrocellulose using Proteinase K treatment followed by phenol–chloroform extraction and ethanol precipitation. Isolated RNA were subjected to small RNA libraries preparation (New England Biolabs), following the manufacturer’s instructions.
cDNA products were then subjected to PCR amplification for 20–24 cycles and size-fractionated on columns. PCR products representing cDNA inserts of 20–50 nts were recovered and subject to sequencing on aIon Proton™ System for Next-Generation Sequencing

tag: hits-clip antibody

value: 2D4 clone from Wako Chemicals

value: P19 stem cell line


title: flg22 3 hrs; pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 62

source_name: flg22 3 hrs; pad4-1 sid2-2

value: pad4-1 sid2-2

value: JEps

value: leaf

value: TTGCGCT


title: cnc1jhd2_K4_biorep2_techrep1

value: Anti-Histone H3 (tri methyl K4) antibody; Abcam ab8580


title: cnc1jhd2_K4_biorep2_techrep2


title: CLIP_AGO2_1

description: HITS-CLIP


title: flg22 3 hrs; dde2-2 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 59

source_name: flg22 3 hrs; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs


title: flg22 1 hr; Col-0; rep2

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 137

source_name: flg22 1 hr; Col-0

value: JEPS

value: 1 hr

value: TTGGAT


title: flg22 3 hrs; dde2-2 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 58

source_name: flg22 3 hrs; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: CGAGAT

value: umn


title: cnc1jhd2_K4_biorep1_techrep2


title: flg22 3 hrs; dde2-2 ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 57

source_name: flg22 3 hrs; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS

value: 3 hrs


title: flg22 3 hrs; sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 56

source_name: flg22 3 hrs; sid2-2

value: JEPs

value: ATCCT


title: EWE5 rep2

first: Björn

last: Schwalb

address: Fassberg 11

institute: MPI

description:
labeled RNA
Barcode: GTCGTA

data_processing:
Acquisition of data obtained from 4tU-Seq experiments was performed as described (Schulz et al., 2013), with minor modifications. Briefly, paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0) (Dobin et al., 2013). SAMTools was used to quality filter SAM files (Li et al., 2009). Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f163) were selected. Further processing of the data was carried out using R/Bioconductor (Gentleman et al., 2004; Ihaka and Gentleman, 1996).
We used a spike-in (RNAs) normalization strategy essentially as described before in (Schwalb et al., 2016) to allow observation of global shifts in 4sU-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015). Those size factors were used to correct for library size and sequencing depth variations.
Piled-up counts for every genomic position were summed up over replicates, using fragment coverage i.e. counting both sequenced bases covered by reads and unsequenced bases spanned between proper mate-pair reads.
Genome_build: S. cerevisiae genome (sacCer3, Version R64-1-1, released 03Feb2011, http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz)
Supplementary_files_format_and_content: tabular containing read counts according to Sc.cerevisiae.feature.anno_Steinmetz_2013.gtf

growth_protocol: inoculate strain from O/N culture at OD600 0.1, grow at 30C in YPD to OD600 0.8, label with 5mM 4thiouracil final conc. for 6 minutes, spin 1 min, discard supernatant, freeze in lN2

extract_protocol:
add spike-ins before cell lysis, extract total RNA with phenol/chloroform, purify labeled RNA
using NUGen Ovation Universal RNA-Seq System starting with 100 ng RNA input

tag: genotype

value: MATa ade- can1-100 cyh2r his3-11,15 leu2-3,112 trp1-1 ura3 hsp82- DHSE-lacZ med10-1002


title: flg22 3 hrs; dde2-2 ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 63

source_name: flg22 3 hrs; dde2-2 ein2-1 pad4-1

value: dde2-2 ein2-1 pad4-1

value: jepS

value: leaf

value: AACAGAGT


title: wild_type_K4_biorep2_techrep2

value: wild type

value: Anti-Histone H3 (tri methyl K4) antibody; Abcam ab8580


title: flg22 3 hrs; ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 61

source_name: flg22 3 hrs; ein2-1 sid2-2

value: ein2-1 sid2-2

value: JePs

value: CATACGT


title: flg22 3 hrs; pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 55

source_name: flg22 3 hrs; pad4-1

value: JEpS

value: ACTGT


title: wild_type_K4_biorep2_techrep1


title: EWE4 rep1

description:
labeled RNA
Barcode: AAGAGG

treatment_protocol: label with 5mM 4thiouracil final conc. for 6 minutes

value: MATa ade- can1-100 cyh2r his3-11,15 leu2-3,112 trp1-1 ura3 hsp82- DHSE-lacZ med21-1002


title: EWE4 rep2

description:
labeled RNA
Barcode: GGAGAA


title: EWE3 rep2

description:
labeled RNA
Barcode: GTCGTA

value: MATa ade- can1-100 cyh2r his3-11,15 leu2-3,112 trp1-1 ura3 hsp82- DHSE-lacZ med7-1002


title: flg22 3 hrs; ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 54

source_name: flg22 3 hrs; ein2-1

value: JePS

value: 3 hrs

value: GTACT

value: umn


title: CLIP_AGO2_3

description: HITS-CLIP

value: 2D4 clone from Wako Chemicals

value: P19 stem cell line


title: flg22 3 hrs; dde2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 53

source_name: flg22 3 hrs; dde2-2

value: jEPS

value: leaf

value: GCTCT


title: EWE3 rep1

description:
labeled RNA
Barcode: AAGCCT


title: EWE+ rep2

description:
labeled RNA
Barcode: GTGCTT

value: MATa ade- can1-100 cyh2r his3-11,15 leu2-3,112 trp1-1 ura3 hsp82- DHSE-lacZ


title: flg22 3 hrs; Col-0; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 52

source_name: flg22 3 hrs; Col-0

value: JEPS

value: GCAT


title: flg22 2 hrs; fls2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 51

source_name: flg22 2 hrs; fls2

value: 2 hrs

value: CGGT


title: flg22 2 hrs; dde2-2 ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 50

value: dde2-2 ein2-1 pad4-1 sid2-2

value: jeps

value: TCGT


title: EWE+ rep1

description:
labeled RNA
Barcode: ACCTCA


title: wild_type_K4_biorep1_techrep1

value: wild type

value: Anti-Histone H3 (tri methyl K4) antibody; Abcam ab8580


title: cnc1jhd2_K4_biorep1_techrep1


title: flg22 2 hrs; ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 49

source_name: flg22 2 hrs; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps

value: AGCT


title: EWE5 rep1

description:
labeled RNA
Barcode: AAGCCT

value: MATa ade- can1-100 cyh2r his3-11,15 leu2-3,112 trp1-1 ura3 hsp82- DHSE-lacZ med10-1002


title: flg22 2 hrs; dde2-2 ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 47

source_name: flg22 2 hrs; dde2-2 ein2-1 sid2-2

value: dde2-2 ein2-1 sid2-2

value: jePs

value: AACAGAGT

value: umn


title: Delta_set1 T= 90 min

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: Illumina index 22

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using bowtie2 (v2.2.5 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: sacCer3
Supplementary_files_format_and_content: read_count.csv contains counts of reads aligning to each gene in each sample.   tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv.   tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample.   These files are sufficient for differential expression and differential tail length analysis.

source_name: Delta_set1 T= 90 min

growth_protocol: Yeast cells were grown in rich media according to standard lab protocols

extract_protocol:
Total RNA was extracted from snap frozen cell pellets Trizol extraction. 1 microgram of this was input into the library preperation.
PAT-seq (Harrison et al 2015). Cluster Generation: 9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012. Sequencing chemistry: 1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012

treatment_protocol: Yeast were grown at 30°C in rich YPD medium (2% bacto-tryptone, 1% yeast extract, and 2% glucose). For synchronization, yeast cells were grown to an OD600 of 0.3 – 0.4 and arrested in the presence of 5 µg/ml alpha factor peptide for approximately 2 hrs; cells were checked under the microscope to ensure that at least 95% of cells were devoid of budding. Alpha factor was removed by three consecutive washes in 10 mM Tris-HCl pH7.5 and the cell cycle was continued by resuspending the cells in pre-warmed (30°C) YPD medium.  15 ml culture aliquots were collected in 15 min intervals.

tag: time point

value: T= 90 min after release


title: Delta_set1 T= 120 min

description: Illumina index 46

source_name: Delta_set1 T= 120 min

value: T= 120 min after release


title: Delta_set1 T= 75 min

description: Illumina index 19

source_name: Delta_set1 T= 75 min

value: T= 75 min after release


title: Delta_set1 T= 60 min

description: Illumina index 16

source_name: Delta_set1 T= 60 min

value: T= 60 min after release


title: Delta_set1 T= 45 min

description: Illumina index 14

source_name: Delta_set1 T= 45 min

value: T= 45 min after release


title: flg22 2 hrs; dde2-2 ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 46

source_name: flg22 2 hrs; dde2-2 ein2-1 pad4-1

tag: genotype/variation

value: dde2-2 ein2-1 pad4-1

value: jepS

value: 2 hrs

value: leaf

value: TTGCGCT


title: flg22 2 hrs; ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 44

source_name: flg22 2 hrs; ein2-1 sid2-2

value: ein2-1 sid2-2

tag: concise genotype name

value: JePs

value: CAGAGT


title: wild_type_K4_biorep1_techrep2

value: wild type

value: Anti-Histone H3 (tri methyl K4) antibody; Abcam ab8580


title: flg22 2 hrs; ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 43

source_name: flg22 2 hrs; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

tag: hrs after flg22 infiltration

value: GACACT


title: flg22 2 hrs; pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 45

source_name: flg22 2 hrs; pad4-1 sid2-2

value: pad4-1 sid2-2

value: JEps

tag: tissue

value: CATACGT

value: umn


title: Delta_set1 T= 15 min

description: Illumina index 10

source_name: Delta_set1 T= 15 min

value: T= 15 min after release


title: Delta_set1 T= 30 min

description: Illumina index 12

source_name: Delta_set1 T= 30 min

value: T= 30 min after release


title: Delta_set1 T=0 min

description: Illumina index 8

source_name: Delta_set1 T=0 min

value: T=0 min after release


title: flg22 2 hrs; dde2-2 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 42

source_name: flg22 2 hrs; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs

value: 2 hrs

value: leaf

tag: barcode

value: CGAGAT


title: flg22 2 hrs; dde2-2 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 41

source_name: flg22 2 hrs; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: TTGGAT

tag: gaiix lane


title: Delta_set1 T=pre

description: Illumina index 6

source_name: Delta_set1 T=pre

value: T=pre unsyncronised


title: flg22 2 hrs; dde2-2 ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 40

source_name: flg22 2 hrs; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS

value: ATCCT

tag: machine location


title: flg22 2 hrs; sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 39

source_name: flg22 2 hrs; sid2-2

value: JEPs

value: ACTGT


title: flg22 2 hrs; pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 38

source_name: flg22 2 hrs; pad4-1

value: JEpS

value: GTACT

value: umn


title: WT T= 105 min

description: Illumina index 23

source_name: WT T= 105 min

tag: strain

value: T= 105 min after release


title: WT T= 90 min

description: Illumina index 20

source_name: WT T= 90 min

value: T= 90 min after release


title: flg22 2 hrs; ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 37

source_name: flg22 2 hrs; ein2-1

value: JePS

value: 2 hrs

value: GCTCT


title: WT T= 120 min

description: Illumina index 31

source_name: WT T= 120 min

value: T= 120 min after release


title: flg22 2 hrs; dde2-2 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 48

source_name: flg22 2 hrs; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: jEps

value: leaf

value: TGTGCGAT


title: Delta_set1T= 105 min

description: Illumina index 30

source_name: Delta_set1T= 105 min


title: flg22 2 hrs; Col-0; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 35

source_name: flg22 2 hrs; Col-0

value: JEPS

value: CGGT


title: flg22 2 hrs; dde2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 36

source_name: flg22 2 hrs; dde2-2

value: jEPS

value: GCAT


title: WT T= 75 min

description: Illumina index 17

source_name: WT T= 75 min

value: T= 75 min after release


title: WT T= 45 min

description: Illumina index 13

source_name: WT T= 45 min

value: T= 45 min after release


title: WT T= 60 min

description: Illumina index 15

source_name: WT T= 60 min

value: T= 60 min after release


title: WT T= 30 min

description: Illumina index 11

source_name: WT T= 30 min

value: T= 30 min after release


title: flg22 1 hr; fls2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 34

source_name: flg22 1 hr; fls2

value: 1 hr

value: TCGT

value: umn


title: flg22 1 hr; ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 32

source_name: flg22 1 hr; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps


title: flg22 1 hr; dde2-2 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 31

source_name: flg22 1 hr; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: AACAGAGT


title: WT T=0 min

description: Illumina index 7

source_name: WT T=0 min

value: T=0 min after release


title: WT T=pre

description: Illumina index 5

source_name: WT T=pre

value: T=pre unsyncronised


title: flg22 1 hr; dde2-2 ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 29

source_name: flg22 1 hr; dde2-2 ein2-1 pad4-1

value: dde2-2 ein2-1 pad4-1

value: jepS

value: leaf

value: CATACGT


title: flg22 1 hr; dde2-2 ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 33

source_name: flg22 1 hr; dde2-2 ein2-1 pad4-1 sid2-2

value: dde2-2 ein2-1 pad4-1 sid2-2

value: jeps

value: AGCT


title: flg22 1 hr; dde2-2 ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 30

source_name: flg22 1 hr; dde2-2 ein2-1 sid2-2

value: dde2-2 ein2-1 sid2-2

value: jePs

value: TTGCGCT


title: flg22 1 hr; ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 26

source_name: flg22 1 hr; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

value: 1 hr

value: CGAGAT

value: umn


title: CSTF2tau_sCLIP_R1

city: Cologne

first: Yulia

last: Kargapolova

address: Robert-Koch-Straße 21

department: CMMC

institute: Cologne University

description: co-immunoprecipitated RNA

data_processing:
Library strategy: CLIP-Seq
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human reference assembly, version hg19, using STAR
Normalized bedGraph files were generated using bedtools
Peaks were called using CLIPper
Genome_build: hg19

source_name: brain; derived from metastatic site: bone marrow; cell line

growth_protocol: BE(2)-C cells were passaged in Dulbecco’s Modified Eagle’s Medium (high glucose) with the following components added: heat inactivated fetal bovine serum at a final concentration 10% and Penicillin-Streptomycin at a final concentration 1%.

extract_protocol:
The RNA-protein interactions were preserved in living cells by means of UV-irradiation. Next, the cells were solubilized and the RNA was partially digested. The RNA-protein complexes were purified by immunoprecipitation (IP), and the bound RNA was ultimately eluted from the RBP.
sCLIP protocol based on Illumina Truseq small RNA library preparation  kit

tag: cell line

value: WT

tag: antibody

value: anti-CSTF2tau A301-486A Bethyl


title: CSTF2tau_sCLIP_R2

description: co-immunoprecipitated RNA


title: CSTF2tau_sCLIP_R3

description: co-immunoprecipitated RNA


title: flg22 1 hr; ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 27

source_name: flg22 1 hr; ein2-1 sid2-2

value: ein2-1 sid2-2

value: JePs

value: GACACT


title: 6 days, 41 kPa

city: Amherst

first: Alyssa

middle: D

last: Schwartz

state: MA

address: 686 N pleasant St, Goessmann 159

department: Chemical Engineering

institute: University of Massachusetts Amherst

description: 6 days, 41 kPa

data_processing:
Reads were mapped to the reference genome using Tophat2 with a bowtie aligner
Normalized read counts were determined using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking files were generated using cufflinks to identify Fragments Per Kilobase of transcript per Million mapped reads

source_name: Human Breast Cancer Cell Line

growth_protocol: Cells grown for the indicated amount of time on the indicated stiffness in DMEM with 10% FBS

extract_protocol:
Total RNA was collected using
Libraries were prepared following the protocol for the TRUseq LT ()

value: 6 days

tag: protocol

value: 41 kPa


title: flg22 1 hr; dde2-2 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 25

source_name: flg22 1 hr; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs

value: leaf

value: TTGGAT


title: flg22 1 hr; dde2-2 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 24

source_name: flg22 1 hr; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: ATCCT


title: 6 days, 4 kPa

description: 6 days, 4 kPa

value: 4 kPa


title: flg22 1 hr; dde2-2 ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 23

source_name: flg22 1 hr; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS

value: 1 hr

value: ACTGT


title: 6 days, 1 kPa

description: 6 days, 1 kPa

value: 1 kPa


title: 6 days, 8 kPa

description: 6 days, 8 kPa

value: 8 kPa


title: 24 hours, 41 kPa

description: 24 hours, 41 kPa

value: 24 hours


title: flg22 1 hr; ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 20

source_name: flg22 1 hr; ein2-1

value: JePS

value: GCAT

value: umn


title: WT T= 15 min

description: Illumina index 9

source_name: WT T= 15 min

value: T= 15 min after release


title: flg22 1 hr; pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 21

source_name: flg22 1 hr; pad4-1

value: JEpS

value: leaf

value: GCTCT


title: 24 hours, 8 kPa

description: 24 hours, 8 kPa


title: flg22 1 hr; dde2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 19

source_name: flg22 1 hr; dde2-2

value: jEPS

value: CGGT


title: flg22 1 hr; Col-0; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 18

source_name: flg22 1 hr; Col-0

value: JEPS

value: TCGT


title: flg22 1 hr; pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 28

source_name: flg22 1 hr; pad4-1 sid2-2

value: pad4-1 sid2-2

value: JEps

value: CAGAGT


title: flg22 0 hrs; dde2-2 ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 16

value: dde2-2 ein2-1 pad4-1 sid2-2

value: jeps

value: 0 hrs

value: TGTGCGAT


title: flg22 0 hrs; ein2-1 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 15

source_name: flg22 0 hrs; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps

value: AACAGAGT


title: flg22 0 hrs; dde2-2 ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 13

source_name: flg22 0 hrs; dde2-2 ein2-1 sid2-2

value: dde2-2 ein2-1 sid2-2

value: jePs

value: CATACGT

value: umn


title: flg22 0 hrs; dde2-2 ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 12

source_name: flg22 0 hrs; dde2-2 ein2-1 pad4-1

value: dde2-2 ein2-1 pad4-1

value: jepS

value: leaf


title: time 0

description: time 0


title: flg22 0 hrs; pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 11

source_name: flg22 0 hrs; pad4-1 sid2-2

value: pad4-1 sid2-2

value: GACACT


title: flg22 0 hrs; dde2-2 pad4-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 14

source_name: flg22 0 hrs; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: jEps

value: TTGCGCT


title: flg22 0 hrs; ein2-1 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 10

source_name: flg22 0 hrs; ein2-1 sid2-2

value: ein2-1 sid2-2

value: JePs

value: 0 hrs

value: CGAGAT


title: flg22 0 hrs; dde2-2 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 7

source_name: flg22 0 hrs; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: ACTGT


title: flg22 0 hrs; ein2-1 pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 9

source_name: flg22 0 hrs; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

value: TTGGAT


title: flg22 1 hr; sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 22

source_name: flg22 1 hr; sid2-2

value: JEPs

value: 1 hr

value: GTACT

value: umn


title: flg22 0 hrs; sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 5

source_name: flg22 0 hrs; sid2-2

value: leaf

value: GCTCT


title: flg22 0 hrs; pad4-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 4

source_name: flg22 0 hrs; pad4-1

value: JEpS

value: GCAT


title: flg22 0 hrs; dde2-2 ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 6

source_name: flg22 0 hrs; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS


title: flg22 0 hrs; Col-0; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 1

source_name: flg22 0 hrs; Col-0

value: JEPS

value: 0 hrs

value: AGCT


title: flg22 0 hrs; dde2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 2

source_name: flg22 0 hrs; dde2-2

value: jEPS

value: TCGT


title: flg22 0 hrs; ein2-1; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 3

source_name: flg22 0 hrs; ein2-1

value: JePS

value: CGGT


title: Clr3_PAR-CLIP_2

city: Oxford

first: Beth

last: Watts

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: crosslinked RNA

data_processing:
PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. pombe genome (ASM294v2.25 from Pombase.org) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Crosslinking sites were normalised to RNA abundance which was determined by RNA-Seq from GEO GSE89914
genome build: S. pombe genome version ASM294v2.28
processed data files format and content: PAR-CLIP: Clr3 crosslinking sites are provided as .table text files. Column headers are as follows: Chromosome, position, m (the number of mutations at certain positions), r (the number of reads (coverage) at the same position), p-value, strand, occ  (m normalised to RNA abundance).

organism: Schizosaccharomyces pombe

source_name: Yeast cell extract

growth_protocol: Cells were grown at 30 °C to OD600 ∼0.5 in CSM minimal medium (Formedium) supplemented with 10 mg/l uracil, 100 µM 4-thiouracil and 4 % glucose. After reaching OD600∼0.5, another 900 µM 4-thiouracil were added and cells were grown further for 4 h (OD600∼1.3-1.6)

extract_protocol:
Cells were UV-irradiated (12 J/cm2 at 365 nm) and lysed by bead beating and the lysate was sonicated. Immunoprecipitation was performed on a rotating wheel for 2 h at 4 °C with rabbit IgG-conjugated Protein G magnetic Dynabeads (Invitrogen). Crosslinked RNA was partially digested with RNase T1 and prepared for cDNA library preparation.
Data acquisition were performed as described by Schulz and Schwalb et al. (Cell, 2013) with minor modifications. Following adapter ligation, RNA was recovered by Proteinase K digestion for 2 h at 55 °C, and subsequent acidic phenol/chloroform extraction. Reverse transcription was done for 1 hr at 44 °C using SuperScript III RTase (Invitrogen). PCR amplification was performed using the NEXTflex barcode primer kit (Bioo Scientific).

value: h+, ura4-delta18, leu1-32, ade6-M216, imr1R(NcoI)::ura4+, clr3-3HA-TAP::kan MX

tag: method

value: PAR-CLIP


title: 24 hours, 4 kPa

description: 24 hours, 4 kPa

source_name: Human Breast Cancer Cell Line

value: 24 hours

value: 4 kPa


title: noXL_PAR-CLIP

description: crosslinked RNA


title: 24 hours, 1 kPa

description: 24 hours, 1 kPa

value: 1 kPa


title: flg22 0 hrs; fls2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 17

source_name: flg22 0 hrs; fls2

value: leaf

value: umn


title: Clr3_PAR-CLIP_1

description: crosslinked RNA


title: Leucoraja_4_RNASeq

city: San Francisco

first: Duncan

last: Leitch

state: California

department: Physiology

institute: University of California - San Francisco

data_processing:
All reads were trimmer for low complexity or low quality ends (Sickle version 1.3).
Forward and reverse reads were pooled. A transcriptome was assembled using Trinity (version 2.1.0)
Estimates of relative abundance for differential expression were performed using RSEM (version 1.1.17)
Genome_build: de novo assembled transcriptome Leucoraja_assembly.fasta (assembled contigs)
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each sample

molecule: polyA RNA

organism: Leucoraja erinaceus

source_name: Liver

extract_protocol:
Tissues were removed, preserved in RNAlater solution at -20C, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Library Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Adult

value: Liver

tag: tissue description

value: 4 mg sample from liver


title: Y881-920F_36.2

city: Stanford

first: Stefan

last: Oliver

address: 300 Pasteur Drive, Grant Rm S366

department: Pediatrics

institute: Stanford University School of Medicine

data_processing:
Quality control checks of FastQ files was performed using FastQC v0.11.4 Babraham Bioinformatics
Reads were aligned and BAM files generated using STAR v2.5
BAM files containing the aligned reads were used to generate RPKM values, which were calculated using the RNA-seq pipeline in Partek Genomics Suite 6.6
Genome_build: hg19

organism:
Homo sapiens
Human alphaherpesvirus 3

source_name: Y881-920F infected MeWo cells; 36hpi

growth_protocol: MeWo cells were were propagated in culture medium [MEM supplemented with 10% fetal bovine serum (Life Technologies, Grand Island, NY), non-essential amino acids (100μM; Cellgro, Manassas, VA), penicillin-G/streptomycin (100 units/ml; Life Technologies, Grand Island, NY), amphotericin (0.5 mg/ml; Cellgro, Manassas, VA)

extract_protocol:
Total RNA was extracted from melanoma cells using an RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared from HOW MUCH RNA using a TruSeq RNA Preparation Kit

treatment_protocol: Infection with varicella-zoster virus

value: MeWo

tag: virus phenotype

value: Hyperfusogenic

tag: time post infection


title: Leucoraja_1_RNASeq

source_name: Ampullary receptor cells

value: Ampullary receptor cells

value: electroreceptor cells


title: Leucoraja_3_RNASeq

source_name: Body skin

value: Body skin

value: non-electroreceptor covered skin


title: Y881F_36.2

source_name: Y881F infected MeWo cells; 36hpi


title: pOka-WT_36.2

source_name: pOka infected MeWo cells; 36hpi

value: Wild type


title: flg22 0 hrs; dde2-2 sid2-2; rep1

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 8

source_name: flg22 0 hrs; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs

value: 0 hrs

value: ATCCT


title: None_36.2

source_name: Unfected MeWo cells; 36hpi

value: Not Applicable


title: Y920F_36.2

source_name: Y920F infected MeWo cells; 36hpi


title: Y881-920F_24.2

source_name: Y881-920F infected MeWo cells; 24hpi


title: Y881-920F_12.2

source_name: Y881-920F infected MeWo cells; 12hpi


title: Y920F_12.2

source_name: Y920F infected MeWo cells; 12hpi


title: Y881F_12.2

source_name: Y881F infected MeWo cells; 12hpi


title: pOka-WT_12.2

source_name: pOka infected MeWo cells; 12hpi


title: None_12.2

source_name: Unfected MeWo cells; 12hpi


title: Y881-920F_36.1


title: Leucoraja_2_RNASeq

source_name: Ampullary canals

value: Ampullary canals

value: structural canal to electroreceptor cells


title: Y920F_36.1


title: Y881F_36.1


title: Y881-920F_24.1


title: Y881F_24.1

source_name: Y881F infected MeWo cells; 24hpi


title: pOka-WT_24.1

source_name: pOka infected MeWo cells; 24hpi


title: None_24.1

source_name: Unfected MeWo cells; 24hpi


title: Y881-920F_12.1


title: Y920F_24.1

source_name: Y920F infected MeWo cells; 24hpi


title: Y920F_12.1


title: Sample ERCC2 capture replicate 1 with 50.0 ng cDNA input

city: Nijmegen

first: Kees

last: Albers

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Center

description:
The synthetic ERCC controls (Thermo Fisher Scientific, Waltham, MA, USA) were diluted 1:100, and 46 ul was used for cDNA synthesis after mixing with human PBMC total RNA using Superscript III Reverse Transcriptase (Thermo Fisher Scientific). Samples were purified using Qiaquick (Qiagen, Venlo, The Netherlands) columns, and cDNA was quantified using the Qubit ssDNA assay (Thermo Fisher Scientific). Of each sample 1 and 2 ng cDNA was used for MIP capture, and all capture experiments were performed in duplo.
processed data file:
all_samples_molecule_counts.txt
cdna_mips_ercc.txt

data_processing:
Match each read pair to a designed smMIP probe (allowing two mismatches);
Remove likely extension-ligation dimers;
For all reads assigned to a given smMIP probe, identify the molecule counts from the unique molecular identifiers;
Determine the read-dependent threshold for UMIs due to sequencing errors;
Estimate normalized expression levels from error-corrected molecule counts integrating replicates using a dedicated Bayesian model.
Genome_build: Reads for the HEK/K562 allelic ratio experiment were mapped to hg19. For all other experiments, no read mapping was performed.
Supplementary_files_format_and_content:
Tab-delimited file with molecule counts for each smMIP and sample, corrected and uncorrected for sequencing errors in the molecular identifiers.
all_samples_molecule_counts.txt: txt file with molecule counts for all experiments
cdna_mips_ercc.txt: txt file with probe design for ERCC experiments
cdna_mips_geuvadis.txt: txt file with probe design for PBMC and EBV experiments
cdna_mips_ase-K562-HEK293.txt: txt file with probe design for allelic ratio experiments

organism:
Homo sapiens
synthetic construct

source_name: ERCC RNA mixed with PBMC RNA

growth_protocol: Primary cells and cell lines were grown according to the description provided for each sample.

extract_protocol:
The isolated total RNA was quantified using the Qubit RNA HS assay kit (Thermo Fisher Scientific, Waltham, MA, USA). cDNA synthesis of 2-5 µg of RNA was performed with iScript (BIO-RAD, Hercules, CA, USA) reverse trancriptase. After cDNA synthesis, the cDNA was purified using Qiaquick (Qiagen, Venlo, The Netherlands) purification columns, and cDNA quantity was measured using the Qubit ssDNA assay kit (Thermo Fisher Scientific).
Single-molecule inversion probes applied to cDNA. Main steps are 1) MIP phosphorylation 2) MIP capture 3) Exonuclease treatment; 4) PCR amplification
Targeted RNA-Seq using cDNA-smMIPs

treatment_protocol: Except for the PBMC stimulation experiment, cells were not stimulated. In the PBMC experiment, cells were stimulated with heat-killed Candida Albicans.

tag: cell type

value: ERCC/PBMC

tag: amount cdna (ng) input used for smmip capture

tag: number of pcr cycles

tag: cdna sample id


title: Sample ERCC2 capture replicate 2 with 50.0 ng cDNA input


title: seb1-1_3_RNA-Seq

description: total RNA

data_processing:
RNA-Seq: Paired-end reads were trimmed by quality (less than Phred score 20) and reads shorter than 20 nt were removed using Trimmomatic (Galaxy Version 0.32.3). The resulting reads were aligned to the S. pombe genome (ASM294v2.28) using TopHat (Galaxy version 0.9). Gene body counts were generated using using HTSeq (version 0.6.1.p1) and the package DESeq2 in R/Bioconductor was used for differential expression analysis.
genome build: S. pombe genome version ASM294v2.28
processed data files format and content: RNA-Seq: Bedgraph files are provided to visualise the data. The values in the bedGraph files is the coverage normalised to library size.

source_name: Yeast cell extract

growth_protocol: S. pombe were grown in YES media at 30°C to OD600 ∼0.5

extract_protocol:
Total RNA was extracted from three separate cultures of WT and mutants grown to mid-log phase and DNase-treated.
Ribodepletion and library preparation were performed by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics according to the TruSeq protocol. Note that with the TruSeq protocol the cDNA strand is sequenced. Thus all the strand information needs to be reversed after mapping the reads to the genome.

tag: genotype

value: h-, seb1-1::natMX

value: RNA-Seq


title: Sample ERCC2 capture replicate 2 with 5.0 ng cDNA input


title: Y920F_24.2

value: MeWo


title: Y881F_12.1

value: Hyperfusogenic


title: Sample ERCC2 capture replicate 1 with 5.0 ng cDNA input


title: seb1-1_2_RNA-Seq

description: total RNA


title: seb1-1_1_RNA-Seq

description: total RNA


title: Y881F_24.2


title: Sample ERCC2 capture replicate 2 with 10.0 ng cDNA input


title: WT_3_RNA-Seq

description: total RNA

value: h-


title: WT_1_RNA-Seq

description: total RNA


title: Sample ERCC2 capture replicate 1 with 10.0 ng cDNA input


title: Sample ERCC2 capture replicate 2 with 1.0 ng cDNA input


title: WT_2_RNA-Seq

description: total RNA


title: Sample ERCC1 capture replicate 2 with 50.0 ng cDNA input


title: Sample ERCC2 capture replicate 1 with 1.0 ng cDNA input


title: Sample ERCC1 capture replicate 1 with 50.0 ng cDNA input


title: Sample ERCC1 capture replicate 2 with 5.0 ng cDNA input


title: Sample ERCC1 capture replicate 1 with 5.0 ng cDNA input


title: 30_c_28_48

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

description: Sampled after move to 28C for 48 hours

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,
Genome_build: PRJNA13023; https://www.ncbi.nlm.nih.gov/genome/405?genome_assembly_id=29037
Supplementary_files_format_and_content: tab-delimited text files include raw counts per gene

organism: Galdieria sulphuraria

source_name: Rep C - Autotrophic Batch Culture

growth_protocol: 42°C/28°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions using 2xGS Medium (M. B. Allen (1959). Studies with cyanidium caldarium, an anomalously pigmented chlorophyte. Archiv für Mikrobiologie, vol. 32, no. 3, p. 270–277.)

extract_protocol:
RNA was extracted using Roboklon’s Universal RNA Purification Kit by following the “plant tissue samples” protocol (Roboklon, Berlin - Germany). RNA quality and concentration was assessed using a Nanodrop photospectrometer ND-1000 (Peqlab Biotechnologie GmbH, Erlangen -Germany).
The samples were synthetized to Illumina HiSeq2000 compatible RNA-Seq libraries strictly following "Illumina TruSeq RNA Sample Prep v2 LS Protocol" (Illumina, San Diego - USA). All reagents were scaled by 2/3 to the volume proposed in the protocol. The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA). The quality of all libraries was assessed using the Bioanalyzer (Agilent Technologies, Santa Clara - USA). The libraries were sequenced in paired-end mode (2x100bp) on two lanes with an Illumina HiSeq2000 sequencer at the BMFZ (Biologisch-Medizinisches Forschungszentrum, Düsseldorf - Germany).

tag: temperature

tag: sampling

value: wild type

tag: truseq adapter index

tag: adapter sequence

value: ATTCCT


title: 19_a_46_48

description: Sampled after move to 46C for 48 hours

source_name: Rep A - Autotrophic Batch Culture

tag: strain

value: ATGTCA


title: 21_c_46_48

description: Sampled after move to 46C for 48 hours

value: CGTACG


title: 28_a_28_48

description: Sampled after move to 28C for 48 hours

value: GTGAAA


title: Sample ERCC1 capture replicate 1 with 10.0 ng cDNA input


title: Sample ERCC1 capture replicate 2 with 10.0 ng cDNA input


title: 12_c_28_48

description: Sampled after move to 28C for 48 hours

value: GTTTCG


title: 11_b_28_48

description: Sampled after move to 28C for 48 hours

source_name: Rep B - Autotrophic Batch Culture

value: CTTGTA


title: 10_a_28_48

description: Sampled after move to 28C for 48 hours


title: 2_b_42_n

description: Sampled after two weeks at 42C

value: CGATGT


title: Sample ERCC1 capture replicate 2 with 1.0 ng cDNA input


title: 3_c_42_n

description: Sampled after two weeks at 42C

value: GCCAAT


title: Sample ERCC1 capture replicate 1 with 1.0 ng cDNA input


title: PZN_Sterne2

status: Public on Feb 28 2017

city: Urbana

first: Douglas

middle: A

last: Mitchell

state: IL

address: 1206 W. Gregory Dr. MC-195 Room 3105 IGB

department: Chemistry

institute: University of Illinois at Urbana-Champaign

description:
Bacillus anthracis Sterne 7702
mRNA
Processed data file: NC_005945_transcripts_DMSO_PZN.txt
Processed data file: NC_005945_transcripts_PZN_Az5.txt

data_processing:
Data was processed with the Rockhopper version 1.30 pipeline using B. anthracis Sterne (NC_005945.1) and B. anthracis Ames Ancestor plasmid pXO1 (NC_007322.2) as references.
Default values (allowed mismatches 0.15, minimum seed length 0.33, minimum expression of UTRs and ncRNAs 0.5) were used, with the exception that reverse complement reads were used for mapping.
Genome_build: B. anthracis Sterne: NC_005945.1
Genome_build: B. anthracis Ames Ancestor plasmid pXO1: NC_007322.2
Supplementary_files_format_and_content: Tab-delimited text files include expression values that are counts normalized using the Rockhopper pipeline.

organism: Bacillus anthracis str. Sterne

source_name: Bacterial cells, plantazolicin

growth_protocol: (3) independent 3 mL cultures for each treatment group were grown to optical density (600 nm) of 0.4.

extract_protocol:
Harvested cells were resuspended in 250 μl of 10 mM Tris (pH 8.5) with 15 mg/ml lysozyme and 5 μl proteinase K (20 mg/ml) and digested for 1 h at 22°C with gentle agitation. RNA was extracted using the Qiagen RNeasy Mini Kit. An on-column DNase I digestion was performed using the Qiagen RNase-free DNase set according to manufacturer's instructions. RNA isolation protocol was completed according to manufacturer's instructions, followed by a second DNase I digestion and an RNA cleanup protocol.
Libraries were created using the TruSeq Stranded RNA Sample Prep kit after rRNA depletion using the RiboZero Bacteria kit, following manufacturer's instructions.

treatment_protocol: Samples were treated with 0.25X MIC compound (plantazolicin or Me2-Arg-Az5) or an equivalent volume of DMSO, and allowed to incubate for 10 min at 37 °C. Samples were treated with Qiagen RNAprotect bacterial reagent and harvested at 4000 x g for 10 min.

tag: strain/background

value: Sterne

tag: treatment compound

value: plantazolicin


title: PZN_Sterne3


title: DMSO_Sterne3

description:
Bacillus anthracis Sterne 7702
mRNA
Processed data file: NC_005945_transcripts_DMSO_PZN.txt
Processed data file: NC_005945_transcripts_DMSO_Az5.txt

source_name: Bacterial cells, DMSO

value: DMSO


title: AP bursting-2

city: Heidelberg

first: Carlos

last: Bas Orth

address: Im Neuenheimer Feld 307

department: Anatomy and Cell Biology

institute: Ruprecht-Karls-University Heidelberg

description: stimulated sample, treated with 50 µM bicuculline for 4 hours to induce action potential bursting

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were mapped to mm9 whole genome using TopHat_1.2.0 with default parameters
The aligned read files (accepted_hits.bam) were name sorted and transformed to SAM files with SAMtools_0.1.19
The sorted files were passed to easyRNASeq_2.10.0 to get the raw counts
Differential expression was analyzed using DESeq_1.12.0 and fitted with a generalized linear model assuming a negative binomial distribution
Genome_build: mm9
Supplementary_files_format_and_content: spread sheet provides ENSEMBL Id, gene name, normalized counts, fold-changes, and adjusted p-values

growth_protocol: Primary hippocampal neurons were prepared from newborn C57BL/6NCrl mice according to standard procedures. Neurons were grown in Neurobasal-A medium supplemented with B27, 0.5mM glutamine, and 1% rat serum. On day in vitro (DIV) 8 growth medium was exchanged with transfection medium consisting of a mixture of buffered salt-glucose-glycine solution [10mM Hepes (pH 7.4), 114mM NaCI, 26.1mM NaHCO3, 5.3mM KCI, 1mM MgCI2, 2mM CaCI2, 30mM glucose, 1mM glycine, 0.5mM sodium pyruvate, and 0.001% phenol red] and phosphate free Eagle's minimum essential medium (9:1 vol:vol), supplemented with insulin (7.5μg/ml), transferrin (7.5μg/mI), sodium selenite (7.5ng/ml)

extract_protocol:
Total RNA was isolated using a QIAGEN RNeasy kit with additional on-column DNase I digestion according to the manufacturer's instructions.
Non-strand-specific RNA-seq libraries were prepared from 1.5 µg of each total RNA sample using an Illumina RNA Library prep kit.

treatment_protocol: On day in vitro 12 neurons were treated with vehicle (DMSO) or 50 µM bicuculline to induce action potential (AP) bursting. Cells were harvested after 4 hours of AP bursting.

tag: tissue

value: brain

tag: brain region

value: hippocampus


title: DMSO_Sterne1


title: DMSO_Sterne2


title: 5Az_Sterne1

description:
Bacillus anthracis Sterne 7702
mRNA
Processed data file: NC_005945_transcripts_DMSO_Az5.txt
Processed data file: NC_005945_transcripts_PZN_Az5.txt

source_name: Bacterial cells, Me2-Arg-Az5


title: 5Az_Sterne3


title: Control-2

description: control sample, treated with vehicle (DMSO)

source_name: primary hippocampal neurons_control


title: 5Az_Sterne2


title: AP bursting-1


title: Control-1


title: RxT line in the wild-type background

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

description: Small RNA

data_processing:
After removing barcodes, adapters and low-quality reads, clean reads of size 18-30 nt were mapped to the Arabidopsis genome (TAIR10 version) and perfectly genome matched reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: *txt: The processed data files are tab-delimited text files that include non-redundant clean reads including unique small RNA sequences and their raw counts.

source_name: 13-day-old seedlings, wild-type

growth_protocol: All plants were grown in Murashige and Skoog (MS) medium at 16-h-light/8-h-dark photoperiod.

extract_protocol:
Small RNAs were extracted from whole plants by Trizol reagent (Invitrogen), resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-28 nt were excised, and the RNAs were eluted and purified for small RNA library construction.
Small RNA libraries were constructed as previously described (Mi et al., Cell, 2008, 133, 116-127).

tag: ecotype

tag: line

value: RxT

tag: genotype/variation

value: wild-type

tag: age

value: 13 days

value: seedlings


title: RxT line in the idn2-3 mutant background

description: Small RNA

source_name: 13-day-old seedlings, idn2-3 mutant


title: T-MEM49_01

city: HKSAR

first: Christine

middle: Yee Yan

last: Wai

address: Shatin, N.T.

country: Hong Kong

institute: The Chinese University of Hong Kong

description: MEM49-encoding DNA vaccine treated mice

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for short reads and low-quality sequences, then mapped to the mouse reference genome mm10 using TMAP.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Sailfish.
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing the gene id, transcript id, length of the transcript, expected read count and RPKM value

source_name: ileum of small intestine

extract_protocol:
Ileum sections were isolated within 24h after intragastric challenge and stored in RNAlater RNA stabilization reagent. Total RNA was extracted using the Rneasy Mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard ion proton protocols

treatment_protocol: BALB/c mice were intradermally injected with 100 ug MEM49-encoding DNA vaccine prior to or after shrimp tropomyosin sensitization

tag: stain

value: BALB/c

value: ileum of small intestine

tag: sample group

value: MEM49-encoding DNA vaccine treated


title: P-MEM49_02

description: MEM49-encoding DNA vaccine pre-vaccinated mice


title: PZN_Sterne1


title: positive control _01

description: shrimp tropomyosin-sensitized mice

value: shrimp tropomyosin-sensitized


title: P-MEM49_01

value: MEM49-encoding DNA vaccine pre-vaccinated


title: negative control_02

description: non-sensitized naïve mice

value: non-sensitized naïve


title: T-MEM49_02

description: MEM49-encoding DNA vaccine treated mice


title: P14d8_r2

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

description: transposase-digested genomic DNA

data_processing:
Basecalls and demultiplexing was performed in Illumina BaseSpace
Sequencing reads were mapped to the mouse genome (mm10) using Bowtie2 with parameters "--non-deterministic --mm --very-sensitive-local -X 2000
Unmapped reads, reads with MAPQ <30 and reads aligned to chrM, chrY or unlocalized/unplaced scaffolds were removed with samtools and awk
Duplicate reads were removed using picard MarkDuplicates
Reads mapping to regions blacklisted by ENCODE (lifted over to mm10) were removed with bedtools
Reads were shifted by +4 bp (positive strand) or -5 bp (negative strand) so that the read start represents the center of the Tn5 transposon binding event
Each read was trimmed to 15 bp to account for the Tn5 occupancy steric hindrance
BigWig files of coverage for individual replicates were computed with deepTools bamCoverage (--binSize 10 --normalizeUsingRPKM --smoothLength 30)
BigWig files were rescaled using TMM normalization on high-accessibility 300-bp wide windows as calculated by the R/Bioconductor package csaw
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files of coverage, normalized using RPKMs with 10-bp bins

source_name: tumor-infiltrating lymphocytes

growth_protocol: When the B16-OVA tumor reached a dimeter of 0.25-0.4 cm, Thy1.1+ P14 and CD45.1+ OT-I cells were collected, washed with PBS, and resuspended at a concentration of 20 million cell/ml in PBS, at a 1:1 P14:OT-I ratio. 2-4.5 million CTL were intravenously injected into the retro-orbital vein in anesthetized mice bearing B16-OVA tumors. In selected experiments, anti-PD-L1 Ab (clone #10F.9G2, BioXCell) or control anti-KLH rat IgG2b (BioXCell) were inoculated intra-peritoneally (200 ug/mouse). Two injections of anti-PD-L1 or control IgG were performed, three and six days after adoptive transfer of OT-I CTL.

extract_protocol:
Cell suspensions were prepared from tumors after enzyme digestion.  For sorting of adoptively transferred OT-I and P14 cells, CD8+ T cells were positively selected from tumors using the Dynabeads FlowComp Mouse CD8 selection kit (Thermo Fisher). To ensure adequate cell yield, samples from multiple mice belonging to the same group were pooled prior to enrichment. Enriched CD8+ T cells were then stained with anti-CD8a (53-6.7), anti-CD45.1 (A20), anti-Thy1.1 (OX-7), anti-PD-1 (29F.1A12), anti-Tim-3 (RMT3-23) and Fixable Viability Dye eFluor780. Tumor infiltrating lymphocytes were isolated as live CD8+CD45.1+ (OT-I) or CD8+Thy1.1+ (P14) on BD FACSARIA III or FUSION sorters. ATAC-seq was performed according to Buenrostro et al. (Nature Methods 2013) with minor modifications: 30,000 to 50,000 sorted CD8+ T cells cells were lysed to extract nuclei. Nuclei were resuspended in 50 ul 1xTD Buffer containing 2.5 μl transposase (Nextera, Illumina). The transposase reaction was conducted for 30 minutes at 37°C, with mild shaking.
Library amplification and barcoding were performed with the library amplification kit (KAPA Biosystems) using Index Primers, designed according to Buenrostro et al. (Nature Methods 2013) at a final concentration of 500 nM. PCR reaction was conducted for 10-11 cycles. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and library size distribution was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent). ATAC-seq libraries were quantified prior to pooling and sequencing using the real-time library quantification kit (KAPA Biosystems).

treatment_protocol: Total CD8+ T cells, harvested from spleen and lymph nodes from 6-12-week old OT-I or P14 mice by negative selection were activated in vitro by crosslinked anti-CD3 plus anti-CD28.  On day 2, T cells were removed from the antibody-coated plate and re-cultured at 400,000 cells/mL with low dose (10 U/ml)  IL-2. Every day the cell concentration was adjusted to 400,000 cells/mL until day 5-6, when cells were adoptively transferred into tumor-bearing mice.

tag: cell type

value: CD8+ T cells

tag: treatment


title: P14d8_r1

description: transposase-digested genomic DNA


title: negative control_01

description: non-sensitized naïve mice


title: OTId8_r2

description: transposase-digested genomic DNA

value: C57BL/6J CD45.1 OT-I


title: OTId8-Ig_r2

description: transposase-digested genomic DNA

value: Control IgG


title: OTId8-Ig_r1

description: transposase-digested genomic DNA


title: OTI-aPDL1_r2

data_processing:
Basecalls and demultiplexing was performed in Illumina BaseSpace
Reads were mapped against the mouse mm10 reference using TopHat with RefSeq annotations
Reads per gene were counted using HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene-level raw count table

growth_protocol: When the B16-OVA tumor reached a dimeter of 0.25-0.4 cm, OT-I cells were collected, washed with PBS, and resuspended at a concentration of 20 million cell/ml in PBS. 2-4.5 million CTL were intravenously injected into the retro-orbital vein in anesthetized mice bearing B16-OVA tumors. Mice were sacrificed on day 8 after adoptive T cell transfer, or whenever tumors reached a diameter of 1.2 cm. anti-PD-L1 Ab (clone #10F.9G2, BioXCell) or control anti-KLH rat IgG2b (BioXCell), were inoculated intra-peritoneally (200 ug/mouse). Two injections of anti-PD-L1 or control IgG were performed, three and six days after adoptive transfer of OT-I CTL.

extract_protocol:
Cell suspensions were prepared from tumors. Tumors were dissected, transferred to RPMI medium supplemented with TL Liberase Cocktail (100ug/mL, Roche) and incubated at 37°C for 15 minutes. Then, additional Liberase was added, incubating with mixing for an additional 10 minutes. Tissue suspensions were passed through 70-micron strainers and washed with PBS/2% FBS. For sorting of adoptively transferred OT-I cells, CD8+ T cells were pre-enriched from tumors using the Dynabeads FlowComp Mouse CD8 selection kit (Thermo Fisher). To ensure adequate cell yield, samples from multiple mice belonging to the same group were pooled prior to enrichment. Enriched CD8+ T cells were then stained with anti-CD8a (53-6.7), anti-CD45.1 (A20), anti-Thy1.1 (OX-7), anti-PD-1 (29F.1A12), anti-Tim-3 (RMT3-23) and Fixable Viability Dye eFluor780. Tumor infiltrating lymphocytes were isolated as live CD8+CD45.1+ on BD FACSARIA III or FUSION sorters. Total RNA was extracted from 5,000-30,000 sorted CD8+ T cells using the RNeasy micro kit or the miRNeasy micro kit. RNA quality was evaluated with the Bioanalyzer RNA pico kit (Agilent Technologies).
Poly(A)-selected RNA was amplified using the Smart-seq2 (Clontech) protocol with minor modifications. Briefly, purified RNA was reverse-transcribed using Superscript II, Oligo dT30 VN primers and template switching primers. A pre-amplification step of 8 PCR cycles was performed using the Kapa HiFi Hotstart kit (Kapa Biosystems). The PCR product was purified using AMPureXP beads (Beckman Coulter) and 1 ng was further used for library preparation using the Nextera XT LibraryPrep kit (Illumina). Tagmented DNA was amplified with a 12-cycle PCR reaction and again purified with AMPureXP beads.

treatment_protocol: Total CD8+ T cells, harvested from spleen and lymph nodes of 6-12-week old OT-I mice by negative selection using Dynabeads (Invitrogen), were activated by anti-CD3 (clone 2C11) plus anti-CD28 (clone 37.51) (BD Biosciences) at 1 μg/mL on plates pre-coated with 50 μg/mL goat anti-hamster IgG (MP Biomedicals). On day 2, T cells were removed from the antibody-coated plate and re-cultured at 400,000 cells/mL with low dose (10 U/ml) recombinant IL-2 (Hoffmann-La Roche). Every day the cell concentration was adjusted to 400,000 cells/mL until day 5-6, when cells were adoptively transferred.

value: OT-I CD8+ T cells


title: OTId8-aPDL1_r2

description: transposase-digested genomic DNA


title: OTId8-aPDL1_r1

description: transposase-digested genomic DNA


title: OTI-aPDL1_r1


title: OTI-Ctrl_r3


title: P14_r5

data_processing:
Basecalls and demultiplexing was performed in Illumina BaseSpace
Trimmed reads were mapped to the mouse genome (mm10) using STAR with the ENCODE parameters as per developer’s manual
Unmapped reads and multi-mapping reads were removed prior to counting using featureCounts with GENCODE vM6 annotations
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited raw count table

growth_protocol: When the B16-OVA tumor reached a dimeter of 0.25-0.4 cm, Thy1.1+ P14 and CD45.1+ OT-I cells were collected, washed with PBS, and resuspended at a concentration of 20 million cell/ml in PBS, at a 1:1 P14:OT-I ratio. 2-4.5 million CTL were intravenously injected into the retro-orbital vein in anesthetized mice bearing B16-OVA tumors.

extract_protocol:
Cell suspensions were prepared from tumors. Tumors were dissected, transferred to RPMI medium supplemented with TL Liberase Cocktail (100ug/mL, Roche) and incubated at 37°C for 15 minutes. Then, additional Liberase was added, incubating with mixing for an additional 10 minutes. Tissue suspensions were passed through 70-micron strainers and washed with PBS/2% FBS. For sorting of adoptively transferred OT-I and P14 cells, CD8+ T cells were pre-enriched from tumors using the Dynabeads FlowComp Mouse CD8 selection kit (Thermo Fisher). To ensure adequate cell yield, samples from multiple mice belonging to the same group were pooled prior to enrichment. Enriched CD8+ T cells were then stained with anti-CD8a (53-6.7), anti-CD45.1 (A20), anti-Thy1.1 (OX-7), anti-PD-1 (29F.1A12), anti-Tim-3 (RMT3-23) and Fixable Viability Dye eFluor780. Tumor infiltrating lymphocytes were isolated as live CD8+CD45.1+ (OT-I) or CD8+Thy1.1+ (P14) on BD FACSARIA III or FUSION sorters. Total RNA was extracted from 5,000-30,000 sorted CD8+ T cells using the RNeasy micro kit or the miRNeasy micro kit. RNA quality was evaluated with the Bioanalyzer RNA pico kit (Agilent Technologies).
Libraries were prepared from polyA+ RNA using the Whole Transcriptome Amplification Sequencing Technology SEQR kit (Sigma-Aldrich)

treatment_protocol: Total CD8+ T cells, harvested from spleen and lymph nodes of 6-12-week old OT-I or P14 mice by negative selection using Dynabeads (Invitrogen), were activated by anti-CD3 (clone 2C11) plus anti-CD28 (clone 37.51) (BD Biosciences) at 1 μg/mL on plates pre-coated with 50 μg/mL goat anti-hamster IgG (MP Biomedicals). On day 2, T cells were removed from the antibody-coated plate and re-cultured at 400,000 cells/mL with low dose (10 U/ml) recombinant IL-2 (Hoffmann-La Roche). Every day the cell concentration was adjusted to 400,000 cells/mL until day 5-6, when cells were adoptively transferred.

value: P14 CD8+ T cells


title: OTId8-aPDL1_r3

description: transposase-digested genomic DNA


title: OTI-Ctrl_r2


title: P14_r4


title: P14_r2


title: OTI-Ctrl_r1


title: P14_r3


title: OTI_r3


title: P14_r1


title: positive control _02

description: shrimp tropomyosin-sensitized mice


title: OTI_r2


title: OTId8_r1

description: transposase-digested genomic DNA


title: OTI_r1


title: OTId8-aPDL1_r4

description: transposase-digested genomic DNA


title: invitro.iono

source_name: Spleen and lymph nodes

growth_protocol: Then, cells were restimulated in vitro for 2 hours with the following agents (or combinations thereof): 10 nM phorbol 12-myristate 13-acetate (PMA), 500 nM ionomycin, 2 uM Cyclosporin A (added 15 minutes prior to stimulation) or anti-CD3 (5 ug/ml, immobilized).

extract_protocol:
ATAC-seq was performed according to Buenrostro et al. (Nature Methods 2013) with minor modifications: 30,000 to 50,000 sorted CD8+ T cells cells were lysed to extract nuclei. Nuclei were resuspended in 50 ul 1xTD Buffer containing 2.5 μl transposase (Nextera, Illumina). The transposase reaction was conducted for 30 minutes at 37°C, with mild shaking.
Library amplification and barcoding were performed with the library amplification kit (KAPA Biosystems) using Index Primers, designed according to Buenrostro et al. (Nature Methods 2013) at a final concentration of 500 nM. PCR reaction was conducted for 10-11 cycles. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and library size distribution was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent). ATAC-seq libraries were quantified prior to pooling and sequencing using the real-time library quantification kit (KAPA Biosystems).

treatment_protocol: Total CD8+ T cells, harvested from spleen and lymph nodes of 6-12-week old TCR alpha-chain KO P14 mice by negative selection using Dynabeads (Invitrogen), were activated by anti-CD3 (clone 2C11) plus anti-CD28 (clone 37.51) (BD Biosciences) at 1 μg/mL on plates pre-coated with 50 μg/mL goat anti-hamster IgG (MP Biomedicals). On day 2, T cells were removed from the antibody-coated plate and re-cultured at 400,000 cells/mL with low dose (10 U/ml) recombinant IL-2 (Hoffmann-La Roche). Every day the cell concentration was adjusted to 400,000 cells/mL until day 5-6.

value: C57BL/6J TCRalpha-/- P14

value: ionomycin


title: invitro.CD3-PMA_r1

value: anti-CD3 + PMA


title: invitro.PMA-iono-CsA

value: PMA + ionomycin + cyclosporin A


title: invitro.resting

value: (none)


title: invitro.CD3-PMA_r2


title: invitro.PMA-iono

value: PMA + ionomycin


title: JEJ-71

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

institute: Michigan State University

description: Mice dosed every 4 days for 28 days

data_processing:
Quality control: FASTQC v0.11.2
Removal of adaptors: Trimmomatic v0.32
Removal of artifacts: FASTX v0.0.14
Alignment: TopHat2 v2.0.12
Conversion to SAM format: SAMTools v0.1.19
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Jejunum epithelium

extract_protocol:
Intestinal epithelium scrapings were homogenized in TRIzol (Ambion, Waltham, MA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified using a Nano-drop spectrophotometer (Thermo Scientific, Wilmington, DE) at 260 nm and purity was assessed by calculating the A260/A280 ratio. RNA quality was analyzed using the Caliper LabChip GX (Perkin Elmer, Waltham, MA).
Libraries were were prepared using the Ovation Mouse RNA-Seq System 1-16 sample preparation kit (NuGen, San Carlos, CA), with an additional DNase step. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Male C57BL/6 mice were gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every  4 days for 28 days.

tag: Sex

value: Male

value: Post natal day 56

tag: intestinal segment

value: Jejunum

tag: duration of treatment

value: 28 Days

value: TCDD

tag: dose

tag: dose unit

value: µg/kg


title: JEJ-63

description: Mice dosed every 4 days for 28 days

tag: strain


title: JEJ-69

description: Mice dosed every 4 days for 28 days


title: JEJ-59

description: Mice dosed every 4 days for 28 days


title: JEJ-60

description: Mice dosed every 4 days for 28 days


title: JEJ-66

description: Mice dosed every 4 days for 28 days


title: JEJ-44

description: Mice dosed every 4 days for 28 days


title: JEJ-52

description: Mice dosed every 4 days for 28 days


title: JEJ-40

description: Mice dosed every 4 days for 28 days


title: JEJ-38

description: Mice dosed every 4 days for 28 days


title: JEJ-29

description: Mice dosed every 4 days for 28 days


title: JEJ-42

description: Mice dosed every 4 days for 28 days


title: JEJ-27

description: Mice dosed every 4 days for 28 days


title: JEJ-41

description: Mice dosed every 4 days for 28 days


title: JEJ-49

description: Mice dosed every 4 days for 28 days


title: JEJ-36

description: Mice dosed every 4 days for 28 days


title: JEJ-24

description: Mice dosed every 4 days for 28 days


title: JEJ-13

description: Mice dosed every 4 days for 28 days


title: JEJ-21

description: Mice dosed every 4 days for 28 days


title: JEJ-11

description: Mice dosed every 4 days for 28 days


title: JEJ-10

description: Mice dosed every 4 days for 28 days


title: JEJ-08

description: Mice dosed every 4 days for 28 days

value: Vehicle


title: IL2-65

description: Mice dosed every 4 days for 28 days

data_processing:
Quality control: FASTQC v0.11.3
Removal of adaptors: Trimmomatic v0.33
Removal of artifacts: FASTX v0.0.14
Alignment: TopHat2 v2.1.0
Conversion to SAM format: SAMTools v1.2.0
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Ileal epithelium

value: Distal Ileum


title: JEJ-07

description: Mice dosed every 4 days for 28 days


title: JEJ-03

description: Mice dosed every 4 days for 28 days


title: IL2-67

description: Mice dosed every 4 days for 28 days


title: IL2-68

description: Mice dosed every 4 days for 28 days


title: JEJ-55

description: Mice dosed every 4 days for 28 days


title: JEJ-25

description: Mice dosed every 4 days for 28 days


title: IL2-59

description: Mice dosed every 4 days for 28 days


title: IL2-57

description: Mice dosed every 4 days for 28 days


title: IL2-44

description: Mice dosed every 4 days for 28 days