title: M82 pollen rep1 sRNA-seq

data_processing:
Sequences were trimmed and filtered with Trim Galore! (with the adapter parameter `-a TGGAATTCTCGGGTGCCAAGG'). Mapping to H06 (S. pennellii and M82 sequences) was performed with Bowtie 1.1.1 (Langmead2009) without mismatches (options `-v 0 -a').
sRNA libraries from IL1-1, IL2-5, IL8-3 and two M82 seedlings were mapped and clustered on Heinz genome SL2.50 using ShortStack v3.3.3 (Axtell2013) with default parameters. sRNA counts on the defined loci were analysed with DESeq2 v1.8.1 (Love2014).
Genome_build: Solanum lycopersicum Heinz SL2.50
Supplementary_files_format_and_content: srna_clusters_counts.txt: ShortStack loci and counts in a tab-separated file. H06_sRNA_counts_leaf_flower_pollen.RData: segmentSeq alignment data file

extract_protocol:
TRIzol extraction
sRNAs from leaf (2-week-old seedlings), flower and pollen of M82, \textit{S. pennellii} LA0716 and their F1 were cloned from 10 $\mu$g total RNA using the Illumina TruSeq Small RNA cloning kit and libraries were indexed during the PCR step (12 cycles) according to the manufacturer’s protocol.
TruSeq adapter ligation, size selection on gel and amplification

value: pollen

value: 2 months


title: Spleen Control Ig no TCR SAM24301797

status: Public on Aug 18 2017

type: SRA

city: South San Francisco

first: Jonathan

last: Sitrin

state: CA

address: 1 DNA Way

department: OMNI Human Genetics

country: USA

institute: Genentech, Inc.

library_source: transcriptomic

data_processing:
Alignment, HTSeqGenie and GSNAP
Filtering, HTSeqGenie. Only reads with  unique genomic alignments were analysed
Feature counting, HTSeqGenie. Gene models based on RefSeq
Normalization,  to obtain normalized reads per kilobase gene model per million total reads (nRPKM) values
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated text file, normalized RPKM (nRPKM) for each sample and gene

molecule: total RNA

organism: Mus musculus

source_name: Splenic enriched CD4+ T Cells

growth_protocol: Female NZB x NZW F1 mice (NZB/W F1) were bred and crossed at the Jackson Laboratory then maintained at Genentech under specific pathogen-free conditions.

extract_protocol:
After in vitro culture, cells were lysed with RLT buffer supplemented with 2-mercaptoethanol (Sigma-Aldrich).  RNA was extracted using the RNEasy Mini or Micro Kit, depending on input (Qiagen #74104 and #74004).  For kidney samples, RNEasy cleanup kit (Qiagen #74204) was performed.  For all RNASeq experiments, Nanodrop 8,000 (Thermo Scientific) was used to quantify RNA and integrity was measured using the Bioanalyzer RNA 6,000 Pico Kit (Agilent).
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (Illumina) with 100-500ng input and amplified using ten cycles of PCR.

treatment_protocol: Splenic CD4 T cells were isolated from 21-27 week old (30-100mg/dL proteinuria) NZB/W F1 mice with the Mouse CD4+ T cell Isolation Kit (StemCell #19852) per manufacturer’s instructions and cultured in a sterile round-bottom 96-well culture dish (Costar #3799) at 2.5x105 cells/well with 10U/mL of IL-2 (Corning #354043).  Cells were treated with anti-Ox40 (IgG1) or an isotype control IgG1 (25ug/ml) along with 0, 1:10 or 1:1 ratio of T Cell Activator (anti-CD3/CD28) Dynabeads (ThermoFisher #11452).  After 48hours, cellular RNA was collected for RNASeq.

tag: treatment 1

value: No anti-CD3/CD28 Beads

tag: treatment 2

value: Control Ig

tag: strain

value: NZB/W F1 Female Mice


title: M82 flower rep1 sRNA-seq

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

organism: Solanum lycopersicum

growth_protocol: plants were raised from seeds in compost (Levington M3) and maintained in a growth room at 23 $^{o}$C with 16/8 h light/dark periods with 60\% relative humidity, at a light intensity of 150 $\mu$mol photons m$^{-2}$.s$^{-1}$

tag: cultivar

tag: tissue

value: mature flower

tag: age


title: M82 flower rep2 sRNA-seq


title: M82 rep2 MethylC-seq

library_source: genomic

data_processing:
Reads were trimmed and filtered with Trim Galore! v0.4.2 (default parameters)
then mapped on Heinz genome SL2.50 using Bismark v0.17.0 \cite{Krueger2011} (first in paired-end mode with options `--score-min L,0,-0.2 -p 4 --reorder --ignore\_quals --no-mixed --no-discordant --unmapped', then unmapped read1 was mapped in single-end mode with the same quality parameter `-N 1')
Reads were deduplicated with `bismark\_deduplicate' and methylation calls were extracted using Bismark `methylation\_extractor' (with options `-r2 2' for paired-end reads).
Based on Bismark's cytosine report, methylated and unmethylated counts for cytosines of both strands were pooled into 300-bp bins sliding by 200 bp and separated by context (CG, CHG, and CHH). Bins with fewer than 10 counts or with coverage exceeding the $99^{th}$ percentile in one or more libraries were excluded from the analysis. We also excluded the introgressed regions: ch01 1 -- 86 Mb, ch02 44 -- 54 Mb and ch08 61 Mb -- 65866657 bp (end of chromosome).
Each introgression line was then compared to M82 by fitting a logistic regression on the methylated and unmethylated counts (R glm with `family = binomial'). The p-values were subjected to a Benjamini-Hochberg correction to control the false discovery rate at 5\%. Differentially methylated bins were further filtered by imposing thresholds on the absolute difference in methylation (average of replicates) between M82 and the introgression line: a difference of 25\% in the CG context, 20\% in CHG and 10\% in CHH. DMRs were constructed by merging overlapping differentially methylated bins.
Genome_build: Solanum lycopersicum Heinz SL2.50
Supplementary_files_format_and_content: Bismark cytosine reports: tab-separated values, with columns corresponding to chromosome, cytosine position, strand, methylated counts, unmethylated counts, context, trinucleotide context

molecule: genomic DNA

extract_protocol:
DNA from leaf (2-week-old seedlings), mature flowers or pollen was extracted with the Puregene kit (QIAgen) following manufacturer's instructions.
Bisulfite library preparation was performed with a custom protocol similar to Urich et al. (2015). 1.2 µg DNA was sonicated on a Covaris E220 to a target size of 400bp and purified on XP beads (Ampure, ratio 1.8). DNA was end-repaired and A-tailed using T4 DNA polymerase and Klenow Fragment (NEB) and purified again using XP beads (ratio 1.8×). Methylated Illumina Y-shaped adapters for paired-end sequencing were ligated using Quick-Stick Ligase (Bioline). 450ng of purified (ratio 1.8×), adapter-ligated DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions. DNA was barcoded using 12 cycles of PCR amplification with KAPA HiFi HotStart Uracil+Ready Mix (Kapa Biosystems) with PE1.0 and custom index primers (courtesy of the Sanger Institute)

value: leaf

value: 2 weeks


title: CCJS1916

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using FPKM method (Fragments Per kb per Million reads) according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: RPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: C_albicans SC5314 genome
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

organism: Candida albicans

source_name: Candida albicans

growth_protocol: Strains were grown at 37°C in liquid  Lee’s glucose medium for 6.5 hours.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: tpk2/tpk2 tpk1/tpk1 mutant


title: WT

value: wild type


title: M82 leaf rep2 sRNA-seq


title: H3K27ac_neurons_KO_IP 2 FVBN

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description:
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin

data_processing:
For ChIP-seq, data was aligned using bowtie2 (2.2.5) to the mouse mm9 genome
Samtools (version 0.1.19) was used to sort bam files
TDF files were generated by IGVtools (2.3.67) count function with processed bam files as input
Genome_build: mm9
Supplementary_files_format_and_content: TDF files

source_name: Neurons

growth_protocol: Neurons were grown in Neurobasal media supplemented with B27, Glutamax, and Pen/Strep

extract_protocol:
For cultured neurons, cells were fixed on plate with 1% formaldehyde, nuclei were isolated and then sonicated by bath ultrasonicator (Bioruptor). Lysates were clarified and DNA-histone complexes were isolated by either anti-H3K4me3 (Active motif 39159) or H3K27ac (Active motif 39133) immobilized by protein A dynabeads (Life).
Purified DNA was prepared for sequencing with the TruSeq ChIP sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on either HiSeq2000 (Illumina) with 50bp single reads or NextSeq500 with 75bp single reads.

value: FVB/N

tag: cell type

value: neurons from E16.5 cortex

tag: protocol

value: cultured for 7 days

value: Fmr1 KO

tag: chip antibody

value: H3K27ac (Active motif 39133)


title: M82 leaf rep1 sRNA-seq


title: QTI-Seq (eIF5&5MP,HEK293)

city: Ithaca

first: Ji

last: Wan

state: NY

address: 303 Biotech 526 Campus Road

institute: Cornell University

data_processing:
Library strategy: QTI-Seq
Sequencing reads were mapped to genome and NCBI refseq genes by Tophat ((--bowtie1 --no-novel-juncs -G)
P-site of RPF (13th nt) was extracted
Genome_build: hg19
Supplementary_files_format_and_content: ribosome occupancy file of NCBI Refseq mRNAs (according to psite of RPF)

organism: Homo sapiens

source_name: Human Embryonic Kidney Cells

extract_protocol:
Rnase I Digestion, RNA dephosphorylation, Size Selection
Poly-A Tailing, cDNA synthesis, Size selection, circularization, DNA precipitation, Linearization, PCR amplification

tag: cell line

tag: transfection


title: CCJS1413

value: cyr1/cyr1 mutant


title: M82 pollen rep2 sRNA-seq


title: H3K27ac_neurons_WT_IP 2 FVBN

value: WT


title: QTI-Seq (5MP,HEK293)


title: QTI-Seq (empty vector,HEK293)

value: empty vector


title: QTI-Seq (eIF5,HEK293)


title: H3K4me3_tissue_KO_IP 3

description:
Sample 20
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin

source_name: Cerebellum

extract_protocol:
For cultured neurons, cells were fixed on plate with 1% formaldehyde, nuclei were isolated and then sonicated by bath ultrasonicator (Bioruptor). Lysates were clarified and DNA-histone complexes were isolated by either anti-H3K4me3 (Active motif 39159) or H3K27ac (Active motif 39133) immobilized by protein A dynabeads (Life).
For cerebellar neurons, tissue was collected from NeuroD1 BAC-TRAP mice and snap frozen at P15. Tissue was then homogenized and fixed with 1% formaldehyde and neurons were sorted based on GFP signal. Lysates were clarified and histone-DNA complexes were isolated using Protein G dynabeads (Life)
Purified DNA was prepared for sequencing with the TruSeq ChIP sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on either HiSeq2000 (Illumina) with 50bp single reads or NextSeq500 with 75bp single reads.

value: cerebellar neurons

value: sorted from P15 NeuroD1 BAC-TRAP

value: H3K4me3 (Active motif 39159)


title: Spleen Control Ig Low TCR SAM24301802

value: 0.1:1 anti-CD3/CD28 Beads:Cell

value: Control Ig

value: NZB/W F1 Female Mice


title: H3K4me3_tissue_KO_input 3

description:
Sample 19
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: Spleen Control Ig High TCR SAM24301809

value: 1:1 anti-CD3/CD28 Beads:Cell


title: H3K4me3_tissue_KO_IP 2

description:
Sample 18
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: Ribo-Seq (eIF5&5MP,HEK293)

data_processing:
Library strategy: Ribo-Seq
Sequencing reads were mapped to genome and NCBI refseq genes by Tophat ((--bowtie1 --no-novel-juncs -G)
P-site of RPF (13th nt) was extracted
Genome_build: hg19
Supplementary_files_format_and_content: ribosome occupancy file of NCBI Refseq mRNAs (according to psite of RPF)


title: Ribo-Seq (eIF5,HEK293)


title: H3K4me3_tissue_KO_input 2

description:
Sample 17
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: Ribo-Seq (5MP,HEK293)


title: H3K4me3_tissue_KO_IP 1

description:
Sample 16
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: Ribo-Seq (empty vector,HEK293)


title: H3K4me3_tissue_WT_input 3

description:
Sample 13
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: H3K4me3_tissue_WT_IP 3

description:
Sample 14
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: H3K4me3_tissue_WT_IP 2

description:
Sample 12
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: H3K4me3_tissue_WT_input 2

description:
Sample 11
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: H3K4me3_tissue_WT_input 1

description:
Sample 9
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: H3K4me3_tissue_WT_IP 1

description:
Sample 10
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin


title: H-T3

city: Taichung

first: Chien Chih

last: Lee

address: 2 Yuh-Der Road

country: Taiwan

institute: China Medical University Hospital

data_processing:
Illumina Pipeline v1.5+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using MapSplice 2.2.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, The number of reads falling in the exons were counted and normalized by the size of the exon and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include exon sites, raw_counts, and RPKM values for each Sample

source_name: Huh7 cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina mRNA-seq sample kit (Cat# RS-930-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated for 24 hrs with 0.1% DMSO or 10μM 4β-Hydroxywithanolide E

value: Hepatocellular carcinoma

tag: passages

tag: treatment

value: Cells were treated for 24 hrs with 10μM 4β-Hydroxywithanolide E


title: ZR75-ERX-11-2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: ZR75 cells treated with ERX+E2

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: ZR75 breast cancer cells

extract_protocol: Total RNA samples about 1-2 mg were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 100bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from ZR75 cells that are treated with vehicle or ERX-11 in the presence of E2 and Samples were subjected to RNAseq analysis

value: ESR1 Coregulator Binding Site Inhibitors


title: ZR75-ERX-11-1

description: ZR75 cells treated with ERX+E2


title: M82 seedling rep2 sRNA-seq

value: aerial part

value: 2 weeks


title: H-C3

value: Cells were treated for 24 hrs with 0.1% DMSO


title: H3K4me3_neuronsKO_IP 2 C57B6

description:
Neurons from E16.5 cortex, cultured for 7 days, C57B6 Fmr1 WT/KO mice
crosslinked chromatin

value: neurons from E16.5 cortex

value: cultured for 7 days

value: Fmr1 KO


title: ZR75-control-1

description: ZR75 cells treated with vehicle+E2

value: Control


title: Micro-Tom seedling sRNA-seq

value: Micro-Tom


title: H3K4me3_neuronsKO_input 2 C57B6


title: H3K4me3_neuronsWT_input 2 C57B6

value: WT


title: H3K4me3_neuronsWT_IP 2 C57B6

value: H3K4me3 (Active motif 39159)


title: INPUT WT 0030

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
0030_17835_TTAGGC
Input WT

data_processing:
Library strategy: DRIP-Seq
Encoding is Sanger/Illumina 1.9
Quality control of FastQ sequences was assessed using the FastQC software version 0.10.1.
Reads were aligned against the dm3 UCSC genome 2012 release using Bowtie 0.12.5, allowing 2 mismatches in the read seed and considering all possible alignment sites for each read in both the immunoprecipitated (IP) and input samples (setting an upper limit of 10.000 to limit output file size), in order to compare enrichment of genomic features with multiple copies across the genome (i.e. transposons).
Assessment of the immunoprecipitation was done with SSD metrics and PCA-type plots using the htSeqTools package version 1.4.066. Further quality control information was performed with the FastQC software version 0.10. Identification and removal of potential PCR-amplification artifacts was performed with sambamba v0.5.1 using the markdup option and default settings. Coverage TDF tracks were generated with the IGV software version 2.1.16.
To determine location of potential R-loops across the whole genome in both condtions, we first performed a peak calling using MACS 1.4 in RNH1 untreated samples using the same options as for the ChIPseq analysis.
Then, in order to remove from the analysis those identified peaks not arising from true R-loops, log2 RPKM immunoprecipitated signal over identified peaks was measured both for RNH1 untreated and treated sample pairs, and only those locations showing at least moderate depletion upon RNH1 treatment in both replicates were kept (FC < -1.5). Finally, these results were used with the DiffBind package 1.4.2 in order to determine R-loops specific to normal and dH1 knock down conditions using the edgeR method.
Genome_build: dm3
Supplementary_files_format_and_content: BED files indicate chromosome, start, end and score in MACS 1.4.2 _peaks.bed output format

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)

extract_protocol:
Genomic DNA was subjected to IP with 4μg of mouse monoclonal S9.6 antibody. Immunoprecipitated DNA was eluted and purified using standard protocols.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 15 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

treatment_protocol: Drosophila S2 cells were grown to 5x10^5 cell/ml and incubated for 8 days with 100μg of dsRNA against dH1 added to the culture at days 1, 4 and 7. Genomic DNA was purified, treated with 1mg/mL RNase A, sonicated to 500bp-1000bp fragments, treated or not with 3mL (6 U) of RNase H (RNH) (Invitrogen).

tag: replicate

value: S2 cells


title: R+ 2 dsH1 0030

description:
0030_17835_TGACCA
S9.6 IP for treated dsH1

value: RNAi dH1

value: RNH1 treated

value: Mouse monoclonal S9.6 (a kind gift from Dr. G. Roncador, CNIO, Spain)


title: R- 2 dsH1 0030

description:
0030_17835_GCCAAT
S9.6 IP for untreated dsH1

value: RNH1 untreated


title: M82 seedling rep1 sRNA-seq


title: R- WT 0030

description:
0030_17835_CGATGT
S9.6 IP for RNH1 untreated WT


title: H3K4me3_neuronsWT_IP 1 C57B6


title: INPUT2B dsH1 0030

description:
0030_17835_CAGATC
Input for S9.6 dsH1


title: H3K4me3_neuronsKO_IP 1 C57B6


title: H3K4me3_neuronsWT_input 1 C57B6


title: INPUT WT 0029

description:
0029_17834_TTAGGC
Input WT


title: H3K4me3_tissue_KO_input 1

description:
Sample 15
Cerebellar neurons sorted from P15 C57B/6 NeuroD1 BAC-TRAP, Fmr1 WT/KO
crosslinked chromatin

value: cerebellar neurons

value: sorted from P15 NeuroD1 BAC-TRAP


title: H3K27ac_neurons_KO_IP 1

description:
Sample 8
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin

value: FVB/N

value: H3K27ac (Active motif 39133)


title: ZR75-control-2

description: ZR75 cells treated with vehicle+E2


title: H3K4me3_neuronsKO_input 1 C57B6


title: H3K27ac_neurons_KO_input 1

description:
Sample 7
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin


title: R+ WT 0030

description:
0030_17835_ATCACG
S9.6 IP for RNH1 treated WT


title: H3K27ac_neurons_WT_input 1

description:
Sample 5
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin


title: R- 1 dsH1 0029

description:
0029_17834_GCCAAT
S9.6 IP for untreated dsH1


title: H3K4me3_neurons_KO_IP fvb

description:
Sample 4
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin


title: INPUT1 dsH1 0029

description:
0029_17834_CAGATC
Input for S9.6 dsH1


title: H3K4me3_neurons_KO_input fvb

description:
Sample 3
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin


title: R+ WT 0029

description:
0029_17834_ATCACG
S9.6 IP for RNH1 treated WT


title: 2dH1Inp

description:
2208_16505_GGCTAC
Input for gammaH2AvD RNAi dH1

data_processing:
Encoding is Sanger/Illumina 1.9
Quality control of FastQ sequences was assessed using the FastQC software version 0.10.1.
Reads were aligned against the dm3 UCSC genome 2012 release using Bowtie 0.12.5, allowing 2 mismatches in the read seed and considering all possible alignment sites for each read in both Immunoprecipitated and control Input samples (setting an upper limit of 10.000 to limit output file size), in order to compare enrichment proportion for genomic features with multiple copies across the genome (i.e. transposons).
Identification and removal of potential PCR-amplification artifacts was performed with sambamba v0.5.1 using the markdup option and default settings. Coverage TDF tracks were generated with the IGV software version 2.1.16.
Peak calling between IPs and their respective input control in untreated and dH1-depleted cells was performed with MACS 1.4 using options –g dm and leaving the rest as default (p-value < 1e-05).
Genome_build: dm3
Supplementary_files_format_and_content: BED files indicate chromosome, start, end and score in MACS 1.4.2 _peaks.bed output format

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αgH2Av antibodies (3mL). Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 15 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

treatment_protocol: Drosophila S2 cells were grown to 5x10^5 cell/ml and incubated for 8 days with 100μg of dsRNA against dH1 added to the culture at days 1, 4 and 7.


title: H3K27ac_neurons_WT_IP 1

description:
Sample 6
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin


title: 2dH1gA

description:
2208_16505_CTTGTA
IP

value: rabbit gammaHAvD (Rockland, catalog# 600-401-914, lot# 33026)


title: H3K4me3_neurons_WT_IP fvb

description:
Sample 2
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin

value: neurons from E16.5 cortex


title: H3K4me3_neurons_WT_input fvb

description:
Sample 1
Neurons from E16.5 cortex, cultured for 7 days, FVBN Fmr1 WT/KO mice
crosslinked chromatin

value: cultured for 7 days


title: 2WTInp

description:
2208_16505_CAGATC
Input for gammaH2AvD WT


title: KO_THZ_n2

data_processing:
Data was aligned using Tophat2 (2.1.0) with mm9 as a reference genome
Samtools (version 0.1.19) was used to sort bam files
TDF files were generated by IGVtools (2.3.67) count function with processed bam files as input
HTSeq (0.6.1) was used to generate counts and DESeq2 was used for comparing conditions for differential expression
Genome_build: mm9
Supplementary_files_format_and_content: tdf
Supplementary_files_format_and_content: DESeq data: WTvKO.deseq2.csv
Supplementary_files_format_and_content: count data for dmso and Jq1 treated WT and KO

source_name: Cultured cortical neurons

extract_protocol:
RNA was purified from neurons using Qiagen RNAeasy kit
Purified DNA was prepared for sequencing with the TruSeq RNA sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on NextSeq500 (Illumina) with 75bp single reads.

treatment_protocol: At 7 DIV, neurons were treated for 24 hours with vehicle, Jq1, or THZ1.

value: Fmr1 knockout


title: KO_THZ_n1


title: 1dH1Inp

description:
2208_16505_ACAGTG
Input for gammaH2AvD RNAi dH1


title: WT_THZ_n3

value: wildtype


title: 1dH1gA

description:
2208_16505_GCCAAT
IP


title: WT_THZ_n2


title: 1WTgA

description:
2208_16505_TGACCA
IP


title: 1WTInp

description:
2208_16505_CGATGT
Input for gammaH2AvD WT


title: KO_Jq1_n3


title: KO_Jq1_n2


title: WT_THZ_n1


title: KO_Jq1_n1


title: R+ 1 dsH1 0029

description:
0029_17834_TGACCA
S9.6 IP for treated dsH1


title: VH-treated DBA _3

city: Cincinnati

first: Evan

last: Frank

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: PBS-perfused lung

growth_protocol: mice were housed in a specific pathogen-free facility at 74 degF -/+4deg, 30-70% humidity, and a 10/14 light/dark cycle

extract_protocol:
Animals were sacrificed via pentobarbital/thiopental and exsanguinated.  Lungs were perfused with 10mL PBS via right ventricle.  Right lung lobes were lavaged with PBS, excised, snap-frozen in liquid nitrogen, and stored at -80deg C.  RNA was isolated from lungs using TRI reagent (http://mrcgene.com/) and purified using adsorption columns (miRNeasy, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were anesthetized with isoflurane and suspended on an incline.  Exposure inoculum was administered via oropharyngeal aspiration (see Rao et al, 2013, J Toxicol Environ Health A 66, 1441–52)

value: lung


title: WT_Jq1_n3


title: VH-treated Bl/6 _3


title: R- WT 0029

description:
0029_17834_CGATGT
S9.6 IP for RNH1 untreated WT

value: WT


title: KO_THZ_n3


title: WT_Jq1_n1


title: VH-treated Bl/6 _2


title: VH-treated DBA _1


title: KO_dmso_n3

value: dmso


title: 2WTgA

description:
2208_16505_GATCAG
IP

value: S2 cells


title: VH-treated Bl/6 _1


title: CNT-exposed DBA _2


title: KO_dmso_n2


title: CNT-exposed DBA _1


title: KO_dmso_n1


title: jaki_stage2_rep_01

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1390 Storrs Road, ABL220D

department: Animal Science

institute: University of connecticut

data_processing:
Sequencing adapters were trimmed using Cutadapt and low quality reads were pre-filtered by FASTX-Toolkit before mapping.  The quality of reads after filtering was examined using fastQC.
All filtered reads were aligned to mouse reference genome (GRCm38/mm10) by Tophat (v2.0.10) using SAMtools (v0.1.18) and Bowtie (v2.1.0) with default parameters
Individual mapped reads were fed to Cufflinks (v1.2.1) to contruct transcriptome models and any novel genes and transcripts that did not fit the supplied gene models were also assembled.
Cuffmerge was used to converge individual transcriptome to produce a master gene model.
Cufflinks was run to calculate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) by using RefSeq genes as reference
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Programmed somatic cells

growth_protocol: The reprogramming medium was a 1:1  mix of KSR-ESC medium containing 76% KO-DMEM, 20% KSR, 1% 100x glutamax, 1% 100x  non-essential amino acids, and 0.5x penicillin/streptomycin (Invitrogen), and supplemented with  1% 100x β-mercaptoethanol and 1,000 U/ml LIF (Millipore, Billerica, MA, USA), and Serum-  ESC medium with 76% DMEM, 20% ESC-qualified FBS from Hyclone (Fisher Scientific,  Pittsburg, PA, USA), 1% 100x glutamax, 1% 100x non-essential amino acids, 0.5x  penicillin/streptomycin, 1% 100x β-mercaptoethanol, and 1,000 U/ml LIF.

extract_protocol:
Total RNA was isolated from reprogrammed cells with different treatments using RNeasy Mini kit (Qiagen, Valencia, CA)
500 ng of rRNA-depleted total RNA from each sample was used to prepare the RNA sequencing library following the manufacturer’s instructions by SOLiD Total RNA-seq Kit (Life Technologies, Grand Island, NY).  Finally, sequencing libraries were quantified by using Agilent 2100 bioanalyzer and then barcoded, multiplexed, and sequenced on a 5500xl Genetic Analyzer following the manufacturer's protocols.

treatment_protocol: The RNA samples were collected from the reprogrammed cells at 18 days after retroviral Oct4, Klf4, Sox2, and cMyc (OKSM) transduction of OG-MEFs cultured in LIF containing medium and treated either with the specific Jak inhibitor I (Jaki)[34,43] or DMSO as the control (Ctl) starting at day 3 of viral infection (named hereafter DMSO-Stage 1 (S1) or Jaki-S1, respectively), or from induced colonies picked at day 21 and expanded one more passage (p2) (named hereafter DMSO-Stage 2 (S2) or Jaki-S2, respectively)

value: a hybrid background of B6;CBATg (  Pou5f1-EGFP) 2Mnn/J x B6D2F1/J mice

value: mouse embryonic fibroblasts (MEFs)

tag: time point

value: day 21

tag: agent

value: Jaki

tag: passage


title: CNT-exposed Bl/6 _3


title: jaki_stage2_rep_02


title: WT_dmso_n3


title: VH-treated DBA _2


title: WT_dmso_n2


title: jaki_stage1_rep_02

value: day 3


title: dmso_stage2_rep_01

value: DMSO


title: CNT-exposed Bl/6 _2


title: jaki_stage1_rep_01


title: CNT-exposed Bl/6 _1


title: dmso_stage1_rep_02


title: WT_Jq1_n2


title: dmso_stage1_rep_01


title: CNT-exposed DBA _3


title: Midbrain_pAstros

city: New York

first: Kristen

middle: J.

last: Brennand

address: 1425 Madison Ave

department: Department of Neuroscience & Friedman Brain Institute

institute: Icahn School of Medicine at Mount Sinai

description: Sample 8

data_processing:
Paired-end RNA-seq data was generated with the Illumina HiSeq 2500 platform following the Illumina protocol. The raw sequencing reads were aligned to human hg19 genome using star aligner (version 2.5.0b).
Following read alignment, featureCounts (v1.5.0-p1) was used to quantify the gene expression at the gene level based on Ensembl gene model GRCh37.70.
Genes with at least 1 count per million (CPM) in more than 2 samples were considered expressed and hence retained for further analysis, otherwise removed.
The gene level read counts data was normalized using trimmed mean of M-values normalization (TMM) method to adjust for sequencing library size difference.
To control for potential sex differences in gene expression, sex effects were corrected by linear regression.
Genome_build: hg19

source_name: ScienCell

growth_protocol: Forebrain NPCs were maintained at high density, grown on matrigel (BD Bioscience) in NPC medium (DMEM/F12 (Invitrogen: 10565), 1x N2 (Invitrogen: 17502-048), 1x B27-RA (Invitrogen: 12587-010)) and 20 ng/ml FGF2 (Invitrogen), resuspended in 1% BSA (Gibco) in PBS (Gibco)) and split approximately 1:3-1:4 every week with accutase (Millipore). NPCs could be expanded up to 14 passages. Forebrain NPCs were differentiated to astrocytes by seeding dissociated single cells at 15,000 cells/cm2 density on matrigel-coated plates in astrocyte medium (ScienCell: 1801, astrocyte medium (1801-b), 2% fetal bovine serum (0010), astrocyte growth supplement (1852) and 10U/ml penicillin/streptomycin solution (0503)). Initial NPC seeding density and single cell dissociation are critical, particularly during the first 30 days of differentiation, in order to efficiently generate a homogenous population of astrocytes.

extract_protocol:
Cells were plated at 1,000,000 cells per well of a 6-well plate. Within 24-48 hrs, astrocyte cultures were washed with PBS and lysed with RLT buffer (Qiagen, # 74106) or Qiazol reagent (Qiagen). The total RNA was extracted from 30-day differentiated astrocytes with easy mini kit (Qiagen, # 74106) with on-column DNase Idigestion (Qiagen, #79254).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary astrocyte

tag: gender

value: male


title: HEK293_TnfSnxB_Rep2

city: Columbia

first: Mengqian

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

description: Sample 11

data_processing:
Indexed sequences were sorted by Illumina BaseSpace FASTQ generation | version: 1.0.0
Reads were mapped to the hg38 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Genome_build: GRCh38.77
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: HEK293 cells, treated with 10ng/mL TNFalpha (with presence of 1µM Senexin B) for 2 hours, biological replicate-#2

growth_protocol: HEK293 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well 24 hours prior to treatment.

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using the Illumina TruSeq RNA Sample Prep Kit (RS-122-2001/RS-122-2002)

treatment_protocol: Cells were first pre-treated with 1μM Senexin B or 0.1% DMSO (control) for 1 hour and then treated with or without 10 ng/mL TNF-α for 2 hours.

value: HEK293 (ATCC)

value: pre-treated with 1uM Senexin B for 1 hour, then treated with 10ng/mL TNF-alpha for 2 hours


title: HEK293_TnfSnxB_Rep3

description: Sample 12

source_name: HEK293 cells, treated with 10ng/mL TNFalpha (with presence of 1µM Senexin B) for 2 hours, biological replicate-#3


title: Cerebral_Cortex_pAstros

description: Sample 7

value: female


title: HEK293_Tnf_Rep3

description: Sample 9

source_name: HEK293 cells, treated with 10ng/mL TNFalpha for 2 hours, biological replicate-#3

value: pre-treated with 0.1% DMSO (vehicle control) for 1 hour, then treated with 10ng/mL TNF-alpha for 2 hours


title: HEK293_TnfSnxB_Rep1

description: Sample 10

source_name: HEK293 cells, treated with 10ng/mL TNFalpha (with presence of 1µM Senexin B) for 2 hours, biological replicate-#1


title: 9429_NPCs

description: Sample 5

source_name: AG09429 (Coriell)

value: hiPSC-astrocyte


title: dmso_stage2_rep_02

tag: strain


title: HEK293_Tnf_Rep2

description: Sample 8

source_name: HEK293 cells, treated with 10ng/mL TNFalpha for 2 hours, biological replicate-#2


title: HEK293_Tnf_Rep1

description: Sample 7

source_name: HEK293 cells, treated with 10ng/mL TNFalpha for 2 hours, biological replicate-#1


title: 9429_Astros

description: Sample 4


title: 9319_Astros

description: Sample 3

source_name: AG09319 (Coriell)


title: 3651_NPCs

description: Sample 2

source_name: GM03651 (Coriell)


title: HEK293_SnxB_Rep2

description: Sample 5

source_name: HEK293 cells, treated with 1uM Senexin B for 3 hours, biological replicate-#2

value: treated with 1uM Senexin B for 3 hours


title: HEK293_SnxB_Rep1

description: Sample 4

source_name: HEK293 cells, treated with 1uM Senexin B for 3 hours, biological replicate-#1


title: UT-SCC105 negative control siRNA [RNA-Seq]

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: RNA sequencing data from cSCC

data_processing:
The samples were sequenced with the HiSeq2500 instrument using single-end sequencing with 50bp read length.
The reads obtained from the instrument were base called using the instrument manufacturer’s base calling software and aligned against the human reference genome (GRCh37 assembly, downloaded from UCSC) using TopHat version 2.0.6.
After alignment, the reads were associated with known genes based on RefSeq annotations derived from UCSC and the number of reads aligned within each gene was counted using HTSeq tool (v.0.5.4p3).
The counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.0.1, Bioconductor version 2.12).
Genome_build: GRCh37
Supplementary_files_format_and_content: For statistical testing the data were further log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalized counts are represented as RPKM values.

source_name: Cutaneous squamous cell carcinoma cell line

growth_protocol: cSCC cells were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cSCC cell lysates were harvested 72 hours after siRNA-treatment and serum-starvated 24 hours before harvesting.

tag: source

value: Cutaneous SCC

value: Derived from cSCC tumors

value: Primary cSCC cells

value: Negative control siRNA


title: WT_dmso_n1

value: wildtype

value: dmso


title: HEK293_Ctrl_Rep3

description: Sample 3

source_name: HEK293 cells, treated with vehicle control for 3 hrs, biological replicate-#3

value: treated with 0.1% DMSO (vehicle control) for 3 hours


title: HEK293_Ctrl_Rep2

description: Sample 2

source_name: HEK293 cells, treated with vehicle control for 3 hrs, biological replicate-#2


title: UT-SCC12A AIM2 siRNA [RNA-Seq]

description: RNA sequencing data from cSCC

tag: tissue

value: AIM2 siRNA


title: UT-SCC12A negative control siRNA [RNA-Seq]

description: RNA sequencing data from cSCC


title: UT-SCC105 AIM2 siRNA [RNA-Seq]

description: RNA sequencing data from cSCC


title: BJ_Astros

description: Sample 6

source_name: BJ ATCC CRL-2522


title: HCT116_Tnf_Rep3

description: Sample 11

source_name: HCT116 cells, treated with 10ng/mL TNFalpha for 2 hours, biological replicate-#3

growth_protocol: HCT116 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well 24 hours prior to treatment.

value: HCT116 (ATCC)


title: UT-SCC7 AIM2 siRNA [RNA-Seq]

description: RNA sequencing data from cSCC


title: HCT116_Ctrl_Rep3

description: Sample 9

source_name: HCT116 cells, treated with vehicle control for 3 hrs, biological replicate-#3


title: HCT116_SnxB_Rep3

description: Sample 10

source_name: HCT116 cells, treated with 1uM Senexin B for 3 hours, biological replicate-#3


title: UT-SCC7 negative control siRNA [RNA-Seq]

description: RNA sequencing data from cSCC


title: HCT116_TnfSnxB_Rep3

description: Sample 12

source_name: HCT116 cells, treated with 10ng/mL TNFalpha (with presence of 1µM Senexin B) for 2 hours, biological replicate-#3


title: HCT116_Tnf_Rep2

description: Sample 7

source_name: HCT116 cells, treated with 10ng/mL TNFalpha for 2 hours, biological replicate-#2


title: HEK293_SnxB_Rep3

description: Sample 6

source_name: HEK293 cells, treated with 1uM Senexin B for 3 hours, biological replicate-#3


title: AdEZH2-Simva-1

city: Rochester

first: Suowen

last: Xu

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCh38.p2 (hg38) + Gencode-23 Annotation
Supplementary_files_format_and_content: raw count matrix in tab-delimited text file, one column for each sample

growth_protocol: Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were treated with control adenovirus (AdCon) or EZH2 adenovirus (AdEZH2, #1371, Vector Biolab) for 24 hours, before stimulation with simvastatin (1 µM, dissolved in DMSO) for 48 hours in the presence of adenovirus

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: 3 to 5 passages

tag: treated with

value: EZH2 adenovirus for 24 hrs

tag: stimulated with

value: simvastatin (1 µM, dissolved in DMSO) for 48 hrs


title: AdEZH2-Simva-3

tag: cell type


title: HCT116_SnxB_Rep2

description: Sample 6

source_name: HCT116 cells, treated with 1uM Senexin B for 3 hours, biological replicate-#2


title: AdCon-Simv-3

value: control adenovirus (AdCon) for 24 hrs


title: AdCon-Simv-2


title: 3651_Astros

description: Sample 1

value: female


title: AdCon-Simv-1


title: HEK293_Ctrl_Rep1

description: Sample 1

source_name: HEK293 cells, treated with vehicle control for 3 hrs, biological replicate-#1

value: HEK293 (ATCC)


title: AdCon-Veh-3

value: vehicle (DMSO) for 48hrs


title: AdCon-Veh-2


title: HCT116_Tnf_Rep1

description: Sample 3

source_name: HCT116 cells, treated with 10ng/mL TNFalpha for 2 hours, biological replicate-#1

value: pre-treated with 0.1% DMSO (vehicle control) for 1 hour, then treated with 10ng/mL TNF-alpha for 2 hours


title: AdCon-Veh-1


title: HCT116_Ctrl_Rep1

description: Sample 1

source_name: HCT116 cells, treated with vehicle control for 3 hrs, biological replicate-#1


title: HCT116_SnxB_Rep1

description: Sample 2

source_name: HCT116 cells, treated with 1uM Senexin B for 3 hours, biological replicate-#1

value: treated with 1uM Senexin B for 3 hours


title: SW480 0hr TNF-a input

city: San Diego

first: Shannon

middle: M

last: Lauberth

state: California

address: 9500 Gilman Drive #0322, Bonner Hall 3202

department: Biological Sciences

institute: UCSD

data_processing:
RNA-seq:
Sequenced reads were trimmed for adaptor sequences and mapped to human hg38 reference genome using STAR (Ultrafast Universal RNA-seq Aligner)
Gene expression levels were counted per gene model (not counting dfferentiated splices) and differential expression across samples were determined using edgeR.
Gene Ontology enrichment was performed using Metascape.
ChIP-seq:
Sequenced reads were mapped to the hg38 human reference genome using Bowtie2 software and default parameters.
Mapped reads were then processed to make tag directories using the HOMER module. PCR duplications were removed and only uniquely mapped reads were kept for further analyses.
Genome browser files for resulting reads were generated by using the makeUCSCfile module from HOMER.
Enrichment for p65 and histone modification deposition wer ecalled using findPeaks module from HOMER using preset parameters for transcription factors and histones, respectively and compared to the input samples.
For p53 R273H peak calling, p53 enriched regions were determined by HOMER (comparing to inputs). The resulting regions were split into subpeaks using PeakSplitter software.
For identification of mutp53 and p65 peak colocalization, p65 peaks were first divided into 2 groups with and without uninduced mutp53 binding by using the co-bound option of mergePeak module from HOMER.
Deeptools were used to generate heatmaps and de novo motif analyses were performed using HOMER.
GRO-seq:
Sequenced reads were mapped to the hg38 human reference genome using Bowtie2 software.
Uniquely mapped reads were kept and at most 3 reads at each unique genomic position.
GRO-seq reads were counted 1000 bp around the specified transcription factor peaks and normalized to 10 million total reads using default settings of annotatePeaks module of HOMER.
Genome_build: hg38

source_name: SW480_SW480 0hr TNF-α input

growth_protocol: Human SW480 cells were grown in Dulbecco’s modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS. SW480 cells that stably and inducibly express short hairpins against LacZ or p53 were kindly provided by Xinbin Chen (UC Davis) and were grown in standard DMEM medium containing 1X penicillin and streptomycin (Gemini Bio-Products), 1.5 μg ml-1 puromycin (Sigma), and were induced with 1 μg ml-1 doxycycline (Sigma).

extract_protocol:
For GRO-seq analyses, nuclei were prepared and used for run-on reactions using BrUTP. Following nascent RNA enrichment with anti-BrdU agarose beads (SCBT), RNA was extracted using TRIzol LS reagent and used for library preparation. For ChIP, lysates from sonicated nuclei were prepared and protein-DNA complexes were IP'd with corresponding antibodies. For RNA-seq, total RNA was extracted using TRIzol LS reagent and strand-specific libraries were prepared from 1 mg of RNA
ChIP-seq libraries were prepared according to Illumina's ChIP Truseq protocol. RNA-seq libraries were prepared following the dUTP second strand cDNA method using NEXTflex barcodes. GRO-seq libraries were prepared similarly. Please refer to the methods section for detailed protocols.

treatment_protocol: All cells were treated with 12.5 ng  ml-1 TNF-α (R&D Systems) for 0 or 16 hr before harvesting for GRO-seq, ChIP-seq, and RNA-seq analyses.

value: Human Colon Cancer Cell Line


title: AdEZH2-Simva-2


title: HCT116_Ctrl_Rep2

description: Sample 5

source_name: HCT116 cells, treated with vehicle control for 3 hrs, biological replicate-#2


title: shp53 16 hr TNF-a RNA-seq

source_name: SW480_shp53 16 hr TNF-α RNA-seq

value: 12.5 ng  ml-1 TNF-α for 16 hr


title: shp53 0 hr TNF-a RNA-seq

source_name: SW480_shp53 0 hr TNF-α RNA-seq


title: F1 pollen rep3 sRNA-seq

data_processing:
Sequences were trimmed and filtered with Trim Galore! (with the adapter parameter `-a TGGAATTCTCGGGTGCCAAGG'). Mapping to H06 (S. pennellii and M82 sequences) was performed with Bowtie 1.1.1 (Langmead2009) without mismatches (options `-v 0 -a').
sRNA libraries from IL1-1, IL2-5, IL8-3 and two M82 seedlings were mapped and clustered on Heinz genome SL2.50 using ShortStack v3.3.3 (Axtell2013) with default parameters. sRNA counts on the defined loci were analysed with DESeq2 v1.8.1 (Love2014).
Genome_build: Solanum lycopersicum Heinz SL2.50
Supplementary_files_format_and_content: srna_clusters_counts.txt: ShortStack loci and counts in a tab-separated file. H06_sRNA_counts_leaf_flower_pollen.RData: segmentSeq alignment data file

organism: Solanum lycopersicum x Solanum pennellii

extract_protocol:
TRIzol extraction
sRNAs from leaf (2-week-old seedlings), flower and pollen of M82, \textit{S. pennellii} LA0716 and their F1 were cloned from 10 $\mu$g total RNA using the Illumina TruSeq Small RNA cloning kit and libraries were indexed during the PCR step (12 cycles) according to the manufacturer’s protocol.
TruSeq adapter ligation, size selection on gel and amplification

tag: sample type

value: F1 of Solanum lycopersicum cv M82 x Solanum pennellii LA0716

value: pollen

tag: age

value: 2 months


title: shLacZ 0 hr TNF-a RNA-seq

source_name: SW480_shLacZ 0 hr TNF-α RNA-seq

tag: cell line


title: SW480 16hr TNF-a input

source_name: SW480_SW480 16hr TNF-α input

tag: chip antibody


title: F1 pollen rep4 sRNA-seq


title: 16 hr TNF-a p65 ChIP-seq

source_name: SW480_16 hr TNF-α p65 ChIP-seq

value: anti-p65 (sc372x)


title: 0 hr TNF-a p65 ChIP-seq

source_name: SW480_0 hr TNF-α p65 ChIP-seq


title: 16 hr TNF-a RNAPII ChIP-seq

source_name: SW480_16 hr TNF-α RNAPII ChIP-seq

value: anti-RNA Pol II (N20, sc899)


title: F1 flower rep3 sRNA-seq

value: mature flower


title: 0 hr TNF-a p53 ChIP-seq

source_name: SW480_0 hr TNF-α p53 ChIP-seq


title: shLacZ 16 hr TNF-a RNA-seq

source_name: SW480_shLacZ 16 hr TNF-α RNA-seq


title: F1 pollen rep2 sRNA-seq


title: F1 flower rep4 sRNA-seq


title: 16 hr TNF-a p53 ChIP-seq

source_name: SW480_16 hr TNF-α p53 ChIP-seq


title: HCT116_TnfSnxB_Rep1

description: Sample 4

source_name: HCT116 cells, treated with 10ng/mL TNFalpha (with presence of 1µM Senexin B) for 2 hours, biological replicate-#1

value: HCT116 (ATCC)

value: pre-treated with 1uM Senexin B for 1 hour, then treated with 10ng/mL TNF-alpha for 2 hours


title: F1 pollen rep1 sRNA-seq


title: 0 hr TNF-a H3K27ac ChIP-seq

source_name: SW480_0 hr TNF-α H3K27ac ChIP-seq


title: F1 flower rep2 sRNA-seq


title: F1 flower rep1 sRNA-seq


title: F1 leaf rep4 sRNA-seq

value: leaf

value: 2 weeks


title: 16 hr TNF-a H3K4me1 ChIP-seq

source_name: SW480_16 hr TNF-α H3K4me1 ChIP-seq

value: anti-H3K4me1 (ab8895)


title: 0 hr TNF-a H3K4me1 ChIP-seq

source_name: SW480_0 hr TNF-α H3K4me1 ChIP-seq


title: F1 leaf rep3 sRNA-seq


title: 0 hr TNF-a GRO-seq

source_name: SW480_0 hr TNF-α GRO-seq


title: F1 leaf rep2 sRNA-seq


title: 16 hr TNF-a GRO-seq

source_name: SW480_16 hr TNF-α GRO-seq


title: 22Rv1-335-6h

city: Chicago

first: WEN-CHING

last: CHAN

state: IL

department: Biological Sciences Division

institute: The University of Chicago

data_processing:
Illumina Casava1.7 software used for basecalling.
All RNA-seq reads were used to align to the hg19 genome assembly using STAR v2.5.1b with default configurations.
Transcripts were assembled from the aligned reads using Cufflinks v2.2.1 with the default configurations to generate FPKM (Fragments Per Kilobase Million) tables.
Using 1.5 as the fold change cutoff, DEGs (Differentially expressed genes) were detected using both Tuxedo suite (FPKM-based method) and featureCounts-DESeq2 (v2_1.6.3) or edgeR (v3.6.8) (read count-based method) with default configurations.
Genes detected by at least more than one method were collected to create a high-confidence DEG lists.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Count tables were generated using featureCount (v1.14.2) based on Ensembl annotation (GRCh37).

source_name: prostate cancer cells

extract_protocol:
Total RNA was isolated using the 'RNeasy Mini' kit (Qiagen) following the manufacturer's instructions. Quality of extracted RNA was evaluated using a 2200 TapeStation system (Agilent). Samples with a RIN score ≥ 7 were selected for making libraries.
RNA sequencing (RNA-seq) libraries were built using the 'Stranded mRNA-Seq' kit for Illumina plateforms (KAPA) with OligodT magnetic beads to enrich the samples for informative mRNA species. Libraries were run on a 2200 TapeStation system (Agilent) to confirm fragment size. Libraries were then quantified by qPCR using the 'Library Quantification' kit (KAPA).
Sequencing was done on a HiSeq 2000 sequencing system (Illumina) in a 100bp, paired-end run, with three samples per lane

value: SGRM - CORT108335 at 6 hours


title: F1 leaf rep1 sRNA-seq


title: 22Rv1-297-6h

value: SGRM - CORT108297 at 6 hours


title: 22Rv1-335-2h

value: SGRM - CORT108335 at 2 hours


title: S. pennellii pollen rep2 sRNA-seq

organism: Solanum pennellii

tag: cultivar


title: 22Rv1-297-2h

tag: treatment

value: SGRM - CORT108297 at 2 hours


title: IL8-3 rep2 MethylC-seq

data_processing:
Reads were trimmed and filtered with Trim Galore! v0.4.2 (default parameters)
then mapped on Heinz genome SL2.50 using Bismark v0.17.0 \cite{Krueger2011} (first in paired-end mode with options `--score-min L,0,-0.2 -p 4 --reorder --ignore\_quals --no-mixed --no-discordant --unmapped', then unmapped read1 was mapped in single-end mode with the same quality parameter `-N 1')
Reads were deduplicated with `bismark\_deduplicate' and methylation calls were extracted using Bismark `methylation\_extractor' (with options `-r2 2' for paired-end reads).
Based on Bismark's cytosine report, methylated and unmethylated counts for cytosines of both strands were pooled into 300-bp bins sliding by 200 bp and separated by context (CG, CHG, and CHH). Bins with fewer than 10 counts or with coverage exceeding the $99^{th}$ percentile in one or more libraries were excluded from the analysis. We also excluded the introgressed regions: ch01 1 -- 86 Mb, ch02 44 -- 54 Mb and ch08 61 Mb -- 65866657 bp (end of chromosome).
Each introgression line was then compared to M82 by fitting a logistic regression on the methylated and unmethylated counts (R glm with `family = binomial'). The p-values were subjected to a Benjamini-Hochberg correction to control the false discovery rate at 5\%. Differentially methylated bins were further filtered by imposing thresholds on the absolute difference in methylation (average of replicates) between M82 and the introgression line: a difference of 25\% in the CG context, 20\% in CHG and 10\% in CHH. DMRs were constructed by merging overlapping differentially methylated bins.
Genome_build: Solanum lycopersicum Heinz SL2.50
Supplementary_files_format_and_content: Bismark cytosine reports: tab-separated values, with columns corresponding to chromosome, cytosine position, strand, methylated counts, unmethylated counts, context, trinucleotide context

extract_protocol:
DNA from leaf (2-week-old seedlings), mature flowers or pollen was extracted with the Puregene kit (QIAgen) following manufacturer's instructions.
Bisulfite library preparation was performed with a custom protocol similar to Urich et al. (2015). 1.2 µg DNA was sonicated on a Covaris E220 to a target size of 400bp and purified on XP beads (Ampure, ratio 1.8). DNA was end-repaired and A-tailed using T4 DNA polymerase and Klenow Fragment (NEB) and purified again using XP beads (ratio 1.8×). Methylated Illumina Y-shaped adapters for paired-end sequencing were ligated using Quick-Stick Ligase (Bioline). 450ng of purified (ratio 1.8×), adapter-ligated DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions. DNA was barcoded using 12 cycles of PCR amplification with KAPA HiFi HotStart Uracil+Ready Mix (Kapa Biosystems) with PE1.0 and custom index primers (courtesy of the Sanger Institute)

tag: introgressin lines


title: IL8-3 rep1 MethylC-seq


title: S. pennellii pollen rep1 sRNA-seq


title: S. pennellii flower rep2 sRNA-seq


title: 22Rv1-RED-6h

value: Dexamethasone (MP Biomedicals) at 6 hours


title: S. pennellii leaf rep2 sRNA-seq


title: 22Rv1-RE

value: Enzalutamide (Selleck Chemicals or Medivation)


title: S. pennellii flower rep1 sRNA-seq


title: S10_SnakeMain

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Raw reads were trimmed and filtered by quality characteristics using Trimmomatic.
The reads for each sample were mapped to a concatonated Potamopyrgus antipodarum transcriptome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-5 were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The DMR that included at least two windows with an edgeR P value < 1e-5 were then selected for further analysis and annotated.
Genome_build: Transcriptome contigs obtained from http://bioweb.biology.uiowa.edu/neiman/download.php were used as the reference genome.
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Potamopyrgus antipodarum

source_name: Foot tissue

growth_protocol: Snails were sampled from two sites representing very different flow regimes. Lake snails were collected from Lake Washington in Seattle, WA, and river snails were collected from the main channel of the Snake River at Ritter Island near Wendell, ID.

extract_protocol:
Genomic DNA from snail foot tissue was prepared as follows. Snail tissue was suspended in 100 μl of 1 x Phosphate Buffered Saline (PBS), then 820 μl DNA extraction buffer (50mM Tris pH8, 10mM EDTA pH8, 0.5% SDS) and 80 μl Proteinase K (20 mg/ml) was added and the sample incubated on a rotator at 55 C for 2-3 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A) was added, the sample mixed and incubated on ice for 15 minutes, then spun at 4 C at 13,000 rpm for 20 minutes. The supernatant was transferred to a fresh tube, then precipitated over night with the same volume 100% isopropanol and 2 μl glycoblue at -20 C. The sample was then centrifuged and the pellet washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. Genomic DNA from ten individuals was pooled into a single sample. Three pooled samples were processed for each sampling location.   Methylated DNA Immunoprecipitation (MeDIP) from genomic DNA was performed as follows. For the snail samples approximately 6 μg of each genomic DNA pool was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 5min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C.   The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube The same volume of Washing Buffer (at least 1 mL) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the washed beads were resuspended in the same volume of 1xIP buffer as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C.  After the incubation the beads were washed three times with 1X IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with 1xIP buffer 3 times. The washed beads were then resuspended in 250μl digestion buffer (50 mM Tris-HCI pH8, 10mM EDTA pH8, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55˚C. After incubation the tube was put again into the magnetic rack for 3 minutes and the supernatant removed to a new microfuge tube. The beads were discarded. 250μl of buffered Phenol-Chloroform-Isoamylalcohol solution were added to the supe and the tube vortexed for 30 sec then centrifuged at 14,000rpm for 5min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250μl chloroform were added to the supernatant from the previous step, vortexed for 30sec and centrifuged at 14,000rpm for 5min at room temperature.  The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in  -20˚C freezer for 1 hour to overnight.   The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20˚C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4˚C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 25μl H2O or TE. DNA concentration was measured in Qubit with ssDNA kit.
For library preparation we used the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. Next generation sequencing (NGS) was performed at the WSU Spokane Genomic Core laboratory using the Illumina® HiSeq 2500 with a PE50 application, with a read size of approximately 50bp and approximately 100 million reads per pool.  Three libraries each were run in one lane comparing river and lake.

treatment_protocol: Samples were obtained by searching the substrate and scraping snails off the underside of rocks and woody debris. The samples were maintained on wet paper towels and kept cool until they reached the laboratory at Washington State University, Pullman, WA. In the laboratory the samples are kept in water in an environmental chamber that is held at 14C with a 12:12 day/night cycle for several days until they were processed for phenotypic and molecular analysis.

value: Foot tissue

tag: location

value: Snake river - main channel


title: IL8-3 seedling RNA-seq

tag: introgression

value: Solanum pennellii introgression in Solanum lycopersicum cv M82

value: aerial part


title: 22Rv1-RED-2h

value: Dexamethasone (MP Biomedicals) at 2 hours


title: S. pennellii leaf rep1 sRNA-seq


title: HCT116_TnfSnxB_Rep2

description: Sample 8

source_name: HCT116 cells, treated with 10ng/mL TNFalpha (with presence of 1µM Senexin B) for 2 hours, biological replicate-#2


title: S9_SnakeMain


title: IL2-5 seedling sRNA-seq


title: cdc22-3_5

city: Hangzhou

first: Xiangwei

last: He

state: Zhejiang

address: NanoTech Bd., Zhejiang Univ., 388 Yuhangtang Rd.

department: Life Sciences Institute

institute: Zhejiang University

description:
ChIP antibody: H3K9me2 (abcam ab1220)
H3K9me2 nucleosome mapping in cdc22-23 mutant cells

data_processing:
Base calls generated with v4.2.2 of the Torrent Suite software. Reads were mapped to S. pombe ASM294v2 assembly using “bwa” with default parameters, and only the uniquely mapped reads were obtained for further analysis. Nucleosome position and occupancy were calculated by using DANPOS(Chen et al., 2013) which normalize data by random sample and adjust clonal signal to 1 read. Reads were adjusted to 73 bases with 5’ fixed when occupancy was counted.
Genome_build: S. pombe ASM294v2 assembly
Supplementary_files_format_and_content: bigWig. Click this link for more information on the bigWig format: https://genome.ucsc.edu/goldenPath/help/bigWig.html

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: growth on YE5S liquid media at 30 degree, logohase cell pellets were harvested and treated with 20mg/ml zymolase for 1h at 37 degree.

extract_protocol:
nucelosome digested by 240U/ml (final) micrococonuclease for 16min in lysis buffer (0.5mM spermidine, 1mM DTT, 0.075% NP40, 50mM NaCl, 10mM Tris(pH8.0), 5mM MgCl2, 5mM CaCl2 plus proteinase inhibitors)
The KAPA library preparation kit for Ion Torrent (KK8301)

tag: genotype

value: cdc22-23 mutant


title: S8_SnakeMain


title: IL1-1 seedling sRNA-seq

city: Heidelberg

first: Quentin

institute: Olivia Newton-John Cancer Research Institute


title: S6_Washington

value: Lake Washington


title: LAPC4-335-6h


title: cdc22-3_3


title: LAPC4-335-2h


title: cdc22-3_1


title: S4_Washington


title: 16 hr TNF-a H3K27ac ChIP-seq

source_name: SW480_16 hr TNF-α H3K27ac ChIP-seq

value: Human Colon Cancer Cell Line

value: 12.5 ng  ml-1 TNF-α for 16 hr


title: S5_Washington


title: X2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: photon irradiation

data_processing:
Concurential mapping with STAR_2.4.0i versus hg19 and mm10 genome folowing Encode RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20"
FeatureCounts counting (subread-1.5.0-p3-Linux-x86_64) with " --primary -g gene_name -p -s 1 -C" options
Supplementary_files_format_and_content: table_featurecounts.txt: Human and Mouse genes count tables

organism: mixed sample

source_name: photon irradiation

growth_protocol: The cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 7% fetal bovine serum (Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol:
One million non-irradiated, P or X irradiated CAL33 cells (CR-MI group) were injected subcutaneously into the flank of 6-week-old NMRI-Foxn1nu/Foxn1nu female mice (Janvier Labs, Le Genest-Saint-Isle, France, n=10/group). The tumor volume (v = L x l2 x 0.52) was determined following measurement with a caliper. When the tumors reached one cm3, the mice were sacrificed and the tumors collected. Total RNA was extracted from tumors with the AllPrep® DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany).
Libraries were generated from 1µg of total RNA using Truseq Stranded mRNA kit (Illumina). Libraries were then quantified with KAPA library quantification kit (Kapa biosystems) and pooled. 4nM of this pool were loaded on a Nextseq 500 high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2 × 75bp paired-end chemistry

treatment_protocol: Cell irradiations. Five million cells were seeded onto 12 cm2 tissue culture flasks, 48 h prior to the irradiations, which were carried out at the Centre Antoine Lacassagne, Nice, France (four independent experiments) with either protons (P, 63 MeV Cyclotron MEDICYC, CAL, Nice, France) or photons (X, 6 MeV Dual energy Clinac 21EX Linear Accelerator, Varian Inc., Palo Alto, CA, USA). The cells were irradiated three times, one week apart with 8 Gy, and processed 6h after irradiation. Cells were re-seeded after each irradiation and kept in culture until the next irradiation. After the third irradiation, the cells were expended in culture for three weeks.

value: head and neck carcinoma

value: Human cells injected in Mice


title: psg55-2_5

description:
ChIP antibody: H3K9me2 (abcam ab1220)
H3K9me2 nucleosome mapping in wt cells

value: wild type


title: psg55-2_3


title: LAPC4-RED-6h


title: LAPC4-297-2h


title: 22Rv1-R

value: R1881 (Sigma-Aldrich)


title: X1

description: photon irradiation


title: P3

description: proton irradiation

source_name: proton irradiation


title: LAPC4-RED-2h


title: S12_SnakeSide

growth_protocol: Snails were sampled from two sites representing very different flow regimes. Lake snails were collected from Lake Lytle in Rockaway Beach, OR, and river snails were collected from a side channel of the Snake River at Ritter Island near Wendell, ID.

value: Snake river - side channel


title: IL2-5 rep2 MethylC-seq

last: Gouil

address: Studley Road

value: leaf

value: 2 weeks


title: psg55-2_1


title: LAPC4-RE

value: Enzalutamide (Selleck Chemicals or Medivation)


title: S10_SnakeSide

value: Foot tissue


title: P2

description: proton irradiation


title: P1

description: proton irradiation


title: X3

description: photon irradiation


title: IL1-1 rep2 MethylC-seq


title: O3

description: control

source_name: control


title: S3_Lytle

value: Lytle lake


title: S2_Lytle


title: LAPC4-R


title: LAPC4-Veh

value: Vehicle


title: 22Rv1-Veh


title: S1_Lytle


title: LAPC4-297-6h

value: SGRM - CORT108297 at 6 hours


title: IL1-1 rep1 MethylC-seq


title: S. pimpinellifolium seedling sRNA-seq

organism: Solanum pimpinellifolium

value: aerial part


title: O2

description: control


title: O1

description: control


title: PDX 14-07 (vehicle) 2

status: Public on Aug 17 2017

city: Melbourne

first: Shom

last: Goel

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Data were analyzed, with all the default parameters, by Torrent Suite (Thermo Fisher) for base caliing, alignment, and filtering,  and ampliSeqRNA analysis plugin (Thermo Fisher) to generate read counts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt  file includes read counts for all Samples.

growth_protocol: Tumors were implanted orthotopically and treated once tumors reached appropriate size (see Methods of accompanying manuscript)

extract_protocol:
RNA was extracted using Macherey Nagel kit.
cDNA libraries were constructed using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher)
The Ion AmpliSeq Transcriptome Human Gene Expression Kit is designed for targeted amplification of over 20,000 human RefSeq genes. A short amplicon (~110 bp) is amplified for each targeted gene (Thermo Fisher).

treatment_protocol: Abemaciclib 90mg/kg by gavage daily vs vehicle

value: PDX tumor

tag: agent

value: control


title: PDX 14-07 (vehicle) 1


title: MCF7 abemaciclib 7 days (replicate 2)

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of RNA collection was between 60-70%.

treatment_protocol: Abemaciclib concentration 500nM for MDA-MB_361 and MDA-MB453; 250nM for MCF7

value: MCF7 breast carcinoma cell line

value: abemaciclib


title: MCF7 abemaciclib 7 days (replicate 3)


title: S11_SnakeSide


title: PDX 14-07 (abemaciclib) 1

value: Abemaciclib


title: MCF7 abemaciclib 7 days (replicate 1)


title: MCF7 control (replicate 3)


title: MCF7 control (replicate 2)


title: IL2-5 rep1 MethylC-seq

growth_protocol: plants were raised from seeds in compost (Levington M3) and maintained in a growth room at 23 $^{o}$C with 16/8 h light/dark periods with 60\% relative humidity, at a light intensity of 150 $\mu$mol photons m$^{-2}$.s$^{-1}$


title: MDA-MB-453 abemaciclib 7 days (replicate 3)

value: MDA-MB-453 breast carcinoma cell line


title: MCF7 control (replicate 1)


title: MDA-MB-453 control (replicate 3)


title: MDA-MB-453 abemaciclib 7 days (replicate 1)


title: MDA-MB-453 control (replicate 2)


title: MDA-MB-361 abemaciclib 7 days (replicate 3)

value: MDA-MB-361 breast carcinoma cell line


title: MDA-MB-453 control (replicate 1)


title: MDA-MB-361 abemaciclib 7 days (replicate 2)


title: MDA-MB-361 control (replicate 2)


title: MDA-MB-361 control (replicate 3)


title: PDX 14-07 (abemaciclib) 2


title: MDA-MB-361 control (replicate 1)


title: MDA-MB-361 abemaciclib 7 days (replicate 1)


title: EED22.2 without Dox

city: Seattle

first: Hannele

last: Ruohola-Baker

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
ChIP-seq reads were aligned to hg19 using Bowtie 2.
RNA-seq reads were aligned to hg19 using Tophat-1.3.3
Peaks were called with MACS2 2.1.1.20160309
Differentially expressed genes were identified with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks call were generated using MACS2. RNA-seq read counts were generated with htseq-counts

source_name: Naïve hESC

growth_protocol: human ESC and primed mouse ESC were grown on a feeder layer of irradiated primary mouse embryonic fibroblasts in ESC medium: DMEM/F-12 media supplemented with 20% knock-out serum replacer, 0.1 mM nonessential amino acids (NEAA), 1 mM sodium pyruvate, and penicillin/streptomycin (all from Invitrogen, Carlsbad, CA) and 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO). For naïve hESCs [Elf-1(NIHhESC-12-0156), (64)], ESC medium was supplemented with 1µM GSK3 inhibitor (CHIR99021, Selleckchem), 1µM of MEK inhibitor (PD0325901, Selleckchem), 10ng/mL human LIF (Chemicon), 5ng/mL IFG1 (Peprotech) and 10ng/mL bFGF: Elf1 2i/L/I/F.

extract_protocol:
RNA was extracted from cells using Trizol
Cells were dissociated using trypsin, washed once in cold PBS and counted. Approximately 4.5 M cells were fixed and chromatin was sonicated as previously described
11 ul of Dynabeads (Invitrogen) and 3 ug of H3K27me3 antibody (Active Motif) were conjugates and incubated with chromatin at 4C O/N. Chromatin-antibody-beads complexes were washed and sequencing libraries prepared as previously described (73). Input libraries were prepared from 5ng of purified DNA using Nextera Library Preparation Kit
Libraries were sequenced on NextSeq500


title: H3K27me3 EED22.2 without Dox

value: H3K27me3 (Cat #39157, Active Motif)


title: shLACZ

city: Pardess hana

first: Uri

last: Weissbein

state: Please Select

address: Haalon 4

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem

description:
LAC-Z Knockdown by shRNA TRCN0000072224
Poly(A)+ RNA
Processed data file: Samples_FPKM.txt

data_processing:
Reads were mapped to the HG19 human reference genome using Tophat (version 2.0.4).
Fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks (version 2.0.2).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Samples_FPKM.txt: Tab-delimited text file includes FPKM values for each sample.

source_name: Human embryonic stem cells

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plus kit (Marcherey-Nagel). mRNA was enriched by Poly-A selection. Sequencing libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina).
Libraries were prepared using the Illumina TruSeq RNA prep kit.

value: Embryonic stem cell line

tag: differentiation status

value: Undifferentiated

value: LAC-Z Knockdown


title: EED22.2 with Dox


title: shGFP

description:
GFP Knockdown by shRNA TRCN0000072194
Poly(A)+ RNA
Processed data file: Samples_FPKM.txt

value: GFP Knockdown


title: sh2652

description:
TSPYL5 Knockdown by shRNA TRCN0000322652
Poly(A)+ RNA
Processed data file: Samples_FPKM.txt

value: TSPYL5 Knockdown


title: H3K27me3 EED22.2 with Dox


title: sh2581

description:
TSPYL5 Knockdown by shRNA TRCN0000322581
Poly(A)+ RNA
Processed data file: Samples_FPKM.txt


title: bulk 293T

first: Junyue

last: Cao

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: bulk RNAseq with RNA extracted from HEK293T cells with three replicates

data_processing:
Base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2)
RT barcode (10bp) and UMI (8bp) sequence in Read1 is attached to the read name of Read2. Reads not matching to the expected RT barcodes were discarded. Read2 were then adaptor clipped using trim_galore/0.4.1 with default settings.
Trimmed reads were mapped to the human reference genome (hg19), mouse reference genome (mm10), C.elegans reference genome (PRJNA13758) or a chimeric reference genome of hg19, mm10 and PRJNA13758, using STAR/v 2.5.2b (38) with default settings and gene annotations (GENCODE V19 for human; GENCODE VM11 for mouse, WormBase PRJNA13758.WS253.canonical_gene set for C.elegans).
Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, and read 2 end-coordinate.
Mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index (ED < 2, including insertions and deletions).
To generate digital expression matrices, we calculated the number of strand-specific UMIs mapping to the exonic and intronic regions of each gene, for each cell; generally, fewer than 3% of total UMIs strand-specifically mapped to multiple genes. For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded.
Genome_build: human reference genome (hg19), mouse reference genome (mm10), C.elegans reference genome (PRJNA13758)
Supplementary_files_format_and_content: Processed data file is a sparsematrix in R: each row corresponds to genes, and each column corresponds to single cell, number in the matrix is the UMI count data.

molecule: polyA RNA

source_name: cell line

growth_protocol: All cultured cell lines were cultured at 37°C with 5% CO2, and were maintained in high glucose DMEM (Gibco cat. no. 11965) supplemented with 10% FBS and 1X Pen/Strep (Gibco cat. no. 15140122; 100U/ml penicillin, 100µg/ml streptomycin).

extract_protocol:
All cell lines were trypsinized, spun down at 300xg for 5 min (4°C). and washed once in 1X PBS. L2 stage worms were disscociated with SDS-DTT solution and pronase to generate single cell suspension. Detailed protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."
library construction protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."

treatment_protocol: For c.elegans, a synchronized L2 population was obtained by two cycles of bleaching gravid adults to isolate fertilized eggs allowing the eggs to hatch in the absence of food to generate a population of starved L1 animals.


title: MDA-MB-453 abemaciclib 7 days (replicate 2)


title: I2I3_plusP_100uM_exp2_rep3 [SC144]

city: Stanford

first: Sur

last: Herrera Paredes

address: 371 Serra Mall,  Gilbert Building Room 109

department: Biology

institute: Stanford University

data_processing:
Illumina Casava version 1.8 was used for basecalling
Quality assessment of the sequencing reads was performed using the FASTX-Toolkit version 0.0.13.2
cutadapt version 1.3 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using Tophat version 2.1.1 with parameters set to allow only one mismatch (-N 1)
The Python package HTSeq version 0.6.1p1 was used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis wild-type Col-0 seeds were germinated in axenic condition on Johnson medium plus 0.5% sucrose with either 1 mM Pi or ~5 µM Pi [traces of Pi from the agar, (Difco)] in a vertical position for 7 days; then transferred (10 seedlings per plate) to 30 µM Pi and 100 µM Pi media (without sucrose) alone or with one of the bacterial synthetic communities at 10^5 c.f.u / mL of medium, for another 7 days. Plants were grown in a growth chamber in a 16-h light/8-h dark regime (24°C/21°C).

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings according to Logemann, et al. (PMID: 2441623). Frozen seedlings were pulverized in liquid nitrogen. Samples were homogenized in 400 µl of Z6-buffer; 8 M guanidinium-HCl, 20 mM MES, 20 mM EDTA pH 7.0. Following the addition of 400 µl phenol:chloroform:isoamylalcohol; 25:24:1, samples were vortexed and centrifuged (20000 g, 10 min) for phase separation. The aqueous phase was transferred to a new 1.5 ml tube and 0.05 volumes of 1N acetic acid and 0.7 volumes 96 % ethanol were added. The RNA was precipitated at -20 °C overnight. Following centrifugation, (20,000 g, 10 min, 4 °C) the pellet was washed with 200 µl sodium-acetate (pH 5.2) and 70 % ethanol. The RNA was dried, and dissolved in 30 µl of ultrapure water and stored at -80 °C until use.
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

tag: ecotype background

tag: bacteria

tag: phosphate

value: whole seedling

tag: replicate

tag: experiment

tag: extraction

tag: plate

tag: well

tag: index

value: CGGCTAT-GTACTGA

tag: sample


title: I2I3_plusP_100uM_exp2_rep2 [SC143]

tag: tissue

value: CGGCTAT-CAGGACG


title: I2I3_plusP_100uM_exp2_rep1 [SC142]

value: CGGCTAT-TAATCTT


title: P3I1_plusP_100uM_exp2_rep2 [SC137]

value: CGGCTAT-TATAGCC


title: P3I1_plusP_100uM_exp2_rep3 [SC138]

value: CGGCTAT-ATAGAGG


title: P3I1_plusP_100uM_exp2_rep1 [SC136]

value: TAATGCG-GTACTGA


title: I1I2_plusP_100uM_exp2_rep2 [SC140]

value: CGGCTAT-GGCTCTG


title: P2P3_plusP_100uM_exp2_rep3 [SC135]

value: TAATGCG-CAGGACG


title: P2P3_plusP_100uM_exp2_rep1 [SC133]

value: TAATGCG-AGGCGAA


title: P1P2_plusP_100uM_exp2_rep3 [SC132]

value: TAATGCG-GGCTCTG


title: No Bacteria_plusP_100uM_exp2_rep3 [SC129]

description: No Bacteria_plusP_100uM

source_name: No Bacteria_plusP_100uM_exp2

value: No Bacteria

value: TAATGCG-TATAGCC


title: P1P2_plusP_100uM_exp2_rep1 [SC130]

value: TAATGCG-ATAGAGG


title: I2I3_plusP_30uM_exp2_rep2 [SC125]

value: CTGAAGC-AGGCGAA


title: I2I3_plusP_30uM_exp2_rep1 [SC124]

value: CTGAAGC-GGCTCTG


title: I1I2_plusP_30uM_exp2_rep3 [SC123]

value: CTGAAGC-CCTATCC


title: No Bacteria_plusP_100uM_exp2_rep1 [SC127]

description: No Bacteria_plusP_100uM

value: whole seedling

value: CTGAAGC-CAGGACG


title: I1I2_plusP_30uM_exp2_rep2 [SC122]

value: CTGAAGC-ATAGAGG


title: P3I1_plusP_30uM_exp2_rep1 [SC118]

value: GAATTCG-TAATCTT


title: P3I1_plusP_30uM_exp2_rep3 [SC120]

value: GAATTCG-GTACTGA


title: I1I2_plusP_30uM_exp2_rep1 [SC121]

value: CTGAAGC-TATAGCC


title: pES6

description:
Control cells
Poly(A)+ RNA
Processed data file: Samples_FPKM.txt

tag: cell line

tag: cell type

value: Embryonic stem cell line

value: Undifferentiated

tag: treatment

value: Control


title: I1I2_plusP_100uM_exp2_rep1 [SC139]

value: CGGCTAT-CCTATCC


title: P3I1_plusP_30uM_exp2_rep2 [SC119]

value: GAATTCG-CAGGACG


title: I1I2_plusP_100uM_exp2_rep3 [SC141]

value: CGGCTAT-AGGCGAA


title: P2P3_plusP_30uM_exp2_rep2 [SC116]

value: GAATTCG-GGCTCTG


title: P2P3_plusP_30uM_exp2_rep3 [SC117]

value: GAATTCG-AGGCGAA


title: P2P3_plusP_30uM_exp2_rep1 [SC115]

value: GAATTCG-CCTATCC


title: P2P3_plusP_100uM_exp2_rep2 [SC134]

value: TAATGCG-TAATCTT


title: No Bacteria_plusP_30uM_exp2_rep3 [SC111]

description: No Bacteria_plusP_30uM

source_name: No Bacteria_plusP_30uM_exp2

value: No Bacteria

value: ATTCAGA-CAGGACG


title: P1P2_plusP_30uM_exp2_rep3 [SC114]

value: whole seedling

value: GAATTCG-ATAGAGG


title: P1P2_plusP_100uM_exp2_rep2 [SC131]

value: TAATGCG-CCTATCC


title: P1P2_plusP_30uM_exp2_rep1 [SC112]

value: ATTCAGA-GTACTGA


title: I2I3_minusP_100uM_exp2_rep3 [SC108]

value: ATTCAGA-GGCTCTG


title: I2I3_minusP_100uM_exp2_rep2 [SC107]

value: ATTCAGA-CCTATCC


title: No Bacteria_plusP_100uM_exp2_rep2 [SC128]

description: No Bacteria_plusP_100uM

value: CTGAAGC-GTACTGA


title: No Bacteria_plusP_30uM_exp2_rep1 [SC109]

description: No Bacteria_plusP_30uM

value: ATTCAGA-AGGCGAA


title: No Bacteria_plusP_30uM_exp2_rep2 [SC110]

description: No Bacteria_plusP_30uM

value: ATTCAGA-TAATCTT


title: I2I3_minusP_100uM_exp2_rep1 [SC106]

value: ATTCAGA-ATAGAGG


title: I1I2_minusP_100uM_exp2_rep3 [SC105]

value: ATTCAGA-TATAGCC


title: P3I1_minusP_100uM_exp2_rep3 [SC102]

value: GAGATTC-TAATCTT


title: I1I2_minusP_100uM_exp2_rep2 [SC104]

value: GAGATTC-GTACTGA


title: P3I1_minusP_100uM_exp2_rep2 [SC101]

value: GAGATTC-AGGCGAA


title: P3I1_minusP_100uM_exp2_rep1 [SC100]

value: GAGATTC-GGCTCTG


title: I1I2_minusP_100uM_exp2_rep1 [SC103]

value: GAGATTC-CAGGACG


title: P2P3_minusP_100uM_exp2_rep1 [SC097]

value: GAGATTC-TATAGCC


title: P1P2_minusP_100uM_exp2_rep1 [SC094]

value: whole seedling

value: CGCTCAT-TAATCTT


title: P2P3_minusP_100uM_exp2_rep2 [SC098]

value: GAGATTC-ATAGAGG


title: P1P2_minusP_100uM_exp2_rep3 [SC096]

value: CGCTCAT-GTACTGA


title: P2P3_minusP_100uM_exp2_rep3 [SC099]

value: GAGATTC-CCTATCC


title: No Bacteria_minusP_100uM_exp2_rep2 [SC092]

description: No Bacteria_minusP_100uM

source_name: No Bacteria_minusP_100uM_exp2

value: No Bacteria

value: CGCTCAT-GGCTCTG


title: I2I3_minusP_30uM_exp2_rep3 [SC090]

value: CGCTCAT-ATAGAGG


title: pES6_5AZA

description:
5-aza-2'-deoxycytidine
Poly(A)+ RNA
Processed data file: Samples_FPKM.txt

value: Embryonic stem cell line

value: Undifferentiated


title: P1P2_plusP_30uM_exp2_rep2 [SC113]

value: GAATTCG-TATAGCC


title: P1P2_minusP_100uM_exp2_rep2 [SC095]

value: CGCTCAT-CAGGACG


title: I2I3_minusP_30uM_exp2_rep2 [SC089]

value: CGCTCAT-TATAGCC


title: No Bacteria_minusP_100uM_exp2_rep1 [SC091]

description: No Bacteria_minusP_100uM

value: CGCTCAT-CCTATCC


title: No Bacteria_minusP_100uM_exp2_rep3 [SC093]

description: No Bacteria_minusP_100uM

value: CGCTCAT-AGGCGAA


title: I2I3_minusP_30uM_exp2_rep1 [SC088]

value: TCCGGAG-GTACTGA


title: I1I2_minusP_30uM_exp2_rep1 [SC085]

value: TCCGGAG-AGGCGAA


title: I1I2_minusP_30uM_exp2_rep2 [SC086]

value: whole seedling

value: TCCGGAG-TAATCTT


title: P3I1_minusP_30uM_exp2_rep1 [SC082]

value: TCCGGAG-ATAGAGG


title: P3I1_minusP_30uM_exp2_rep2 [SC083]

value: TCCGGAG-CCTATCC


title: I1I2_minusP_30uM_exp2_rep3 [SC087]

value: TCCGGAG-CAGGACG


title: P1P2_minusP_30uM_exp2_rep3 [SC078]

value: ATTACTC-TAATCTT


title: P2P3_minusP_30uM_exp2_rep2 [SC080]

value: ATTACTC-GTACTGA


title: P2P3_minusP_30uM_exp2_rep3 [SC081]

value: TCCGGAG-TATAGCC


title: P2P3_minusP_30uM_exp2_rep1 [SC079]

value: ATTACTC-CAGGACG


title: P1P2_minusP_30uM_exp2_rep2 [SC077]

value: ATTACTC-AGGCGAA


title: P1P2_minusP_30uM_exp2_rep1 [SC076]

value: ATTACTC-GGCTCTG


title: No Bacteria_minusP_30uM_exp2_rep3 [SC075]

description: No Bacteria_minusP_30uM

source_name: No Bacteria_minusP_30uM_exp2

value: No Bacteria

value: ATTACTC-CCTATCC


title: No Bacteria_minusP_30uM_exp2_rep2 [SC074]

description: No Bacteria_minusP_30uM

value: ATTACTC-ATAGAGG


title: No Bacteria_minusP_30uM_exp2_rep1 [SC073]

description: No Bacteria_minusP_30uM

value: ATTACTC-TATAGCC


title: I2I3_plusP_100uM_exp1_rep1 [SC070]

value: CGGCTAT-TAATCTT


title: I2I3_plusP_100uM_exp1_rep2 [SC071]

value: CGGCTAT-CAGGACG


title: P1P2_plusP_100uM_exp1_rep3 [SC060]

value: whole seedling

value: TAATGCG-GGCTCTG


title: P3I1_plusP_100uM_exp1_rep1 [SC064]

value: TAATGCG-GTACTGA


title: P3I1_plusP_100uM_exp1_rep3 [SC066]

value: CGGCTAT-ATAGAGG


title: I1I2_plusP_100uM_exp1_rep2 [SC068]

value: CGGCTAT-GGCTCTG


title: I1I2_plusP_100uM_exp1_rep1 [SC067]

value: CGGCTAT-CCTATCC


title: P3I1_plusP_100uM_exp1_rep2 [SC065]

value: CGGCTAT-TATAGCC


title: I1I2_plusP_100uM_exp1_rep3 [SC069]

value: CGGCTAT-AGGCGAA


title: No Bacteria_plusP_100uM_exp1_rep3 [SC057]

description: No Bacteria_plusP_100uM

source_name: No Bacteria_plusP_100uM_exp1

value: TAATGCG-TATAGCC


title: P3I1_minusP_30uM_exp2_rep3 [SC084]

value: TCCGGAG-GGCTCTG


title: P2P3_plusP_100uM_exp1_rep3 [SC063]

value: TAATGCG-CAGGACG


title: P2P3_plusP_100uM_exp1_rep2 [SC062]

value: TAATGCG-TAATCTT


title: No Bacteria_plusP_100uM_exp1_rep1 [SC055]

description: No Bacteria_plusP_100uM

value: No Bacteria

value: CTGAAGC-CAGGACG


title: P1P2_plusP_100uM_exp1_rep1 [SC058]

value: TAATGCG-ATAGAGG


title: P1P2_plusP_100uM_exp1_rep2 [SC059]

value: TAATGCG-CCTATCC


title: I2I3_plusP_30uM_exp1_rep2 [SC053]

value: CTGAAGC-AGGCGAA


title: No Bacteria_plusP_100uM_exp1_rep2 [SC056]

description: No Bacteria_plusP_100uM

value: whole seedling

value: CTGAAGC-GTACTGA


title: I1I2_plusP_30uM_exp1_rep1 [SC049]

value: CTGAAGC-TATAGCC


title: I1I2_plusP_30uM_exp1_rep3 [SC051]

value: CTGAAGC-CCTATCC


title: P3I1_plusP_30uM_exp1_rep1 [SC046]

value: GAATTCG-TAATCTT


title: I1I2_plusP_30uM_exp1_rep2 [SC050]

value: CTGAAGC-ATAGAGG


title: I2I3_plusP_100uM_exp1_rep3 [SC072]

value: CGGCTAT-GTACTGA


title: P3I1_plusP_30uM_exp1_rep3 [SC048]

value: GAATTCG-GTACTGA


title: I2I3_plusP_30uM_exp1_rep1 [SC052]

value: CTGAAGC-GGCTCTG


title: P3I1_plusP_30uM_exp1_rep2 [SC047]

value: GAATTCG-CAGGACG


title: P2P3_plusP_30uM_exp1_rep2 [SC044]

value: GAATTCG-GGCTCTG


title: P2P3_plusP_30uM_exp1_rep3 [SC045]

value: GAATTCG-AGGCGAA


title: P3N3_plusP_100uM_exp2_rep2 [SC0431]

value: AGCGATA-CAGGACG


title: P3N3_plusP_100uM_exp2_rep3 [SC0432]

value: AGCGATA-GTACTGA


title: P2P3_plusP_30uM_exp1_rep1 [SC043]

value: GAATTCG-CCTATCC


title: No Bacteria_plusP_100uM_exp2_rep3 [SC0426]

description: No Bacteria_plusP_100uM

value: No Bacteria

value: AGCGATA-ATAGAGG


title: P2N3_plusP_100uM_exp2_rep1 [SC0427]

value: whole seedling

value: AGCGATA-CCTATCC


title: P1P2_plusP_30uM_exp1_rep3 [SC042]

value: GAATTCG-ATAGAGG


title: I2I3_plusP_30uM_exp1_rep3 [SC054]

value: CTGAAGC-TAATCTT


title: No Bacteria_plusP_100uM_exp2_rep1 [SC0424]

description: No Bacteria_plusP_100uM

value: TCTCGCG-GTACTGA


title: P2N3_plusP_100uM_exp2_rep3 [SC0429]

value: AGCGATA-AGGCGAA


title: P2N3_plusP_100uM_exp2_rep2 [SC0428]

value: AGCGATA-GGCTCTG


title: No Bacteria_plusP_100uM_exp2_rep2 [SC0425]

description: No Bacteria_plusP_100uM

value: AGCGATA-TATAGCC


title: P3N3_plusP_30uM_exp2_rep2 [SC0422]

value: TCTCGCG-TAATCTT


title: P3N3_plusP_30uM_exp2_rep3 [SC0423]

value: TCTCGCG-CAGGACG


title: P1P2_plusP_30uM_exp1_rep2 [SC041]

value: GAATTCG-TATAGCC


title: P2N3_plusP_30uM_exp2_rep2 [SC0419]

value: TCTCGCG-CCTATCC


title: P3N3_plusP_30uM_exp2_rep1 [SC0421]

value: TCTCGCG-AGGCGAA


title: P2N3_plusP_30uM_exp2_rep1 [SC0418]

value: TCTCGCG-ATAGAGG


title: P2N3_plusP_30uM_exp2_rep3 [SC0420]

value: TCTCGCG-GGCTCTG


title: No Bacteria_plusP_30uM_exp2_rep1 [SC0415]

description: No Bacteria_plusP_30uM

value: No Bacteria

value: TCCGCGA-CAGGACG


title: No Bacteria_plusP_30uM_exp2_rep3 [SC0417]

description: No Bacteria_plusP_30uM

value: whole seedling

value: TCTCGCG-TATAGCC


title: No Bacteria_plusP_30uM_exp2_rep2 [SC0416]

description: No Bacteria_plusP_30uM

value: TCCGCGA-GTACTGA


title: P3N3_minusP_100uM_exp2_rep1 [SC0412]

value: TCCGCGA-GGCTCTG


title: P2N3_minusP_100uM_exp2_rep3 [SC0411]

value: TCCGCGA-CCTATCC


title: P3N3_minusP_100uM_exp2_rep2 [SC0413]

value: TCCGCGA-AGGCGAA


title: P1P2_plusP_30uM_exp1_rep1 [SC040]

value: ATTCAGA-GTACTGA


title: No Bacteria_minusP_100uM_exp2_rep3 [SC0408]

description: No Bacteria_minusP_100uM

value: CGGCTAT-GTACTGA


title: P3N3_plusP_100uM_exp2_rep1 [SC0430]

value: AGCGATA-TAATCTT


title: No Bacteria_minusP_100uM_exp2_rep2 [SC0407]

description: No Bacteria_minusP_100uM

value: CGGCTAT-CAGGACG


title: No Bacteria_minusP_100uM_exp2_rep1 [SC0406]

description: No Bacteria_minusP_100uM

value: CGGCTAT-TAATCTT


title: P3N3_minusP_30uM_exp2_rep1 [SC0403]

value: CGGCTAT-CCTATCC


title: P2N3_minusP_30uM_exp2_rep2 [SC0401]

value: CGGCTAT-TATAGCC


title: P3N3_minusP_30uM_exp2_rep2 [SC0404]

value: CGGCTAT-GGCTCTG


title: No Bacteria_minusP_30uM_exp2_rep2 [SC0398]

description: No Bacteria_minusP_30uM

value: TAATGCG-TAATCTT


title: No Bacteria_plusP_30uM_exp1_rep3 [SC039]

description: No Bacteria_plusP_30uM

source_name: No Bacteria_plusP_30uM_exp1

value: No Bacteria

value: ATTCAGA-CAGGACG


title: P2N3_minusP_30uM_exp2_rep1 [SC0400]

value: whole seedling

value: TAATGCG-GTACTGA


title: No Bacteria_minusP_30uM_exp2_rep3 [SC0399]

description: No Bacteria_minusP_30uM

value: TAATGCG-CAGGACG


title: P2N3_minusP_30uM_exp2_rep3 [SC0402]

value: CGGCTAT-ATAGAGG


title: P3N3_plusP_100uM_exp1_rep2 [SC0395]

value: AGCGATA-CAGGACG


title: P3N3_plusP_100uM_exp1_rep3 [SC0396]

value: AGCGATA-GTACTGA


title: P2N3_plusP_100uM_exp1_rep3 [SC0393]

value: AGCGATA-AGGCGAA


title: No Bacteria_minusP_30uM_exp2_rep1 [SC0397]

description: No Bacteria_minusP_30uM

value: TAATGCG-AGGCGAA


title: P3N3_plusP_100uM_exp1_rep1 [SC0394]

value: AGCGATA-TAATCTT


title: P3N3_minusP_100uM_exp2_rep3 [SC0414]

value: TCCGCGA-TAATCTT


title: P2N3_minusP_100uM_exp2_rep2 [SC0410]

value: TCCGCGA-ATAGAGG


title: P2N3_plusP_100uM_exp1_rep2 [SC0392]

value: AGCGATA-GGCTCTG


title: No Bacteria_plusP_100uM_exp1_rep2 [SC0389]

description: No Bacteria_plusP_100uM

value: AGCGATA-TATAGCC


title: No Bacteria_plusP_100uM_exp1_rep3 [SC0390]

description: No Bacteria_plusP_100uM

value: AGCGATA-ATAGAGG


title: No Bacteria_plusP_30uM_exp1_rep2 [SC038]

description: No Bacteria_plusP_30uM

value: ATTCAGA-TAATCTT


title: P2N3_minusP_100uM_exp2_rep1 [SC0409]

value: TCCGCGA-TATAGCC


title: No Bacteria_plusP_100uM_exp1_rep1 [SC0388]

description: No Bacteria_plusP_100uM

value: No Bacteria

value: TCTCGCG-GTACTGA


title: P3N3_plusP_30uM_exp1_rep2 [SC0386]

value: whole seedling

value: TCTCGCG-TAATCTT


title: P3N3_plusP_30uM_exp1_rep1 [SC0385]

value: TCTCGCG-AGGCGAA


title: P3N3_plusP_30uM_exp1_rep3 [SC0387]

value: TCTCGCG-CAGGACG


title: P3N3_minusP_30uM_exp2_rep3 [SC0405]

value: CGGCTAT-AGGCGAA


title: No Bacteria_plusP_30uM_exp1_rep3 [SC0381]

description: No Bacteria_plusP_30uM

value: TCTCGCG-TATAGCC


title: P2N3_plusP_30uM_exp1_rep2 [SC0383]

value: TCTCGCG-CCTATCC


title: P2N3_plusP_30uM_exp1_rep1 [SC0382]

value: TCTCGCG-ATAGAGG


title: No Bacteria_plusP_30uM_exp1_rep2 [SC0380]

description: No Bacteria_plusP_30uM

value: TCCGCGA-GTACTGA


title: No Bacteria_plusP_30uM_exp1_rep1 [SC037]

description: No Bacteria_plusP_30uM

value: ATTCAGA-AGGCGAA


title: P3N3_minusP_100uM_exp1_rep2 [SC0377]

value: TCCGCGA-AGGCGAA


title: No Bacteria_plusP_30uM_exp1_rep1 [SC0379]

description: No Bacteria_plusP_30uM

value: TCCGCGA-CAGGACG


title: P3N3_minusP_100uM_exp1_rep1 [SC0376]

value: TCCGCGA-GGCTCTG


title: P2N3_minusP_100uM_exp1_rep1 [SC0373]


title: I2I3_minusP_100uM_exp1_rep3 [SC036]

value: ATTCAGA-GGCTCTG


title: No Bacteria_minusP_100uM_exp1_rep3 [SC0372]

description: No Bacteria_minusP_100uM

source_name: No Bacteria_minusP_100uM_exp1

value: CGGCTAT-GTACTGA


title: P3N3_minusP_30uM_exp1_rep2 [SC0368]

value: CGGCTAT-GGCTCTG


title: P3N3_minusP_30uM_exp1_rep1 [SC0367]

value: CGGCTAT-CCTATCC


title: No Bacteria_minusP_100uM_exp1_rep1 [SC0370]

description: No Bacteria_minusP_100uM

value: No Bacteria

value: whole seedling

value: CGGCTAT-TAATCTT


title: No Bacteria_minusP_100uM_exp1_rep2 [SC0371]

description: No Bacteria_minusP_100uM

value: CGGCTAT-CAGGACG


title: P2N3_minusP_30uM_exp1_rep3 [SC0366]

value: CGGCTAT-ATAGAGG


title: P2N3_plusP_100uM_exp1_rep1 [SC0391]

value: AGCGATA-CCTATCC


title: P2N3_minusP_30uM_exp1_rep2 [SC0365]

value: CGGCTAT-TATAGCC


title: No Bacteria_minusP_30uM_exp1_rep3 [SC0363]

description: No Bacteria_minusP_30uM

source_name: No Bacteria_minusP_30uM_exp1

value: TAATGCG-CAGGACG


title: No Bacteria_minusP_30uM_exp1_rep1 [SC0361]

description: No Bacteria_minusP_30uM

value: TAATGCG-AGGCGAA


title: P1P3_plusP_100uM_exp2_rep3 [SC0360]

value: AGCGATA-GTACTGA


title: No Bacteria_minusP_30uM_exp1_rep2 [SC0362]

description: No Bacteria_minusP_30uM

value: TAATGCG-TAATCTT


title: P2N3_plusP_30uM_exp1_rep3 [SC0384]

value: TCTCGCG-GGCTCTG


title: I2I3_minusP_100uM_exp1_rep2 [SC035]

value: ATTCAGA-CCTATCC


title: P1P3_plusP_100uM_exp2_rep1 [SC0358]

value: AGCGATA-TAATCTT


title: P2I1_plusP_100uM_exp2_rep1 [SC0355]


title: P2I1_plusP_100uM_exp2_rep2 [SC0356]

value: AGCGATA-GGCTCTG


title: P2I1_plusP_100uM_exp2_rep3 [SC0357]

value: AGCGATA-AGGCGAA


title: P3N3_minusP_100uM_exp1_rep3 [SC0378]

value: TCCGCGA-TAATCTT


title: P2N3_minusP_100uM_exp1_rep2 [SC0374]

value: TCCGCGA-ATAGAGG


title: P2N3_minusP_100uM_exp1_rep3 [SC0375]

value: whole seedling

value: TCCGCGA-CCTATCC


title: P1I1_plusP_100uM_exp2_rep3 [SC0354]

value: AGCGATA-ATAGAGG


title: P1I1_plusP_100uM_exp2_rep1 [SC0352]

value: TCTCGCG-GTACTGA


title: No Bacteria_plusP_100uM_exp2_rep2 [SC0350]

description: No Bacteria_plusP_100uM

value: No Bacteria

value: TCTCGCG-TAATCTT