title: 2-1-INPUT

first: Eric

last: Batchelor

address: 10 Center Dr

department: LP/CCR/NCI

institute: National Institutes of Health

description: harvested 3 h after replacing medium

data_processing:
Reads were trimmed to remove bases on both ends with quality scores below 20.
Reads were aligned to hg19 using Bowtie v2.2.5 (Langmead and Salzberg, Nature Methods 2012) with default parameters.
Read coverage of the genome was computed using bedtools genomecov v2.25.0; signal was normalized to the number of reads.
For each sample, peaks were called using MACS v2.1.1.20160309 (Zhang et al., Genome Biology 2008) with false discovery rate cutoff q < 0.05. Input DNA sequenced on the same lane as the sample (same first digit) was used as control (-c). Model building was bypassed in favor of a fixed 200-bp extension size (--nomodel, --extsize 200).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files generated by bedtools, which contain read coverage of the genome, were converted to bigWig format.
Supplementary_files_format_and_content: Tab-delimited files generated by MACS contain information about peaks of p53 binding.

source_name: Input DNA

growth_protocol: MCF-7 cells were cultured in RPMI containing 10% fetal bovine serum, 100 U/mL penicillin G, 100 µg/mL streptomycin sulfate, and 250 ng/mL amphotericin B. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
Samples were prepared as described by Barski et al. (Cell, 2007) with minor changes. Briefly, 40,000,000 cells were cross-linked with 1% formaldehyde for 10 min. Cross-linking was stopped by the addition of glycine to 125 mM final concentration, and cells were washed twice with PBS. Cells were then harvested by scraping, and the pellet was washed once with PBS + 0.5% BSA and resuspended in RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and 200 mM NaCl) supplemented with cOmplete™ protease inhibitor tablet (Roche, 11697498001) to a final concentration of 5,000,000 cells/mL. Samples were sonicated for 15 min with 20-sec pulses, 40-sec resting, using the Q700 Sonicator (QSONICA) to produce chromatin fragments of 300 bp on average. After clarification by centrifugation, sonicated extracts (other than input DNA) were subjected to immunoprecipitation. 4 µg of antibody was mixed with 40 µL of Dynabeads Protein A (ThermoFisher, 10002D) and incubated at 4°C for 6 h with rotation. Chromatin from 5,000,000 cells was added to the Protein A-antibody complexes and incubated overnight at 4°C with rotation. Immunoprecipitates were washed twice with RIPA buffer, twice with RIPA buffer + 300 mM NaCl, twice with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and twice with TE buffer. The beads were then resuspended in TE buffer + 0.25% SDS + 500 µg/mL proteinase K (New England Biolabs, P8102S) and incubated overnight at 65°C. After elution, the DNA was recovered from the eluate by phenol chloroform extraction followed by ethanol precipitation in the presence of 20 µg of glycogen (Roche, 10901393001) and dissolved in TE buffer.
Samples were quantified using a Quant-iT™ PicoGreen™ dsDNA Assay Kit (ThermoFisher, P11496), and fragment sizes were assessed using a Bioanalyzer (Agilent) with a High Sensitivity DNA Kit (Agilent, 5067-4626). Libraries were then prepared using TruSeq ChIP Library Preparation Kits (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer's instructions. Briefly, DNA was end-repaired, and 3’ ends were adenylated to prepare for adapter ligation. After ligation of adapters, ligation products were purified and size-selected for fragments of length 250-300 bp. Fragments with adapters were enriched by 18 cycles of PCR, then pooled for sequencing.

treatment_protocol: MCF-7 cells were plated on 15-cm dishes. After 24 h, cells were treated for 3 h with 400 ng/mL neocarzinostatin (Sigma, N9162) to induce DNA double-strand breaks; "untreated" cells were given fresh medium.

value: Breast carcinoma


title: 1_10_MNT2

status: Public on Aug 02 2017

type: SRA

city: Bethesda

state: MD

country: USA

description: harvested 3 h after replacing medium

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF-7, untreated, biological replicate 2

tag: cell type

tag: cell line

tag: chip antibody

value: p53 (Santa Cruz Biotechnology, sc-126 X)


title: ChIP-seq RNApolII R1-D567 Radiated cells

city: Dallas

first: Ganesh

middle: V

last: Raj

state: TX

address: 5323 Harry Hines Blvd

department: Department of Urology

institute: UT SOUTHWESTERN MEDICAL CENTER

data_processing:
Basecalling was done using bcl2fastq/2.17
Fastq files were trimmed for quality and adapters using fastq-mcf (ea-utils/1.1.2-806)
Fastq files were mapped to hg19 (UCSC) using bowtie/2.2.3
Reads with mapping quality less than 10 were removed using samtools/1.2-2-gf8a6274
Duplicates were removed using picard-tools/1.127
Normalized bigwig files were made using homer/v4.8.3
Peak calling was done using MACS/2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files contain normalized read coverage
Supplementary_files_format_and_content: narrowPeak files are bed files with peaks in narrowPeak format

growth_protocol: RPMI 1640 medium supplemented with 10% (vol/vol) FBS in a 5% CO2 incubator at 37 °C

extract_protocol:
ChIP was performed using HighCell ChIP kit following manufacturer's protocol (Diagenode). ChIP DNA was isolated and purified (IPure Kit, Diagenode) from samples.
Next- generation sequencing library preparation using KAPA Hyper Prep kit (KAPA Biosystems) using TruSeq adapters (Integrated DNA Technologies). A quality check of the purified libraries was carried out using the Bioanalyzer 2100 (Agilent).

treatment_protocol: Cells were radiated with 10 Gy, and fixed in formaldehyde. They were lysed to carry out ChIPs using RNApolII antibody (Biolegend, 920101) and Androgen Receptor (SCBT, sc-816)

value: Transcription activator-like effector nuclease genetically-engineered cell lines derived from CWR-R1 PCa cells

tag: sample group

value: radiated cells

value: RNApolII antibody (Biolegend, 920101)


title: 1_1_INPUT

description: harvested 3 h after replacing medium


title: 1_12_MYT2

description: harvested 3 h after treatment with 400 ng/mL neocarzinostatin

source_name: MCF-7, NCS-treated, biological replicate 2


title: AB1235_L1_S12_R1 IL4_normal

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

library_source: transcriptomic

data_processing:
Illumina RTA v. 2.4.6 software (NextSeq System Suite v2.0) was used for basecalling.
Bcl files output by Illumina NextSeq500 sequencer were converted to fastq format with Bcl2fastq v2.16.
The reads were aligned to the mouse mm10 genome with TopHat2 (v. 2.0.8) set for first strand mRNA and a median fragment size of 280b in Partek Flow (Build 4.0.15.0702).
Aligned reads were mapped to the mouse RefSeq transcriptome (2015-0804) with the Partek Flow (Build 4.0.15.0702) EM algorithm function, then exported as counts per gene.
Read counts per gene were normalized as Reads per Million (aligned) reads by sample (RPM), shifted by +1, converted to log2, and normalized by the upper quantile across samples with JMP/Genomics 7.0 (SAS Institute Inc., Cary N.C.).
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Tab-delimited text file with counts per gene per sample (output of Partek E/M mapping algorithm)
Supplementary_files_format_and_content: Tab-delimited text file with normalized and filtered counts per gene per sample (as described)

molecule: total RNA

organism: Mus musculus

source_name: Liver Tissue

growth_protocol: Male mice were obtained from Taconic Farms at 6-8 weeks of age, all genotypes are on a C57Bl6 background.

extract_protocol:
Livers were perfused and approximately 10-20 mg of liver tissue was collected for RNA isolation.  Samples were homogenized in 750 ul of Trizol reagent in a Precellys homogenizer with stainless steel beads. A chloroform extraction was performed and RNA was isolated using MagMAX-96 Total RNA Isolation Kit (Life Technologies) according to manufacturer’s protocol with DNase treatment.
Libraries were prepared with Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Product # RS-122-2101) using nominal input of 3 ug total RNA per sample following the standard protocol document “Illumina TruSeq Stranded mRNA Sample Preparation Guide” (Part # 15031047 Revision E, October 2013).

treatment_protocol: Wild type, IL-4 knockout and IL-10/IL-4 double knockout mice on normal or high fat diet;. mice were fed with either normal chow or 60%kcal from fat diet (Harlan TD.06414) for 15 weeks

tag: background strain

tag: genotype

value: IL-4 KO

tag: tissue

value: liver

tag: diet

value: normal


title: AB1232_L1_S15_R1 IL4_normal


title: 2-9-MNT1

description: harvested 3 h after replacing medium

source_name: MCF-7, untreated, biological replicate 1


title: AB1223_L1_S23_R1 WT_normal

value: wild type


title: MU1

description: harvested 3 h after replacing medium

data_processing:
Paired-end reads were trimmed using Trimmomatic v0.36 (Bolger et al., Bioinformatics 2014) to remove Nextera adapter sequences and bases on the 3’ end with quality scores below 30.
Reads were aligned to hg19 using Bowtie v2.2.9 (Langmead and Salzberg, Nature Methods 2012) with parameter -X 2000 to ensure that long fragments were able to align.
Properly paired alignments were extracted, and duplicate fragments were removed from this set using Sambamba v0.6.6 (Tarasov et al., Bioinformatics 2015).
Fragment coverage of the genome was computed using bedtools genomecov (v2.25.0); signal was normalized to the number of properly paired reads with duplicates removed.
To identify nucleosome positions, fragments were processed as described by Buenrostro et al. (Nature Methods, 2013): fragments of length 180-247 bp were considered to be one nucleosome, and fragments of length 315-473 bp were considered to be two nucleosomes and split into two fragments.
Nucleosome positions were identified using DANPOS v2.2.2 (Chen et al., Genome Research 2013) with parameters -p 1, -a 1, -jd 20, and --clonalcut 0. Fragments shorter than 100 bp were used as the background signal (parameter -b). Read counts in DANPOS were normalized to the number of properly paired reads with duplicates removed (parameter -c).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files generated by bedtools, which contain fragment coverage of the genome, were converted to bigWig format.
Supplementary_files_format_and_content: wig files generated by DANPOS, which contain nucleosome occupancy values at each base pair across the genome, were converted to bigWig format.

source_name: MCF-7, untreated

growth_protocol: MCF-7 cells were cultured in RPMI containing 10% fetal bovine serum, 100 U/mL penicillin G, 100 µg/mL streptomycin sulfate, and 250 ng/mL amphotericin B. MCF-7 sh-p53 cells were cultured in base medium plus 0.125 µg/mL puromycin. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
Cells were harvested 3 h after treatment following the protocol of Buenrostro et al. (Current Protocols in Molecular Biology, 2015), with modifications, as follows. Cells were incubated for 5 min with 0.25% trypsin at 37°C and 5% CO2. Fresh medium was then added to the trypsin in a 3:1 ratio, and cells were centrifuged at 500x g for 5 min at 4°C. Cells were resuspended in 1.0 mL of cold PBS, then counted using a Millipore Scepter 2.0 handheld cell counter. 150,000 cells were removed and centrifuged at 500x g for 5 min at 4°C. These cells were then resuspended in 150 µL of lysis buffer (10 mM Tris-HCl, pH 7.5; 10 mM NaCl; 3 mM MgCl2; 0.1% IGEPAL CA-630), incubated on ice for 5 min, and centrifuged at 500x g for 10 min at 4°C. The nuclear pellet was resuspended in 60 µL of resuspension buffer consisting of 3 parts water and 1 part 2x TD Reaction Buffer from the Nextera DNA Library Preparation Kit (Illumina, FC-121-1030). 10 µL of resuspended nuclei (representing 25,000 cells) was removed and combined with 10 µL of 2x TD Reaction Buffer and 5 µL of TDE1 transposase from the same kit, as suggested by Takaku et al. (Genome Biology, 2016). This mixture was incubated at 37°C for 30 min, gently shaking, then purified with a MinElute PCR Purification Kit (Qiagen, 28004).
Purified DNA was amplified and barcoded by 8 cycles of PCR using NEBNext® High-Fidelity 2X PCR Master Mix (New England BioLabs, M0541) and the barcoding primers used by Buenrostro et al. (Nature Methods, 2013); amplified fragments were then purified again with the MinElute kit. Size selection was performed by gel electrophoresis, selecting fragments of length 100-600 bp. Size-selected fragments were then quantified by qPCR, amplified by 4-7 additional cycles of PCR with the NEBNext master mix, and purified again using the MinElute kit.

treatment_protocol: 640,000 MCF-7 or 1,000,000 MCF-7 sh-p53 cells were plated on 6-cm dishes one day prior to treatment. Cells were treated with 400 ng/mL neocarzinostatin (Sigma, N9162) to induce DNA double-strand breaks; "untreated" cells were given fresh medium.

tag: passages


title: 2-11-MYT1

source_name: MCF-7, NCS-treated, biological replicate 1


title: SN2

source_name: MCF-7 sh-p53, NCS-treated

value: MCF-7 sh-p53


title: AB1231_L1_S16_R1 WT_fatty

value: high fat diet


title: SU2

description: harvested 3 h after replacing medium

source_name: MCF-7 sh-p53, untreated


title: 2190

city: Gainesville

first: Thomas

middle: C

last: Foster

state: Florida

address: 1149 Newell Drive Bldg 59

department: Neuroscience

institute: University of Florida-McKnight Brain Institute

description:
Bisulfite converted
Processed data file: Aging-Young-CG-mat.csv
Processed data file: Aging-Young-CHG-mat.csv
Processed data file: Aging-Young-CHH-mat.csv
Processed data file: AI-AU-CG-mat.csv
Processed data file: AI-AU-CHG-mat.csv
Processed data file: AI-AU-CHH-mat.csv

data_processing:
WGBS data was analyzed using the DMAP2 pipeline available at the University of Florida high performance computer clusters. Briefly, quality assessment and trimming of fastq files were performed with FastQC and trimmomatic. Alignment to the rn5 genome was executed with BSMAP (default parameters). DNA methylation calling at CpG, CHG and CHH was performed with the ‘cscall’ program (mindepth=5; minsamples=3 for minimum coverage of 15x for each site in each group).
Annotation was performed using the Rnor_5.0.78.gtf file, and all sites were annotated according to promoters and gene body (exons and introns) regions using the "genediffmeth" program at the university's clusters.
Genome_build: rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *.csv: Comma-separated values files contain the DNA methylation ratios per biological replicate for each site (indicated by chromosome number and coordinate).

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Rats were anesthetized with isoflurane, decapitated and the brain was rapidly removed. The prelimbic and infralimbic mPFC was collected. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC. Genomic DNA was isolated with the DNeasy Blood & Tissue kit (Qiagen, catalog number: 69504). Bisulfite conversion was performed with the EZ DNA Methylation-Direct kit (Zymo Research, catalog number: D5020).
Whole-genome bisulfite sequencing (WGBS) libraries were constructed with the Illumina TruSeq DNA Methylation kit (Illumina, catalog number: EGMK91324). Following size selection and amplification, the concentration of each library was quantified using the Qubit dsDNA HS Assay and size distribution was evaluated with the High Sensitivity D1000 Screen Tape in the Tapestation system (Agilent Technologies).

tag: strain/background

value: Fischer 344

value: medial prefrontal cortex

tag: age

value: Aged

tag: age impairment

value: Impaired

tag: rat identifier


title: 2176

description:
Bisulfite converted
Processed data file: Aging-Young-CG-mat.csv
Processed data file: Aging-Young-CHG-mat.csv
Processed data file: Aging-Young-CHH-mat.csv

value: Young


title: 2191


title: 2189

value: Unimpaired


title: 2181


title: 2185


title: 121448


title: 2175


title: 2184


title: 2180


title: 2182


title: 2173


title: 121445


title: 121413


title: MN1

source_name: MCF-7, NCS-treated

value: Breast carcinoma


title: 121437


title: 1935


title: 1932


title: 1929


title: 1930


title: 1931


title: 1928


title: 1936


title: 1927


title: 1925


title: 1920


title: 1926


title: 1924


title: 1919


title: Taf13_GC-Ile-Val_3IAA_2

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Flag Immunoprecipitation

data_processing:
We used Bowtie2 to map the paired-end 25bp reads to Saccer3 version of yeast genomic sequence obtained from UCSC.
We used Bowtie2 to map the paired-end 25bp reads to ASM294v2.20 version of pombe genomic sequence obtained from pombase.
We counted the properly paired reads from the S. pombe alignments.
Genome_build: SacCer3
Genome_build: PomBase ASM294v2.20
Supplementary_files_format_and_content: We generated wig files from fragments of size 25-140 bp aligned to S. cerevisiae genome with a scaling factor of (10000/number of fragments mapped to S. pombe) to create spike-normalized coverage file (Supplementary file .wig)

organism: Saccharomyces cerevisiae

source_name: Flag IP - Rpb3-3XFlag / Taf13-3V5-IAA7 - GC-Ile-Val 30 deg, + 500 uM 3-IAA 30 min

growth_protocol: For each yeast strain and condition, two liters of S. cerevisiae were grown at 30 deg in YPD (+ 100 μl Antifoam 204) to an absorbance of ~0.7-1.0.

extract_protocol:
Cells were rapidly harvested by vacuum filtration through a 90 mm diameter 0.45 micron nitrocellulose filter, followed by a 100 ml wash with the cell culture media.  The cell paste was scraped off with a pre-chilled spatula and plunged into liquid nitrogen to flash freeze cells.  For spike-in normalization, an 8 liter batch of S. pombe was grown in YE (+ Antifoam 204) to a similar absorbance and harvested as described above.  2.5 g S. cerevisiae were combined with 0.25 g S. pombe in a mortar pre-chilled on dry ice and liquid nitrogen. Frozen cells were lysed with a 4.5” OD mortar and large pestle. Cells were ground for 1 min, liquid nitrogen was then added to the cells and ground for 1 min.  The grinding and addition of liquid nitrogen was repeated for a total of 6 minutes.  The frozen powdered ground cells were transferred to a cold conical tube and stored at -80 deg.
DNA isolated from IPs was prepared for sequencing as previously described (Skene and Henikoff, eLIFE 2017), except for the following changes.  End Repair and A-tailing was performed in a 20 ml volume containing up to 50 ng DNA and the following final concentrations:  1X T4 DNA ligase buffer (NEB #B0202S), 0.5 mM each dNTP, 0.25 mM ATP, 2.5% PEG 4000, 2.5 U T4 PNK (NEB #M0201S), 0.05 U T4 DNA polymerase (Invitrogen #18005025), and 0.05 U Taq DNA polymerase and reactions were incubated at 12 deg 15 min, 37 deg 15 min, 72 deg 20 min, then put on ice and immediately used in adapter ligation reactions.  Adapter Ligation was performed in a 50 ml volume containing 100:1 adapter:insert molar ratios, 1X Rapid DNA ligase buffer (Enzymatics #B101L) and 3000 U DNA ligase (Enzymatics #L6030-HC-L).  A single post-ligation cleanup was performed using 0.4X vol AMPure XP reagent (Beckman Coulter #A63881) and DNA eluted in 40 ul 0.1X TE.  Library Enrichment was performed in a 25 μl volume containing 16.25 μl DNA from previous step and the following final concentrations:  1X KAPA buffer, 0.3 mM each dNTP, 0.5 mM each P5 and P7 PCR primer, and 0.5 U KAPA HS HIFI polymerase (#KK2502).  DNA was amplified with the following program:  98 deg 45 sec, [98 deg 15 sec, ramp to 60 deg @ 1 deg/sec, 60 deg 20 sec, ramp to 98 deg @ 1 deg/sec] 8-10X, 72 deg 1 min.  A post-PCR cleanup was performed using 1.4X vol AMPure XP reagent and DNA was eluted into 40 ml 0.1X TE.  Libraries were sequenced on the Illumina HiSeq2500 platform using 25 bp paired-ends at the Fred Hutchinson Cancer Research Center Genomics Shared Resources facility.

treatment_protocol: Cells were then induced for protein degradation by the addition of 10 ml 200X 3-IAA (500 μM final working concentration) dissolved in DMSO, or 10 ml DMSO for the no 3-IAA controls, for 30 minutes at 30 deg.

tag: strain

tag: antibody

value: Anti-FLAG M2 Magnetic Beads


title: Taf11_GC-Ile-Val_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf11-3V5-IAA7 - GC-Ile-Val 30 deg, + DMSO 30 min


title: Taf11_GC-Ile-Val_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf11-3V5-IAA7 - GC-Ile-Val 30 deg, + 500 uM 3-IAA 30 min


title: Taf13_GC-Ile-Val_3IAA_1

description: Flag Immunoprecipitation


title: 121412


title: Taf11_GC-Ile-Val_3IAA_1

description: Flag Immunoprecipitation


title: Taf13_GC-Ile-Val_DMSO_1

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf13-3V5-IAA7 - GC-Ile-Val 30 deg, + DMSO 30 min


title: Taf13_GC-Ile-Val_DMSO_2

description: Flag Immunoprecipitation


title: Taf11_GC-Ile-Val_DMSO_1

description: Flag Immunoprecipitation


title: WT_GC-Ile-Val_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / WT - GC-Ile-Val 30 deg, + 500 uM 3-IAA 30 min


title: WT_GC-Ile-Val_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / WT - GC-Ile-Val 30 deg, + DMSO 30 min


title: WT_GC-Ile-Val_3IAA_1

description: Flag Immunoprecipitation


title: Taf13_YPD_HS_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf13-3V5-IAA7 - YPD 30 deg with 37 deg heat shock 30 min, + DMSO 30 min


title: WT strain

city: Guangzhou

first: Yin

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: SYSU

description: Pooled samples from three independently grown flasks

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Neurospora crassa OR74A whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

molecule: polyA RNA

organism: Neurospora crassa

source_name: hyphae

growth_protocol: Strains were growthed in minimal slants for two weeks and cultivated in 2% glucose media in constant light for 2 days.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The wild type and upf1 knockout strains were cultured in the same condition, no specific treatment.

value: 2 days


title: UPF1 strain


title: Jo_1_4

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

country: United Kingdom

institute: University of Bath

data_processing:
Sequencing data was aligned against human reference genome hg38 using Tophat2: tophat --library-type fr-firststrand <reference_genome.gtf> -1 <forward_strand.fa> -2 <reverse_strand.fa> -o <output.sam>
Output SAM files were then sorted and converted to BAM files (samtools sort -@ 8 –o output.bam output.sam) and indexed (samtools index –b output.bam) in Samtools
To identify novel lncRNA, all potential transcripts were initially assembled from the merged BAM files of the control, Jo-1 and IBM samples by use of Cufflinks2. Bedtools was employed to identify novel lncRNAs that did not overlap with genes annotated in GenCode v23. Novel lncRNAs were identified as those genes that contained > 1 exon, length > 200bp, FPKM > 1 and which had a low protein coding potential as assessed using the coding potential calculator 0.9-r2.
The list of novel lncRNAs (GTF) was merged with Gencode v23, to produce a master list of mRNA and lncRNAs genes.
Using this master list (GTF), Differential expression of protein coding genes (protein coding genes.txt) and lncRNAs  (long non-coding RNAs.txt) was assessed with the geometric option (DESeq) in Cuffdiff v2.2.1.3 39 using a significance threshold of q <0.05: cuffdiff --FDR=0.05 --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled -u <reference_genome.gtf> <control_1.bam>,<control_x.bam> <activated_1.bam>,<activated_x.bam> -o <output_file_name>using Cuffdiff (V2.2.1.2)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mean FPKM values for each group and differential expression between groups

source_name: Skeletal Muscle Biopsy

extract_protocol:
Skeletal muscle biopises were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient

value: Jo_1 myositis muscle


title: Jo_1_2


title: 1918


title: Taf13_YPD_HS_DMSO_1

description: Flag Immunoprecipitation


title: Taf11_YPD_HS_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf11-3V5-IAA7 - YPD 30 deg with 37 deg heat shock 30 min, + 500 uM 3-IAA 30 min


title: Jo_1_3


title: Taf11_YPD_HS_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf11-3V5-IAA7 - YPD 30 deg with 37 deg heat shock 30 min, + DMSO 30 min


title: IBM_4

value: Inclusion Body Myositis Muscle


title: Taf11_YPD_HS_DMSO_1

description: Flag Immunoprecipitation


title: Taf11_YPD_HS_3IAA_1

description: Flag Immunoprecipitation


title: Taf13_YPD_HS_3IAA_1

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf13-3V5-IAA7 - YPD 30 deg with 37 deg heat shock 30 min, + 500 uM 3-IAA 30 min


title: Jo_1_1


title: WT_YPD_HS_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / WT - YPD 30 deg with 37 deg heat shock 30 min, + 500 uM 3-IAA 30 min


title: WT_GC-Ile-Val_DMSO_1

description: Flag Immunoprecipitation


title: IBM_2


title: Control_3

value: Non-inflammed Muscle


title: IBM_1


title: Taf13_YPD_HS_3IAA_2

description: Flag Immunoprecipitation


title: Control_2


title: WT_YPD_HS_DMSO_1

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / WT - YPD 30 deg with 37 deg heat shock 30 min, + DMSO 30 min


title: Control_4


title: Taf2_YPD_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf2-3V5-IAA7 - YPD 30 deg + 500 uM 3-IAA 30 min


title: WT_YPD_HS_DMSO_2

description: Flag Immunoprecipitation


title: Taf2_YPD_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf2-3V5-IAA7 - YPD 30 deg + DMSO 30 min


title: Control_1


title: WT_YPD_HS_3IAA_1

description: Flag Immunoprecipitation


title: MN2: MCF-7 MYC-GFP, NCS-treated

description: treated with NCS

data_processing:
Reads were trimmed using Partek Flow (Partek, St. Louis, MO) to remove bases on both ends with quality scores below 20.
Reads were aligned to the human transcriptome (hg19, RefSeq Transcripts 2016-05-02) using TopHat v2.1.0 (Kim et al., Genome Biology 2013) with parameters --mate-inner-dist 82, --mate-std-dev 134.
Unaligned reads were then aligned to the S. pombe transcriptome (ASM294v2) using TopHat v2.1.0 with the same parameters.
A "pombe score" representing the amount of S. pombe RNA in each sample, and thus proportional to the number of cells in each sample, was calculated as follows: From the reads mapped to the S. pombe transcriptome, reads with the same start position, reads that mapped to more than one location, and unpaired reads were removed. The remaining reads were quantified using the Partek E/M algorithm. For each transcript, the number of reads mapping to that transcript was divided by the transcript length to yield RPK (reads per kilobase of transcript). From the top 50 expressed transcripts as measured by average RPK over all 12 samples, the transcript with the lowest average correlation with all the others across all 12 samples was removed; this procedure was performed iteratively until a set of 10 highly correlated transcripts was reached. This served to identify transcripts that collectively best represented the quantity of spike-in RNA in each sample. The pombe score for each sample was then calculated as the geometric mean of the expression (RPK) of those 10 genes in that sample.
Reads mapped to the human transcriptome (not filtered) were quantified using the Partek E/M algorithm. For each transcript, the number of reads quantified to that transcript was divided by the transcript length to yield RPK, then divided by the pombe score for the sample to normalize to the number of cells.
Genome_build: hg19, ASM294v2
Supplementary_files_format_and_content: pombe_transcript_reads.txt: tab-delimited text file with metadata about pombe transcripts and raw read counts for each sample
Supplementary_files_format_and_content: pombe_scores.txt: tab-delimited text file with pombe scores for each sample
Supplementary_files_format_and_content: human_transcript_reads.txt: tab-delimited text file with metadata about human transcripts and raw read counts for each sample
Supplementary_files_format_and_content: human_transcript_rpk_norm_pombe.txt: tab-delimited text file with metadata about human transcripts and RPK values for each sample, normalized to the pombe score

source_name: MCF-7 MYC-GFP, NCS-treated

growth_protocol:
MCF-7 GFP and MCF-7 MYC-GFP clonal cells were cultured in RPMI containing 10% tetracycline-free FBS (Clontech, 631106), 100 U/mL penicillin G, 100 µg/mL streptomycin sulfate, 250 ng/mL amphotericin B, and 0.5 µg/mL puromycin. Cells were cultured at 37°C and 5% CO2.
S. pombe cells expressing human equilibrative nucleoside transporter 1 (hENT1) and thymidine kinase (tk) (h+ leu1‐32::[hENT1 leu1+] his7‐366::[hsv‐tk his7+] ura4‐D18 ade6‐M210) (Hodson et al., Nucleic Acids Research 2003) were grown at 30°C in EMM containing 225 mg/L of each of adenine, histidine, lysine, and uracil.

extract_protocol:
After 1 h of labeling with EU (3.5 h after initial treatment), for each cell line and treatment, three plates of cells were incubated for 5 min with 0.25% trypsin at 37°C and 5% CO2. After trypsinization, cells in each plate were counted using a Millipore Scepter 2.0 handheld cell counter. Then, for each cell line and treatment, three more plates of cells were lysed directly and RNA harvested using Qiagen QIAshredder and RNeasy Mini Plus kits. EU-labeled RNA from S. pombe was added to each cell lysate at 150 ng of total RNA per million MCF-7 cells, where the number of cells was taken to be the average count of the three replicates of that cell line and treatment.
For each sample, EU-labeled RNA was isolated from total RNA using a Click-iT® Nascent RNA Capture Kit (ThermoFisher, C10365). Specifically, 5.0 μg of total RNA was used in a click reaction in which EU-labeled RNA was biotinylated according to manufacturer’s protocol. 1.0 μg of biotinylated RNA was bound to streptavidin-coated magnetic beads to isolate EU-labeled RNA according to manufacturer’s protocol. EU-labeled RNA was then used as a template for first-strand cDNA synthesis with a SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech, 634889), following manufacturer’s protocol and shaking at 1000 rpm during thermal cycling. Second-strand cDNA synthesis and amplification (6 cycles of PCR) were then performed with the same kit, and amplified cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter, A63880). Concentration and size distribution of amplified cDNA were assessed using a Bioanalyzer (Agilent) with a High Sensitivity DNA Kit (Agilent, 5067-4626). For each sample, 136.45 pg of amplified cDNA was fragmented, tagged with adapter sequences, and amplified using a Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) according to manufacturer’s protocol. DNA libraries were then purified again using Agencourt AMPure XP beads, and fragment size distribution was assessed using a Bioanalyzer. DNA concentration was measured using a Quant-iT™ High-Sensitivity dsDNA Assay Kit (ThermoFisher, Q33120) on a microplate reader, and equimolar amounts of DNA were pooled for sequencing.

treatment_protocol:
400,000 MCF-7 GFP or MCF-7 MYC-GFP cells were plated on 6-cm dishes 2 days prior to treatment. Expression of GFP or MYC-GFP was induced with 150 ng/mL doxycycline 18 h prior to treatment. Cells were treated with 400 ng/mL neocarzinostatin (Sigma, N9162) to induce DNA double-strand breaks or with fresh medium containing 150 ng/mL doxycycline as a control. After 2.5 h, medium was replaced with fresh medium containing 0.5 mM 5-ethynyl uridine (EU) and 150 ng/mL doxycycline.
S. pombe cells were grown overnight in medium containing 0.5 mM 5-ethynyl uridine (EU).
S. pombe cells were harvested during logarithmic phase, and RNA was extracted using TRIzol® LS Reagent (ThermoFisher, 10296010) according to manufacturer’s standard protocol.

value: MCF-7 MYC-GFP

tag: passage


title: MN3: MCF-7 MYC-GFP, NCS-treated

description: treated with NCS

tag: cell type


title: IBM_3


title: Med14_YPD_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Med14-3V5-IAA7 - YPD 30 deg + DMSO 30 min


title: MC3: MCF-7 MYC-GFP, untreated

description: not treated with NCS

source_name: MCF-7 MYC-GFP, untreated

tag: cell line


title: Taf2_YPD_DMSO_1

description: Flag Immunoprecipitation


title: MN1: MCF-7 MYC-GFP, NCS-treated

description: treated with NCS


title: Med14_YPD_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Med14-3V5-IAA7 - YPD 30 deg + 500 uM 3-IAA 30 min


title: GN3: MCF-7 GFP, NCS-treated

description: treated with NCS

source_name: MCF-7 GFP, NCS-treated

value: MCF-7 GFP


title: Taf2_YPD_3IAA_1

description: Flag Immunoprecipitation


title: Taf13_YPD_DMSO_1

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf13-3V5-IAA7 - YPD 30 deg + DMSO 30 min


title: MC2: MCF-7 MYC-GFP, untreated

description: not treated with NCS


title: Taf13_YPD_3IAA_1

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf13-3V5-IAA7 - YPD 30 deg + 500 uM 3-IAA 30 min


title: GN2: MCF-7 GFP, NCS-treated

description: treated with NCS


title: Taf1_YPD_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf1-3V5-IAA7 - YPD 30 deg + 500 uM 3-IAA 30 min


title: Med14_YPD_3IAA_1

description: Flag Immunoprecipitation


title: GC3: MCF-7 GFP, untreated

description: not treated with NCS

source_name: MCF-7 GFP, untreated


title: Taf1_YPD_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf1-3V5-IAA7 - YPD 30 deg + DMSO 30 min


title: GC2: MCF-7 GFP, untreated

description: not treated with NCS


title: KO_IP6

city: Edinburgh

first: Emily

last: Osterweil

address: Hugh Robson building

institute: University of Edinburgh

description:
TRAP IP
Ribosome bound mRNA

data_processing:
Alignment to ensembl V80 with STAR aligner 2.4.0i
read count per gene level with feature count 1.4.6-p2
DEseq2 run with betaprior=FALSE. Littermates were paired for this analysis
Genome_build: mm10
Supplementary_files_format_and_content: read count data used for DESeq2 (WTKOIN and WTKOIP). IP and IN data are in separate files with sample IDs on first column. DESeq2 output from IP comparison and IN comparison (ip.Res and in.Res). All in csv format

source_name: CA1 pyramidal cells

growth_protocol: All experiments are done with p25 -p32 male littermate paired mice.

extract_protocol:
Hippocampus was rapidly removed and homogenised. RNA samples were amplified with RNAseq V2 ovation kit before library construction.
Libraries were constructed using Wafergen’s PrepX Complete ILMN 32i DNA Library Kit (cat number 400076) using the Apollo 324. Ligation of adapters was performed using Illumina Adapters within the Multiplexing Sample Preparation Oliogonucleotide Kit.

tag: tissue/cell type

value: CA1 pyramidal cells

value: Fmr1 KO

tag: gender

value: male


title: GC1: MCF-7 GFP, untreated

description: not treated with NCS


title: Taf1_YPD_DMSO_1

description: Flag Immunoprecipitation


title: Taf11_YPD_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf11-3V5-IAA7 - YPD 30 deg + 500 uM 3-IAA 30 min


title: WT_IP6

description:
TRAP IP
Ribosome bound mRNA

value: WT


title: WT_IP5

description:
TRAP IP
Ribosome bound mRNA


title: Taf7_YPD_DMSO_1

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf7-3V5-IAA7 - YPD 30 deg + DMSO 30 min


title: KO_IP4

description:
TRAP IP
Ribosome bound mRNA


title: KO_IP5

description:
TRAP IP
Ribosome bound mRNA


title: Taf11_YPD_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf11-3V5-IAA7 - YPD 30 deg + DMSO 30 min


title: KO_IN6

description:
Input
Total RNA

source_name: Hippocampus

value: Hippocampus


title: Med14_YPD_DMSO_1

description: Flag Immunoprecipitation


title: WT_IP4

description:
TRAP IP
Ribosome bound mRNA


title: Taf11_YPD_DMSO_1

description: Flag Immunoprecipitation


title: Mpos3

city: Medford

first: Benjamin

middle: E

last: Wolfe

state: MA

address: 200 Boston Ave

department: Microbiology

institute: Tufts University

description: RNA-Seq from Serratia grown with Mucor present, replicate 3

data_processing:
Basecalls performed using CASAVA
Transcripts were aligned to Serratia BW106 draft genome (Accesson No. BioSample SAMN05449653) using Rockhopper Reference Assembly, using standard options: Strand-specific checked yes, max bases between paired reads: 500, allowed mismatches: 0.15, minimum seed length 0.33, minimum expression of UTRs and ncRNAs: 0.5,
Differential Gene expression and Operon identification performed by Rockhopper
Genome_build: BioSample SAMN05449653 Serratia BW106
Supplementary_files_format_and_content: RNAseqFungalNetworks_forGEO.xlsx contains raw and normalized counts

organism: Serratia sp. BW106

source_name: experimental biofilm

growth_protocol: Experimental biofilms were created by inoculating organisms onto cheese curd agar medium. See Wolfe et al. 2014 Cell 158 422-433

extract_protocol:
RNA was extracted using a phenol-chloroform
RNA libraries were prepared using the NEBNext RNA Ultra Kit for Illumina

treatment_protocol: Serratia was grown either alone or with a Mucor spp.

tag: condition


title: Taf7_YPD_3IAA_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / Taf7-3V5-IAA7 - YPD 30 deg + 500 uM 3-IAA 30 min


title: Mpos4

description: RNA-Seq from Serratia grown with Mucor present, replicate 4


title: Taf7_YPD_3IAA_1

description: Flag Immunoprecipitation


title: MC1: MCF-7 MYC-GFP, untreated

description: not treated with NCS


title: Taf11_YPD_3IAA_1

description: Flag Immunoprecipitation


title: Taf7_YPD_DMSO_2

description: Flag Immunoprecipitation


title: Mneg4

description: RNA-Seq from Serratia grown alone, replicate 4

value: alone


title: KO_IN5

description:
Input
Total RNA

tag: genotype


title: Mpos1

description: RNA-Seq from Serratia grown with Mucor present, replicate 1


title: WT_YPD_3IAA_1

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / WT - YPD 30 deg + 500 uM 3-IAA 30 min


title: KO_IN4

description:
Input
Total RNA


title: WT_YPD_3IAA_2

description: Flag Immunoprecipitation


title: WT_IN6

description:
Input
Total RNA


title: GN1: MCF-7 GFP, NCS-treated

description: treated with NCS


title: Taf1_YPD_3IAA_1

description: Flag Immunoprecipitation


title: WT_YPD_DMSO_2

description: Flag Immunoprecipitation

source_name: Flag IP - Rpb3-3XFlag / WT - YPD 30 deg + DMSO 30 min


title: WT_IN5

description:
Input
Total RNA


title: Mneg3

description: RNA-Seq from Serratia grown alone, replicate 3


title: WT_YPD_DMSO_1

description: Flag Immunoprecipitation


title: R2-NI_S8

status: Public on Aug 01 2017

city: St Louis

first: Carolina

middle: B

last: Lopez

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

description:
Replicate pool 2
Sample 8

data_processing:
fastq files were aligned to Release 79 of human reference All cDNA GRCh38 using Kallisto.
Transcript-level count data were importd into R using the Tximport package
Expression data was normalized using the VOOM function from the Limma package in R, and batch effects were corrected with the ComBat function of the SVA package in R.
Differentially expressed genes (2-fold and ≤ 1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: human transcriptome, build 38 (Homo_sapiens.GRCh38.cdna.all.fa)
Supplementary_files_format_and_content: TxiCounts.txt: raw gene counts
Supplementary_files_format_and_content: TxiAbundance.txt: non-normalized transcripts per million (TPM), summarized to the gene level
Supplementary_files_format_and_content: normData_batchCorrect.txt: transcripts per million (TPM), normalized using Limma VOOM, and summarized to the gene level

source_name: viral contents: none

growth_protocol: 3x10^6 A549 cells were plated in 100mm culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours

extract_protocol:
RNA samples from FISH-FACS-sorted cells were prepared as follows: RNA extracted from TRIzol reagents was re-purified by PicoPureTM RNA isolation kit (Thermo Fisher Scientific).
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: A549 were either mock infected with, PBS or infected with SeV HD at MOI 1.5 for 24 hrs. cells were trypsinized, resuspended in 1% FBS in PBS, fixed and permeabilized in 100% methanol for at least 15min on ice. Hybridization was performed in100μl hybridization buffer in presence of 1.25μM RNA FISH probes for 16 h in a humidified chamber at 37°C. Cells were resuspended in GLOX anti-fade media for sorting based on different accumulaiton of viral contants


title: WT_IN4

description:
Input
Total RNA


title: WTC4_RNA_Seq

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: sample 2

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads (Trim Galore).
Sequences were aligned to the genome by STAR software; aligned sequences were assembled to form transcripts by Cufflinks software.
The differential expression genes were identified with DESeq.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel spreadsheets with statistical analysis

organism: Arabidopsis thaliana

source_name: Wild-type leaf explants at time 4 days on Callus Inducing Medium

growth_protocol: Plants were grown at 22 ºC with a 16-h light (~ 5000 Lux) and 8-h dark photoperiod in growth chamber for 12 days.

extract_protocol:
RNA extraction using Trizol protocols(Life Technology, USA)
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina)

treatment_protocol: First pair leaves were cut from 12-d-old plants. The leaf explants were cultured for 0 and 4 days on Callus Inducing Medium under continuous dark at 22 ºC.

tag: tissue

value: whole leaf explants with callus

value: wildtype Col-0


title: lbd16C4_RNA_Seq

description: sample 4

source_name: lbd16-2 muant leaf explants at time 4 days on Callus Inducing Medium


title: R2-INT_S7

description:
Replicate pool 2
Sample 7

source_name: viral contents: both FL and DVG


title: lbd16C0_RNA_Seq

description: sample 3

source_name: lbd16-2 muant leaf explants at time 0 on Callus Inducing Medium

value: whole leaf explants


title: WTC0_RNA_Seq

description: sample 1

source_name: Wild-type leaf explants at time 0 DAC on Callus Inducing Medium


title: R1-DVG_S2

description:
Replicate pool 1
Sample 2

source_name: viral contents: DVG


title: ChIPseq H3K27me3 TBT rep 4

city: Irvine

first: Bassem

middle: Merit

last: Shoucri

state: CA

address: 4351 Natural Sciences 2

institute: University of California Irvine

data_processing:
RNA-Seq and ChIP-Seq deep sequencing reads (fastq data) were aligned to the mouse genome reference sequence GRCm38/mm10 using the STAR aligner, and the resulting bam format aligned reads were subjected to QC analysis using fastQC (Babraham Institute) followed by extraction of uniquely mapped reads using samtools.
For RNA-seq data analysis, uniquely mapped reads were assigned to the mm10 gene model and on-exon reads were counted using Bioconductor package “Rsubread.” The assigned read counts were normalized in the Bioconductor package “DESeq2” using the regularized log transformation. Differential expression was assessed in DESeq2 using the function DESeqDataSetFromMatrix with alpha = 0.01. Differentially expressed genes were defined by Benjamini-Hochberg corrected p-values (p-adj < 0.01) and fold change (absolute value of log2[fold change] > 0.2).
For ChIP-seq data, from the bam file data of uniquely mapped reads, gDNA areas enriched with the H3K4me3 or H3K27me3 histone marks were detected using SICER with the following  arguments: W-200, G=600, FDR cutoff = 0.001. The output BED files of SICER were then subjected to detection of differential enrichment of the histone marks using Bioconductor package “DiffBind” with the default parameters of function dba.analyze.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA_counts.txt was generated in Rsubread as indicated above. log.2.norm.counts.txt was generated in DESeq2 as described above.
Supplementary_files_format_and_content: *islands-summary-FDR1e-3 files contain H3K27me3 or H3K4me3 islands determined for each treatment and replicate in SICER as described above (window size = 200bp, gap size = 600bp, FDR cutoff = 0.001); file format: chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold. *DiffPeaks.txt files contain differential binding sites between DMSO and TBT replicates as determined in DiffBind and indicated above.

source_name: bone marrow-derived mesenchymal stem cells

growth_protocol: Identical to RNA-Seq growth protocol.

extract_protocol:
MSCs were fixed at room temperature for 10 min with 1% paraformaldehyde (Ted Pella, Redding, CA) in unsupplemented DMEM, washed with ice cold PBS, then quenched for 5 min with 125 mM glycine. Fixed cells were washed, scraped from plates, centrifuged, then resuspended in 1 mL PBS / 10^7 cells. Equal numbers of cells were spun down, flash frozen in liquid N2, and stored at -80°C. To isolate nuclei, cell pellets were lysed at 4°C for 10 min with mild detergents (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X 100, protease inhibitors). Nuclei were spun down, washed for 10 min at room temperature (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, protease inhibitors), and finally lysed in 300 uL of nuclear lysis buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, protease inhibitors). Chromatin was sonicated in 0.5 mL thin-walled PCR tubes (BrandTech, Essex, CT) using a QSonica Q800R2 (QSonica, Newtown, CT) with the following settings: 30 min, 30 sec ON / 30 sec OFF, amplitude 40%. 1% Triton-X 100 was added to sonicated lysate prior to high-speed, cold centrifugation to remove debris. 5 ug of DNA was immunoprecipitated with pre-blocked Protein A/G Dynabeads (Thermo, Waltham, MA) complexed to 2.5 ug of antibody (anti-H3K4me3, ab8580, RRID:AB_306649, Abcam, Cambridge, UK; anti-H3K27me3, ab6002, RRID:AB_305237, Abcam). Beads were washed four times with LiCl buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and once with TE + 50 mM NaCl. Beads were resuspended in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) and incubated at 65°C for 30 min to release chromatin from beads. Eluate and input controls were reverse crosslinked overnight at 65°C. DNA was isolated using the Zmyo ChIP DNA Clean & Concentrator kit (Zymo Research) following RNAse A (0.2 mg/mL, 2 hr, 37°C) and Proteinase K (0.2 mg/mL, 2 hr, 55°C) treatment.
Size distribution of ChIP-enriched genomic DNA fragments was evaluated using D1000 high-sensitivity DNA screen tape to be 100-300 bp, peaking at about 200 bp. ChIP-seq deep sequencing libraries were synthesized using NEBNext Ultra Library Prep Kit (New England Biolabs, Ipswich, MA). Libraries were subjected to size distribution analysis using Tapestation (125 bp – 300 bp, peaking at 200 bp) and quantified using the KAPA kit to pool up for NextSeq500 sequencing (75 nt, single) to generate fastq data.

treatment_protocol: Treatments were carried out as in the RNA-Seq experiments, except in 10 cm plates.

tag: agent

value: TBT


title: R2-FL_S5

description:
Replicate pool 2
Sample 5

source_name: viral contents: Full-length (FL) genome


title: ChIPseq H3K27me3 TBT rep 2


title: R2-DVG_S6

description:
Replicate pool 2
Sample 6


title: ChIPseq H3K27me3 TBT rep 1


title: R1-NI_S4

description:
Replicate pool 1
Sample 4


title: ChIPseq H3K27me3 DMSO rep 4

value: DMSO


title: ChIPseq H3K27me3 DMSO rep 3


title: R1-FL_S1

description:
Replicate pool 1
Sample 1


title: ChIPseq H3K27me3 TBT rep 3


title: ChIPseq H3K27me3 DMSO rep 1


title: ChIPseq H3K27me3 DMSO rep 2


title: ChIPseq H3K4me3 TBT rep 4


title: ChIPseq H3K4me3 TBT rep 2


title: ChIPseq H3K4me3 TBT rep 3


title: ChIPseq H3K4me3 DMSO rep 2


title: ChIPseq H3K4me3 DMSO rep 3


title: ChIPseq H3K4me3 TBT rep 1


title: Mneg1

description: RNA-Seq from Serratia grown alone, replicate 1


title: R1-INT_S3

description:
Replicate pool 1
Sample 3


title: RNAseq TBT rep 5

description:
RNA_counts.txt
log2.norm.counts.txt

growth_protocol: Bone marrow-derived multipotent mesenchymal stromal cells from the long bones of C57BL/6 mice (MSCs) were purchased at passage 6 (OriCell, Cyagen Biosciences, Santa Clara, CA) and stored at passage 8 or 9 in liquid N2. Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% calf bovine serum (CBS), 10 mM HEPES, 1 mM sodium pyruvate, 100 IU/mL penicillin, and 100 ug/mL streptomycin.

extract_protocol:
Cells were lysed in TriPure (Roche, Basel, Switzerland) and total RNA isolated with MiniPrep columns (Zymo Research, Irvine, CA)
Integrity of total RNA was evaluated using Tapestation high-sensitivity RNA screen tapes (Agilent Technologies, Santa Clara, CA). Range of the RNA integrity number (RIN) was 8.0 - 8.6. Strand-specific, barcode-indexed RNA-seq deep sequencing libraries were synthesized from total RNA with ERCC spike-in controls (ThermoFisher Scientific, Waltham, MA) using Ovation RNA-Seq Systems 1-16 for Mouse (NuGen Technologies, San Carlos, CA). Size distribution of the libraries were determined by Tapestation to be 200 – 800 bp, peaking at 300 bp. RNA-seq libraries were quantified using KAPA Illumina library quantification kit (KAPA Biosystems, Wilmington, MA), and up to 12 libraries were pooled in each run of the Illumina NextSeq500 deep sequencer (75 nt + 75 nt, paired-end) to generate fastq raw read sequence files.

treatment_protocol: MSCs were plated at 15,000 cells/cm2 in 12-well plates, and were allowed to attach and acclimate for 24 hours prior to 48 hours of chemical treatment with 0.1% DMSO, 100 nM Rosiglitazone, 100 nM AGN194204, or 50 nM Tributyltin.


title: RNAseq TBT rep 6

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq TBT rep 3

description:
RNA_counts.txt
log2.norm.counts.txt


title: ChIPseq H3K4me3 DMSO rep 1


title: RNAseq 4204 rep 5

description:
RNA_counts.txt
log2.norm.counts.txt


title: ChIPseq H3K4me3 DMSO rep 4


title: RNAseq TBT rep 2

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq 4204 rep 6

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq 4204 rep 4

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq ROSI rep 4

description:
RNA_counts.txt
log2.norm.counts.txt

value: ROSI


title: RNAseq ROSI rep 5

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq 4204 rep 3

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq ROSI rep 2

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq TBT rep 4

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq ROSI rep 1

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq DMSO rep 6

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq DMSO rep 5

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq ROSI rep 6

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq DMSO rep 4

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq DMSO rep 2

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq DMSO rep 3

description:
RNA_counts.txt
log2.norm.counts.txt


title: ChIPseq Input TBT


title: ChIPseq Input DMSO


title: RNAseq DMSO rep 1

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq 4204 rep 1

description:
RNA_counts.txt
log2.norm.counts.txt


title: RNAseq 4204 rep 2

description:
RNA_counts.txt
log2.norm.counts.txt


title: Jak2VF/+ vector LSK, biological rep3

city: Syracuse

first: Golam

last: Mohi

state: New York

address: 766 Irving Avenue

department: Pharmacology

institute: SUNY Upstate Medical University

description: Gene expression data

data_processing:
Base calling performed using Illumina Real Time Analysis (RTA) v2. The RTA software is part of the NextSeq Control Software (NCS).
Reads were aligned to the mouse genome sequences (mm10) using Partek Flow, Version 3.0 (Partek Incorporated). Bowtie2 algorithm was used in Partek Flow.
BAM files generated from allignment were mapped using the template sequence Ensembl mouse release 86.
Biological interpretation for gene set analysis was done with one way ANOVA in Partek Flow, Version 3.0 (Partek Incorporated). Genes having a fold change greater than 1.5 and a significance value of less than 0.05 (P< 0.05) in Jak2VF/+Hmga2 compared to Jak2VF/+ vector were listed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: LSK from  Jak2VF/+ vector mice, 32weeks after BMT

growth_protocol: Bone marrow cells from 5-fluorouracil-primed Mx1Cre; Jak2V617F/+ (referred as Jak2VF/+) and mice were transduced with lentiviruses expressing vector alone or Hmga2 by two rounds of spin infection. Transduced bone marrow cells (1X10^6) were injected into retro-orbital veins of lethally irradiated (2X 550 cGy) C57BL/6 recipient mice. BM cells were harvested at 32 weeks after BMT.

extract_protocol:
Total RNA from LSK were extracted from LSK with RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Harvested bone marrow cells were stained with antibodies. LSK (Lin-Sca-1+c-kit+) cells were sorted with FACS AriaIII (BD)

value: bone marrow

value: LSK (Lin-Sca-1+c-kit+) hematopoietic stem cells

tag: genotype/variation

value: Jak2VF/+ vector transduced


title: Jak2VF/+ Hmga2 LSK, biological rep3

description: Gene expression data

source_name: LSK from  Jak2VF/+ Hmga2 mice, 32weeks after BMT

value: Jak2VF/+ Hmga2 transduced


title: Jak2VF/+ Hmga2 LSK, biological rep2

description: Gene expression data


title: Jak2VF/+ vector LSK, biological rep1

description: Gene expression data


title: Jak2VF/+ Hmga2 LSK, biological rep1

description: Gene expression data


title: Casnaive-96

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

state: California

address: UC Santa Barbara

department: NRI

institute: UCSB

data_processing:
Reads were mapped to the mm10 mouse genome using Bowtie2.
Duplicate reads removed using samtools.
Reads were summarized on a gene annotation using RsubReads.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of counts for each cell (as column) and each gene (as row)

extract_protocol:
After dissection, the naïve or IVA DRG neurons were filtered through a 35um mesh and resuspended in 2ml of complete media before being layered on a Percoll solution (density of 1.040) as described in (Delree et al., 1989) to remove myelin debris. The lower 5ml fraction was washed in PBS and the pellet was resuspended in C1 cell wash buffer. Cells were counted and resuspended at a concentration of 310 cells per ul, stained for viability on ice for 30 minutes and then captured by the C1 from Fluidigm using the large chip. Cells were imaged at 4X magnification. Cell lysis, reverse transcription and pre-amplification were performed on the C1 as described by the manufacturer.
cDNA was diluted and library prepared for Illumina sequencing using the Nextera kit and according to the Fluidigm protocol. Libraries were sequenced on a NextSeq 500 using a high-output 150 cycles chip. Up to 192 cells were sequenced at once and cells from all conditions were combined on each sequencing run.

value: CAST/Ei

value: dorsal root ganglia

tag: treatment

value: none (naive)


title: Jak2VF/+ vector LSK, biological rep2

description: Gene expression data


title: Casnaive-94


title: Casnaive-95


title: Casnaive-93


title: Casnaive-88


title: Casnaive-89


title: Casnaive-85


title: Casnaive-87


title: Casnaive-86


title: Casnaive-84


title: Casnaive-83


title: Casnaive-82


title: Casnaive-91


title: Casnaive-81


title: Casnaive-80


title: Casnaive-79


title: Casnaive-78


title: Casnaive-76


title: Casnaive-75


title: Casnaive-90


title: Casnaive-92


title: Casnaive-73


title: Casnaive-74


title: Casnaive-66


title: Casnaive-65


title: Casnaive-68


title: Casnaive-64


title: Casnaive-67


title: Casnaive-69


title: Casnaive-62


title: Casnaive-61


title: Casnaive-71


title: Casnaive-77


title: Casnaive-60


title: Casnaive-63


title: Casnaive-58


title: RNAseq TBT rep 1

description:
RNA_counts.txt
log2.norm.counts.txt


title: Casnaive-72


title: Casnaive-59


title: Casnaive-70


title: Casnaive-54


title: Casnaive-53


title: Casnaive-48


title: Casnaive-50


title: Casnaive-45


title: Casnaive-47


title: Casnaive-43


title: Casnaive-44


title: Casnaive-51


title: Casnaive-40


title: Casnaive-57


title: Casnaive-38


title: Casnaive-52


title: Casnaive-37


title: Casnaive-39


title: Casnaive-46


title: Casnaive-55


title: Casnaive-42


title: Casnaive-41


title: Casnaive-56


title: Casnaive-36


title: Casnaive-33


title: Casnaive-32


title: Casnaive-34


title: Casnaive-49


title: Casnaive-31


title: Casnaive-29


title: Casnaive-27


title: Casnaive-25


title: Casnaive-26


title: Casnaive-24


title: Casnaive-22


title: Casnaive-23


title: Casnaive-17


title: Casnaive-20


title: Casnaive-19


title: Casnaive-21


title: Casnaive-11


title: Casnaive-9


title: Casnaive-6


title: Casnaive-16


title: Casnaive-14


title: Casnaive-15


title: Casnaive-18


title: RNAseq ROSI rep 3

description:
RNA_counts.txt
log2.norm.counts.txt


title: Casnaive-8


title: Casnaive-5


title: Casnaive-28


title: Casnaive-10


title: ZCF8_del_mut_Rep2

city: Würzburg

first: Tobias

last: Ludwig

address: Josef-Schneider-Straße 2

country: Germany

institute: Institute for Molecular Infection Biology

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. albicans Build 21 transcriptome using STAR v2.5.2b with parameters --runThreadN 3 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Raw read counts per reference feature were calculated using HTSeq v0.6.1
Raw read counts were normalized and analysed for differentially expressed genes using DESeq2 v1.14.1
Genome_build: Candida albicans Build 21
Supplementary_files_format_and_content: tab-delimeted text files include raw read counts for each sample, tab-delimited text files contain the mean of normalized counts, log2 fold change, log2 fold change standard error, wald statistics, p-value and adjusted p-value for each replicate pair after differential gene expression analysis sample

organism: Candida albicans

source_name: yeast cell

growth_protocol: C. albicans reference strain and deletion mutants were grown on Todd-Hewitt agar at 37°C for 24 h.

extract_protocol:
Total RNA was extracted using RiboPure(TM) RNA purification kit for yeast (Ambion, Life Technologies)
Library construction was carried out by GATC Biotech (Konstanz, Germany) following standard operating procedures. Briefly, the steps included poly(A)+ RNA selection, mRNA fragmentation, random primer cDNA synthesis, adaptor ligation and Illumina(HiSeq2500) sequencing

value: deletion mutant


title: Casnaive-13


title: Casnaive-7


title: ZFU2_del_mut_Rep2


title: ZCF8_del_mut_Rep1


title: Casnaive-4


title: Casnaive-35


title: ZFU2_del_mut_Rep1


title: Casnaive-3


title: TRY4_del_mut_Rep2


title: Casnaive-12


title: WT_TRY4_ZFU2_ZCF8_Rep2

value: wildtype


title: TRY4_del_mut_Rep1


title: Casnaive-1


title: WT_TRY4_ZFU2_ZCF8_Rep1


title: Casinjur-101

treatment_protocol: After dissociation cells were plated on bare plastic at high density (5000 to 10000 cells per cm2) and allowed to grow for 48 h with the addition of ara-c 24 h after plating. After 48 hr cells were lifted using trypsin and lightly triturated to ensure dissociation of all processes.

value: injured


title: Casinjur-99


title: Casinjur-97


title: Casinjur-94


title: Casinjur-103


title: Casinjur-98


title: Casinjur-100


title: Casinjur-92


title: Casinjur-95


title: Casinjur-93


title: Casinjur-91


title: Casinjur-90


title: Casinjur-96


title: Casinjur-87


title: pgc2

city: Miami

first: Mary Lou

last: King

state: FL

department: Cell Biology

institute: University of Miami, Miller School of Medicine

data_processing:
Raw reads from PGC and endoderm samples were aligned to each genome version using Tophat2 v2.1.0
Aligned reads were sorted and counted with Samtools v1.2 and HTSeq v0.6.0, respectively.
Raw count data were filtered to remove transcripts with FDR > 0.1, and CPM < 3 in at least three samples.
Filtered counts were TMM normalized and GLMTagwise dispersion was estimated.
Data from alignment to v7.1 and v9.1 were merged and normalized generating 13,469 total unique transcripts. Note: for transcripts identified in both genome versions, the counts from v9.1 were used.
EdgeR v3.12.0 was used for differential gene expression analysis. Transcripts were considered to be differentially expressed if the FDR corrected (Benjamini–Hochberg) p value was < 0.05.
Bowtie2 v2.2.6 was used to create index reference genomes for Xenopus laevis v7.1 and v9.1 (xenbase.org, September, 2015)
Genome_build: 7.1 and 9.1
Supplementary_files_format_and_content: csv

organism: Xenopus laevis

source_name: stage 12-14 Xenopus laevis embryos

extract_protocol:
Primordial germ cells and stage-matched endoderm cells were isolated from stage 12-14 Xenopus laevis embryos and collected into RNA lysis buffer as described by Butler et al. (2016). Total RNA was extracted using the RNAqueous-Micro Total RNA Isolation Kit per the manufacturer’s protocol (Ambion).
Three 1ng aliquots of each rRNA-depleted sample were used as template for preparation of sequence-able template DNA molecules using the ScriptSeq v2 RNASeq Library Preparation Kit (Illumina, Part # SSV21124). The quality and size distribution of the amplified libraries were determined utilizing an Agilent 2100 Bioanalyzer High Sensitivity DNA Chip. Libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems, Boston, MA), and equimolar concentrations were diluted prior to loading onto the flow cell of the Illumina cBot cluster station. The libraries were extended and bridge amplified to create sequence clusters using the Illumina HiSeq PE Cluster Kit v4, and sequenced on an Illumina HiSeq Flow Cell v4 with 100-bp paired-end reads plus index read using the Illumina HiSeq SBS Kit v4. Real time image analysis and base calling were performed on the instrument using the HiSeq Sequencing Control Software version 2.2.58. Three DNA libraries were prepared from Xenopus laevis primordial germ cell RNA and three from matched endoderm cell RNA.

value: PGC


title: Casinjur-86


title: pgc1


title: Casnaive-2


title: Casinjur-85


title: Casinjur-102


title: endo3

value: Endoderm


title: Casinjur-82


title: Casinjur-89


title: Casinjur-81


title: Histone H3K36me3 ChIP-seq Cdk7as Rep2

first: David

middle: L.

last: Bentley

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description: Chromatin IP against histone H3K36me3

data_processing:
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for RNA-seq
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: bigwig files for ChIP-seq

source_name: HCT116 Cdk7as (Larochelle et al Mol. Cell 25:839, 2007)

growth_protocol: HCT1161 WT and Cdk7as mutant cells were grown in McCoy's medium 10% FCS and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: WT HCT116 and Cdk7as cells were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq or RNA-seq

value: Cdk7as mutant

value: rabbit anti  H3K36me3 (Kim et al PNAS 108:13564, 2011 )


title: endo1


title: endo2


title: Casinjur-80


title: Casinjur-88


title: pgc3


title: Casinjur-77


title: Casinjur-79


title: Histone H3K36me3 ChIP-seq WT Rep2

description: Chromatin IP against histone H3K36me3


title: YTHDC2-PARCLIP-repl.1

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description:
PAR-CLIP
small RNA fragments crosslinked with YTHDC2 with 4SU
processed data file:
YTHDC2_PARCLIP.xlsx

data_processing:
Gene structure annotations were downloaded from hg38 RefSeq. Dataanalyses were performed as previously described (Wang, Boxuan Simen Zhao, et al.2015; Dominissini et al. 2012). Briefly, after removing adapters, sequencing reads werealigned to the reference genome (mm10) using TopHat (v2.0.14) (Kim et al. 2013). ForRIPSeq, RPKM were calculated by Cuffnorm (Trapnell et al. 2012). RIP-seq targetswere defined as genes enriched in the IP (log2(RIP/input) >= 1), and RIP-seq non-targets were defined as genes depleted in the IP (log2(RIP/input) <= -1). For m 6 A-seq,the longest isoform was used if multiple isoforms were detected. Aligned reads wereextended to 100 nt (average fragment size) and converted from genome-basedcoordinates to isoform-based coordinates to eliminate interference from introns in peakcalling. To call m 6 A peaks, the longest isoform of each human gene was scanned usinga 100 nt sliding window with 10 nt steps. To reduce bias from potentially inaccurategene structure annotation and the arbitrary usage of the longest isoform, windows withreads counts less than 1/20 of the top window in both m 6 A IP and input sample wereexcluded. For each gene, the reads count in each window was normalized by themedian count of all windows of that gene. A negative binomial model was used toidentify the differential windows between IP and input samples by using the edgeRpackage (Robinson et al. 2009). The window was called positive if FDR < 1% andlog2(enrichment score) ≥ 1. Overlapping positive windows were merged. The followingfour numbers were calculated to obtain the enrichment score of each peak (or window):read count of the IP sample in the current peak/window (a), median read count of the IPsample in all 100 nt windows on the current mRNA (b), read count of the input sample inthe current peak/window (c), and median read count of the input sample in all 100 ntwindows on the current mRNA (d). The enrichment score of each window wascalculated as (a × d)/(b × c). For CLIP-seq, we used a modified version of PARalyzer(Corcoran et al. 2011) to allow for all mutations, rather than just T to C mutations, forpeak calling, while filtering out all SNPs and potential sequencing errors. Consensusmotif was determined using HOMER (Heinz et al. 2010)
For ParCLIP data, PARalyzer was used for peak calling.
Genome_build: hg38
Supplementary_files_format_and_content: Excel

source_name: HeLa

extract_protocol: NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

value: HeLa

value: N terminal Flag-HA tagged YTHDC2 HeLa stable expression cell line

tag: par-clip antibody

value: Anti-FLAG M2 Magnetic Beads (M8823 SIGMA)


title: Casinjur-75


title: Casinjur-74


title: Casinjur-76


title: Casinjur-78


title: RNAseq Cdk7as Rep2

description: rRNA depleted total RNA

data_processing:
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for RNA-seq
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: bigwig files for ChIP-seq, TDF files for RNA-seq

growth_protocol: McCoy's 10% FCS, 10mM NM-PP1, 24hr

extract_protocol: Ribosomal RNA was removed using the NEB ribosome removal kit and libraries were prepared using the NEB ultra directional kit, with RNA fragmentation for 8 min and 15 PCR cycles.


title: RNAseq Cdk7as Rep3

description: rRNA depleted total RNA


title: Casinjur-73


title: RNAseq Cdk7as Rep1

description: rRNA depleted total RNA


title: Casinjur-72


title: RNAseq HCT116 Rep3

description: rRNA depleted total RNA


title: RNAseq HCT116 Rep2

description: rRNA depleted total RNA


title: RNAseq HCT116 Rep1

description: rRNA depleted total RNA


title: Casinjur-71


title: Casinjur-70


title: Histone H3 ChIP-seq Cdk7as

description: Chromatin IP against histone H3 Cter

value: rabbit anti  H3 Cter (Zhang et al EMBO J, 24:2379, 2005)


title: Casinjur-69


title: Histone H3 ChIP-seq WT

description: Chromatin IP against histone H3 Cter


title: Casinjur-67


title: YTHDC2-PARCLIP-repl.2


title: Casinjur-68


title: HCE ChIP-seq Cdk7as Rep2

description: Chromatin IP against human capping enzyme

value: rabbit anti-HCE (Glover-Cutter et al NSMB. 15:71, 2008)


title: HCE ChIP-seq WT Rep2


title: HCE ChIP-seq Cdk7as Rep1


title: Casinjur-64


title: Casinjur-66


title: Casinjur-62


title: Casinjur-65


title: RNA pol II Ser2-P ChIP-seq Cdk7as Rep2

description: Chromatin IP against RNA pol II Ser2-P

value: rat monoclonal anti-Ser2-P 3E10 (Chromotek)


title: Casinjur-59


title: RNA pol II Ser2-P ChIP-seq Cdk7as Rep1

description: Chromatin IP against RNA pol II Ser2-P


title: Casinjur-60


title: RNA pol II Ser2-P ChIP-seq WT Rep2

description: Chromatin IP against RNA pol II Ser2-P


title: Casinjur-58


title: RNA pol II Ser5-P ChIP-seq WT  Rep2

description: Chromatin IP against RNA pol II Ser5-P

value: rat monoclonal anti-Ser5-P 3E8 (Chromotek)


title: RNA pol II Ser5-P ChIP-seq Cdk7as  Rep2

description: Chromatin IP against RNA pol II Ser5-P


title: Casinjur-57

value: CAST/Ei


title: RNA pol II Ser5-P ChIP-seq WT  Rep1

description: Chromatin IP against RNA pol II Ser5-P


title: RNA pol II Ser5-P ChIP-seq Cdk7as  Rep1

description: Chromatin IP against RNA pol II Ser5-P


title: Casinjur-55

value: dorsal root ganglia


title: Casinjur-56


title: RNA pol II ChIP-seq DMSO control

description: Chromatin IP against RNA pol II

growth_protocol: McCoy's 10% FCS, 0.1% DMSO, 1hr

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: Casinjur-63


title: Casinjur-54


title: RNA pol II ChIP-seq WT Rep1

description: Chromatin IP against RNA pol II


title: RNA pol II ChIP-seq THZ1

description: Chromatin IP against RNA pol II

growth_protocol: McCoy's 10% FCS, 1mM THZ1, 0.1% DMSO, 1hr


title: HCE ChIP-seq WT Rep1


title: Casinjur-53


title: RNA pol II ChIP-seqCdk7as Rep1

description: Chromatin IP against RNA pol II


title: Casnaive-173

value: none (naive)


title: Casnaive-174


title: Casnaive-170


title: Casnaive-171


title: RNA pol II Ser2-P ChIP-seq WT Rep1

description: Chromatin IP against RNA pol II Ser2-P

value: wildtype


title: Casnaive-172


title: Casnaive-169


title: N2 L1 Arrest Dnase-seq Biological Replicate W

city: Pasadena

first: Paul

last: Sternberg

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

description:
processed data file (analyzed and merged from biological replicates of same stage):
L1.ce10.noncodingDHS.geneannot.txt
L1arrestassociated.ce10.ncDHS.geneannot.txt
merged.L1.ce10.negative.normalized.bw
merged.L1.ce10.positive.normalized.bw
merged.L1.ce10.total.normalized.bw
L1.ce10.allDHS.bed
L1.ce10.noncodingDHS.bed
L1.ce10.DHSfootprints.FDR0.05.bed
L1arrestassociated.ce10.noncodingDHS.bed
L1arrestassociated.ce10.DHSfootprints.FDR0.05.bed

data_processing:
Reads were analyzed using FastQC and filtered using quality threshold Q20.
50bp single-end reads from embryo replicates B, C, D and L1 arrest X, Y, Z replicates were trimmed to 45bp and mapped to WS220 (ce10) version of C. elegans genome using Bowtie 1.0.0 using settings that did not allow alignments with more than two mismatches, disallowing reads with more than two read alignments, and only permitting alignments in the best alignment “stratum”. 76bp single-end reads from embryo replicate A and L1 arrest replicates W and V did not need trimming and were mapped using identical settings.
Potential PCR duplicates were removed using software SAMtools (Li et al. 2009).
Raw DNaseI hypersensitive peaks were identified by detecting read enrichment in 150bp consecutive nucleotides using HOTSPOT peak caller specifically designed for DNase-seq (version 3; John et al. 2011). We filtered raw peak calls obtained from HOTSPOT using the irreproducibility discovery rate (IDR) framework developed for ENCODE, which uses a non-parametric copula mixture model to filter peaks into reproducible or irreproducible categories (Li et al. 2011; Landt et al. 2012). Peaks are filtered on the combination of their rank or score as well as their consistency across replicates at an IDR level of 0.1. Peaks overlapping Repeatmasker repeats were omitted. Blacklist regions from ENCODE representing known ce10 genomic regions exhibiting signal artifacts in ChIP-seq experiments were removed (ENCODE Project Consortium 2012). Overlapping peaks were merged to yield 41,825 and 23,670 DHS peaks across embryo and L1 arrest biological replicates, respectively.
Footprints were identified with DNase2TF software package using a FDR threshold of 0.05 (Sung et al. 2014) to identify decreased read coverage within noncoding DHS in regions between 6-40bp with a strand shift in reads in each biological replicate. Replicate data within each stage were merged and used to identify additional TF footprints.
Genome_build: WS220 (ce10)
Supplementary_files_format_and_content: DHS peak locations were annotated in exons (if 75% of region was located in exon), introns, promoter (<300bp from ATG), and intergenic regions (>300bp from ATG) using custom scripts and WormBase WS241 gene models. Pseudogenes, tRNAs, and ncRNAs were excluded from annotation.

organism: Caenorhabditis elegans

source_name: N2 L1 Arrest

growth_protocol: Wild-type N2 worms were grown synchronously for at least two generations. Embryos at around the 40-cell stage or L1 arrest larvae were collected and frozen at -80°C. Freeze-thaw cycles in a nuclei purification buffer and a Dounce homogenizer were used to isolate nuclei. Nuclei (blue) were purified by spinning on Optiprep density gradient medium and visualized with DAPI (see Methods).

extract_protocol:
After treating with 45ug/mL boiled RNase A for 30 minutes, DNA was purified and concentrated using column purification. The DNA sample was run on 1% agarose, stained with SYBR Gold, and the gel piece containing DNA fragments less than 500bp was isolated and purified. DNA sample yield was measured using a Qubit fluorimeter.
50 base pair single ended sequencing library for embryo replicates B, C, D and L1 arrest X,Y,Z. 76 base pair single ended sequencing library for embryo replicate A and L1 arrest replicates W and V.
Illumina HiSeq2500

treatment_protocol: Embryo and L1 arrest larvae nuclei were treated with 0, 20, 40, 80, 120, 160 U/mL DNaseI in 1X DNaseI digestion buffer (containing CaCl2, spermine, spermidine, protease inhibitor) each for 3 minutes at 37°C. DNaseI treatment follows the conditions from the Stamatoyannopoulos lab protocol (Thurman et al. 2012). DNaseI treatment was quenched with STOP buffer containing 20mg/mL Proteinase K and incubated 55°C overnight.

tag: Stage

value: L1 Arrest

tag: library preparation

tag: flowcell sample id


title: N2 L1 Arrest Dnase-seq Biological Replicate V

tag: strain

value: 76 base pair single ended sequencing library


title: N2 L1 Arrest Dnase-seq Biological Replicate Z

value: 50 base pair single ended sequencing library


title: N2 L1 Arrest Dnase-seq Biological Replicate X


title: N2 L1 Arrest Dnase-seq Biological Replicate Y


title: N2 Embryo Dnase-seq Biological Replicate D

description:
processed data file (analyzed and merged from biological replicates of same stage):
embryo.DNaseI.motifanatomy.txt
embryo.DNaseI.motifassocgenes.txt
embryo.DNaseI.motifGO.txt
embryo.DNaseI.novelmotifs.txt
embryo.ce10.noncodingDHS.geneannot.txt
merged.embryo.ce10.negative.bw
merged.embryo.ce10.positive.bw
merged.embryo.ce10.total.bw
Embryo.ce10.allDHS.bed
embryo.ce10.noncodingDHS.bed
embryo.ce10.DHSfootprints.FDR0.05.bed

source_name: N2 Embryo

value: Mid-Embryogenesis (roughly 40 cell stage)


title: N2 Embryo Dnase-seq Biological Replicate C


title: Casnaive-166


title: Casnaive-165


title: N2 Embryo Dnase-seq Biological Replicate B


title: N2 Embryo Dnase-seq Biological Replicate A


title: Casnaive-164


title: Casnaive-161


title: Casnaive-160


title: Casnaive-162


title: Casnaive-163


title: Casnaive-159


title: WT_P21_2_ATAC

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description:
processed data file:
ATAC-Dev-Ret_M_N-P21.free.bw

data_processing:
Basecalls performed using CASAVA
After trimming nextra adapter with cutadapt(v 1.13), we used BWA (version 0.5.9-r26-dev, default parameter) to align the reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads. Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1804” version 0.1.18 (r982:295)).
center 80bp of nucleosome free reads were used generate bigwig file to view on IGV (version 2.3.40).
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

source_name: retina

extract_protocol: ATAC-seq library preparation was performed as described (Buenrostro et al., 2013) with minor modifications. Briefly, for each experiment, 2 × 105 - 5 × 105 dissociated retinal cells were washed twice with PBS (Lonza, 17-516F) containing Proteinase Inhibitor Cocktail (Sigma-Aldrich P8340), incubated with 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.3% IGEPAL CA-630) on ice for 10 min and centrifuged at 500 g for 10 min at 4°C. After centrifugation, the pellet was immediately incubated with 50 μL of Tn5 transposition reaction mix (25 μL TD buffer, 2.5 μL TDE1 (Nextera DNA Library Prep Kit, Illumina, FC-121-1030) and 22.5 μL nuclease-free water) at 37°C for 30 min. After purification with QIAGEN MinElute PCR Purification Kit (QIAGEN, 28006), transposed DNA fragments were amplified with NEBNext High-Fidelity 2 × PCR Master Mix (New England Biolabs, M0541) for 5 cycles using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. 5 μL of each library was amplified in a 25 μL qPCR reaction with KAPA SYBRFAST qPCR Kit (Kapa Biosystems, KK4603) to estimate the optimum number of additional cycles to finish amplification of the remaining 45 μL library.

tag: developmental stage

value: postnatal day 21

value: retina


title: WT_P14_ATAC

description:
processed data file:
ATAC-Dev-Ret_M_N-P14.free.bw

value: postnatal day 14


title: Casnaive-158


title: WT_P10_2_ATAC

description:
processed data file:
ATAC-Dev-Ret_M_N-P10.free.bw

value: postnatal day 10


title: Casnaive-156


title: Casnaive-157


title: Casnaive-30


title: Casnaive-155


title: WT_P10_1_ATAC


title: WT_P3_2_ATAC

description:
processed data file:
ATAC-Dev-Ret_I_N-P3.free.bw

value: postnatal day 3


title: Casnaive-167


title: Casnaive-152


title: Casnaive-168


title: Casnaive-153


title: WT_P3_1_ATAC


title: WT_P0_ATAC

description:
processed data file:
ATAC-Dev-Ret_I_N-P0.free.bw

value: postnatal day 0


title: Casnaive-151


title: WT_E17.5_ATAC

description:
processed data file:
ATAC-Dev-Ret_E_N-E17.5.free.bw

value: embryonic day 17.5


title: WT_E14.5_ATAC

description:
processed data file:
ATAC-Dev-Ret_E_N-E14.5.free.bw

value: embryonic day 14.5


title: WT_P7_ATAC

description:
processed data file:
ATAC-Dev-Ret_M_N-P7.free.bw

value: postnatal day 7


title: Casnaive-149

value: CAST/Ei

value: dorsal root ganglia


title: Casnaive-150

value: none (naive)


title: WT_P21_1_ATAC


title: Casnaive-148


title: YTHDC2-m6Aseq-KO-IP-repl.2

description:
m6A-seq
fragmented polyA RNA immunoprecipitated with anti-m6A antibody
processed data file:
YTHDC2_m6Aseq.xlsx

data_processing:
Gene structure annotations were downloaded from UCSC mm10 RefSeq. Data analyses were performed as previously described (Wang, Boxuan Simen Zhao, et al.2015; Dominissini et al. 2012). Briefly, after removing adapters, sequencing reads werealigned to the reference genome (mm10) using TopHat (v2.0.14) (Kim et al. 2013). ForRIPSeq, RPKM were calculated by Cuffnorm (Trapnell et al. 2012). RIP-seq targetswere defined as genes enriched in the IP (log2(RIP/input) >= 1), and RIP-seq non-targets were defined as genes depleted in the IP (log2(RIP/input) <= -1). For m 6 A-seq,the longest isoform was used if multiple isoforms were detected. Aligned reads wereextended to 100 nt (average fragment size) and converted from genome-basedcoordinates to isoform-based coordinates to eliminate interference from introns in peakcalling. To call m 6 A peaks, the longest isoform of each human gene was scanned usinga 100 nt sliding window with 10 nt steps. To reduce bias from potentially inaccurategene structure annotation and the arbitrary usage of the longest isoform, windows withreads counts less than 1/20 of the top window in both m 6 A IP and input sample wereexcluded. For each gene, the reads count in each window was normalized by themedian count of all windows of that gene. A negative binomial model was used toidentify the differential windows between IP and input samples by using the edgeRpackage (Robinson et al. 2009). The window was called positive if FDR < 1% andlog2(enrichment score) ≥ 1. Overlapping positive windows were merged. The followingfour numbers were calculated to obtain the enrichment score of each peak (or window):read count of the IP sample in the current peak/window (a), median read count of the IPsample in all 100 nt windows on the current mRNA (b), read count of the input sample inthe current peak/window (c), and median read count of the input sample in all 100 ntwindows on the current mRNA (d). The enrichment score of each window wascalculated as (a × d)/(b × c). For CLIP-seq, we used a modified version of PARalyzer(Corcoran et al. 2011) to allow for all mutations, rather than just T to C mutations, forpeak calling, while filtering out all SNPs and potential sequencing errors. Consensusmotif was determined using HOMER (Heinz et al. 2010)
Genome_build: mm10
Supplementary_files_format_and_content: Excel

source_name: Seminiferous tubules

extract_protocol:
Illumina TruSeq Stranded mRNA Library Prep Kit
Testes were isolated from mice, and seminiferous tubules were isolated.

value: Ythdc2 knockout

value: testis

tag: tissue compartment

value: Seminiferous tubules

tag: age

tag: m6a-seq antibody

value: Synaptic Systems anti-N6-methyladenosine polyclonal rabbit antibody (Cat. 202 003, Lot 202003/65)


title: YTHDC2-m6Aseq-KO-Input-repl.2

description:
m6A-seq
fragmented polyA RNA
processed data file:
YTHDC2_m6Aseq.xlsx

value: none (input)


title: YTHDC2-m6Aseq-KO-IP-repl.1


title: Casnaive-147


title: Casnaive-146


title: Casnaive-145


title: YTHDC2-m6Aseq-KO-Input-repl.1


title: YTHDC2-m6Aseq-control-Input-repl.2

value: wild type


title: YTHDC2-m6Aseq-control-IP-repl.2


title: Casnaive-142


title: Casnaive-154


title: Casnaive-141


title: Casnaive-143


title: YTHDC2-m6Aseq-control-IP-repl.1


title: Casnaive-144


title: YTHDC2-RIP-seq-Input-repl.2

description:
RIP-seq
rRNA-depleted RNA
processed data file:
YTHDC2_RIPseq.xlsx

tag: rip-seq antibody


title: YTHDC2-RIP-seq-Input-repl.1


title: YTHDC2-m6Aseq-control-Input-repl.1


title: YTHDC2-RIP-seq-IP-repl.1

description:
RIP-seq
Full length RNA co-immunoprecipitated with YTHDC2
processed data file:
YTHDC2_RIPseq.xlsx

value: Santa Cruz anti-YTHDC2 polyclonal goat antibody (Cat. sc-249370, Lot J0212)


title: Casnaive-138


title: YTHDC2-RIP-seq-IP-repl.2


title: Casnaive-137


title: Casnaive-136


title: YTHDC2-CLIP-seq-repl.2

description:
CLIP-seq
small RNA fragments crosslinked with YTHDC2
processed data file:
YTHDC2_CLIPseq.xlsx

extract_protocol:
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®
Testes were isolated from mice, and seminiferous tubules were isolated.

value: 12 weeks

tag: clip-seq antibody


title: Casnaive-140


title: Casnaive-135


title: YTHDC2-CLIP-seq-repl.1


title: C57injur-113

value: injured


title: C57injur-115


title: C57injur-109


title: C57injur-111


title: C57injur-108


title: C57injur-106


title: C57injur-110


title: C57injur-105


title: C57injur-107


title: Casnaive-139


title: C57injur-101


title: C57injur-99


title: C57injur-103


title: C57injur-102


title: C57injur-97


title: C57injur-98


title: C57injur-104


title: C57injur-96


title: MBD_rep1

city: Montpellier

first: Daniel

last: Grimanelli

address: 911 Av Agropolis

country: France

institute: IRD

description: chromatin

data_processing:
Quality filtering and base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.2)
Reads with Q>30 were mapped to the reference genome -TAIR10- using Bowtie2. parameters used: 1 mismatch
Bining and read counts /coverage relative to annotations performed using bedtools2
Genome_build: TAIR10
Supplementary_files_format_and_content: BED files with coordinates and coverage

source_name: Arabidopsis inflorescences, WT

extract_protocol:
500 ug of inflorescence tissues were collected for each genotype and cross linked with 1% formaldehyde in water for 10 min with vacuum. Cross linking was stopped by adding glycine to a final concentration of 0.125M. Liquid Nitrogen was used to grind the tissues  to a fine powder, which was mixed to 30ml of Extraction Buffer 1 (0.4M sucrose, 10mM Tris-HCl pH 8, 10mM MgCl, 5mM BME, 0.1mM PMSF, 1 tab Protease inhibitors (Roche Biochemicals) per 50mls), mixed gently and let on ice for 15 min. The solution was filtered twice with Miracloth into a fresh 50ml falcon tube, and spinned for 20 minutes at 4000 rpm in a centrifuge at 4°C. The pellet was resuspended in 1ml of Extraction Buffer 2 ( 0.25M sucrose, 10mM Tris-HCl pH 8, 10mM MgCl2, 1% Triton X-100, 5mM BME, 0.1mM PMSF, Protease inhibitors (Roche Biochemicals, 1 mini tab per 5mls) and transferred to 1.5ml eppendorf tube, followed by 10 min centrifugation (12,000 g at 4 degrees). The resulting pellet was resuspend in 300ul of Extraction Buffer 3 (1.7M sucrose, 10mM Tris-HCl pH 8, 0.15% Triton X-100, 2mM MgCl2, 5mM BME, 0.1mM PMSF, protease inhibitor (Roche Biochemicals, 1 mini tab per 5mls), layered on top of 300ul of Extraction Buffer 3 in a clean tube and spin for 1 hour at 16,000 at 4 degrees. The chromatin pellet was then resuspended in 300ul of Nuclei Lysis Buffer (50mM Tris-HCl ph 8, 10mM EDTA, 1% SDS, Protease inhibitors (Roche Biochemicals, 1 mini tab per 5mls) and sonicated with a Diagenode Bioruptor machine (10 cycles, 30 seconds/1 minute ON/OFF), spinned at full speed for 5 minutes at 4 degrees to pellet debris, the supernatant collected to a fresh tube, and the chromatin solution brought to 3ml with ChIP Dilution Buffer (1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl pH 8, 167mM NaCl). 1ml of chromatin was added to new low-binding tubes and pre-cleared with 50ul of agorose beads for 1h on a rotating wheel. 1ml of pre-cleared chromatin was mixed with 80µl of equilibrated agarose beads and 3µg of anti-GFP antibody, and incubated overnight at 4°C on a ratting wheel. Beads were washed with the following sequence: twice 5min with Low Salt Wash Buffer (150mM NaCl, 0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl pH8.1), twice 5min with High Salt Wash Buffer (500mM NaCl, 0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl (pH8.1)), twice 5min with LiCl Wash Buffer (0.25 LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1), and twice 5min with TE Buffer:  (10mM Tris-HCl pH 8, 1mM EDTA). Immune complexes were eluted twice with 250ul of Elution Buffer (1% SDS, 0.1 M NaHCO3) by incubating 65 degrees for 15 minutes with gentle agitation (mix tubes during incubation), and combining both two eluates. 20ul 5M NaCl was added to the combined eluates, which were reverse-cross linked at 65°C overnight, and treated with 2ul of 10mg/ml proteinase K for one hour at 45°C.  Note:  Don’t forget to get your total DNA out of the freezer and reverse X-link with other samples (Add 500 ul of Elution buffer + 20ul 5M NaCl). The resulting DNA fragments were purified using Diagenode ChIP purification kit (catalogue #C03010011), and resuspended in 50ul of distilled water.
Library constructed using Illumina’s TruSeq ChIP Sample Prep Kit, and following manufacturer’s protocol.

tag: tissues

value: inflorescences

tag: genotypes

value: WT; mCGBP-VENUS

tag: antibodies

value: Anti-GFP Abcam (ab6556, GR136046-1)


title: MBD_rep2

description: chromatin


title: C57injur-94

tag: tissue


title: CG_input1, rep1

extract_protocol:
500 ug of inflorescence tissues were collected for each genotype and cross linked with 1% formaldehyde in water for 10 min with vacuum. Cross linking was stopped by adding glycine to a final concentration of 0.125M. Liquid Nitrogen was used to grind the tissues  to a fine powder, which was mixed to 30ml of Extraction Buffer 1 (0.4M sucrose, 10mM Tris-HCl pH 8, 10mM MgCl, 5mM BME, 0.1mM PMSF, 1 tab Protease inhibitors (Roche Biochemicals) per 50mls), mixed gently and let on ice for 15 min. The solution was filtered twice with Miracloth into a fresh 50ml falcon tube, and spinned for 20 minutes at 4000 rpm in a centrifuge at 4°C. The pellet was resuspended in 1ml of Extraction Buffer 2 ( 0.25M sucrose, 10mM Tris-HCl pH 8, 10mM MgCl2, 1% Triton X-100, 5mM BME, 0.1mM PMSF, Protease inhibitors (Roche Biochemicals, 1 mini tab per 5mls) and transferred to 1.5ml eppendorf tube, followed by 10 min centrifugation (12,000 g at 4 degrees). The resulting pellet was resuspend in 300ul of Extraction Buffer 3 (1.7M sucrose, 10mM Tris-HCl pH 8, 0.15% Triton X-100, 2mM MgCl2, 5mM BME, 0.1mM PMSF, protease inhibitor (Roche Biochemicals, 1 mini tab per 5mls), layered on top of 300ul of Extraction Buffer 3 in a clean tube and spin for 1 hour at 16,000 at 4 degrees. The chromatin pellet was then resuspended in 300ul of Nuclei Lysis Buffer (50mM Tris-HCl ph 8, 10mM EDTA, 1% SDS, Protease inhibitors (Roche Biochemicals, 1 mini tab per 5mls) and sonicated with a Diagenode Bioruptor machine (10 cycles, 30 seconds/1 minute ON/OFF), spinned at full speed for 5 minutes at 4 degrees to pellet debris, the supernatant collected to a fresh tube, and the chromatin solution brought to 3ml with ChIP Dilution Buffer (1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl pH 8, 167mM NaCl). 1ml of chromatin was added to new low-binding tubes and pre-cleared with 50ul of agorose beads for 1h on a rotating wheel. 1ml of pre-cleared chromatin was mixed with 80µl of equilibrated agarose beads and 3µg of anti-GFP antibody, and incubated overnight at 4°C on a ratting wheel. Beads were washed with the following sequence: twice 5min with Low Salt Wash Buffer (150mM NaCl, 0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl pH8.1), twice 5min with High Salt Wash Buffer (500mM NaCl, 0.1% SDS, 1% TritonX-100, 2mM EDTA, 20mM Tris-HCl (pH8.1)), twice 5min with LiCl Wash Buffer (0.25 LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1), and twice 5min with TE Buffer:  (10mM Tris-HCl pH 8, 1mM EDTA). Immune complexes were eluted twice with 250ul of Elution Buffer (1% SDS, 0.1 M NaHCO3) by incubating 65 degrees for 15 minutes with gentle agitation (mix tubes during incubation), and combining both two eluates. 20ul 5M NaCl was added to the combined eluates, which were reverse-cross linked at 65°C overnight, and treated with 2ul of 10mg/ml proteinase K for one hour at 45°C.  Note:  Don’t forget to get your total DNA out of the freezer and reverse X-link with other samples (Add 500 ul of Elution buffer + 20ul 5M NaCl). The resulting DNA fragments were purified using Diagenode ChIP purification kit (catalogue #C03010011), and resuspended in 50ul of distilled water.
Library constructed at FASTERIS using Illumina’s TruSeq ChIP Sample Prep Kit, and following manufacturer’s protocol.

tag: genotype/variation

value: WT; mCHHBP-VENUS

tag: chip antibody


title: CHH_input1, rep 2


title: CHH_input1, rep 1


title: C57injur-92

tag: treatment


title: CG_input2, rep 2


title: C57injur-112


title: C57injur-90


title: C57injur-89


title: C57injur-91


title: mCHH;drm1drm2cmt2cmt3 rep1

description: chromatin

data_processing:
Quality filtering and base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.2)
Reads with Q>30 were mapped to the reference genome -TAIR10- using Bowtie. parameters used: 1 mismatch (-v1), and only keeping reads that uniquely mapped to the genome (-m1)
Bining and read counts /coverage relative to annotations performed using bedtools2
ChIP peaks detection performed using MACS
Genome_build: TAIR10
Supplementary_files_format_and_content: BED files with coordinates and coverage

tag: genotype

value: drm1drm2cmt2cmt3; mCHHBP-VENUS

tag: antibody


title: C57injur-100


title: mCHH;drm2 rep1

description: chromatin

source_name: Arabidopsis inflorescences, drm2

value: drm2; mCHHBP-VENUS


title: mCHH_protocol_validation_input

description: chromatin

tag: cultivar


title: cmt2_H9_rep1

description: chromatin

value: cmt2; mCHHBP-VENUS


title: mCG_protocol_validation_input

description: chromatin


title: mCHH rep2

description: chromatin


title: mCHH rep1

description: chromatin


title: mCG rep2

description: chromatin


title: mCG_protocol_validation_chip

description: chromatin


title: C57injur-87

tag: strain

value: dorsal root ganglia


title: C57injur-95


title: C57injur-84


title: C57injur-85


title: C57injur-83


title: C57injur-93


title: C57injur-82


title: C57injur-81


title: C57injur-79


title: stripped root 25ºC rep2

city: Columbia

first: Md Shakhawat

last: Hossain

state: Missouri

address: 201 Life Science Center 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: Glycine max reference genome version 1.0
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions

organism: Glycine max

source_name: stripped root

growth_protocol: Seeds from soybean cultivar Williams 82 were surface sterilized with 30% bleach, rinsed several times with sterilized double-distilled H2O (dd H2O), once with 0.01 M HCl for 10 min, and then thoroughly rinsed several times with sterilized ddH2O. Sterilized seeds were placed on nitrogen-free B&D agar medium (Broughton & Dilworth, 1971) in large, glass petri dishes and allowed to germinate in a growth chamber in the dark at 25°C and 80% humidity.

extract_protocol:
Root hairs and stripped roots were isolated after 3 hours of incubation as described by Wan et al. (2005). Genomic DNA was extracted using the DNeasy® Plant Mini Kit (Qiagen) following the manufacturer’s instructions.
One µg of gDNA was spiked with 5ng of unmethylated Lambda DNA (Promega), and randomly sheared to an average of 300 bp using the Covaris S220 instrument. Sheared DNA was end-repaired, A-tailed and ligated using TruSeq DNA sample preparation kit (Illumina, San Diego, CA). Bisulfite treatment was performed twice using the EpiTect Bisulfite kit (Qiagen) following the manufacturer's protocol for DNA isolated from formalin-fixed paraffin-embedded tissue (FFPE) tissue samples. The bisulfite-converted library was amplified (9 cycles) by PCR with KAFA HiFi Uracil+ DNA polymerase (Kapa Biosystems) according to the manufacturer’s conditions.

treatment_protocol: After three days of germination, half of the seedlings (approximately 1000) were transferred to another chamber for heat (40°C) treatment and remaining half were kept in a chamber at 25°C, considered the mock control. To avoid drying, we maintained high humidity (80%) in the growth chamber.

tag: cell type

value: root without root hair

value: Williams 82 (wild type)

value: root


title: stripped root 40ºC rep1