title: mRNACo_ded1-95_37dgC_replicate3

city: Cleveland

first: Ulf-Peter

last: Guenther

state: OH

address: 10900 Euclid Ave

department: Biochemistry/ RNA Center

institute: Case Western Reserve University

description: replicate 3

data_processing:
Basecalling with Illumina Casava software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie
Transcriptome alignment with TopHat
Further read analyses by custom scripts in Rstudio
More detailed information on additonal software in the methods section of the accompanying article.
Genome_build: sacCer3
Supplementary_files_format_and_content: mRNACo quantification in .tabular format (columns 1-13:tracking_id:1; class_code:2; nearest_ref_id:3; gene_id:4; gene_short_name:5; tss_id:6; locus:7; length:8; coverage:9; FPKM:10; FPKM_conf_lo:11; FPKM_conf_hi:12; FPKM_status:13); all other data files in .txt format (columns 1-7: chr:7; position:2; strand:3; sequence:4; gene:5; gene feature:6; normalized counts)

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were grown to an OD600 of ~  0.4 in YPD medium and subjected to temperature shifts as indicated

extract_protocol:
Cells were rapidly sedimented and snap-frozen on dry ice. Whole cell extracts were generated by breaking the cells with glass beads.
Detailed information available in the Methods section of the article.

treatment_protocol: Cells were treated  with cycloheximide (56 ug / ml) prior to harvesting

tag: strain (genetic background)

value: thermo-sensitive ded1-95

tag: temperature

value: 37 dgC for 5 min

tag: molecule type

value: mRNA


title: Non-hepatocyte_Input

status: Public on Jan 24 2017

type: SRA

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

country: USA

institute: Beth Israel Deconess Medical Center

library_source: genomic

data_processing:
ChIP-seq data were aligned using Bowtie2 to the mm9 mouse genome
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. Low signal peaks (log2 CPM<2) were removed, and differential peaks were defined at log2 FC≥1 and log2 FDR≤0.25.
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual.
Extracted DNA (1-10ng, or all if less) was used to generate sequencing libraries by following the “on-bead” sequencing library preparation method. Briefly, DNA was processed through end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment (NEB M0212) and index adaptor ligation using the Quick Ligase (NEB M2200). AMPure XP beads were left in all the reactions to clean up the DNA using PEG(Polyethylene Glycol 8000)/NaCl solution. After ligation, DNA was eluted from AMPure XP beads and then PCR-amplified using the PfuUltra II Hotstart PCR Master Mix (Agilent 600850). Gel electrophoresis/extraction was performed using the E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction (Qiagen) to select library fragments between 250 and 600bp. Quantity and quality of the libraries were analyzed by Qubit and Agilent Bioanalyzer, respectively, and the libraries were pooled at a final concentration of 12pM and sequenced by HiSeq2500 or NextSeq 500 systems.

tag: strain

tag: tissue

value: Liver


title: B_HS_LPS_2

city: Ames

first: Angelica

middle: G

last: Van Goor

state: Iowa

address: 1221 Kildee Hall

institute: USDA-NIFA

library_source: transcriptomic

data_processing:
Clipped barcode adapter sequences -FASTX Clipper, Version 0.0.13. Discard sequences shorter than: 30 bp, minimum quality score: 30, and minimum percent of bases that must have this quality: 80.
Mapped reads to GalGal 4.0  -TopHat, Version 2.0.9.  Bowtie version: 2.1.0. Quality scale: phredd, Anchor length: 8, Maximum number of mismatches: 0, Minimum intron length: 70, Maximum intron length: 5000, Minimum isoform fraction: 0.15, Maximum number of alignments: 20, Minimum intron length that may be found during split-segment: 50, Maximum intron length that may be found during split-segment: 500000, Number of mismatches allowed in each segment: 2, Minimum length of read segments: 20, Bowtie 2 speed and sensitivity: sensitive (slower)
Count reads to chicken genome -HTSeq, Version 0.6.1. Use acceptedhits.bam from tophat2 output, Minimum mapping quality 0 because of only high quality data phred 30 going in, Bed file for overlap is output from tophat junctions.bed, GFF file was downloaded from NCBI Gallus_gallus.Galgal4.78.gtf, Mode: intersection-nonempty for stringency, Strandspecificity: none because sequencing wasn’t strand specific, Minimum quality: default 0, Feature type: exon, Feature attribute: gene_id, Feature counts output file: name of samplefeaturecounts.txt

molecule: polyA RNA

organism: Gallus gallus

source_name: Chicken splenic tissue

growth_protocol: Chickens were raised with ad libitim access to feed and water that met all NRC requirements.

extract_protocol:
The total RNA was isolated from 4 chicken spleens per treatment group (32 birds total) with the RNAqueous kit (Ambion) using all manufacturers recommendations as previously described (Cheeseman et al. 2007), and treated with DNA-free kit (Ambion).
Only samples with an RNA Integrity Number (RIN) greater than 9 were used for cDNA library construction using the TruSeq RNA Library preparation kit v2 (Illumina) that preferentially amplifies PolyA mRNA. The cDNA libraries created from the spleen of 32 chickens were run on the HiSeq 2500 machine (Illumina) with the option of 100 bp single end reads at the Iowa State University DNA Facility. Four lanes were used for RNA-sequencing with 8 multiplexed samples per lane (one sample per each treatment).
Individually barcoded samples with 8 different bar codes per lane for multiplexing.

treatment_protocol: Chickens were treated with a themal stimulation (heat stress or thermoneutral) and/or an inflammatory stimulus (LPS or PBS).

tag: chicken breed

value: Broiler

tag: thermal treatment

value: Heat stress

tag: inflammatory stimulus treatment

value: LPS


title: B_TN_LPS_2

value: Thermoneutral


title: WAT Adipocyte H3K4me1 rep1

source_name: inguinal WAT

value: adipose

tag: chip antibody


title: Hepatocyte_H3K27ac

value: H3K27ac (Active Motif, 39133)


title: mRNACo_ded1-95_30dgC_replicate3

description: replicate 3

molecule: total RNA

growth_protocol: Cells were grown to an OD600 of ~  0.4 in YPD medium

value: 30 dgC


title: Hepatocyte_Input


title: BAT_adipocyte_PPARg_rep4

description: 10min fixation, 8min-shearing, 1M nuclei

source_name: BAT

value: PPARG (Santa Cruz, sc-7196X)


title: mRNACo_WT_37dgC_replicate3

description: replicate 3

value: wild-type DED1


title: Hepatocyte_H3K4me3


title: BAT_adipocyte_H3K4me1_rep2


title: BAT_adipocyte_PPARg_rep1

description: 4min fixation, 4min-shearing, 1M nuclei


title: BAT_adipocyte_PPARg_rep2

description: 10min fixation, 4min-shearing, 500K nuclei


title: mRNACo_WT_30dgC_replicate3

description: replicate 3


title: BAT_adipocyte_PPARg_rep3

description: 10min fixation, 4min-shearing, 1M nuclei


title: WAT_adipocyte_H3K27ac

source_name: Pool of epididymal and inguinal WAT


title: mRNACo_ded1-95_30dgC_replicate2

description: replicate 2


title: BAT_adipocyte_H3K4me1_rep1


title: BAT_adipocyte_H3K27ac_400K


title: BAT_adipocyte_H3K27ac_200K


title: mRNACo_WT_37dgC_replicate2

description: replicate 2


title: BAT_adipocyte_H3K27ac_10K


title: BAT_adipocyte_H3K27ac_20K


title: Whole_WAT_Input

source_name: epididymal WAT


title: BAT_adipocyte_H3K27ac_100K


title: mRNACo_ded1-95_37dgC_replicate1

description: replicate 1


title: WAT_non-adipocyte_H3K27ac


title: BAT_Non-adipocyte_Input


title: WAT_adipocyte_Input


title: BAT_non-adipocyte_H3K27ac


title: mRNACo_ded1-95_30dgC_replicate1

description: replicate 1


title: BAT _adipocyte_Input


title: mRNACo_WT_37dgC_replicate1

description: replicate 1


title: mRNACo_ded1-95_37dgC_replicate2

description: replicate 2


title: BAT_adipocyte_H3K27ac_50K


title: BAT_adipocyte_H3K27ac


title: TRAP-rep3

data_processing:
RNA-seq data were aligned using TopHat2 (Trapnell et al., 2009) to the mm9 mouse genome.
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were assigned to transcripts, normalized and quantified using featureCounts (Liao et al., 2014) and EdgeR (Robinson et al., 2010).
Low expressed genes (log2 CPM <1) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥0.5 and log2 false discovery rate (FDR)≤0.25
Gene set enrichment analysis was performed using RDAVIDWebService (Fresno and Fernandez, 2013) and GOstats (Falcon and Gentleman, 2007).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for each sample

extract_protocol:
TRAP was performed as previously described (Long et al., Cell Metab 2014) with modifications. Adipose tissues were homogenized and processed to immunoprecipitation using anti-GFP antibody. Immunoprecipitates were washed and subjected to RNA extraction using Qiagen Micro RNeasy kit according to the manufacturer’s instructions. For input RNA, 5% of homogenates were mixed with TRIzol and processed according to the manufacturer’s instructions to extract total RNA. Isolated RNA was quantified by Qubit, and RNA integrity was analyzed by Agilent Bioanalyzer.
Extracted RNA (100ng) was processed for ribosomal RNA removal using the Epicentre rRNA depletion kit according to the manufacturer’s instructions. Ribosomal RNA-depleted RNA was subsequently used to generate paired-end sequencing libraries using the Illumina RNA TruSeq Library Kit according to the manufacturer’s instructions. Quantity and quality of RNA-Seq libraries were analyzed by Qubit and Agilent Bioanalyzer, respectively, and the libraries were pooled at a final concentration of 12pM and sequenced by HiSeq2500


title: TRAP-rep1


title: iCLIP_Ded1p_HTBH

description: replicate 2

growth_protocol: Cells were grown to an OD600 of ~  1.0 in YPD medium

treatment_protocol: Cells were irradiated with UV light prior to harvesting

value: WT-DED1 with c-terminal HTBH-Tag

value: Ded1p-protected RNA


title: TRAP-rep2


title: Input-rep2


title: iCLIP_Ded1p_His6Flag3

description: replicate 1

value: WT-DED1 c-terminus tagged with His/3xFlag


title: Input-rep1


title: WAT_non-adipocyte_Input


title: Brassica_oleracea_Y2

city: Wuhan

first: Chen

last: Daozong

state: Hubei

address: Shizishan Street · Hongshan District

country: China

institute: Huazhong agricultural university

data_processing:
Basecalls performed using Illumina Casava1.7 software.
Raw data was saved as fastq files, and the high-quality clean reads were obtained after filtering the dirty reads with adaptors or two N and low quality reads.
Clean reads of each sample were mapped to the genome of Brassica rapa using Tophat, allowing no more than two mismatched bases.
Mapped reads were normalized using the DESeq Bioconductor package.
Gene expression levels were calculated as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) using Cufflinks and Cuffdiff.
Genome_build: Arabidopsis genome
Supplementary_files_format_and_content: Microsoft Excel files include the expression of gene(FPKM) in each sample, the length of each gene, gene symbol, the description of gene and so on.

organism: Brassica oleracea

source_name: Petals

growth_protocol: Plants were grown in the greenhouse

extract_protocol:
The petals on half-open flowers were collected in liquid nitrogen from the four samples, respectively, and kept at -80°C. Total RNA was extracted by guanidine isothiocyanate method and then treated with RQ1 DNase (Promega) to remove DNA.
Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80°C until used for sequencing.

value: Petals

tag: developmental stage

value: half-open flowers

tag: phenotype

value: yellow flower


title: mRNACo_WT_30dgC_replicate2

description: replicate 2

value: mRNA


title: pgrmc2_3-709

city: La Jolla

first: Inigo

last: Narvaiza

state: CA

address: 10010 N Torrey Pines Rd

department: Laboratory of Genetics

institute: Salk Institute

description: mRNA

data_processing:
Libraries were sequenced using single-end 50 bp reads at a depth of 10-15 million reads per library, (50 bp fragments)
Single-end sequencing reads were mapped to the mouse reference genome (mm9, NCBI37) using STAR (version 2.2.0.c, default parameters) (Dobin et al. 2013).  Only reads that aligned uniquely to a single genomic location were used for downstream analysis (MAPQ > 10)
Gene expression values were calculated for read counts on exons of annotated RefSeq genes using HOMER. Differentially expressed genes were calculated from three replicates per condition using EdgeR and a threshold of padj < 0.05 was used to call differentially expressed genes.
Genome_build: mm9, NCBI37
Supplementary_files_format_and_content: read_count.txt.gz - tab-delimited text file showing read counts normalized to 10e7 mapped reads from all experiments and gene annotation information for RefSeq protein-coding genes (mm9 assembly)

source_name: 3T3-L1 cells

growth_protocol: CELLS were GROWN IN DMEM SUPPLEMENTED WITH 10%BCS

extract_protocol:
Cells were lysed in Trizol and RNA was extracted using the Direct-Zol RNA extraction kit (Zymo Research)
PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit and analyzed on an Illumina HiSeq 2500 sequencer.  (Single-end 50 bp)

treatment_protocol: Cells were plated into 6-well plates at 150000 cells/ well. 2 days after cell reached confluency, cells  were induced to differentiate with DMEM 1-% FBS, insulin 1ug/mL, dexamethasone 0.4 ug/mL ind IBMX 0.5 mM

tag: passage

tag: cell line

tag: protocol


title: pgrmc2_1-707

description: mRNA


title: gfp_3-703

description: mRNA

value: Gfp


title: pgrmc2_2-708

description: mRNA


title: mono_ded1-95_37dgC_replicate2

description:
replicate 2
Total_MPnorm_TS5_normCounts.txt

value: thermo-sensitive ded1-95

value: 37 dgC for 5 min

value: Monosome-protected RNA


title: mono_ded1-95_30dgC_replicate2

description:
replicate 2
Total_MPnorm_TS0_normCounts.txt


title: Brassica_oleracea_Y1


title: gfp_2-702

description: mRNA


title: gfp_1-701

description: mRNA


title: mono_WT_37dgC_replicate2

description:
replicate 2
Total_MPnorm_WT5_normCounts.txt


title: mono_ded1-95_37dgC_replicate1

description:
replicate 1
Total_MPnorm_TS5_normCounts.txt


title: mRNACo_WT_30dgC_replicate1

description: replicate 1


title: E12.5_Heart_ATAC_rep1

first: Fei

last: Gu

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

description: ATAC-seq DNA

data_processing:
Library strategy: ATAC-seq
Basecalls performed using CASAVA version 1.8.2
ATAC-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.5.9, peaks were called using MACS 2
genome build: mm9
processed data files format and content: bigwig

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Boston Children’s Hospital.

extract_protocol:
Isolated cardiomyocytes from mouse E12.5 ventricles were immediately centrifuged at 500 x g, 4 degrees, 10 minutes with nonionic detergent. Nuclei pellets were resuspend in a Tn5 transposase reaction mix (Nextera) and incubated at 37 degrees for 30 minutes. Tn5-cleaved euchromatin was purified using a Qiagen MinElute PCR Purification kit.
Amplification of transposed DNA fragments was performed using Illumina adapters and NEBNext High-Fidelity 2x PCR Master Mix (NEB). Appropriate cycle number was determined after five initial PCR cycles via qRT-PCR using SYBER Green I (Life Technologies). Libraries were purified using a Qiagen MinElute PCR Purification kit.

treatment_protocol: Mouse tissues for ChIP were minced by homogenizer in PBS containing 1% formaldehyde, then incubated on a rotator for 15 min at room temperature before adding Glycine to quench the crosslinking reagents.

tag: sample type

value: Primary tissue

tag: background strain

value: mixed background of C57BL/6 and 129S1

value: Heart

tag: age


title: Adult_Lung_VecadCre_p300_rep3

description:
Flagbio_DNA
input: Adult_Lung_p300_input

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.5.9, peaks were called using MACS 2
genome build: mm9
processed data files format and content: bigwig

source_name: Endothelial in Lung

extract_protocol:
Nuclei were isolated by homogenization in hypotonic buffer and then resuspended in ChIP buffer for sonication. Sonication conditions were titrated to achieve sufficient fragmentation (mean fragment size 500 bp) while avoiding degradation of p300 protein.
ChIP-seq libraries were prepared with KAPA Hyper Prep Kit (Kapa Biosystems)

value: Endothelial in Lung

value: Adult (8 weeks)


title: Adult_Lung_VecadCre_p300_rep2


title: mono_ded1-95_30dgC_replicate1

description:
replicate 1
Total_MPnorm_TS0_normCounts.txt

tag: strain (genetic background)

value: 30 dgC


title: E10.5_T2_input

description: mRNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the gencode M1 (mm9) genome assembly using tophat version 2.0.7, reads were count using htseq-count version 0.5.3
genome build: mm9
processed data files format and content: text file with FPKM values

source_name: Endothelial in Embryo

extract_protocol:
RNA extraction protocol not provided.
RNA-seq libraries were prepared with ScriptSeq v2 RNA-seq library kit.

value: Endothelial in Embryo


title: mono_WT_37dgC_replicate1

description:
replicate 1
Total_MPnorm_WT5_normCounts.txt

value: wild-type DED1

tag: temperature


title: Adult_Lung_VecadCre_p300_rep1


title: Adult_Lung_EIIaCre_p300_rep2

source_name: Lung

value: Lung


title: Adult_Heart_VecadCre_p300_rep3

description:
Flagbio_DNA
input: Adult_Heart_p300_input

source_name: Endothelial in Heart

value: Endothelial in Heart


title: mono_WT_30dgC_replicate1

description:
replicate 1
Total_MPnorm_WT0_normCounts.txt

tag: molecule type


title: Adult_Lung_p300_input

description: Total DNA


title: RPrunoff_ded1-95_37dgC_replicate1

description: replicate 1

value: Ribosome-protected RNA


title: Adult_Heart_VecadCre_p300_rep1


title: Adult_Heart_EIIaCre_p300_rep2


title: RPrunoff_ded1-95_30dgC_replicate1

description: replicate 1


title: RPrunoff_WT_37dgC_replicate1

description: replicate 1


title: Adult_Heart_VecadCre_p300_rep2


title: Adult_Heart_EIIaCre_p300_rep1


title: Adult_Heart_p300_input

description: Total DNA


title: mono_WT_30dgC_replicate2

description:
replicate 2
Total_MPnorm_WT0_normCounts.txt


title: E10.5_T2_Trap


title: RPrunoff_WT_30dgC_replicate1

description: replicate 1


title: F3P12

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC
The reads for each sample for both CNV and DMR analyses were mapped to the zebrafish (Danio rerio) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-7 were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The DMR that included at least two windows with an edgeR P value < 1e-7 were then selected for further analysis and annotated.
Genome_build: GRCz10
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Danio rerio

source_name: Sperm

growth_protocol: Adult EK strain zebrafish were housed at a maximum density of 10 fish/L in a flow-through dechlorinated water system maintained at 26-29 °C on a 14:10 hour light: dark photoperiod. Eggs were collected ≤ 1 hour post fertilization and placed into metal-free, plastic culture dishes in E2 medium. Following 24 hours of MeHg-exposure, the embryos were rinsed three times with E2 medium and transferred to 2-L tanks (60 embryos per tank) containing static E2 medium for rearing. Starting at 5 days post fertilization (dpf), larvae were fed 5-100 micron Golden Pearl Reef & Larval Fish Diet.  Platinum Grade Artemia nauplii were fed to the larvae starting at 9 dpf. At 21 dpf, the fish were transferred to 1-L flow-through tanks and reared using standard husbandry techniques until 4 months of age. At this point, the zebrafish were ready for subsequent breeding and behavioral assays. Juvenile and adult fish were fed a combination of Platinum and Gold grade Artemia nauplii and Aquarian™ flake food.

extract_protocol:
One hundred μl of sperm suspension was used then 820 μl DNA extraction buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) and 80 μl 0.1 M Dithiothreitol (DTT) added and the sample incubated at 65 oC for 15 minutes. Proteinase K (80 μl, 20 mg/ml) was added and the sample incubated on a rotator at 55 oC for 2 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A, Madison, WI) was added, the sample mixed and incubated on ice for 15 minutes, then spun at 4 oC at 13,000 rpm for 20 minutes. The supernatant was transferred to a fresh tube, then precipitated over night with the same volume 100% isopropanol and 2 μl glycoblue at -20 oC. The sample was then centrifuged and the pellet washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop. Zebrafish sperm DNA pools were generated using 2 μg of genomic DNA from each individual for 3 pools each of control and MeHg exposed animals. Each pool contained 2 individuals for a total of n=6 per exposure group. The resulting 6 μg of genomic DNA per pool was diluted to 150 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with a probe sonicator using 5 x 20 pulses at 20% amplitude. Fragment size (200-800 bp) was verified on a 1.5% agarose gel. Sonicated DNA was diluted to 400 μl with 1xTE and heated to 95 oC for 10 minutes, then incubated in ice water for 10 minutes. Then 100 μl of 5 x immunoprecipitation (IP) buffer (50 mM Sodium Phosphate pH 7, 700 mM NaCl, 0.25% Triton X-100) and 5 μg of 5-mC monoclonal antibody (Diagenode, Denville, NJ, C15200006-500) were added and the sample incubated on a rotator at 4 oC overnight. The next day Protein A/G Agarose Beads from Santa Cruz were prewashed with 1xPBS/0.1% BSA and resuspended in 1 x IP buffer. Eighty μl of the bead slurry were added to each sample and incubated at 4 oC for 2 hours on a rotator. The bead-DNA-antibody complex was washed 3 times with 1 x IP buffer by centrifuging at 6,000 rpm for 2 minutes and resuspending in 1 x IP buffer. After the last wash the bead-complex was resuspended in 250 μl of digestion buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) with 3.5 μl Proteinase K (20mg/ml) per sample and incubated on a rotator at 55 oC for 2 hours. After incubation, DNA was extracted with the same volume of Phenol-Chloroform-Isoamyalcohol and then with the same volume chloroform. To the supernatant from chloroform extraction 2 μl glycoblue, 20 μl 5M Sodium Chloride and 500 μl 100% cold ethanol were added.   DNA was precipitated at -20 oC overnight, then spun for 20 minutes at 13,000 rpm at 4 oC, washed with 75% ethanol and air-dried. Dry pellet was resuspended in 20 μl H2O and concentration measured in Qubit using the Qubit ssDNA Assay Kit
The MeDIP pools were used to create libraries for next generation sequencing (NGS) at the University of Reno, NV, Genomics Core Laboratory using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. NGS was performed at that same laboratory using the Illumina HiSeq 2500 with a PE50 application, with a read size of approximately 50 bp and approximately 100 million reads per pool.

treatment_protocol: The newly fertilized eggs were then transferred to 12-well (non-treated) culture plates (10 eggs/well) and rinsed twice with E2 medium. The fertilized eggs (n= 10) were exposed to 1.5 ml of E2 medium containing MeHg (0, 1, 3, 10, 30, and 100 nM nominal concentration as methylmercury chloride—CH3ClHg, with ethanol as the vehicle [< 0.01% total volume]).

tag: treatment

value: MeHg-exposed

tag: generation


title: E13.5_Myf5Cre_p300_rep2

description:
Flagbio_DNA
input: E11.5_p300_input

source_name: Skeletal Muscle in Embryo

tag: tissue

value: Skeletal Muscle in Embryo


title: E12.5_Heart_ATAC_rep2

description: ATAC-seq DNA


title: F3P11


title: ribo_ded1-95_37dgC_replicate2

description: replicate 2


title: E13.5_Myf5Cre_p300_rep1

description:
Flagbio_DNA
input: E11.5_p300_input


title: E11.5_Tie2Cre_p300_rep3

description:
Flagbio_DNA
input: E11.5_p300_input


title: F3P10


title: E11.5_Tie2Cre_p300_rep2

description:
Flagbio_DNA
input: E11.5_p300_input


title: ribo_ded1-95_30dgC_replicate2

description: replicate 2


title: Adult_Lung_EIIaCre_p300_rep1


title: E11.5_Tie2Cre_p300_rep1

description:
Flagbio_DNA
input: E11.5_p300_input


title: E11.5_EIIaCre_p300_rep3

description:
Flagbio_DNA
input: E11.5_p300_input

source_name: Whole Embryo

value: Whole Embryo


title: ribo_WT_37dgC_replicate2

description: replicate 2

source_name: Whole cells


title: E13.5_Myf5Cre_p300_rep3

description:
Flagbio_DNA
input: E11.5_p300_input


title: ribo_WT_30dgC_replicate2

description: replicate 2


title: E11.5_EIIaCre_p300_rep2

description:
Flagbio_DNA
input: E11.5_p300_input


title: ES_p300_rep2

description:
Flagbio_DNA
input: ES_P300_input_2

source_name: ES cell

value: ES cell


title: ribo_ded1-95_37dgC_replicate1

description: replicate 1

value: thermo-sensitive ded1-95

value: 37 dgC for 5 min


title: ribo_ded1-95_30dgC_replicate1

description: replicate 1


title: F3P7

value: control


title: F1P6


title: ES_P300_input_rep1

description: Total DNA


title: ES_p300_rep1

description:
Flagbio_DNA
input: ES_P300_input_1


title: E11.5_p300_input

description: Total DNA

value: Primary tissue

value: mixed background of C57BL/6 and 129S1


title: ribo_WT_30dgC_replicate1

description: replicate 1


title: ribo_WT_37dgC_replicate1

description: replicate 1


title: F1P3


title: F3P9


title: F1P2


title: F3P8


title: e7_KO969

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

data_processing:
Illumina Casava software used for basecalling.
The sequencing raw reads were mapped onto the mouse genome reference mm10 using GSNAP (version 2013-11-27). Uniquely and properly mapped read pairs were used for further analysis..
Expression levels of genes, the FPKM (fragments per kilobase of exon per million mapped reads) measure was calculated by cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: shank2 exon 7 deletion mutant

extract_protocol:
Total RNA from hippocampi was extracted using TRIZOL.
Poly(A) mRNA (5 μg) was isolated and fragmented using Illumina Truseq RNA Sample Prep Kit with poly-T oligo-attached magnetic beads. The adaptor-ligated library was size-selected by band excision after agarose gel electrophoresis and purified using QIAquick gel extraction kit (Qiagen).

treatment_protocol: Eight to fifteen weeks old male Shank2 knock-out (KO) and wild type (WT) littermates were used for behavioral experiments. Mice were kept on a 12 h light/dark cycle, and the behavioral experiment was performed during light phase of the cycle. Food and water were provided ad libitum. The Animal Care and Use Committee of Seoul National University approved the animal protocols.

tag: strain

value: mixed C57BL/6J and C57BLl/6N

tag: genotype/variation

value: Shank2 KO (exon 7 deletion mutant)

value: hippocampi


title: e6-7_KO864

source_name: shank2 exon 6,7 deletion mutant

value: Shank2 KO (exon 6,7 deletion mutant)


title: e7_KO990


title: e7_WT999

source_name: shank2 exon 7 deletion control wild-type

value: wild-type (exon 7 deletion control)


title: E11.5_EIIaCre_p300_rep1

description:
Flagbio_DNA
input: E11.5_p300_input


title: e6-7_KO777


title: F1P1


title: e6-7_WT865

source_name: shank2 exon 6,7 deletion control wild-type

value: wild-type (exon 6,7 deletion control)


title: ES_P300_input_rep2

description: Total DNA


title: GBM062811_Input

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

data_processing:
Image scanning and basecalls were performed using BioScope (v. 1.2.1)
ChIP-seq reads were aligned to hg19 geneome assembly using BioScope (v. 1.2.1)
Mapped reads were filtered to remove low quality, ambiguous and redundant reads
Peaks were called using the MACS (v. 1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contains SOX2 peak coordinates in BED format

organism: Homo sapiens

source_name: HOT1 (orthotopic tumor)

growth_protocol: Tumor sample was obtained from patient at the University of Texas Southwestern Medical Center at the time of craniotomy and tumor resection after written informed consent under an Institutional Review Board approved clinical protocol. The tumor tissue was dissociated with papain, and a suspension of 5x10^4 cells was stereotactically injected into the right caudate of 6-week-old NOD-SCID mice. Tumor growth was monitored using MRI  and by following the neurological status of the animals.

extract_protocol:
A NOD-SCID mouse harboring HOT1 tumor derived from a human glioblastoma patient sample was euthanized. Three slices of tumor sample (~1 mm thick, ~100 mg total) were obtained from the dissected brain within three minutes after sacrificing the mouse, and were immediately placed in 1 ml of pre-warmed DMEM (37C) containing 1% formaldehyde, and homogenized with a POLYTRON for 30 seconds. After 10 minutes of incubation at room temperature 111 µl 1.25 M glycine was added, and after 5 minutes of incubation at room temperature the cells were pelleted by centrifugation at 700g. The cell pellet was washed twice with 1 ml of ice-cold PBS. The cell pellet was then lysed in 1 ml ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors, Roche) and sonicated at 4C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 15 minutes). The sheared chromatin with an average fragment length of ~500 bp was centrifuged at 10,000 g for 10 minutes at 4C. 100 μl of the supernatant was used for ChIP or as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4C overnight with 6 μg/ml of SOX2 antibody (Cell Signaling Technology, rabbit monoclonal antibody). Immunoprecipitation was carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65C in 192 mM NaCl for 16 hours. DNA fragments were purified using QiaQuick PCR Purification kit (Qiagen) and eluted twice with 30 μl EB buffer according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.
Libraries were prepared according to SOLiD 5500 instructions accompanying the ChIP-seq kit with barcoding beta protocol. AMPure® XP beads were used in this protocol. Briefly, DNA was end-repaired using a combination of 5X reaction buffer, dNTP mix (10mM), end polishing enzyme 1 and 2, and nuclease free water included in the kit. Binding and washing of end-paired DNA was performed using AMPure® XP beads and 70% ethanol respectively. Then, the end-paired DNA was eluted with elution buffer included in the kit. Then,  the 5500 barcoded adaptors were liagted to the DNA and purified using 70% ethanol. Purified adaptor ligated DNA was PCR amplified for 10-15cycles. Amplified DNA was purified and ~1μL of purified amplified product was run on a 2% E-Gel® EX Gel to confirm the removal of any primer dimers.This product was quantified using qPCR. Following qPCR quantitation, the SOLiD™ ChIP-Seq fragment library was subjected to templated bead preparation.

tag: host strain

value: NOD-SCID mouse


title: F1P5


title: GBM062811_SOX2_ChIP

institute: University of Texas Southwestern Medical Center

value: HOT1 tumor derived from a human glioblastoma patient sample

tag: chip antibody

value: Monoclonal (rabbit) against SOX2

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody cat. #

tag: chip antibody lot #


title: HP1g_ChIPSeq_siHP1γ

city: Beijing

first: Pinchao

last: Mei

address: Dongdansantiao 5hao

department: Dept. Biochem & Mol Biol

institute: Peking Union Medical College & Chinese Academy of Medical Science

data_processing:
Basecalls performed using FastQC v0.11.2
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 version 2.3.3 with the follow setting: -p 8
Data were filtered using trim galore version 0.3.7, and the following specifications:-q 25 --stringency 5 --length 50
peaks were called using MACS version 1.4.2 with the following setting: -g mm -m 10, 30 -p  10e-5 --nomodel --shiftsize 200 -w
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using wigToBigWig with default setting.

source_name: mouse stem cells E14

growth_protocol: Embryonic stem cell lines were cultured in KnockoutTM DMEM (Life Technology) supplemented with 15% FBS (Clonetech), 1% Non-essential amino acids, 1% L-Glutamine, 10-4 M β-Mercaptoethanol and 103 U/ml LIF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according toThruPLEX® DNA-seq Kit Instruction Manual (CAT. NO. R400406). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Transfection of ES cells was performed by electroporation with NeonTM transfection system (Invitrogen). Basically, 5×106 trypsinized cells were washed once with PBS, and resuspended in 90 μl Buffer R. The single cell suspension was then gently mixed with siRNA (20 μM) and subjected to electroporation (1400 V/10 ms/3 pulse). Cells were subsequently seeded in a 10 cm dish, and cultured for additional 48h before harvesting for further experiments.

tag: Sex

value: male

tag: cell type

value: embryonic stem cell line derived from mouse inner-cell masses

tag: stain

value: HP1gamma (Millipore, MAB3450, lot 2021184)

tag: trasfection

value: tranfected with siHP1g for 48h


title: e7_WT993


title: e7_KO994


title: input DNA_siGFP

value: tranfected with siGFP for 48h


title: e7_WT628


title: 13.5 dpc wt pancreas 1

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

country: Germany

institute: TU Dresden

data_processing:
basecalling: bcl2fastq 1.8.4
alignment: alignment of single-end data against mm10 with gsnap version 2014-12-17; splice sites were supported by using Ensembl version 69 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-69.ss.mm10.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.4.6 (-a EnsemblGene-69.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 69 gtf file
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.mm10.e69.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 2 Conditions and their 3 replicates

source_name: embryonic pancreas

extract_protocol:
Total RNA was prepared using  the Rneasy Kit and on column genomic digestion (Qiagen)
Total RNA with an integrity number of ≥ 8 was used. mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB)

value: pancreas

tag: dpc

value: wild type


title: H3K27me3_ChIPSeq_siHP1γ


title: 13.5 dpc wt pancreas 3


title: e6-7_WT778

value: mixed C57BL/6J and C57BLl/6N


title: E12.5_Heart_H3K27ac_rep2

description:
ChIP_DNA
input: E12.5_Heart_input

source_name: Heart

tag: sample type

value: Primary tissue

tag: background strain

value: mixed background of C57BL/6 and 129S1

value: Heart

tag: age

tag: antibody

value: anti-H3K27Ac (Active Motif, catalog number 39133)


title: E12.5_Heart_H3K27ac_rep1

description:
ChIP_DNA
input: E12.5_Heart_input

tag: tissue


title: Orychophragmus_violaceus_W2

organism: Orychophragmus violaceus

source_name: Petals

value: Petals

tag: developmental stage

value: half-open flowers

tag: phenotype

value: white-violet flower


title: E12.5_Heart_p300_rep2

description:
Flagbio_DNA
input: E12.5_Heart_input


title: HP1g_ChIPSeq_siGFP


title: E12.5_Heart_p300_rep1

description:
Flagbio_DNA
input: E12.5_Heart_input


title: 15.5 dpc wt pancreas 2

tag: strain

tag: genotype/variation


title: 15.5 dpc wt pancreas 1


title: F1P4

tag: treatment

value: MeHg-exposed

tag: generation


title: Orychophragmus_violaceus_W1


title: 14.5 + 2 + JTE + CTGF 3

data_processing:
basecalling: bcl2fastq 1.8.4
alignment: alignment of single-end data against mm10 with gsnap version 2014-12-17; splice sites were supported by using Ensembl version 67 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-69.ss.mm10.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.4.6 (-a EnsemblGene-69.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 69 gtf file
gene expression: DESeq2 version 1.6.2 and the count file from featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.mm10.e69.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 5 Conditions and their 3 replicates
Supplementary_files_format_and_content: tab delimited spreadsheet (deseq.comparisons.xls) containing 4 comparisons which were done with DESeq2; columns 1-7 are standard output from DESeq2; columns 8-13 normalised counts for the samples; columns 14-15 normalised mean counts for the two conditions, columns 16-22 gene information from Ensembl (gene name, chromosome, start, end, strand, biotype, description)

tag: condition

value: 15 uM of JTE013 and 50 ng/ml CTGF


title: E12.5_Heart_input

description: Total DNA


title: e6-7_WT809

value: wild-type (exon 6,7 deletion control)

value: hippocampi


title: 14.5 + 2 + JTE + CTGF 2


title: Orychophragmus_violaceus_P2

value: violet flower


title: 14.5 + 2 + JTE + CTGF 1


title: Orychophragmus_violaceus_P1


title: 15.5 dpc wt pancreas 3


title: E12.5_FB_H3K27ac_rep2

description:
ChIP_DNA
input: E12.5_FB_input

source_name: Fore Brain

value: Fore Brain


title: Aubrieta_cultorum_PI2

organism: Aubrieta x cultorum

value: pink flower


title: E12.5_FB_H3K27ac_rep1

description:
ChIP_DNA
input: E12.5_FB_input


title: 14.5 + 2 + JTE 2

value: 15 uM of JTE013


title: Matthiola_incana_W2

organism: Matthiola incana

value: white flower


title: E12.5_FB_p300_rep2

description:
Flagbio_DNA
input: E12.5_FB_input


title: Aubrieta_cultorum_PI1


title: 14.5 + 2 control 3

value: standard condition


title: E12.5_FB_p300_rep1

description:
Flagbio_DNA
input: E12.5_FB_input

value: Primary tissue


title: Matthiola_incana_RB2


title: E12.5_FB_input

description: Total DNA

value: mixed background of C57BL/6 and 129S1


title: Matthiola_incana_W1


title: 14.5 + 2 control 2


title: 14.5 S1pr2 null 3

value: S1pr2 null


title: Carcinoma

city: Saint-Petersburg

first: Ekaterina

last: Matyunina

address: Pudogsakya str 7

country: Russia

institute: The Biomedical Center

description:
anchor: NlaIII
tag count: 21,749,743
tag length: 27

data_processing:
The SOLiD-generated RNA-Seq reads was in 27 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences.
The reads were mapped to the zebrafish NCBI RefSeq (Reference Sequence) mRNA database with a criterion of maximum 2 nucleotide mismatches.
The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript.
Genome_build: danRer7
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Hepatocellular carcinoma of  transgenic fishes

extract_protocol:
mRNA was purified using Dynabeads Oligo(dT) EcoP (Invitrogen)
Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA-SAGE (serial analysis of gene expression) sequencing was performed on ABI SOLiD platform by Mission Biotech (Taiwan) according to manufacturer’s protocol and 10–23 million reads were generated from each sample

treatment_protocol: One-month-old transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone-free water.

value: Hepatocellular carcinoma

tag: genotype

value: Tg(fabp10:LexPR-LexA:EGFP; cryB:mCherry-NLS-Cre; fabp10:loxP-mCherry-loxP-EGFP-krasV12) line


title: NormM

description:
anchor: NlaIII
tag count: 25,263,861
tag length: 27

source_name: Normal liver of transgenic fishes under mifepristone

value: Normal liver


title: CarcinomaM

description:
anchor: NlaIII
tag count: 23,397,434
tag length: 27

source_name: Hepatocellular carcinoma of transgenic fishes after mifepristone withdrawal


title: Norm

description:
anchor: NlaIII
tag count: 25884343
tag length: 27

source_name: Normal liver of transgenic fishes


title: 14.5 S1pr2 null 1


title: Matthiola_incana_LP2

value: Petals

value: half-open flowers

value: modena flower


title: Matthiola_incana_RB1


title: Matthiola_incana_LP1


title: 13.5 dpc wt pancreas 2

value: pancreas

value: wild type


title: 14.5 S1pr2 null 2


title: Matthiola_incana_DP2

value: lavender flower


title: 14.5 wt 3

value: wildtype


title: Matthiola_incana_DP1


title: H3K27me3_ChIPSeq_siGFP

tag: Sex

value: male

tag: cell type

value: embryonic stem cell line derived from mouse inner-cell masses

tag: chip antibody

value: tranfected with siGFP for 48h


title: 14.5 + 2 control 1

value: standard condition


title: 14.5 wt 2


title: Iberis_amara_PI1

organism: Iberis amara

value: violet flower


title: 14.5 wt 1


title: Malcolmia_maritima_P2

organism: Malcolmia maritima

value: white-violet flower


title: Iberis_amara_PI2


title: Iberis_amara_P2

value: pink flower


title: Malcolmia_maritima_P1


title: Malcolmia_maritima_LP2


title: Homo sapiens Donor 2 Th1 Input

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
Basecalls performed using CASAVA
Polony  identification, base  calling  and  QC  statistics were performed using GOAT and Bustard module
Reads (in fastq files) were filtered to remove adapters using fastq-mcf and for quality using seqkt and aligned to the human (hg19) with Bowtie2 (default settings). Bigwig files for visualization in the UCSC genome browser were generated using a custom pipeline; duplicate reads were first removed, coverage calculated with genomeCoverageBed and tag density calculated in 10bp windows. unionBedGraphs was then used to subtract input signals and bigwig files generated using bedGraphToBigWig. Regions of significant enrichment were identified using MACS version 1.4 (Zhang et al., 2008) using input or total histone H3 as background, with the setting --keep-dup=1. A p-value threshold of 10-7 was used, unless stated otherwise.
Genome_build: hg19
Supplementary_files_format_and_content: peak

source_name: In vitro differentiated Th1 cells

growth_protocol: Bulk human CD4+ T-cells were isolated by positive magnetic selection (Miltenyi Biotec). Cells were activated for 72 hours by plate bound anti-CD3 and anti-CD28 antibodies (2 µg/ml, BD Pharmingen) and were then cultured for 10 days with rhIL-2 (Biolegend, 10ng/ml). Conditions for T cell polarization were: rhIL-12 (10 ng/ml, Biolegend) and anti-IL-4 (10 µg/ml, R&D) for Th1.

extract_protocol:
Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detergent. Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 20 µl of anti-T-bet serum. Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNase A, proteinase K and phenol:chloroform extraction followed by ethanol precipitation.
Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 150 bp single-end read sequencing with an Illumina NextSeq sequencer.

treatment_protocol: Human T cells were formaldehyde crosslinked on day 13 after restimulation witn anti-CD3/CD28.

value: input

tag: treatment/agent


title: Malcolmia_maritima_LP1


title: Homo sapiens Donor 2 Th1 T-bet

value: anti-T-bet SY4530FB


title: Erysimum_cheiri_P2

organism: Erysimum cheiri

value: yellow flower


title: 14.5 + 2 + JTE 3

value: 15 uM of JTE013


title: Lobularia_maritima_W2

organism: Lobularia maritima

value: Petals

value: half-open flowers

value: white flower


title: Erysimum_cheiri_P1


title: Lobularia_maritima_W1


title: Lobularia_maritima_P2


title: Erysimum_cheiri_O2


title: Homo sapiens Donor 1 Th1 Input


title: Raphanus_sativus_W2

organism: Raphanus sativus


title: Erysimum_cheiri_O1


title: 14.5 + 2 + JTE 1


title: Raphanus_sativus_W1


title: Erysimum_cheiri_B2

value: orange flower


title: Lobularia_maritima_P1


title: Iberis_amara_P1


title: Raphanus_sativus_LP2


title: Erysimum_cheiri_B1


title: DMS-MapSeq_ded1-95_replicate2

description:
replicate 2
total_DMSMapSeq_norm_TS5_normCounts.txt

data_processing:
Basecalling with Illumina Casava software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie
Transcriptome alignment with TopHat
Further read analyses by custom scripts in Rstudio
More detailed information on additonal software in the methods section of the accompanying article.
Genome_build: sacCer3
Supplementary_files_format_and_content: mRNACo quantification in .tabular format (columns 1-13:tracking_id:1; class_code:2; nearest_ref_id:3; gene_id:4; gene_short_name:5; tss_id:6; locus:7; length:8; coverage:9; FPKM:10; FPKM_conf_lo:11; FPKM_conf_hi:12; FPKM_status:13); all other data files in .txt format (columns 1-7: chr:7; position:2; strand:3; sequence:4; gene:5; gene feature:6; normalized counts)

source_name: Whole cells

growth_protocol: Cells were grown to an OD600 of ~  0.6 in YPD medium

treatment_protocol: Cells were treated with dimethyl sulfate (5% (v/v) final concentration) prior to harvesting

tag: strain (genetic background)

value: thermo-sensitive ded1-95

tag: temperature

value: 37 dgC for 5 min

tag: molecule type

value: mRNA


title: Raphanus_sativus_LP1


title: Homo sapiens Donor 1 Th1 T-bet

tag: antibody


title: Eruca_sativa_Y1

tag: tissue

value: brownness flower


title: DMS-MapSeq_WT_replicate1

description:
replicate 1
total_DMSMapSeq_norm_WT5_normCounts.txt

value: wild-type DED1


title: Raphanus_sativus_DP1

tag: developmental stage


title: DMS-MapSeq_WT_replicate2

description:
replicate 2
total_DMSMapSeq_norm_WT5_normCounts.txt


title: Erysimum_cheiri_Y2

organism: Eruca vesicaria subsp. sativa

tag: phenotype


title: 30-TEX(-)TAP(+)

status: Public on Jan 23 2017

city: Paris

first: Anna

last: ZHUKOVA

address: 28 rue du Dr. Roux

country: France

institute: Institut Pasteur

data_processing:
reads were cleaned from adapter sequences with AlienTrimmer version 0.4.0
reads were cleaned from duplicates and low quality reads using PRINSEQ version 0.20.3
reads were aligned to the reference genome of L. interrogans serovar Manilae strain L495 chromosome LMANv2 using Rockhopper, allowing 5% of read length mismatches, and using 35% of read length as minimal seed.
the produced alignments were filtered to remove data with 0 scores, sorted and indexed with SAMTools version 0.1.19
coverage graphs representing the numbers of mapped reads per nucleotide were generated based on the sorted reads using BEDTools version 2.17.0
Genome_build: LMANv2
Supplementary_files_format_and_content: Wiggle Track Format (WIG)

organism: Leptospira interrogans serovar Manilae

source_name: cells

growth_protocol: grown aerobically at 30°C or 37°C in EMJH with shaking at 100 rpm to mid log phase (~1 x 10 8 Leptospira/ml)

extract_protocol:
Cells were collected by centrifugation for 15 min at 4,000 x g. Pelleted cells were resuspended in 700 μl of TRIzol, and RNA was purified according to the manufacturer's instructions (Invitrogen, Saint Aubin, Ile de France, France). DNA was degraded by using a Turbo DNA-free kit according to the manufacturer's instructions (Invitrogen). One microgram of DNase-treated RNA per sample was used to generate cDNA with the iScript cDNA synthesis kit according to the manufacturer's instructions (Bio-Rad, Marnes-la-Coquette, France). Ribosomal RNA was depleted by specific rRNA modified capture hybridization approach ("MicrobExpress" kit, AM1905, Ambion), allowing an enrichment of messager RNA.
cDNA librairies were prepared by ligation with an excess of 5 adapter (Illumina TruSeq Small RNA kit) and by reverse transcription using a random primer (RPO primer: 5 ′ CCTTGGCACCCGAGAATTCCANNNNNN-3). The first strand cDNA/RNA hybrids were then run on a 2% Low Range Agarose (Biorad). cDNAs ranging from 120 to 250 bp were extracted from a gel slice by using the Qiaquick gel extraction kit (Qiagen) and PCR amplified for 14 cycles using the Illumina primer RP1, and one of the indexed primers (Illumina TruSeq Small RNA kit). The resulting PCR products were purified with Agencourt AMPure Beads XP (Beckman).

treatment_protocol: see Samples section

tag: strain

tag: serovar

value: Manilae

tag: molecule

value: cDNA treated with TAP


title: 30-TEX(-)TAP(-)

value: untreated cDNA


title: 37-RNAseq

value: total RNA


title: 30-RNAseq


title: 37-TEX(-)TAP(+)


title: 37-TEX(+)TAP(+)

value: cDNA treated with TEX and TAP


title: 37-TEX(-)TAP(-)


title: PARP-1KO_ESC_Input_ChIPseq_Rep2

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
ChIP-seq reads were subjected to quality-control using FastQC
trimmed to remove adapter sequences
and aligned to the mouse reference genome (mm9) using Bowtie 0.12.7 allowing for one mismatch during alignment.
The data were then converted to wiggle (WIG) file format using PeakRanger
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file for visualization

source_name: embryonic stem cells

growth_protocol: mES cells were maintained on a feeder layer in mESC growth medium: Dulbecco’s modified Eagle’s medium (Gibco; 11965) containing 2 mM L-glutamine (Sigma), supplemented with 15% (v/v) FBS (Atlanta Biologicals; S12450), 0.1 mM nonessential amino acids (Sigma; M7145), 1 mM sodium pyruvate (Invitrogen; 11360070), 1000 units/mL mLIF (Millipore; ESG1106), penicillin and streptomycin (Invitrogen; 15140), and 0.1 mM b-mercaptoethanol (Sigma).  The cells were passaged twice to eliminate feeder cells before being used in experiments.

extract_protocol:
mESCs were passaged twice without a feeder layer and then grown in geletin-coated plates to ~70 to 80% confluence.  The cells were cross-linked using 1% paraformaldehyde at room temperature for 10 min., followed by quenching in 125 mM glycine for 5 min. at 4°C.  The crosslinked cells were collected, and the nuclei were released by gentle pipetting three times in lysis buffer [10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x protease inhibitor cocktail (Roche)].  The nuclei were collected by gentle centrifugation and resuspended in sonication buffer [1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1x protease inhibitor cocktail (Roche)].  The nuclei were then incubated in sonication buffer on ice for 10 min., and sonicated at 4°C using a Biorupter (Diagenode) high setting, three cycles of 5 min. sonication (30 seconds on/30 seconds off) with 5 min. intervals) to generate genomic DNA fragments of 200 - 500 bp in length.  The sonicated chromatin was clarified by centrifugation and pre-cleared with agarose beads.
Aliquots of the pre-cleared chromatin were immunoprecipitated with various antibodies at 4°C overnight, followed by collection of the immunoprecipitates using protein A (Millipore) or G (Invitrogen) agarose beads (protein A beads for H3K4me3, H3K27me3, and PARP-1 antibodies; protein G beads for Sox2 and Oct4 antibodies).  The beads were collected by gentle centrifugation and washed in low salt wash buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1x protease inhibitor cocktail), high salt wash buffer (low salt wash buffer containing 500 mM NaCl), and LiCl wash buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1x protease inhibitor cocktail).  The immunoprecipitated genomic DNA was eluted and the crosslinks were reversed by incubation in elution buffer (100 mM NaHCO3, 1% SDS) at 65°C overnight.  The genomic DNA was then deproteinized by digestion with proteinase K and extraction with phenol:chloroform:isoamyl alcohol, followed by precipitation with ethanol. Approximately 50 ng of ChIPed DNA (quantified using a NanoDrop) was used to prepare each ChIP-seq library. The genomic DNA fragments were end-polished, dA-tailed, and ligated to Y-adaptors containing barcode sequences.  After agarose gel-based size selection and purification, the DNA was amplified for 13 - 15 cycles by PCR using Phusion high-fidelity DNA polymerase (NEB).  The final ChIP-seq libraries were subjected to quality control assessment using a Bioanalyzer (Agilent), followed by 50 bp sequencing using an Illumina HiSeq 2000 Sequencing System.

tag: genoptype


title: DMS-MapSeq_ded1-95_replicate1

description:
replicate 1
total_DMSMapSeq_norm_TS5_normCounts.txt

extract_protocol:
Cells were rapidly sedimented and snap-frozen on dry ice. Whole cell extracts were generated by breaking the cells with glass beads.
Detailed information available in the Methods section of the article.


title: WT_ESC_Input_ChIPseq_Rep2

value: wild type


title: WT_ESC_Input_ChIPseq_Rep1


title: PARP-1KO_ESC_Oct4_ChIPseq_Rep2

value: Oct4 (Santa Cruz; sc-8628)


title: WT_ESC_Oct4_ChIPseq_Rep2


title: 30-TEX(+)TAP(+)


title: Eruca_sativa_Y2


title: PARP-1KO_ESC_Oct4_ChIPseq_Rep1


title: Raphanus_sativus_DP2

value: violet flower


title: WT_ESC_Oct4_ChIPseq_Rep1


title: WT_ESC_Sox2_ChIPseq_Rep2

value: Sox2 (Santa Cruz; sc-17320)


title: PARP-1KO_ESC_Sox2_ChIPseq_Rep2


title: PARP-1KO_ESC_Sox2_ChIPseq_Rep1


title: e6-7_KO776

source_name: shank2 exon 6,7 deletion mutant

value: mixed C57BL/6J and C57BLl/6N

tag: genotype/variation

value: Shank2 KO (exon 6,7 deletion mutant)

value: hippocampi


title: Erysimum_cheiri_Y1

value: Petals

value: half-open flowers

value: yellow flower


title: WT_ESC_Sox2_ChIPseq_Rep1


title: ESC_PARP-1_ChIPseq_Rep2

value: PARP-1 (Active Motif; 39561)


title: ESC_H3K27me3_ChIPseq_Rep2

value: H3K27me3 (Millipore; 170622)


title: ESC_PARP-1_ChIPseq_Rep1


title: ESC_H3K4me3_ChIPseq_Rep1

value: H3K4me3 (Active Motif; 3915)


title: ESC_H3K4me3_ChIPseq_Rep2


title: PARP-1KO_ESC_Input_ChIPseq_Rep1


title: ESC_H3K27me3_ChIPseq_Rep1


title: WT_ESC_RNAseq_Rep2

data_processing:
mRNA-seq reads were subjected to quality-control using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed to remove adapter sequences,
aligned to the mouse reference genome (mm9) using Tophat  {Trapnell, 2009 #5} before transcript assembly using Cufflinks {Trapnell, 2010 #6}
The data were then converted to wiggle (WIG) file format using PeakRanger {Feng, 2011 #7} for visualization using the Integrative Genomics Viewer (IGV2.3)
Cuffdiff {Trapnell, 2010 #6} was used to identify genes that showed significant differential regulation upon PARP-1 depletion, with a false discovery rate (FDR) cutoff of 5%.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file for visualization. Lane 2 and Lane 3 were merged for both replicate 1 samples.

extract_protocol:
total RNA was extracted from mESCs using Trizol reagent, The integrity of the RNA was assessed and verified using an Experion Automated Electrophoresis System (Bio-Rad) before mRNA-seq libraries were prepared using methods described previously
polyA+ RNA was enriched using Dynabeads oligo(dT)25 (Invitrogen), heat fragmented, and reverse transcribed using random hexamers in the presence of dNTPs.  Second strand cDNA synthesis was performed with dNTPs, but replacing dTTP with dUTP.  After end-repair, dA-tailing, ligation to adaptors containing barcode sequences, and size selection using AMPure beads (Agencourt), the synthesized second-strand was digested using uracil DNA glycosylase (Enzymatics).  A final PCR reaction was performed using Phusion high-fidelity DNA polymerase (NEB)


title: WT_ESC_RNAseq_Rep1_Lane2 and 3


title: Parp1KO_ESC_RNAseq_Rep2


title: Mut_+Dox_rep_2_CEBPB_ChIP

description: ChIP-enriched DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta PARylation site mutant in doxycycline treated condition

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to (1) “bed” files for later Metagene and read-density analyses and (2) “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using the BEDTools software package  (Quinlan et al, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: peaks.bed

growth_protocol: 3T3-L1 cells (Green and Kehinde, 1975) were obtained from the American Type Cell Culture (ATCC, CL-173TM) and maintained in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
3T3-L1 cells were cultured and treated as described above.  The cells were cross-linked with 1% paraformaldehyde in PBS for 10 minutes at 37°C and quenched in 125 mM glycine in PBS for 5 minutes at 4°C.  The cells were then collected and lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and 1x RCPIC).  A crude nuclear pellet was collected by centrifugation, resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 7.9, 1 mM DTT, and 1x RCPIC), and incubated on ice for 10 minutes.  The chromatin was sheared at 4°C by sonication using a Bioruptor UC200 at the high setting for four 5-minute cycles of 30 seconds on and 60 seconds off to generate chromatin fragments of ~300 bp in length.  The soluble chromatin was diluted 1:10 with dilution buffer (20 mM Tris-HCl, pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT and 1x RCPIC) and pre-cleared with protein A agarose beads.  The pre-cleared supernatant was used in immunoprecipitation reactions with antibodies against the factor of interest or with rabbit IgG as a control.  The immunoprecipitated material was washed once with low salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM aprotinin, and 1 mM leupetin), once with high-salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM aprotinin, and 1 mM leupetin), once with LiCl wash buffer (10 mM Tris-HCl, pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM aprotinin, and 1 mM leupetin), and once with 1x Tris-EDTA (TE).  The immunoprecipitated material was eluted in elution buffer (100 mM NaHCO3, 1% SDS) and was then digested with proteinase K and RNase H to remove protein and RNA, respectively.  The immunoprecipitated genomic DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The immunoprecipitated DNA was purified further using the MinElute PCR Purification Kit from Qiagen.
After purification, 5-10 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, For the spike in normalization, 100pg of PhiX DNA were added. DNA was then end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (greather than 250 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina NextSeq (NS500579) per the manufacturer’s instructions.

treatment_protocol: 3T3-L1 cells were plated in 15cm plates, grown to confluence, and then grown for another two days under contact inhibition. For the induction of C/EBP beta,cells were treated with 1μg/ml of doxycycline for 8 hours. For PARP inhibitor treatment condition, BYK204165 were treated 1 hour prior to the doxycycline induction.

tag: cell line

value: Mouse preadipocytes

tag: treated with

value: Doxycycline

tag: ChIP

value: C/EBP beta (Santa Cruz; sc-150x; J2215)


title: Mut_+Dox_rep_1_CEBPB_ChIP

tag: cell type

value: expressing doxycycline inducible C/EBP beta PARylation site mutant


title: WT_-Dox_rep_2_CEBPB_ChIP

description: ChIP-enriched DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta wildtype in vehicle treated condition

value: Vehicle


title: WT_+Dox_+BYK_rep_1_CEBPB_ChIP

description: ChIP-enriched DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta wildtype in doxycycline and PARP inhibitor BYK204165 treated condition

value: Doxycycline + BYK204165


title: WT_+Dox_rep_1_CEBPB_ChIP

description: ChIP-enriched DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta wildtype in doxycycline treated condition


title: WT_+Dox_rep_2_CEBPB_ChIP

value: expressing doxycycline inducible C/EBP beta wildtype


title: WT_+Dox_+BYK_rep_2_CEBPB_ChIP


title: Mut_-Dox_rep_2_CEBPB_ChIP

description: ChIP-enriched DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta PARylation site mutant in vehicle treated condition


title: WT_-Dox_rep_1_CEBPB_ChIP


title: WT_+Dox_+BYK_rep_2_Input

description: Input DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta wildtype in doxycycline and PARP inhibitor BYK204165 treated condition

value: none (input)


title: WT_+Dox_+BYK_rep_1_Input


title: WT_+Dox_rep_2_Input

description: Input DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta wildtype in doxycycline treated condition


title: WT_+Dox_rep_1_Input


title: Mut_-Dox_rep_2_Input

description: Input DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta PARylation site mutant in vehicle treated condition


title: Mut_-Dox_rep_1_Input


title: Mut_+Dox_rep_2_Input

description: Input DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta PARylation site mutant in doxycycline treated condition


title: WT_-Dox_rep_2_Input

description: Input DNA from 3T3-L1 cells expressing doxycycline inducible C/EBP beta wildtype in vehicle treated condition


title: Parp1KO_ESC_RNAseq_Rep1_Lane2 and 3


title: EFT_723_pH5.65

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

data_processing:
Demultiplexing and file conversion performed by bcl2fastq version bcl2fastq-1.8.3
RNAseq reads were imported to CLC Genomics Workbench 6.5 (CLC bio, Boston, MA), trimmed, and then mapped to F. succinogenes S85 genome assembly (CP001792).  Fastq files were imported into the CLCBio RNA-sequencing pipeline.  Default settings were used for mismatch, insertion, and deletion costs.
Total gene counts from the CLCBio mapping were used for DESeq2 analysis to normalise and determine significant gene expression differences
Genome_build: ASM2466v1
Supplementary_files_format_and_content: Tab deliminated file includes read counts for each gene across the samples used in this study

organism: Fibrobacter succinogenes subsp. succinogenes S85

source_name: Bacterial fermentation

growth_protocol: Fibrobacter succinogenes S85 was grown at 37oC in a 500-ml (vessel capacity 1.3 L) culture using a water-jacketed BioFlo110 bioreactor (New Brunswick Scientific, Edison, NJ). Temperature, pH, and agitation were monitored and controlled in the bioreactor via the BioCommand 2.62 software.   Cells were harvested from a 50 ml chemostat sample by centrifugation (7,600 × g, 4°C for 4 min) at each ph point.

extract_protocol:
Cells were pelleted from a 50 ml chemostat sample by centrifugation (7,600 × g, 4°C for 4 min), flash frozen in liquid nitrogen, and stored at -80°C. Ten milliliters of TRIzol reagent (Life Technologies) were added to the frozen cell pellet and mixed until the pellet was fully dissolved. Following the manufacturer’s protocol TRIzol was used to extract Total RNA. The aqueous phase containing RNA was further processed with a Qiagen RNeasy mini kit (Qiagen, Valencia, CA), following the manufacturer’s instructions, including the on-column DNaseI (Qiagen) treatment. Quantity of RNA was measured with NanoDrop and quality was assessed with Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) on a RNA 6000 Nano Chip.  Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit for Gram-negative Bacteria (Epicentre, Madison, WI) following the manufacturer’s protocol.
RNA-seq libraries were constructed using an Epicentre Scriptseq mRNA-Seq library preparation kit (Illumina compatible).  Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ mRNA-Seq Library preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was eluted with 20 µl of Buffer EB provided in the Min-Elute PCR purification kit (Qiagen) according to the ScriptSeq™ mRNA-Seq Library preparation kit protocol. Twelve PCR cycles were used during library amplification and samples were purified using the Min-Elute PCR purification kit and eluted with 20 µl of buffer EB.  The final RNA-seq libraries were quantified with a Qubit Fluorometer and library quality was assessed with Agilent Bioanalyzer and a DNA 7500 chip. Final libraries were normalized using the Illumina’s Library dilution calculator and pooled into a stock.  Pooled samples were prepared for sequencing based on the manufactures recomendations and sequenced on an Illumina MiSeq.

tag: ph


title: KD_RBM_rep1

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

data_processing:
RNA-seq reads that pass the Illumina filter were aligned to the S. pombe genome reference sequences using TopHat with default mapping parameters
The raw read count for each gene was produced by HTSeq
DESeq package was used to identify the differentially expressed genes between  rbm10Δ cells and WT
Genome_build: ASM294v2
Supplementary_files_format_and_content: tab-delimited text files include read cout for each Sample

organism: Schizosaccharomyces pombe

source_name: Yeast

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype


title: KD_WT_rep2

value: Wild type


title: EFT_671_pH5.65


title: KD_RBM_rep2


title: OE_RBM_rep1


title: EFT_699_pH5.65


title: Mut_-Dox_rep_1_CEBPB_ChIP

organism: Mus musculus


title: EFT_672_pH6.1


title: EFT_642_pH6.1


title: Axonal_2

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

data_processing:
We used reaper (PMID:23816787) to process the raw fastq files, to remove the Illumina sRNA 3’ adapter sequence (TGGAATTCTCGGGTGCCAAGG).
Trimmed sequences were collapsed to unique reads using tally (PMID:23816787), assigning their total counts to each sequence identifier. Only reads >= than 10nt were kept.
Reads were mapped to miRNA hairpins from miRBase v21 using bowtie1 (PMID:19261174) with an iterative process: first only perfect hits, second one mismatch for unmapped reads > 10nt, third two mismatches for unmapped reads > 20nt, finally three mismatches for unmapped reads > 30nt. A read was assigned to a mature miRNA if at least 16nt overlapped the mature coordinates within the hairpin.
Genome_build: miRBase v21 miRNA hairpins
Supplementary_files_format_and_content: fasta of unique sequences. Example sequence id line is of the format >seq_5.w18.x126044, where seq_# is a counter, w## is the length of the read and x##### is the number of times that read was sequenced.

organism: Xenopus laevis

source_name: distal axons from stage 37/38 embryo eye cultures

growth_protocol: Xenopus laevis embyros were grown in 0.1X Modified Bath’s Saline at 14-22 oC until stage 37/38. A total of 1000 whole eyes were extracted from stage 37/38 Xenopus laevis embryos, anesthesized in 1.5 mM MS222 (3-aminobenzoic acid ethyl ester methanesulphonate salt) and subsequently cultured in 60% L15 for 48hrs.

extract_protocol:
Total RNA was extracted from the axonal fraction by phenol-chloroform extraction (Trizol).
Small RNAs between 22-30nt were size-selected by cutting from a gel. Libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina) and sequenced on MiSeq sequencer (Illumina).

treatment_protocol: Eye explants and contaminating cells were manually removed to isolate distal axons only.

value: axons

tag: Stage

value: stage 37/38


title: EFT_652_pH5.65


title: Mut_+Dox_rep_1_Input


title: EFT_655_pH6.1


title: EFT_455_pH6.7


title: EFT_401_pH6.7


title: OE_WT_rep2


title: WT_-Dox_rep_1_Input


title: EFT_389_pH6.7


title: Axonal_1


title: OE_WT_rep1


title: 34Fc2: ski2KO dom34KO short and long footprints

status: Public on Jan 22 2017

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description: Reads split into 15-18 nt and 25-34 nt bins for downstream analysis

data_processing:
Library strategy: ribosome profiling
Base calling was performed at UC Riverside or Johns Hopkins sequencing facilities with CASAVA 1.8
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009) and the parameters: -y -a -m 1 --best --strata. Reads were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Wig files beginning with "end3" are aligned by 3' ends, all others by 5' ends.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

organism: Saccharomyces cerevisiae

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.

value: ski2KO dom34KO

tag: target molecule

value: Ribosome-protected RNA 15-34 nt


title: KD_WT_rep1


title: 33Mc: ski2KO mRNA-Seq

data_processing:
Base calling was performed at UC Riverside or Johns Hopkins sequencing facilities with CASAVA 1.8
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009) and the parameters: -y -a -m 1 --best --strata. Reads were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Wig files beginning with "end3" are aligned by 3' ends, all others by 5' ends.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

value: Total RNA 15-34 nt


title: 46F: dom34KO suppressor tRNA short and long footprints

value: dom34KO SUP4-o

tag: cell culture treatment

value: CSM-His media


title: 33F2: ski2KO short and long footprints


title: Japanese macaque sperm

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

description: Bisulfite-Seq

data_processing:
Basecalls performed using CASAVA
The reads were analyzed by Bismark version 0.8.3 using the reference genome of rhesus macaque.
Genome_build: rheMac3
Supplementary_files_format_and_content: The first, second, third and the last columns indicate chromosome name,  genomic postion of a CpG site, methylation levels (min. 0, max. 1), and the number of mapped reads, respectively.  The txt file was generated by original perl script.

organism: Macaca fuscata

source_name: Sperm

extract_protocol: The library for Bisulfite-Seq was constructed by the post-bisulfite adaptor tagging method, and subjected to 100-bp single-end sequencing on Illumina HiSeq1500.

tag: tissue

value: sperm


title: 60F: suppressor tRNA short and long footprints


title: 34Mc: ski2KO dom34KO mRNA-Seq


title: OE_RBM_rep2


title: 23Fs: ski2KO dom34KO suppressor tRNA short footprints

description: Wig files divided into narrow size bins for downstream analysis.

value: ski2KO dom34KO SUP4-o

value: Ribosome-protected RNA 15-24 nt


title: 33Fs: ski2KO short footprints previous replicate

description: Serves as technical replicate to short reads in 33F2


title: 34Fs: ski2KO dom34KO short footprints previous replicate

description: Serves as technical replicate to short reads in 34F2


title: 22Fs: ski2KO suppressor tRNA short footprints

value: ski2KO SUP4-o


title: WT_IgG

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Short reads (50bp, single end) were aligned to the mouse reference genome (mm10) using bowtie aligner version 2.2.4
Reads with multiple alignments were removed with samtools (v1.1) and de-duplicated with picard (v1.130)
To identify peaks from ChIP-seq reads, we used the HOMER package makeTagDirectory followed by the findPeaks command with the ‘histone’ parameter. Peaks displaying 4-fold enrichment and poison P-value of 1x10-4 against background IgG ChIP were considered significant and were used for further analysis.
To visualize individual ChIP-seq data on Integrative Genomics Viewer (IGV), we converted bam output files from picard into normalized bigwig format using the bamCoverage function in deepTools (v1.6) with options – fragmentLength 200 –normalizeUsingRPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Thymus

extract_protocol:
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as MECs.
Chromatin IPed with specific Abs was eluted from the Protein-G beads, treated with 1µg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample.

value: Aire+/+

value: MECs

tag: antibody

value: IgG


title: human MBD1-captured

data_processing:
Basecalls performed using CASAVA
The reads were mapped by bowtie.
The map counts were processed by MEDIPS
Genome_build: hg19 (human) or panTro3 (chimpanzee)
Supplementary_files_format_and_content: The first colmn shows genomic position and the second colmn shows MEDIPS score.

organism: Homo sapiens

source_name: human PBLs

extract_protocol:
Genomic DNA was prepared by a standard procedure from female PBLs.  Samples from 4 individuals for each species were pooled, and the pooled samples were flagmented into 200-600 bp by sonication. Methylated DNA fragments were collected by using  the His-tagged MBD1.
The sequence libraries were constructed for total and MBD1-collected DNA fragments by using paired-end sequencing kit (Illumina), and deeply sequenced on Illumina Genome Analyzer II with 75-bp paired-end sequencing.

tag: sequenced dna

tag: gender

value: female

value: peripheral blood leukocyte


title: WT_H3K27ac_rep_2

tag: strain

tag: antibody vendor/catalog


title: Aire_KO_H3K27ac_rep_1

value: Aire-/-


title: Aire_KO_TOP1_rep_1

value: Abcam/ab3825 and ab85038


title: WT_TOP1_rep_2


title: WT_gH2AX_rep_1


title: WT_TOP1_rep_1


title: Aire_KO_TOP2A_rep_2


title: Aire_KO_TOP2A_rep_1


title: WT_TOP2A_rep_2


title: WT_TOP2A_rep_1


title: DDX5-/- mESCs Line #2 (miRNA-seq)

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: miRNA

data_processing:
CAP-miRSeq pipeline was used to process the miRNA-seq data
edgeR was used to call differential miRNAs
Genome_build: mm10, mirbase v21, GENCODE M9
Supplementary_files_format_and_content: miRNAseq_expression.tsv.gz contains a TSV, with each miRNA on a row and their expression in the columns. Expression is given as 'weighted tag count' as output by mirDeep2 software.

source_name: embryonic stem cells_DDX5KO

growth_protocol: Wild-type (MPI-II) and DDX5 knockout mESCs were cultured in plates coated with feeder cells in DMEM/High Glucose medium (Hyclone) supplemented with b-mercaptoethanol(10mM), sodium pyruvate(10mM), non-essential amino acids(10mM), GlutaMAX(10mM), 15% fetal bovine serum (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), and 1 μM MEK inhibitor PD0325901 and 3μM GSK3 inhibitor CH99021.

extract_protocol:
Generation of DDX5 Knockout mESCs: Two sets of oligonucleotides were separately cloned into a U6-gRNA vector to create paired sgRNA target sites for SpCas9-nickase in the second exon of Ddx5, encoding the DDX5 protein. CRISPR/Cas9 target sites in Ddx5 (NM_007840.3) were designed by http://zifit.partners.org/ZiFiT/CSquare9Nuclease.aspx. Then these two sets of oligonucleotides were synthesized and inserted into the Bbs I site of the U6-gRNA vector. The sequences of two sets of oligonucleotides were as follow: Ddx5-Target1-F: 5’-CACCGAGACCGCGGCCGGGATCGA-3’, Ddx5-Target1-R: 5’-AAACTCGATCCCGGCCGCGGTCTC-3’, Ddx5-Target2-F: 5’-CACCGGAAAGAAGTTTGGAAATCC-3’, Ddx5-Target2-R: 5’-AAACGGATTTCCAAACTTCTTTCC-3’.  To generate a stable DDX5-/- mESC line, 2 × 106 mESCs were transfected with 20 μg U6-gRNA vector and 50 μg U6-cas9 plasmids. Cells were selected with 500 μg/ml of G418 (Sigma) after 24 hr of infection and were maintained in selection for 72 hr. Single clones were separated and were seeded in each well of a 48-well plate. Individual wells were inspected by microscopy to exclude polyclonal cell lines. Monoclonal cell lines were expanded. Then, DNA and protein of monoclonal cell lines were extracted to detect the genotype through DNA sequencing after PCR and Western blot.
Illumina miRNA-seq kit

value: Mus musculus

value: MPI-II

tag: passages

value: DDX5 KO

value: Ddx5 knockout MPI-II embryonic stem cells


title: DDX5-/- mESCs Line #1 (miRNA-seq)

description: miRNA

tag: genotype/variation


title: DDX5-/- mESCs Line #3 (miRNA-seq)

description: miRNA


title: WT_Aire_rep_1

value: Aire


title: DDX5+/+ mESCs Rep #1 (miRNA-seq)

description: miRNA

source_name: embryonic stem cells_wildtype

value: wild type

value: Ddx5 wild-type MPI-II embryonic stem cells


title: DDX5+/+ mESCs Rep #2 (miRNA-seq)

description: miRNA


title: DDX5-/- mESCs Line #2

description: Ddx5 knockout MPI-II embryonic stem cells

data_processing:
rsem v1.2.17/bowtie2 v2.2.0 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 25 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab separated text file containing ensembl transcript accession, gene name and normalised abundance estimates for each transcript

extract_protocol:
Extracted using TRIzol using the manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Generation of DDX5 Knockout mESCs: Two sets of oligonucleotides were separately cloned into a U6-gRNA vector to create paired sgRNA target sites for SpCas9-nickase in the second exon of Ddx5, encoding the DDX5 protein. CRISPR/Cas9 target sites in Ddx5 (NM_007840.3) were designed by http://zifit.partners.org/ZiFiT/CSquare9Nuclease.aspx. Then these two sets of oligonucleotides were synthesized and inserted into the Bbs I site of the U6-gRNA vector. The sequences of two sets of oligonucleotides were as follow: Ddx5-Target1-F: 5’-CACCGAGACCGCGGCCGGGATCGA-3’, Ddx5-Target1-R: 5’-AAACTCGATCCCGGCCGCGGTCTC-3’, Ddx5-Target2-F: 5’-CACCGGAAAGAAGTTTGGAAATCC-3’, Ddx5-Target2-R: 5’-AAACGGATTTCCAAACTTCTTTCC-3’.  To generate a stable DDX5-/- mESC line, 2 × 106 mESCs were transfected with 20 μg U6-gRNA vector and 50 μg U6-cas9 plasmids. Cells were selected with 500 μg/ml of G418 (Sigma) after 24 hr of infection and were maintained in selection for 72 hr. Single clones were separated and were seeded in each well of a 48-well plate. Individual wells were inspected by microscopy to exclude polyclonal cell lines. Monoclonal cell lines were expanded. Then, DNA and protein of monoclonal cell lines were extracted to detect the genotype through DNA sequencing after PCR and Western blot.

value: embryonic stem cells

value: DDX5 knockout


title: WT_Aire_rep_2


title: DDX5-/- mESCs Line #4


title: DDX5-/- mESCs Line #3


title: WT_ATAC-seq_fibroblast_rep_1

data_processing:
Short reads (50bp, forward; 34bp, reverse) were aligned to the mouse reference genome (mm10) using bowtie aligner version 2.2.4
Reads with multiple alignments were removed with samtools (v1.1) and de-duplicated with picard (v1.130)
Reads mapping to mitochondrial DNA were removed before analysis.
To identify peaks from ATAC-seq reads, we used the HOMER package makeTagDirectory followed by the findPeaks command with the ‘factor’ parameter.
To visualize individual ATAC-seq data on Integrative Genomics Viewer (IGV), we converted bam output files into normalized bigwig format using the bamCoverage function in deepTools (v1.6) with options – fragmentLength 200 –normalizeUsingRPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Ear

extract_protocol:
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as MECs and CD45-EpCAM-CD31-Ter-119-Sca-1+ as earskin fibroblasts
Cells were suspended in 100ul of cold hypotonic lysis buffer [10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2 and 0.1% NP40], followed by immediate centrifugation at 550g for 30 min. The pellet was re-suspended in 5ul of transposition reaction mix [1ul of Tagment DNA Enzyme and 2.5uL of Tagment DNA Buffer from Nextera DNA Sample Prep Kit (Illumina), 1.5ul H2O], and was incubated for 60 min at 37°C for DNA to be fragmented and tagged. For library preparation, two sequential 7-cycles of PCR were performed in order to enrich small tagmented DNA fragments. After the first PCR, the libraries were selected for small fragments (less than 600bp) using SPRI beads followed by a second round of PCR with the same conditions in order to obtain the final library

value: fibroblasts


title: 23F: ski2KO dom34KO suppressor tRNA long footprints

value: ski2KO dom34KO SUP4-o

value: CSM-His media

value: Ribosome-protected RNA 25-34 nt


title: Aire_KO_ATAC-seq_MEC_rep_2

value: MECs


title: DDX5-/- mESCs Line #1


title: WT_H3K4me1_rep_2

value: Aire+/+

value: Abcam and Millipore/ab8895  and 07-436


title: human WG

value: whole genome

value: female

value: peripheral blood leukocyte


title: Aire_KO_ATAC-seq_MEC_rep_1

value: Aire-/-


title: 22F: ski2KO suppressor tRNA long footprints previous replicate

value: ski2KO SUP4-o


title: WT_ATAC-seq_MEC_rep_2


title: WT_ATAC-seq_MEC_rep_1


title: DDX5+/+ mESCs Rep #1

description: Ddx5 wild-type MPI-II embryonic stem cells

value: MPI-II


title: WT_H3K27ac_rep_1


title: DDX5-/- mESCs Line #4 (miRNA-seq)

description: miRNA

value: Mus musculus

value: DDX5 KO

value: Ddx5 knockout MPI-II embryonic stem cells


title: Aire_KO_gH2AX_rep_2


title: 11F: ski2KO dom34KO previous replicate

description: Serves as biological replicate to long reads in 34F2

value: ski2KO dom34KO


title: WT_gH2AX_rep_2


title: Aire_KO_gH2AX_rep_1


title: WT_RYBP_ChIPSeq

data_processing:
Reads were aligned to the mouse mm10 genome using bowtie2 v2.2.5
Peaks were discovered using MACS 1.4 (RYBP, CBX7)
Peaks were discovered using Dfilter (H2AK119ub)
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: MPI-II_wild type

extract_protocol:
ChIP experiments were performed as previously described (Huang et al., 2013). Briefly, 1 × 107 cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). The cells were sonicated in SDS lysis buffer containing 1 × protease inhibitor cocktails and 1 mM PMSF to achieve a chromatin sized of 100-500 bp. The sonicated chromatin was incubated with indicated antibodies coupled with dynabeads protein A and G (1:1 mixed) overnight at 4°C with rotation. Immune complexes were washed with the following buffers: low salt wash buffer (0.1% SDS, 1%Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris-HCl (pH 8.0)) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: Embryonic stem (ES) cell line

value: wild type

tag: chip antibody

value: DEDAF (Millipore, AB3637, lot 2426983)


title: DDX5-/-_Input

source_name: MPI-II_DDX5 knock-out

value: DDX5 knock-out


title: WT_PolII_rep_2

value: MECs

value: PolII


title: WT_ATAC-seq_fibroblast_rep_2

value: Aire+/+

value: fibroblasts


title: WT_Input


title: WT_PolII_rep_1


title: WT_H3K27me3_rep_1


title: chimpanzee MBD1-captured

organism: Pan troglodytes

source_name: chimpanzee PBLs

value: female


title: WT_H3K27me3_rep_2


title: chimpanzee WG

value: whole genome

value: peripheral blood leukocyte


title: WT_H3K4me1_rep_1

value: Abcam and Millipore/ab8895  and 07-436


title: DDX5-/-_H2AK119ub_ChIPSeq

value: MPI-II

value: H2AK119ub (Cell signaling, D27C4, lot 8240)


title: WT_H2AK119ub_ChIPSeq


title: yes_kcl5_TGCTGGG_RNAseq

status: Public on Jan 21 2017

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Excluded one KCl replicate due to low library size
Using Trimmomatic v. 0.32, trimmed adapters and set min. read length to 25 (RF) or 20 (RNA-seq) and set max length to 35 (RF)
Removed rRNA reads using STAR v. 2.3.1z8
Aligned RF and RNA-seq reads to non-degenerate mouse transcriptome using Bowtie2 v. 2.2.2
Counted reads using BEDTools v. 2.20.1
Differentially transcribed or translated genes were identified using a permuted t-test with replacement after integration into a digital gene expression (DGE) object using the edgeR package
Genome_build: Ensembl 75 (mouse) transcriptome with degenerate sequences removed. We also removed several positions in the transcriptome for translation efficiency calculations: 9 nt before the first nt of each start codon, 15 nt after the last nt of each start codon, 15 nt before the first nt of each stop codon, and 15nt after the last nt of each stop codon
Supplementary_files_format_and_content: ASCII files with counts for each sample

source_name: Mouse neurons_yes_kcl

extract_protocol:
DNAse I treated total RNA was purified with RNeasy MinElute columns (Qiagen).
Double stranded cDNA was generated using Nugen Ovation RNAseq system V2, starting from 68 ng of total RNA. Standard Illumina sequencing libraries were generated from 1-2 ug of cDNA.

tag: age

value: FVB

value: brain cortex


title: yes_kcl4_TCAAACA_RNAseq


title: no_kcl1_GACACCGGT_RF

data_processing:
Library strategy: Ribosomal footprinting
Excluded one KCl replicate due to low library size
Using Trimmomatic v. 0.32, trimmed adapters and set min. read length to 25 (RF) or 20 (RNA-seq) and set max length to 35 (RF)
Removed rRNA reads using STAR v. 2.3.1z8
Aligned RF and RNA-seq reads to non-degenerate mouse transcriptome using Bowtie2 v. 2.2.2
Counted reads using BEDTools v. 2.20.1
Differentially transcribed or translated genes were identified using a permuted t-test with replacement after integration into a digital gene expression (DGE) object using the edgeR package
Genome_build: Ensembl 75 (mouse) transcriptome with degenerate sequences removed. We also removed several positions in the transcriptome for translation efficiency calculations: 9 nt before the first nt of each start codon, 15 nt after the last nt of each start codon, 15 nt before the first nt of each stop codon, and 15nt after the last nt of each stop codon
Supplementary_files_format_and_content: ASCII files with counts for each sample

source_name: Mouse neurons_no_kcl

extract_protocol:
Cell lysate was treated with DNase and clarified, and a portion was taken for RNAseq analysis. Remainder was treated with RNaseI(100U/ul; Invitrogen)for 45 min at room temperature and gentle mixing on a Nutator followed by inactivation of RNase by treatment with SUPERase-In(Thermo Fisher). Ribosomes and protected mRNA fragments were separated from free RNA by pelleting with ultracentrifugation on 1M Sucrose cushion at 200,000g for 4 h at 40C. RNA was isolated from the pellet using miRNeasy kit from Qiagen. Ribosome protected fragments (26-nt to 34-nt size)were purified on a 15% polyacrylamide TBE-urea gel and after dephosphorylation linker ligation was performed at room temperature for 2.5h using miRNA cloning linker from NEB. Linker ligated product was separated from unligated product on a 15% polyacrylamide gel.
Reverse transcription was performed using SuperScript III(Invitrogen)per the manufacturer’s protocol. Left over RNA was hydrolysed by treatment with 1N NaOH and precipitated cDNA was circularized using CircLigase(NEB). Circularized cDNA was subjected to rRNA depletion using biotinylated subtraction oligo pool directed against rRNA. Ribosome depleted product was PCR amplified using Phusion polymerase(NEB)and different indexing primers and the final product was purified on 8% polyacrylamide non-denaturing gels. Resuspended library was quantified and fragment size measured on high-sensitivity DNA chip on the Agilent BioAnalyzer.


title: no_kcl1_ACTGTCG_RNAseq


title: no_kcl2_GTTCTCA_RNAseq


title: no_kcl2_ACATCTCTT_RF


title: no_kcl3_TTGCCCC_RNAseq