title: At gel purified RBS-seq rep 1 (2)

city: Adelaide

first: Alice

middle: Louise

last: Burgess

state: SA

address: Frome road

department: Genetics and Evolution

country: Australia

institute: University of Adelaide

description: gel purified RNA

data_processing:
Illumina Casava1.8 software used for base calling.
Sequenced reads were trimmed to remove adaptor sequences, filtered for low-quality reads, then mapped to tRNA reference sequences or in silico bisulfite converted tRNA reference sequences using CLC Genomics Workbench 7 (Qiagen) with parameters: mismatch cost =1, insertion cost =3, deletion cost =1, length fraction = 0.8, similarity fraction = 0.9
Methylation percentages of cytosines were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Methylation percentage = (#C divided by #C+#T) times by 100)
tRNA abundance measurements from the Arabidopsis thaliana RNA-seq library were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Read counts were normalized to reads per million (RPM)
Genome_build: TAIR10 annotated transfer RNAs and the plantRNA database (http://plantrna.ibmp.cnrs.fr)
Supplementary_files_format_and_content: Excel file with methylation percentages for cytosine residues in tRNAs from A. thaliana, G. biloba, B. rapa, N. occulata, C. taxifolia and T. durum from bisulfite treated RNA, enriched for tRNAs.
Supplementary_files_format_and_content: Excel file with RPM values for tRNAs from Arabidopsis wild type tRNA enriched RNA-seq.
Supplementary_files_format_and_content: Excel file with Arabidopsis tRNA consensus reference sequences.

organism: Arabidopsis thaliana

source_name: 10 days after germination seedlings

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH) and RNA was gel purified to enrich for tRNAs
RNA libraries were prepared for sequencing using standard Illumina protocols except BS treated RNA was not fragmented.

value: seedling

value: wild type


title: At gel purified RBS-seq rep 3 (2)

status: Public on Oct 01 2015

type: SRA

description: gel purified RNA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: At gel purified RBS-seq rep 2 (2)

description: gel purified RNA


title: 4C-seq: ind13_Kc_1

city: Freiburg

first: Fidel

last: Ramirez

address: Stübeweg 51

department: Bioinformatics Unit

country: Germany

institute: Max Planck Institute for Immunobiology and Epigenetics

description: ligated DNA

library_source: genomic

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.3
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: cultured fruit fly cells

growth_protocol: S2 cells were cultured in Schneider's medium (Gibco) supplemented with 10% FCS and 0.05% Pluronic F-68 (Sigma-Aldrich) on shaking incubators at 27C at a density of 2-16 million/ml.

extract_protocol: 4C-seq in S2 and Kc cells was carried out as described by Splinter et al.63 with minor modifications as following: 50-100 million S2 cells or Kc cells, fixed, were used for two biological replicates. DpnII (NEB) was used as the primary and Csp6I (ThermoScientific) as the secondary restriction enzyme. For each viewpoint, two 50ul PCR reactions (8 cycles with 5C annealing temperature, followed by 18 cycles with 63C) with 160ng of template each were prepared and the combined products cleaned up by a one-step purification using 1.6 volumes of AMPure XP magnetic beads (Beckmann Coulter) according to manufacturer's instructions. These viewpoint libraries were eluted in 20ul elution buffer (10mM Tris-HCl pH 8.5) and the molarities for each individual sample were estimated using the bioanalyzer DNA 7500 kit (Agilent Technologies). All different viewpoint libraries for one biological replicate were mixed equimolarly and sequenced on separate lanes on an Illumina HiSeq2500 DNA sequencer.

tag: cell line

value: Kc

tag: restriction enzyme(s)

value: DpnII, Csp6I

tag: replicate

value: biological 1


title: At gel purified RNA-seq

description: gel purified RNA


title: 4C-seq: ind11_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.25
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

value: biological 2


title: nop2a-2 gel purified RBS-seq rep 1

description:
gel purified RNA
experiment 1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, filtered for low-quality reads, then mapped to in silico bisulfite converted tRNA reference sequences using CLC Genomics Workbench 7 (Qiagen) with parameters: mismatch cost =1, insertion cost =3, deletion cost =1, length fraction = 0.8, similarity fraction = 0.9
Methylation percentages of cytosines were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Methylation percentage = (#C divided by #C+#T) times by 100)
Genome_build: TAIR10 annotated transfer RNAs
Supplementary_files_format_and_content: Excel file with methylation percentages for cytosine residues in tRNAs from A. thaliana wild type and RMTase mutants from bisulfite treated RNA, enriched for tRNAs
Supplementary_files_format_and_content: Excel file with A. thaliana tRNA reference sequences with corresponding gene identifiers and chromosome co-ordinates

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH) and gel purified RNA to enrich for tRNAs. RNA was bisulfite converted prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except RNA fragmentation was not performed.


title: At total RNA RBS-seq rep 3 (2)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequence, filtered for low-quality reads, then mapped to rRNA reference sequences or in silico bisulfite converted rRNA reference sequences using CLC Genomics Workbench 7 (Qiagen) with parameters: mismatch cost =1, insertion cost =3, deletion cost =1, length fraction = 0.8, similarity fraction = 0.9
Methylation percentages of cytosines were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Methylation percentage = (#C divided by #C+#T) times by 100)
Arabidopsis TAIR10 rRNA sequences were used for guided reference assemby of rRNAs from other species using RNA-seq libraries and alignments made using CLC genomics workbench 7 (Qiagen)
Genome_build: TAIR10 annotated ribosomal RNAs for Arabidopsis thaliana and species specific rRNA sequences for plants other than Arabidopsis thaliana
Supplementary_files_format_and_content: Excel file with methylation percentages for cytosine residues in rRNAs from A. thaliana, G. biloba, B. rapa, N. occulata, C. taxifolia and T. durum from bisulfite treated total RNA.
Supplementary_files_format_and_content: Excel file with rRNA reference sequences from A. thaliana, G. biloba, B. rapa, N. occulata, C. taxifolia and T. durum.

source_name: 10 days after germination seedlings grown on soil

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH) total RNA was used either with or without bisulfite conversion before Illumina library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except BS treated RNA was not fragmented.


title: At total RNA RBS-seq rep 2 (2)


title: trdmt1 trm4b gel purified RBS-seq rep 1

description:
gel purified RNA
experiment 1

value: trdmt1 trm4b


title: trm4a gel purified RBS-seq rep 1

description:
gel purified RNA
experiment 1


title: At total RNA RBS-seq rep 1 (2)


title: trm4b-1 gel purified RBS-seq rep 1

description:
gel purified RNA
experiment 1


title: At gel purified RBS-seq rep 1 buds

description:
gel purified RNA
experiment 2

source_name: mixed buds

value: mixed buds


title: trm4b-2 gel purified RBS-seq rep 1 buds

description:
gel purified RNA
experiment 2


title: nsun5-2 gel purified RBS-seq rep 1

description:
gel purified RNA
experiment 1


title: At gel purified RBS-seq rep 1

description:
gel purified RNA
experiment 1


title: trdmt1 gel purified RBS-seq rep 1

description:
gel purified RNA
experiment 1


title: trdmt1 total RNA RBS-seq rep 1 plate

description: experiment 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequences, filtered for low-quality reads, then mapped to in silico bisulfite converted rRNA reference sequences using CLC Genomics Workbench 7 (Qiagen) with parameters: mismatch cost =1, insertion cost =3, deletion cost =1, length fraction = 0.8, similarity fraction = 0.9
Methylation percentages of cytosines were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Methylation percentage = (#C divided by #C+#T) times by 100)
Genome_build: TAIR10 annotated ribosomal RNAs
Supplementary_files_format_and_content: excel file with methylation percentages for cytosine residues in rRNAs from A. thaliana wild type and RMTase mutants from bisulfite treated total RNA.
Supplementary_files_format_and_content: excel file with methylation percentages for cytosine residues in rRNAs from A. thaliana wild type and RMTase mutants from bisulfite treated total RNA.
Supplementary_files_format_and_content: excel file with ribosomal RNA reference sequences and gene identifiers and or accession numbers.

source_name: 10 days after germination seedlings grown on 1/2 MS media plates

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH) and total RNA was bisulfite converted prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except RNA fragmentation was not performed.


title: At gel purified RBS-seq rep 2

description:
gel purified RNA
experiment 1


title: At gel purified RBS-seq rep 3

description:
gel purified RNA
experiment 1


title: At total RNA RBS-seq rep 1 plate

description: experiment 2


title: trm4a total RNA RBS-seq rep 1 plate

description: experiment 2


title: trm4b-1 total RNA RBS-seq rep 1 plate

description: experiment 2


title: nop2b-2 total RNA RBS-seq rep 1

description: experiment 1

source_name: 10 days after germination seedlings gown on soil


title: nsun5-2 total RNA RBS-seq rep 2

description: experiment 1


title: 4C roX2 S2

description: ligated DNA

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.3
Each mate file  was mapped using Bowtie2 adding the --local parameter to accommodate for reads containing a ligation site.
All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 500 bp apart. Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10,000 bp, 25,000 bp, 50,000 bp and 100,000 bp. Replicates were merged into one dataset.
Genome_build: dm3
Supplementary_files_format_and_content: Processed files contain matrices of corrected Hi-C contact counts for different bin resolution.

growth_protocol: S2 cells were cultured in Schneider’s medium (Gibco) supplemented with 10% FCS and 0.05% Pluronic F-68 (Sigma-Aldrich) on shaking incubators at 27°C at a density of 2-16 million/ml. Clone8 (cl.8+) cells were grown in Shields and Sang M3 Insect Medium (Sigma-Aldrich) supplemented with 2% FCS, 5µg/ml insulin and 2.5% fly extract on 15cm cell culture dishes.

extract_protocol:
4C in S2 cells was carried out as described (Splinter et al., 2012) with minor modifications: 50 million S2 cells, fixed as described above were used. DpnII was used as the primary and Csp6I as the secondary restriction enzyme.
50 million S2 cells were collected and resuspended in 22.5ml of fresh medium. Clone8 cells were washed with PBS and 22.5ml of fresh medium added. 37% formaldehyde solution was added to obtain a final concetration of 1%, followed by incubation at room temperature for 10min. 1.25ml 2.5M glycine solution was added and incubated for another 5 min at RT followed by 10min on ice.


title: nsun5-1 total RNA RBS-seq rep 2

description: experiment 1


title: nsun5-1 total RNA RBS-seq rep 3

description: experiment 1


title: nop2c-2 total RNA RBS-seq rep 2

description: experiment 1


title: nsun5-1 total RNA RBS-seq rep 1

description: experiment 1


title: nop2c-1 total RNA RBS-seq rep 3

description: experiment 1


title: trdmt1 trm4b total RNA RBS-seq rep 1 plate

description: experiment 2


title: nop2c-1 total RNA RBS-seq rep 1

description: experiment 1


title: At total RNA RBS-seq rep 3

description: experiment 1


title: nop2c-2 total RNA RBS-seq rep 1

description: experiment 1


title: nop2a-2 total RNA RBS-seq rep 1

description: experiment 1


title: At total RNA RBS-seq rep 1

description: experiment 1


title: At total RNA RBS-seq rep 2

description: experiment 1


title: nop2b-1 total RNA RBS-seq rep 1

description: experiment 1


title: nop2a-2 total RNA RBS-seq rep 2

description: experiment 1


title: 4C-seq: ind22_Kc_2

description: ligated DNA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.34
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3


title: nop2b-1 total RNA RBS-seq rep 2

description: experiment 1


title: IR [miRNA]

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

country: China

institute: Tongji University

description:
small RNA
ischemia-reperfusion

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome and mature miRNA annotation using Bowtie v0.12.7 with default parameters.
Read counts (RC) were caculated following the miRDeep2 pipeline from Friedländer et al, Nature Biotechnology, 2008.
Genome_build: mm10

organism: Mus musculus

source_name: Liver cell

extract_protocol:
small RNA was extracted from the livers using miRNA isolation kit(Ambion, USA) following the manufacturer’s instruction. The quality of the purified RNA was assessed using a BioAnalyzer 2100 with the parameters: RIN>7.5, concentration>200 ng/μl. RNA samples were stored at -80℃
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were housed in a stainless steel with ad libitum access to filtered tap water and commercial feed in a specific pathogen free animal room of the supervision and testing center.

value: Liver

tag: gender

value: Male

tag: strain

tag: age

value: 8-10 weeks


title: nop2b-1 total RNA RBS-seq rep 3

description: experiment 1


title: WI [miRNA]

description:
small RNA
warm ischemia


title: Dmel Input male

description: genomic DNA

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.85
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

source_name: salivary gland

extract_protocol: Chromatin was obtained from male 3rd instar larvae salivary glands as previously described (PMID: 16547175). In brief, collected salivary glands (10 per ChIP) were fixed, sonicated for 8 min (pulsed eight times for 30 sec, paused for 30 sec, high) in a Bioruptor (Cosmo Bio), and chromatin immunoprecipitated with the respective antibody.

tag: developmental stage

value: third instar

tag: Sex

value: male

tag: chip antibody

value: none (input)


title: IR

description: ischemia-reperfusion

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.0.9 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.0.2. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

extract_protocol:
Total RNA was extracted from the livers using miRNA/mRNA isolation kit(Ambion, USA) following the manufacturer’s instruction. The quality of the purified RNA was assessed using a BioAnalyzer 2100 with the parameters: RIN>7.5, concentration>200 ng/μl. RNA samples were stored at -80℃
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8-10 week


title: Sham [miRNA]

description:
small RNA
sham


title: Dmel MSL1 ChIP male

description: genomic DNA

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.84
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

source_name: salivary glands

value: polyclonal MSL1 antibody raised against the N-terminus (AA1-584)


title: nsun5-2 total RNA RBS-seq rep 1

description: experiment 1


title: HFD_MeDIP-seq

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

data_processing:
Data filtering was applied to remove adapter sequences, contamination and low-quality reads from raw reads.
Raw reads were aligned to the reference mouse genome (UCSC mm9) using BWA with default parameter.
Peak calling was performed by using MACS.
Differentially methylated regions were identified by using MEDIPS
Genome_build: mm9
Supplementary_files_format_and_content: peak files

source_name: Epididymal fat

growth_protocol: Male 4 week old C57BL/6J mice were randomly assigned to a standard chow diet (STD) or a high-fat diet (HFD - 60% kcal from fat - Research Diets Inc., New Brunswick, New Jersey, USA) for 5 months.

extract_protocol:
Genomic DNA was isolated from epididymal white adipose tissues of STD and HFD mice, respectively, using the AllPrep DNA/RNA Mini Kit (Qiagen, Germany) according to the manufacturer's instructions.
Purified DNA (>50 ng/per sample) was then sent to Beijing Genomics Institute (BGI at Shenzhen, China) for libraries preparation according to Illumina's instructions for MeDIP-seq

value: epididymal white adipose tissue

tag: diet

value: high-fat


title: WI

description: warm ischemia


title: STD_MeDIP-seq

value: regular chow


title: nop2c-1 total RNA RBS-seq rep 2

description: experiment 1

value: seedling


title: nop2a-2 total RNA RBS-seq rep 3

description: experiment 1


title: LMP2a-H3K27ac

city: Boston

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

country: USA

institute: Harvard Medical School

data_processing:
Mapping using bowtie with following parameters -S -t -p 2 -k 1 -m 1 -q
Call Peaks using MACS default parameters
Genome_build: mm9

source_name: B220+ LMP2a B cells

growth_protocol: B220+ B cells from splenocytes were purified using the Magnetic Cell Sorting-based B-Cell Isolation Kit or B220 MicroBeads, according to the manufacturer’s protocol (Miltenyi Biotec). The cells were cultured in RPMI1640 medium containing 10% FBS, streptomycin/penicillin, 2-mercaptoethanol and MEM non-essential Amino Acid (all obtained from GIBCO)

extract_protocol:
Mouse splenic B220+ B cells were cross-linked in 1% (vol/vol) formaldehyde, lysed in Lysis Buffer [50 mM Tris•HCl, pH 8.1, 10 mM EDTA, 1% SDS, and protease inhibitors (Roche)] and sonicated for 20 × 20-s cycles on ice. Lysate was diluted 10-fold with Dilution Buffer (16.7 mM Tris•HCl, pH 8.1, 1.2 mM EDTA, 167 mM NaCl, 1.1% Triton X-100, 0.01% SDS, and protease inhibitors) and ChIP grade rabbit polyclonal antibodies (Abcam) against Histone H3 (mono methyl K4), Histone H3 (tri methyl K4) and Histone H3 (acetyl K27) were added to immune precipitate H3K4me1-DNA, H3K4me3-DNA and H3K27ac-DNA complexes, respectively. Protein-DNA complexes were captured with the addition of protein A agarose/salmon sperm DNA and then washed one time for 15 min at 4 °C with rotation, with Low Salt Wash Buffer (20 mM Tris•HCl, pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 1% SDS), one time with High-Salt Wash Buffer (20 mM Tris•HCl, pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 1% SDS), one time with LiCl Wash Buffer (10 mM Tris•HCl, pH 8.1, 1 mM EDTA, 0.25 M LiCl, 1% Nonidet P-40, 1% deoxycholate acid), and two times with TE buffer. Protein–DNA complexes were eluted from the protein A-beads by rotating at room temperature two times for 15 min in 250 μL of Elution Buffer (100 mM NaHCO3, 1% SDS) to a final volume of 500 μL. DNA–protein cross-link was reversed by the addition of 20 μL of 5 M NaCl and incubation at 65 °C for 4 h. DNA was purified using a PCR MinElute column (Qiagen).
Libraries were prepared using ChIP-Seq Library Prep Reagent Set for Illumina from NEB. Briefly, DNA was end-repaired. 3' A base was added and ligated to adaptors. After PCR amplification, DNA was purified and analyzed with Illumina HiSeq.

tag: strain background

tag: genotype/variation

value: EBV LMP2a transgenic

tag: cell type

value: B lymphocytes

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#

tag: chip antibody lot#


title: LMP2a-H3K4me1


title: GFP-H3K4me3

source_name: B220+ GFP B cells

value: GFP transgenic


title: GFP-Input


title: LMP2a-H3K4me3


title: GFP-H3K4me1


title: Sham

description: sham

tag: tissue


title: GFP-H3K27ac


title: KO_Spl_aTreg4

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

description:
Male littermates
Foxp3 allele

data_processing:
Libraries were sequenced using a HiSeq 2000 platform (Illumina) with a standard paired-end protocol.
Reads were first processed with Trimmomatic to remove TruSeq adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded.
Trimmed reads were then aligned to mm10 mouse genome with the STAR spliced-read aligner.
For each gene from the RefSeq annotations, the number of uniquely mapped reads overlapping with the exons was counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/).
Genome_build: mm10
Supplementary_files_format_and_content: count for each gene

source_name: Spleen

extract_protocol:
Sorted cells were lysed with TRIzol and stored at -80 degree. Total RNA was extracted according to the manufacturer’s manual (Life Technologies).
cDNA libraries were generated after SMART amplification (Clontech) and samples were individually indexed. Libraries were sequenced using a HiSeq 2000 platform (Illumina) according to a standard paired-end protocol.

value: Regulatory T cells

tag: genotype

value: 6-8 weeks


title: KO_Spl_rTreg3

description:
Male littermates
Foxp3 allele

value: Male


title: KO_Spl_rTreg4

description:
Male littermates
Foxp3 allele


title: WT_Spl_aTreg3

description:
Male littermates
Foxp3 allele

value: Wild type Foxp3-gfp


title: WT_Spl_aTreg2

description:
Male littermates
Foxp3 allele


title: KO_Spl_aTreg1

description:
Male littermates
Foxp3 allele


title: KO_Spl_rTreg1

description:
Male littermates
Foxp3 allele


title: WT_Thy_mCD4SP3

description:
Male littermates
Foxp3 allele

source_name: Thymus

value: Non-Treg CD4+ single positive


title: WT_Spl_rTreg1

description:
Male littermates
Foxp3 allele


title: KO_Thy_mCD4SP1

description:
Male littermates
Foxp3 allele


title: WT_Spl_aTreg1

description:
Male littermates
Foxp3 allele


title: WT_Spl_rTreg3

description:
Male littermates
Foxp3 allele


title: WT_Spl_rTreg2

description:
Male littermates
Foxp3 allele


title: KO_Thy_mCD4SP2

description:
Male littermates
Foxp3 allele


title: KO_Thy_mCD4SP3

description:
Male littermates
Foxp3 allele


title: WT_Thy_mCD4SP1

description:
Male littermates
Foxp3 allele


title: WT_Thy_mCD4SP2

description:
Male littermates
Foxp3 allele


title: KO_Thy_mCD4SP4

description:
Male littermates
Foxp3 allele


title: LMP2a-Input


title: KO_Spl_rTreg2

description:
Male littermates
Foxp3 allele


title: KO_Spl_aTreg2

description:
Male littermates
Foxp3 allele


title: KO_Spl_aTreg3

description:
Male littermates
Foxp3 allele


title: KO_Thy_Treg4

description:
Male littermates
Foxp3 allele


title: KO_Thy_Treg1

description:
Male littermates
Foxp3 allele


title: KO_Thy_Treg3

description:
Male littermates
Foxp3 allele


title: WT_Thy_Treg2

description:
Male littermates
Foxp3 allele


title: WT_Thy_Treg1

description:
Male littermates
Foxp3 allele


title: KO_Thy_Treg2

description:
Male littermates
Foxp3 allele


title: WT_Thy_Treg3

description:
Male littermates
Foxp3 allele


title: Abcc5 knockout brain 5

city: Amsterdam

first: Koen

last: van de Wetering

address: Plesmanlaan 121

department: Molecular Oncology

country: Netherlands

institute: Netherlands Cancer Institute

description:
ABCC5-5
10_Brain-Mrp5-5_TTAGGCA

data_processing:
The samples were single end sequenced with a length of 51 bp on a HiSeq2000 machine. The reads were aligned using Tophat (Version 2.0.6) against the Mouse reference (build 37). Tophat was supplied with a known set of gene models using a GTF file (Ensembl version 66).
HTSeq-count was used to generate a list with the number of uniquely mapped reads for each gene. All samples were combined into one dataset and genes that have no expression across all samples in the dataset were removed.
In order to determine the differentially expressed genes between groups, the R pacakge EdgeR and Limma were used. The voom function was used to transform the count data to log2 counts per million and the estimation of the variance across the samples. Different groups were defined and the differentially expressed genes were deterimined using lmFit and eBayes. Genes with a p-value < 0.05 were considered differentially expressed.
Genome_build: NCBI build 37
Supplementary_files_format_and_content: The file diffexp.txt conaints absolute counts, normalized and counts and results from the differential expression analysis.

source_name: Abcc5 knockout

extract_protocol:
Whole brains were collected from CO2-asphyxiated wildtype and Abcc5-/- mice, and immediately frozen on dry ice. After homogenization in Trizol (Invitrogen), RNA was extracted according to the manufacturer’s protocol.
Sequencing libraries were generated according to the manufacturer's instructions (TruSeq RNA Sample Preparation v2 Guide; Illumina; Part # 15026495 Rev. F). Briefly, polyadenylated RNA from intact total RNA was purified using oligo-dT beads. Following purification the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, part # 18064-014). Second strand synthesis was performed using Polymerase I and RNaseH. The resulting cDNA was converted to blunt end fragments using an end repair mix (Illumina), followed by 3' end adenylation and ligated to Illumina paired-end sequencing adapters and subsequently amplified by 16 cycles of PCR.

value: FVB/NJ

value: Abcc5 knockout; Abcc5-/-

value: Whole brain


title: Dmel Input female

description: genomic DNA

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.87
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

value: third instar

value: female

value: none (input)


title: Abcc5 knockout brain 3

description:
ABCC5-3
8_Brain-Mrp5-3_GTGAAAC


title: Abcc5 knockout brain 1

description:
ABCC5-1
6_Brain-Mrp5-1_CCGTCCC


title: Wildtype brain 5

description:
WT-5
5_Brain-wildtype-5_ATGTCAG

source_name: Wildtype

value: Wildtype; Abcc5+/+


title: Abcc5 knockout brain 2

description:
ABCC5-2
7_Brain-Mrp5-2_GTCCGCA


title: Wildtype brain 4

description:
WT-4
4_Brain-wildtype-4_AGTTCCG


title: Dmel MSL1 ChIP female

description: genomic DNA

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.86
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Bigwig files for 4C-seq were produced using FourCSeq (Klein et al., 2014). Only reads with mapping quality > 20 where used. For MSL1 the log2ratio of ChIP-input was computed using bamCompare from deepTools (Ramirez et al., 2014). For MNAse data, custom script were created to compute the coverage of the center of paired-end fragments.
processed data files format and content: bigwig files containing 4C-seq counts per fragment for 4C data, bigwig files containing the log2 ratio of ChIP-seq over input for MSL1 data, big2wig files
Genome_build: dm3

value: polyclonal MSL1 antibody raised against the N-terminus (AA1-584)


title: Wildtype brain 3

description:
WT-3
3_Brain-wildtype-3_AGTCAAC


title: Wildtype brain 2

description:
WT-2
2_Brain-wildtype-2_CTTGTAA


title: WT run0141_lane1_index3=5188MID~mouse_align

city: Cincinnati

first: Nupur

last: dasgupta

state: OH

address: 3333, Burnet Avenue

department: human Genetics

institute: CCHMC

description: WT

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Post Binary Alignment/Map (BAM) aligned files of RNASeq data were analyzed using Avadis® NGS software, Version 1.3.0. Reads were filtered to remove 1) duplicate reads, 2) non-primary-matched reads and 3) reads with alignment scores <95. Quantification was performed on the filtered reads against the RefSeq annotation. Post filtering the read counts dropped between ~35-43% for the mRNA
Data normalization was performed with DESeq. The sequencing depth is estimated by the read count of the gene with the median read count ratio across all genes. The method is based on the negative binomial distribution, which allows for less restrictive variance parameter assumptions than does the Poisson distribution. The false discovery rate (FDR) was calculated according to the Benjamini and Hochberg algorithm.  1.5 FC with an FDR of 0.05 was used as selection criteria
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalised values values for each Sample ...

extract_protocol:
Isolated mice tissues from whole brain and brain regions were immediately immersed in RNA Later. RNAs (mRNA and miRNA) were extracted using the Ambion mirVana™ miRNA Isolation Kit (Ambion, AM1560) following manufacture instruction
RNA-Seq as per Illumina

treatment_protocol: The 4L;C* mice were treated with a pharmacological chaperone, isofagamine tartrate (IFG), at 60 mg/kg/d by drinking water.The pregnant dames were given drinking water containing IFG staring 3 to 5 days prior to birth and during the weaning period. After weaning, the pups were continued on 60 mg/kg/d IFG in drinking water for entire course.The brain tissues from all the cohorts (3 mice per cohort) were harvested at the age of 42-45 days. Whole brains were collected from 4L;C* and WT control mice.  Four brain regions were collected as cerebral cortex (CO), brain stem (BS), midbrain (MID) and cerebellum (CB) from 4L;C*, IFG treated 4L;C* and WT mice. The collected brain samples were used for lipid (GC and GS) and RNA (mRNA and miRNA) analyses

value: WT

value: Midbrain

tag: tissue (abbreviation)

value: MID


title: 4L;C* run0141_lane5_index19=5186MID~mouse_align


title: WT run0141_lane5_index10=5753MID~mouse_align

description: WT


title: Wildtype brain 1

description:
WT-1
1_Brain-wildtype-1_CAGATCA


title: 4L;C* run0141_lane5_index11=5754MID~mouse_align


title: 4L;C* run0139_lane6_index8=6913MID~mouse_align


title: 4L;C* run0139_lane5_index3=6912MID~mouse_align


title: 4L;C* run0139_lane5_index1=5755MID~mouse_align


title: 4L;C* run0141_lane5_index7=5188CO~mouse_align

value: Cortex

value: CO


title: 4L;C* run0139_lane2_index9=6914MID~mouse_align


title: Abcc5 knockout brain 4

description:
ABCC5-4
9_Brain-Mrp5-4_ATCACGA


title: 4L;C* run0141_lane5_index5=5186CO~mouse_align


title: WT run0141_lane5_index13=5754CO~mouse_align

description: WT


title: WT run0141_lane5_index15=6912CO~mouse_align

description: WT


title: 4L;C* run0141_lane5_index12=5753CO~mouse_align


title: WT run0141_lane5_index14=5755CO~mouse_align

description: WT


title: 4L;C* run0141_lane1_index18=6914CO~mouse_align


title: WT run0141_lane1_index6=5187CO~mouse_align

description: WT


title: 4L;C* run0141_lane5_index1=5187MID~mouse_align


title: 4L;C* run0144_lane2_index11=6912CB~mouse_align

value: Cerebellum

value: CB


title: 4L;C* run0141_lane3_index1=5753CB~mouse_align


title: 4L;C* run0141_lane3_index2=6913CB~mouse_align


title: WT run0141_lane3_index3=5754CB~mouse_align

description: WT


title: outlier run0141_lane3_index4=6914CB~mouse_align

description: outlier

value: outlier


title: WT run0140_lane1_index25=5187CB~mouse_align

description: WT


title: 4L;C* run0140_lane1_index9=5753BS~mouse_align

value: Brain Stem

value: BS


title: 4L;C* run0140_lane3_index22=6914BS~mouse_align


title: WT run0141_lane3_index10=5755CB~mouse_align

description: WT


title: 4L;C* run0140_lane1_index3=5187BS~mouse_align


title: 4L;C* run0140_lane2_index23=5186CB~mouse_align


title: WT run0140_lane1_index20=6912BS~mouse_align

description: WT


title: WT run0140_lane1_index1=5186BS~mouse_align

description: WT


title: 4L;C* run0140_lane1_index11=5755BS~mouse_align


title: 4L;C* run0141_lane1_index16=6913CO~mouse_align


title: IgG_NE

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Basecalls performed using Real-Time Analysis (RTA) software
BCL2FASTQ Conversion Software was used to generate fastq files
Reads were aligned to the mm10 genome assembly using tophat version 2.0.10 (dependent on bowtie2, version 2.1.0) with parameter --read-realign-edit-dist 2
sam files were converted to bam and technical replicates were merged with samtools
Transcript abundances were calculated with RSEM version 1.2.8
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with RSEM (rsem-calculate-expression) output containing TPM (transcript per milion) and FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped)

source_name: liver

extract_protocol:
Liver tissue (~100 mg) was immersed in 2 mL of hypotonic buffer A [10 mM HEPES (pH 7.9), 2 mM MgCl2, and 2 mM KCl] supplemented with protease and phosphatase inhibitors (Thermo, 78441) and 40 U/mL ribonuclease inhibitor (Invitrogen, 10777-019). Thereafter, samples were ground with a loose (10 times) and tight (30 times) Dounce pestle and centrifuged at 2000 rpm for 5 min at 4oC. The supernatant (cytoplasmic fraction) was transferred to a fresh tube and the pellet (nuclei) was suspended in 0.5 mL of Buffer C [25% glycerol, 20 mM HEPES (pH 7.9), 2 mM MgCl2, 420 mM NaCl, and 0.2 mM EDTA] supplemented with protease, phosphatase, and ribonuclease inhibitors, incubated on ice for 15 min with mixing every 3 min, and centrifuged at 12000 rpm for 10 min at 4oC. The supernatant was diluted with three volumes of buffer A containing inhibitors (nuclear fraction) and kept on ice until IP was performed. Ten micrograms of an anti-hnRNPK antibody (#54) or control IgG (Vector Labs, I-1000) was conjugated to 50 µL of Dynabeads Protein-A (Life Technologies, 10002D) and used in a single IP reaction. Cytoplasmic and nuclear extracts were first incubated with IgG-conjugated Dynabeads for 30 min at 4oC with rotation, separated from the beads using a magnetic stand, and subjected to IP reaction with anti-hnRNPK antibody-conjugated Dynabeads under the same conditions. Beads were washed three times with IP buffer [150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, NP-40 (0.5% vol/vol), and Triton X-100 (1.0% vol/vol)] and RNA was eluted from the beads with 200 µL of RLT buffer supplemented with β-mercaptoethanol from an RNeasy Mini Kit (Qiagen). Thereafter, on-column DNAse I digestion and RNA clean-up were performed according to the RNeasy Mini Kit protocol. The RNA concentration was measured using a Nanodrop instrument and RNA was stored at -80oC.
RNA-sequencing library was prepared from 400 ng of total or immunoprecipitated RNA using an Illumina TruSeq RNA Sample Preparation Kit

value: mixed

tag: cell compartment

value: nucleus

tag: molecule type

value: hnRNPK-bound RNA


title: DT_NE_2

tag: strain

value: high-fat


title: DT_total_2_2

value: total

value: total RNA


title: DT_Cyt_2

value: cytoplasm


title: DT_NE_1


title: DT_total_2_1


title: 4L;C* run0141_lane3_index19=5188CB~mouse_align

tag: age


title: DT_total_1_2


title: IgG_Cyt


title: DT_total_1_1


title: DT_Cyt_1


title: WT_Cyt_2

value: normal


title: WT_NE_2


title: 4L;C* run0140_lane1_index8=5188BS~mouse_align


title: 4L;C* run0140_lane1_index10=5754BS~mouse_align


title: WT_total_2_1


title: WT_NE_1


title: WT_total_2_2


title: OB_total_2_2


title: OB_NE_2


title: WT_total_1_2


title: WT_total_1_1


title: OB_total_2_1


title: OB_Cyt_1


title: OB_NE_1


title: OB_total_1_1


title: OB_Cyt_2


title: WT_Cyt_1


title: Uninduced isolated GFP myotubes, replicate 2

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

description:
replicate 2
Sample 12

data_processing:
Fastq files were aligned with TopHat v. 2.0.11 with the option --b2-very-sensitive
The resulting BAM files were sorted, indexed, and merged (for each sample, the files from the two lanes) using samtools v. 0.1.19
The sorted, indexed, and merged BAM files were coverted into count tables with the function summarizeOverlaps with option 'IntersectionNotEmpty', in the R package GenomicAlignments v. 1.0.6
For each comparison performed for differential expression, a DGElist object was created using the function DGEList, in the R package edgeR v. 3.6.8
On each DGElist object, normalization was performed for RNA composition effects, to scale the raw library sizes for the library sizes that minimize the log-fold changes between the samples for most genes (function R calcNormFactors in edgeR package)
For each normalized DGElist object, common dispersion, as well as tagwise dispersion, were estimated using the R functions estimateCommonDisp and estimateTagwiseDisp, in the package edgeR
Tables of differentially expressed genes were produced with the R function exactTest
Genome_build: mm9
Supplementary_files_format_and_content: The txt file was generated using the GenomicAlignments R package, v 1.0.6 (see above); scores represent raw read counts for features (genes). Columns 1-16 correspond to the 16 samples analyzed, and last column represents the HUGO Symbol for each feature analyzed. The rows identically equal to 0 have been removed.

source_name: Isolated transgenic pmi28 myotubes with inducible GFP transgene

growth_protocol: Transgenic mouse pmi28 myoblasts with inducible msx2 and GFP transgenes were cultured in DMEM supplemented with 20% fetal bovine serum and 1% L-Glutamine and cultured at 37 0C in 5% CO2. Myotubes were obtained by switching the confluent myoblast cultures to a medium with DMEM supplemented with 10% horse serum and 1% L-Glutamine at 37 0C in 5% CO2 for three days. 3 day old heterogenous myotube cultures of pmi28 line were gently washed with PBS and incubated in pre-warmed StemPro Accutase dissociation reagent (Invitrogen, Carlsbad, CA, USA) for 10 minutes at 37 0C. The cell suspension was filtered with a 40 mm nylon filter mesh (BD Falcon, Franklin Lakes, New Jersey, USA). The filter was washed with differentiation medium several times to get rid of mononucleated cells. Myotubes that are trapped on the mesh were retrieved and recultured on gelatin-coated culture dishes in differentiation medium containing 25mM AraC. After three days, the medium was replaced with fresh differentiation medium to get rid of AraC before the treatments were initiated.

extract_protocol:
RNA was extracted with TRIzol (Invitrogen, Carlsbad, CA, USA), DNase-treated with TURBOTM DNase (Ambion, Life Technologies, Waltham, MA, USA),
RNA libraries for sequencing were prepared with 500ng total RNA input using a standard Illumina protocol (TruSeq Stranded mRNA LT Sample Prep Kit -Catalog IDs: RS-122-2101, RS-122-2102), with 12 instead of 15 cycles of PCR amplification.

treatment_protocol: To induce transgene expression, isolated myotube cultures were treated with 2ug/ml doxycycline in growth medium (DMEM supplemented with 20% fetal bovine serum and 1% L-Glutamine) for 24 hours.

tag: cell line

tag: differentiation status

value: myotube

tag: inducible trasngene

value: GFP only

tag: transgene expression


title: Uninduced GFP myoblasts, replicate 2

description:
replicate 2
Sample 10

source_name: Transgenic pmi28 myoblasts with inducible GFP transgene

value: myoblast


title: Induced isolated GFP myotubes, replicate 3

description:
replicate 3
Sample 16


title: Induced isolated GFP myotubes, replicate 2

description:
replicate 2
Sample 15


title: Uninduced isolated GFP myotubes, replicate 3

description:
replicate 3
Sample 13


title: Induced isolated GFP myotubes, replicate 1

description:
replicate 1
Sample 14


title: Uninduced isolated GFP myotubes, replicate 1

description:
replicate 1
Sample 11


title: Uninduced GFP myoblasts, replicate 1

description:
replicate 1
Sample 9


title: Induced isolated msx2 myotubes, replicate 3

description:
replicate 3
Sample 8

source_name: Isolated transgenic pmi28 myotubes with inducible msx2+GFP transgenes

value: msx2 and GFP


title: Uninduced isolated msx2 myotubes, replicate 2

description:
replicate 2
Sample 4


title: Uninduced isolated msx2 myotubes, replicate 1

description:
replicate 1
Sample 3


title: Uninduced msx2 myoblasts, replicate 1

description:
replicate 1
Sample 1

source_name: Transgenic pmi28 myoblasts with inducible msx2+GFP transgenes


title: Induced isolated msx2 myotubes, replicate 2

description:
replicate 2
Sample 7


title: Uninduced isolated msx2 myotubes, replicate 3

description:
replicate 3
Sample 5


title: Uninduced msx2 myoblasts, replicate 2

description:
replicate 2
Sample 2


title: Induced isolated msx2 myotubes, replicate 1

description:
replicate 1
Sample 6


title: Control_H3K4me3_ChIPSeq_R2

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

country: France

institute: Université de Rennes 1

data_processing:
Basecalls performed using CASAVA version 1.8.3
The resulting sequences were quality filtered with Sickle program with –q 33 and mapped back to mouse mm9/NCBI37 genome using Bowtie versions 1.0.0 (seed length 20). Only tags that passed the quality filter and mapped uniquely to the genome were used. The number of mapped reads in each file was normalized according to reads number.
Identification of the H3K4me3 marks’ peaks was performed using MACS 2.0.1  and with two biological replicates samples, including corresponding input (shift size window = 73 bp, nomodel, P-value threshold < 10-5).
To compare ATZ treated versus control H3K4me3 CHIP data sets, differential peak calling was performed using several steps. First,  we selected the set of peaks reproducible in both replicates based on an irreproducible discovery rate (IDR) of 0.05. From selected peaks dataset, we kept only peaks with average expression value in at least above 5% percentile of all peaks. Last, we selected the peaks with fold change above 1.5 and FDR < 5%. The statistical significance was calculated using linear regression model software.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated by coverageBed algorithm in the BEDTools suite. The fourth column in each bedGraph file represents the coverage strength.

source_name: Testes

extract_protocol:
Lysates from testis cells were sonicated, clarified and DNA protein complexes were isolated with anti H3K4me3 antibodies.
Immunoprecipitated DNA was purified from proteins.The DNA concentration was measured with Quantus Fluoremeter (E6150, Promega), using Quantiflor dsDNA system, (E2670, Promega). The libraries were prepared from 50 ng of ChiP and Input material using NEBNext Ultra DNA library Prep Kit for Illumina (NEB #E7370S). Library selection was done using excision fragments from 2% agarose gel including GelGreen stain (Gentaur, 41005), 180-220 bp fragments were excised using Dark reader transilluminator (Clare Chemical research, Dr-46B). The Illumina Hiseq2000 Genome Analyzer was used to perform massively parallel 51 bp sequencing in Single End mode. 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: Mice were treated 3 weeks with atrazine at a concentration of 100 mg/l in drinking water nearly corresponding to 25mg/kg/days. Treatment was stopped two weeks after to observe the effect of atrazine on a complete round of spermatogenesis from moment of treatment.

tag: chip antibody

value: Rabbit anti-H3K4me3 (07-473)

tag: agent


title: Atrazine_H3K4me3_ChIPSeq_R1

value: Atrazine


title: Atrazine_H3K4me3_ChIPSeq_R2


title: Atrazine_input_DNA

value: none, input


title: Flank_H3K27ac_Replicate1

city: Athens

first: Carlos

middle: Rafael

last: Infante

state: GA

address: 500 D.W. Brooks Dr

department: Genetics

institute: University of Georgia

data_processing:
Basecalls were performed CASAVA version 1.8.2.
Illumina reads were aligned to the mouse genome (mm9) or green anole genome (anoCar2) with Bowtie version 1.1.0 with the options "--best --sam -t -l 28 -n 3 -m 1".
ChIP-Seq data quality and fragment size was assessed from aligned reads for each sample using phantompeaktools (https://code.google.com/p/phantompeakqualtools/).
Regions of H3K27ac enrichment were determined using macs2 (version 2.0.10.20130501) with the options “--bdg --SPMR --nomodel --qvalue=0.05”. Extension size was determined for each sample based on the cross-correlation profile of the aligned reads.
BigWig files of H3k27ac signal visualized as fold enrichment compared to background were generated from treatment and control bedGraph files using macs2 bdgcmp with the options " --tdepth=1 --cdepth=1 --method=FE". BedGraph files were converted to BigWig using BEDtools slopBed command and the bedClip and bedGraphToBigWig from UCSC Kent Utilities as implemented in the bdg2bw script by Tao Liu (https://gist.github.com/taoliu/2469050).
Genome_build: mm9 (Mus musculus); anoCar2 (Anolis carolinensis)
Supplementary_files_format_and_content: BigWig files were generated from treatment and control signal files created by macs2 and represent the fold enrichment of the ChIP sample versus the input DNA control. Bed files were created from the first 6 columns of the narrowPeak format files created by macs2 and represent regions with significant H3K27ac enrichment compared to background signal from input DNA controls with a qvalue cutoff of 0.05.

source_name: embryonic flank

growth_protocol: Normal gestation

extract_protocol:
After cross-linking in 1% formaldehyde in PBS for 30 minutes, tissues were rinsed and treated with trypsin for 5 minutes to generate a single cell suspension. Samples were then pre-disrupted with a Branson 450 Sonifier, and then sheared with a Bioruptor (Diagenode) to generate a chromatin size range of 200–600 bp. PureProteome Protein G Magnetic Beads (Millipore) were pre-incubated with H3k27ac antibody before incubating overnight with 100-200 μg of sheared chromatin. After washing, immune complexes were eluted from the beads, and protein-DNA crosslinks were reversed by incubating at 65˚C overnight. After treatment with RNase followed by proteinase K, samples were purified with the QIAquick PCR Purification Kit (Qiagen).
ChIP and input chromatin control libraries were produced using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England BioLabs) as directed by the manufacturer with Illumina-compatible adapters. Libraries were sequenced with 50 bp single-end runs on an Illumina HiSeq 2000 at the HudsonAlpha Institute for Biotechnology.

value: ICR

value: embryonic flank

tag: developmental stage

value: wild type

value: H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294)


title: Flank_Input_DNA


title: Eye_Input_DNA_Replicate1

source_name: embryonic eye

value: embryonic eye


title: Hi-Myc_enzalutamide_AR_ChIP-Seq

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were obtained and mapped to the human genome (mm9 or build 37) using Bowtie to generate BAM files
Duplicates were removed using Samtools
Peak detection was performed with the software MACS (Version 1.4.1) with input as controls.
Genome_build: Build 37 or mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks

source_name: Mouse Prostate, enzalutamide (30 mg/kg) oral gavage x 3 days

growth_protocol: Hi-Myc transgenic mice were fed ad lib

extract_protocol:
Prostates were dissected and then minced in 1.5ml tube with fine scissors. They were crosslinked for 15-minutes in 1% parformaldehyde. After quenching with glycine, the cross-linked chromatin was dounced and then sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with 5 ug of the indicated antibody, washed, eluted, reverse cross-linked, and purified.
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 18 cycles. DNA was purified using Ampure beads and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Mice underwent surgical castration or drug treat via oral gavage

value: Hi-Myc

tag: tissue type

value: prostate tumor

tag: ip antibody

value: AR IP (Epitomics clone ER179(2))


title: Eye_H3K27ac_Replicate1


title: OB_total_1_2

tag: diet

value: total

value: total RNA


title: Eye_H3K27ac_Replicate2

tag: tissue


title: Hi-Myc_bicalutamide_AR_ChIP-Seq

source_name: Mouse Prostate, bicalutamide (30 mg/kg) oral gavage x 3 days


title: VCaP_DHT+Bicalutamide_AR_ChIP-seq

description: Chromatin IP against AR

data_processing:
Alignment: ChIP-seq reads were obtained and mapped to the human genome (hg18, build 36) using either the AB SOLiD pipeline (LNCaP-AR and VCaP) or the Illumina CASAVA pipeline (v1.8.0; CWR22PC). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification and data analysis.
Peak detection was performed with the software MACS (Version 1.4.0) with input as controls.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data are peaks in the standard bed format.

organism: Homo sapiens

source_name: Prostate cancer cells

growth_protocol: LNCaP-AR cells were grown in RPMI containing 10% FBS, VCaP cells were grown in DMEM containing 10% FBS, CWR22PC cells were grown in RPMI containing 10% FBS plus 0.1nM DHT

extract_protocol: ChIP library was prepared for sequencing by the SOLiD (LNCaP-AR and VCaP) or HiSeq2000 (CWR22PC) instruments according to manufacturer recommended procedures.

treatment_protocol: LNCaP-AR cells were grown in charcoal-stripped serum containing phenol-red free media for 72hrs and then treated with vehicle or 1nM R1881 or 1nM R1881 plus 10µM Bicalutamide or 1nM R1881 plus 10µM MDV3100 for 1hr. VCaP and CWR22PC cells were grown in regular media and treated with vehicle or 1nM DHT or 1nM DHT plus 10µM Bicalutamide or 1nM DHT plus 10µM MDV3100 for 1hr.

value: VCaP

tag: cell type

value: Prostate cancer

value: AR (Millipore, 06-680)


title: VCaP_DHT+MDV3100_AR_ChIP-seq

description: Chromatin IP against AR


title: Hi-Myc_Input_DNA

source_name: Mouse Prostate, Vehicle x 3 days

value: Input DNA


title: Hi-Myc_AR_ChIP-Seq


title: Eye_Input_DNA_Replicate2

tag: genotype


title: Control_H3K4me3_ChIPSeq_R1

value: Rabbit anti-H3K4me3 (07-473)


title: VCaP_Vehicle_AR_ChIP-seq

description: Chromatin IP against AR


title: F145

city: Beijing

first: Qi

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

description:
PolyA RNA
The cell line F145 was constructed by a cooperation lab.

data_processing:
Base-calling were performed using CASAVA.
The RNA-seq reads were mapped to mouse mm9 genome assembly using TopHat2 software (version 2.0.4) with the settings: --transcriptome-index, --bowtie1, -N 2 --segment-length 33.
Transcriptomes were assembled from mapped fragments with Cufflinks (version 2.0.2) and the expression of transcripts were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: MGSCv37
Supplementary_files_format_and_content: BedGraph files were generated using the sam2wig.py in Seqgene.

source_name: mouse embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described on mitomycin-C-treated MEF cells with DMEM (Gibco) plus 15% FBS (Gibco), 1,000U/ml LIF (Chemicon), 2mM glutamine (Sigma), 1mM sodium pyruvate (Sigma), 0.1mM β-mercaptoethanol (Sigma) and 0.1mM non-essential amino acids (Invitrogen). Mouse embryonic fibroblast cells (CF1 genetic background), which were used as the feeder cells for the mESC culture, and tail tip fibroblast cells (B6D2F1 genetic background) were isolated from E13.5 fetuses and adult tail tip tissues, respectively, and cultivated with DMEM plus 10% FBS (Gibco).

extract_protocol:
Mouse ES cells and TTF were trypsinized, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Paired-end RNA-Seq libraries were prepared from TTF and mESC.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: embryonic stem cells

tag: strain/background

tag: genotype/variation


title: VCaP_Input_DNA

description: input DNA

value: none (input)


title: LNCaP-AR_R1881+MDV3100_AR_ChIP-seq

description: Chromatin IP against AR

value: LNCaP-AR


title: F145TTF

description: PolyA RNA

source_name: mouse adult tail tip fibroblasts

value: tail tip fibroblasts


title: SIM 64

city: Dublin

first: Finbar

middle: Patrick

last: MacCarthy

address: St. James's Hospital, James's Street,

department: Clinical Medicine

country: Ireland

institute: Institute of Molecular medicine,Trinity Centre for Health Sciences,

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequencing data obtained was assessed prior to analysis using FastQC. QC was performed inputting each read set of a pair separately, with separate assessment of forward and reverse reads. Where necessary, trimming of unsatisfactory quality segments of reads was performed in accordance with FastQC results using Trimmomatic. FastQC was repeated to ensure suitability of trimmed reads for downstream analysis.
Read alignment was performed using TopHat v2.0.3 using NCBI Build 37.2 as reference genome and transcriptome. Unmapped reads, reads that did not align uniquely and those not aligned with the partner read were discarded.
Quality assessment of alignment was performed using PICARD tools. Sequences aligned to the human genome were sorted using SAMtools  and subsequently assigned to genes and counted using  HTSeq-count. Genes which did not have at least 10 read counts in each sample were excluded from further analysis
Normalisation and differential expression analysis was performed using DESeq v1.10.1. In order to reduce multiple testing error p-value was adjusted using the Benjamini-Hochberg procedure. Genes with at least 2-fold change with an adjusted p-value (Q-value) of <0.1 were considered for further analysis
Network and gene ontology analysis was performed using Ingenuity Pathway Analysis (IPA, Ingenuity Systems, Redwood City, CA).
Genome_build: NCBI Homo sapiens build 37.2
Supplementary_files_format_and_content: tab delimited text files

source_name: Endoscopic Biopsy

extract_protocol:
RNA was extracted using the Qiagen RNA minElute kit (Qiagen, Limburg, Netherlands) with slight modification of the manufacturer’s protocol utilising TRIzol reagent.
mRNA purification, cDNA synthesis, Adapter ligation, DNA enrichment, library validation and normalisation were performed with the TruSeq RNA kit (Illumina inc. San Diego, CA) as per the manufacturer’s instructions (sample prep v. 2).

tag: degree of dysplasia

value: Simple intestinal metaplasia

tag: biopsy site

value: Barrett's Oesophagus segment


title: LNCaP-AR_R1881+Bicalutamide_AR_ChIP-seq

description: Chromatin IP against AR

tag: cell line


title: SIM 55


title: LNCaP-AR_Vehicle_AR_ChIP-seq

description: Chromatin IP against AR


title: LNCaP-AR_R1881_AR_ChIP-seq

description: Chromatin IP against AR


title: SIM 41


title: LNCaP-AR_Input_DNA

description: input DNA


title: SIM 38


title: Control_input_DNA

tag: strain

value: none, input


title: LGD 48

value: Low Grade Dsyplasia


title: LGD 58


title: VCaP_DHT_AR_ChIP-seq

description: Chromatin IP against AR


title: LGD 61


title: SIM 26


title: SIM 7


title: LGD 2


title: LGD 62


title: LGD 47


title: LGD 19


title: HGD 43

value: High Grade Dsyplasia


title: HGD 39


title: HGD 40


title: HGD 20


title: HGD 6


title: HGD 21


title: SIM 16


title: HGD 4


title: mA16d#4

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
RNA sequencing data was generated using Illumina Hiseq 2000 paired-end 101bp, and Illumina Genome Analyzer was used for base calling.
Paired-end sequences were mapped to mouse transcriptome using STAR (A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635) with default parameters and maximum 3 mismatches.
Transcripts per milliion (TPM) were calculated based on  Wagner et al., Theory Biosci, 2012, 131:281-285. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
TPM from all samples were log2 converted and quantile normalized
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing log2 TPM (transcript per million) of all samples

source_name: IDH1(R132H)-transduced mouse p53-null neural stem cells deleted of Atrx

growth_protocol: Control and Atrx-deleted mouse p53-null neural stem cells transduced with mutant IDH1(R132H) were cultured in either neural prolferation medium supplemented with 20 ng/ml EGF + bFGF or differentiation medium (neural basal medium + B27 withour growth factor supplement).

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq RNA Sample Preparation kit (Illumina)

treatment_protocol: Differentiation samples were induced for differentiation for 8 days in differentiation medium (neural basal medium + B27 withour growth factor supplement).

value: Neural stem cells


title: Control NSC#2-differentiation

source_name: IDH1(R132H)-transduced mouse p53-null neural stem cells upon 8 day differentiation induction in neural basal medium + B27 without growth factor supplements


title: mA19d#4-differentiation

source_name: IDH1(R132H)-transduced mouse p53-null neural stem cells deleted of Atrx were upon 8 day differentiation induction in neural basal medium + B27 without growth factor supplements


title: mA19d#7


title: mA16d#4-differentiation


title: Control NSC#1-differentiation


title: mA19d#7-differentiation


title: Control NSC#2

source_name: IDH1(R132H)-transduced mouse p53-null neural stem cells


title: Control NSC#1


title: ColxLer Rep B

city: Acton

first: Michael

last: Groszmann

state: ACT

address: Clunies Ross St

department: Agriculture

institute: CSIRO

description: ColxLer Rep B Read 1 and Read 2

data_processing:
Read quality was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed and mapped to the TAIR10 reference genome using BioKanga align (http://sourceforge.net/projects/biokanga/) using default settings and additionally implementing parameters -A5000 and -M5.
Mapped reads were allocated to genomic features (as per TAIR10 annotations) using BioKanga maploci on default settings.
Supplementary_files_format_and_content: Text File - Gene ID and counts of associated aligned reads (pre-normalised counts) for all samples

source_name: Whole aerial tissue 15 day old seedlings

growth_protocol: Plants were grown on agar plates as described in Groszmann et al., 2014 Plant Physiology.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plant MiniKitTM with on column DNA digestion using the QIAGEN RNAse free DNAse setTM. Libraries were prepared and sequenced by a service provider using the illumina True-seq kit and sequenced on an illumina GAIIx or Hi-Seq as mRNA-seq single-ended or pair-ended runs.  (For more details see associated publicaiton).
illumina True-seq kit

value: whole aerial seedling

tag: age

value: 15 day old

value: ColxLer


title: Hi-Myc_Castrate_AR_ChIP-Seq

source_name: Mouse Prostate, Castration 3 days prior

value: Hi-Myc

value: prostate tumor

value: AR IP (Epitomics clone ER179(2))


title: LerxCol Rep A

description: LerxCol Rep A Read 1 and Read 2

value: LerxCol


title: ColxLer Rep A

description: ColxLer Rep A Read 1 and Read 2


title: ColxC24 Rep A

description: ColxC24 Rep A Read 1 and Read 2


title: ColxC24 Rep B

description: ColxC24 Rep B Read 1 and Read 2


title: LerxC24 Rep A

description: LerxC24 Rep A Read 1 and Read 2


title: LerxC24 Rep F

description: LerxC24 Rep F Read 1 and Read 2


title: C24xCol Rep A

description: C24xCol Rep A Read 1 and Read 2


title: LerxC24 Rep B

description: LerxC24 Rep B Read 1 and Read 2


title: C24xCol Rep B

description: C24xCol Rep B Read 1 and Read 2


title: LerxCol Rep B

description: LerxCol Rep B Read 1 and Read 2


title: C24xLer Rep E

description: C24xLer Rep E Read 1 and Read 2


title: LerxC24 Rep G

description: LerxC24 Rep G Read 1 and Read 2


title: C24xLer Rep D

description: C24xLer Rep D Read 1 and Read 2


title: C24xLer Rep B

description: C24xLer Rep B Read 1 and Read 2


title: Col Rep B

description: Col Rep B Read 1 and Read 2

value: Col


title: mA19d#4


title: C24xLer Rep A

description: C24xLer Rep A Read 1 and Read 2


title: Ler Rep G

description: Ler Rep G Read 1 and Read 2

value: Ler


title: Col Rep A

description: Col Rep A Read 1 and Read 2


title: Ler Rep F

description: Ler Rep F Read 1 and Read 2


title: Ler Rep B

description: Ler Rep B Read 1 and Read 2


title: Ler Rep D

description: Ler Rep D Read 1 and Read 2


title: Ler Rep A

description: Ler Rep A Read 1 and Read 2


title: C24 Rep G

description: C24 Rep G Read 1 and Read 2


title: C24 Rep F

description: C24 Rep F Read 1 and Read 2


title: C24 Rep D

description: C24 Rep D Read 1 and Read 2


title: C24 Rep A

description: C24 Rep A Read 1 and Read 2


title: C24 Rep B

description: C24 Rep B Read 1 and Read 2


title: TSCendo-B6#1

city: Jerusalem

first: Yossi

last: buganim

address: Ein Karem 91120

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Illumina bcl2fastq, v2.15.0.4, was used for transforming basecalls to fastq files.
Sequenced reads were quality trimmed at both ends with PHRED score threshold of 32, trimmed for adaptor sequence with Trim Galore, v0.3.7, and filtered for low-quality reads with the FASTX package, v0.0.13. Reads were then mapped to GRCm38 (mouse) using TopHat v2.0.11 with parameters -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 18 --read-realign-edit-dist 5 --b2-i S,1,0.75 --b2-mp 3,1 --b2-score-min L,-0.5,-0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Cufflinks package v2.2.1 with the programs cuffquant and cuffnorm, using parameters -b, -u and a masking file with all IG, TR, rRNA, tRNA, miRNA, snRNA, snoRNA and pseudo entries of the mouse GTF file.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts and FPKM values at gene level for each sample. Fields are Ensembl_Gene_ID, Ensembl_Transcript_ID, Gene_Full_Name, Gene_Symbol, Gene_Biotype, EntrezGene_ID, RefSeq_mRNA, UCSC_ID, First_replicate_count, Second_replicate_count, First_replicate_fpkm, Second_replicate_fpkm. Multiple data is separated by semicolon. Missing data is represented by a question mark.

source_name: endogenous trophoblast stem cells

growth_protocol: TSCs and iTSCs were cultured under TX medium condition as decribed in PMID:24527396. mESCs were cultured in 2i medium and MEFs with DMEM supplemenated with 10% FBS medium

extract_protocol:
Cells were homogenized and RNA was harvested using the RNeasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endogenous trophoblast stem cells


title: Transgenic line biological Rep2_sRNA

city: Paterna

first: Regis

middle: Lopes

last: Correa

state: Valencia

address: CL. Catedrático Agustín Escardino 9

country: Spain

description:
sRNA
GNU20, GNU22

data_processing:
Reads from the RNA-Seq data were mapped to the A. thaliana genome (TAIR 9) using the software BWA v0.5.8c with a maximum set of two mismatches in the first 32 bases of the sequences, and a maximum of more mismatches in total (reads with 225 bp length).
The expression level was estimated by counting the reads mapped to the features (genes) with the software SeqMonk v. 0.13.0. Only the reads mapped to mRNA features were used in further analyses. Expression levels were presented with the FPKM (Fragments per Kilobase per Million reads) metric, analogous to the RPKM (reads per kilobase per million reads) metric, which allows read counts to be normalized by both transcript length and total number of mapped reads in the library for paired-end sequenced data. To remove features with poor statistics and reduce the number of candidates, we used an approach based on a constant threshold of 10 counts in at least one of the libraries (the size of the feature was not taken into account).
The miRCat software (plant version) was initially used to align all 18- to 24-nt long sRNAs sequenced to the A. thaliana TAIR 9 genome, using default parameters. All putative miRNA precursor sequences extracted from the genome by the miRCat software were mapped against the redundant set of  18- to 24-nt long sRNAs with the Bowtie software. The Bowtie output was filtered with an in-house filter tool (FilterPrecursor) in order to identify candidate sequences as miRNA precursors. The software scans the data and identifies patterns of one or two blocks of perfect matching sRNAs, that would correspond to where mature and/or star miRNA sequences align. The filtering was done with the following default parameters: minimum number of mapped reads in the candidate precursors: 10; maximum offset allowed for a single read: 5; maximum percentage of reads mapped out of columns: 25; maximum number of columns in the mapping profile: 2. FilterPrecursor`s source code can be downloaded at: http://code.google.com/p/filter-precursors/downloads/list. The resulting files, containing the 18- to 24-nt sRNAs mapped to the putative miRNA precursors, were then visually inspected using the Tablet software. Sequences having the expected pattern of sRNA mapping to their respective precursors were checked by the RNA folding tool from the UEA sRNA toolkit, using default parameters. The following criteria were used to define a good miRNA candidate: no more than four unpaired nucleotides between the putative mature and star sequences, of which no more than three nucleotides were consecutive and no more than three nucleotides were without a corresponding unpaired nucleotide in the near complementary sequence within the hairpin structure. MiRNAs were then classified according BLAST searches against the miRBase database.
Differential expression analysis for both mRNA and sRNA data was carried out with edgeR statistical software package for R. A Fisher-like exact test based on a negative binomial distribution was performed to test whether group means (wild type versus transgenic) were significantly different from one another. To perform the test, a moderate dispersion estimate for each tag (gene for the RNA-Seq data and miRNA family for the sRNA-Seq data) was obtained based on its individual dispersion, and a common dispersion pondered by a weighting factor. P-values were adjusted for multiple tests with Benjamini-Hochberg correction to return a false discovery rate (FDR). The technical replicates obtained in the sRNA-seq for one wild type and one transgenic library were computed together in the analysis by normalizing the sum of reads per million.
Genome_build: TAIR9
Supplementary_files_format_and_content: The file ´RNA-seq_rpkm.txt` contains the Reads per kilobase of transcript per million (RPKM) for all genes identified in the four samples. The file ´sRNA-Seq_rpkm.txt` contains the expression of all miRNAs identified in the four samples.

source_name: Whole seedlings

growth_protocol: Wild type and transgenic lines of A. thaliana expressing coffee homeobox CAHB12 were grown in a growth chamber at 22 oC (± 2 oC) under a photoperiod of 18h light/ 6h dark.

extract_protocol:
Total RNA was extracted from pools of 50 seedlings harvested 10-days after germination with RNeasy® Plant Mini Kit (Qiagen). 4 μg of RNA were used for cDNA library construction.
Four RNA-seq and Six sRNA-seq libraries were produced, since technical replicates were produced for two of the libraries (wild type and transgenic).

tag: ectopic gene

tag: cultivar

value: Columbia

value: Whole organism

value: 10 days after germination


title: Transgenic line biological Rep1_sRNA

description:
sRNA
GNU18


title: WT biological replicate 2_mRNA

description:
mRNA
GNU15


title: TSCendo#1


title: WT biological replicate 1_mRNA

description:
mRNA
GNU13


title: WT biological replicate 2_sRNA

description:
sRNA
GNU19, GNU21


title: WT biological replicate 1_sRNA

description:
sRNA
GNU17


title: Ler Rep E

description: Ler Rep E Read 1 and Read 2


title: Hi-C S2 GFP RNAi control 1

city: Freiburg

first: Fidel

last: Ramirez

address: Stübeweg 51

institute: Max Planck Institute for Immunobiology and Epigenetics

description: ligated DNA with biotin labeling

data_processing:
Library strategy: Hi-C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.92
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Hi-C: All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 1000 bp apart, that were more than 800 bp from a restriction site or that were duplicated.  Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10.000 bp and restrictrion fragment size (RF).
processed data files format and content: matrices of corrected Hi-C contact counts for different bin resolution.
Genome_build: dm3

source_name: cultured fruit fly cells

extract_protocol: Hi-C was carried out as described (Belton et al., 2012) with a few modifications to account for Drosophila cell and genome size: 50 million fixed insect cells per sample were used and batches of 20 million cells each were digested with 400U HindIII as Hi-C samples with a control 3C sample of 10 million cells. Cohesive ends in Hi-C samples were filled in with dATP, dGTP, dTTP and biotin-14-dCTP. Then DNA was ligated, purified and sonicated. Size selection for ~230bp fragments carried out and then enriched for biotinylated specimen with straptavidin beads. Illumina paired-end adapters and PfuUltra II Fusion DNA polymerase were used for library generation. For all libraries 10 cycles of PCR amplification were used.

tag: restriction enzyme(s)

value: HindIII

tag: replicate

value: biological 1


title: 3F-iTSC#4

source_name: induced trophoblast stem cells

tag: passages

value: induced trophoblast stem cells


title: DGRP male pooled

city: East Lansing

first: Wen

last: Huang

state: MI

address: 474 S Shaw Ln, Anthony Hall 1205F

department: Animal Science

institute: Michigan State University

data_processing:
Alignment to FlyBase 5.49 using TopHat 2.0.8
Gene model assembly using Cufflinks 2.0.2
Merge assemblies from females and males using Cufflinks
Re-estimate gene expression using Cufflinks
Genome_build: BDGP5
Supplementary_files_format_and_content: Table with FPKM reported by Cufflinks

source_name: whole body poly A (+) RNA of DGRP males

growth_protocol: Standard cornmeal-molasses-agar medium, 25°C, 60–75% relative humidity and a 12-hr light-dark cycle

extract_protocol:
Total RNA from adult flies were extracted and 200ng from each of the 192 DGRP lines were pooled
TruSeq

value: whole body

tag: developmental stage

value: 3-5 d old adult

tag: gender

value: male


title: 4F-iTSC#3


title: Hi-C S2 GFP RNAi control 2

description: ligated DNA with biotin labeling

data_processing:
Library strategy: Hi-C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.93
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Hi-C: All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 1000 bp apart, that were more than 800 bp from a restriction site or that were duplicated.  Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10.000 bp and restrictrion fragment size (RF).
processed data files format and content: matrices of corrected Hi-C contact counts for different bin resolution.
Genome_build: dm3

value: biological 2


title: 12F-iTSC#4


title: 3F-iTSC#3


title: Hi-C S2 MSL3 RNAi 2

description: ligated DNA with biotin labeling

data_processing:
Library strategy: Hi-C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.91
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Hi-C: All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 1000 bp apart, that were more than 800 bp from a restriction site or that were duplicated.  Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10.000 bp and restrictrion fragment size (RF).
processed data files format and content: matrices of corrected Hi-C contact counts for different bin resolution.
Genome_build: dm3


title: C24 Rep E

description: C24 Rep E Read 1 and Read 2

tag: tissue

value: whole aerial seedling

value: 15 day old


title: Transgenic line biological Rep1_mRNA

description:
mRNA
GNU14


title: Hi-C S2 MSL2 RNAi 2

description: ligated DNA with biotin labeling

data_processing:
Library strategy: Hi-C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.89
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Hi-C: All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 1000 bp apart, that were more than 800 bp from a restriction site or that were duplicated.  Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10.000 bp and restrictrion fragment size (RF).
processed data files format and content: matrices of corrected Hi-C contact counts for different bin resolution.
Genome_build: dm3


title: Hi-C S2 MSL3 RNAi 1

description: ligated DNA with biotin labeling

data_processing:
Library strategy: Hi-C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.90
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Hi-C: All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 1000 bp apart, that were more than 800 bp from a restriction site or that were duplicated.  Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10.000 bp and restrictrion fragment size (RF).
processed data files format and content: matrices of corrected Hi-C contact counts for different bin resolution.
Genome_build: dm3


title: Hi-C S2 MSL2 RNAi 1

description: ligated DNA with biotin labeling

data_processing:
Library strategy: Hi-C-Seq
Basecalls performed using Illumina bcl2fastq 1.8.88
Reads were mapped using bowtie2 (Langmead & Salzberg, 2012). For 4C, primer sequences were trimmed from reads.
Hi-C: All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 1000 bp apart, that were more than 800 bp from a restriction site or that were duplicated.  Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10.000 bp and restrictrion fragment size (RF).
processed data files format and content: matrices of corrected Hi-C contact counts for different bin resolution.
Genome_build: dm3


title: 12F-iTSC#5

tag: cell type


title: DGRP female pooled

source_name: whole body poly A (+) RNA of DGRP females

value: female


title: Hi-C clone8 Wild type 2

description: ligated DNA with biotin labeling

data_processing:
Basecalls performed using Illumina bcl2fastq 1.8.3
Each mate file  was mapped using Bowtie2 adding the --local parameter to accommodate for reads containing a ligation site.
All reads that mapped multiple times to the genome were discarded as well as read pairs that were less than 500 bp apart. Only reads having a mapping quality of at least 20 were considered. Hi-C matrices of different bin sizes were created by counting the number of times a Hi-C pair connected any two bins. The bin sizes considered were: 10,000 bp, 25,000 bp, 50,000 bp and 100,000 bp. Replicates were merged into one dataset. Merged matrices of Hi-C corrected counts replicates for each cell type were used to compute boundary points as reported in the study publication.
Genome_build: dm3
Supplementary_files_format_and_content: Processed files contain matrices of corrected Hi-C contact counts for different bin resolution and .bed files with the genomic coordinates of boundaries.

extract_protocol:
Hi-C in S2 or clone8 cells was carried out as described (Belton et al., 2012) with a few modifications to account for Drosophila cell and genome size: 50 million fixed insect cells per sample were used and batches of 20 million cells each were digested with 400U HindIII as Hi-C samples with a control 3C sample of 10 million cells. Cohesive ends in Hi-C samples were filled in with dATP, dGTP, dTTP and biotin-14-dCTP. Then DNA was ligated, purified and sonicated. Size selection for ~230bp fragments carried out and then enriched for biotinylated specimen with straptavidin beads. Illumina paired-end adapters and PfuUltra II Fusion DNA polymerase were used for S2 library generation while TruSeq adapters and Q5 DNA polymerase were used for clone8 samples. For all libraries 10 cycles of PCR amplification were used.
50 million S2 cells were collected and resuspended in 22.5ml of fresh medium. Clone8 cells were washed with PBS and 22.5ml of fresh medium added. 37% formaldehyde solution was added to obtain a final concetration of 1%, followed by incubation at room temperature for 10min. 1.25ml 2.5M glycine solution was added and incubated for another 5 min at RT followed by 10min on ice.


title: Hi-C S2 Wild type 2

description: ligated DNA with biotin labeling


title: 4F-iTSC#1


title: NCBP3 replicate3

city: Martinsried

first: Andreas

last: Pichlmair

state: Bayern

address: Am Klopferspitz 18

department: Mann

institute: Max-Planck Institut für Biochemie

data_processing:
Primary data analysis was done using Illumina’s real-time analysis software (RTA)
Sequenced reads containing adaptor sequences were discarded, remaining reads were trimmed (to bp 6-98), then mapped to the GRCh37 genome assembly and ensembl gene-annotation version 70 using tophat v2.0.9 ( parameters: -G, otherwise default settings)
Reads mapping to the mitochondrial genome or rRNA annotations were removed. Transcript/gene levels were quantified against ensembl gene annotation version 70 using cufflinks 2.2.1
Genome_build: GRCh37
Supplementary_files_format_and_content: Table (as tab separated values) with FPKM values, counts, fold changes (sample over control) and p-values for all quantifiable genes as output by cuffdiff

source_name: HeLa (Kyoto)

extract_protocol:
Cells were pelleted by centrifugation at 500 × g for 10 minutes at 4°C, washed twice with ice-cold PBS and lysed in an equal volume of RIP lysis buffer [10 mM HEPES pH 7.0, 100 mM KCl, 5 mM MgCl2, 25 mM EDTA, 0.5% (v/v) Nonidet P-40, 1 mM DTT, protease inhibitor cocktail (EDTA-free, cOmplete; Roche)] for 30 minutes on ice in the presence of 100 U/ml RNase inhibitor (Fermentas).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa (Kyoto)

tag: cell line type

value: BAC-GFP cell line (Poser et al., Nat. Methods 5, 409 (2008))

tag: transgene

tag: antibody

value: GFP-Trap_A (Chromotek, catalog# gta-20, lot# 131213001A)


title: NCBP3 replicate2


title: control replicate1


title: Hi-C S2 Wild type 1

description: ligated DNA with biotin labeling


title: control replicate2


title: control replicate3


title: NCBP3 replicate1


title: NCBP2 replicate3


title: NCBP2 replicate2


title: sub097

city: Austin

first: Russell

last: Poldrack

state: TX

address: 100 East 24th Street, R9975

institute: University of Texas at Austin

data_processing:
Illumina RTA version 1.17 used for base calling, and Casava version 1.8 used for extraction from BCL to fastq format
Paired-end reads aligned to hg19 reference assembly using bowtie 2.2.2 via tophat 2.0.11: tophat --rg-id Paired --rg-library RNAseq --rg-platform ILLUMINA  --mate-inner-dist 100  --b2-very-sensitive -p 15 -r 250
Per-gene read counts were obtained using htseq-count [HTSeq package, version 0.5.4p5]
Read counts were  normalized for library size using the estimateSizeFactors function [DeSeq package, version 1.14.0], and genes were then filtered for a mean read count across sessions of at least 4 and no more than 10,000,
Variance-stabilized read counts were obtained using the varianceStabilizingTransformation in DeSeq (version 1.14.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including gene names and variance-stabilized per-gene read counts

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were harvested by Ficoll gradient from whole blood, and immediately placed in lysis solution to eliminate nuclease activity for RNA isolation. RNA was extracted using the Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing according to "Next-Generation Sequencing RNA-Seq Library Construction", Podnar et. al. Curr Protoc Mol Bio 106:4.21, 2014.

tag: collectiondate

tag: rin


title: sub095

value: Peripheral blood mononuclear cells (PBMCs)


title: sub104


title: sub101


title: NCBP2 replicate1

tag: cell line


title: Hi-C clone8 Wild type 1

description: ligated DNA with biotin labeling


title: sub099


title: Transgenic line biological Rep2_mRNA

description:
mRNA
GNU16

value: Columbia


title: sub094


title: sub086


title: sub093


title: sub081


title: sub091


title: sub085


title: sub088


title: sub083


title: sub074


title: sub078


title: sub079


title: sub076


title: sub069


title: sub068


title: sub062


title: Tjilkuri-H-WG-1-a

city: Urrbrae

first: Jason

middle: A

last: Able

address: GN10b, Waite Main Buiding, Waite Road

department: School of Agriculture, Food and Wine

institute: University of Adelaide

data_processing: Novel miRNA: Raw data were processed by trimming 3' adapter sequences. The non-redundant (NR) set of 3' adapter trimmed reads of 19-26 bp in length were filtered to remove low quality reads. Clean sRNA-seq data was used to identify candidate pre-miRNA hairpins from the International Wheat Genome Sequencing Consortium’s (IWGSC) Chromosomal Survey Sequences (CSS). For each NR 3' adapter trimmed read, all perfect alignment locations in the IWGSC CSS were identified. Using a subset of reads and CSS contigs involved in those perfect alignments, we also identified all imperfect alignments (two-five mismatches). The candidate pre-miRNA hairpins were defined using all pairwise combinations of perfect to imperfect alignments of a given read within a CSS contig. Additional constraints were applied such that the perfect and imperfect alignments were in opposite orientations and separated by 54-1000 bp. A NR set of these regions ±20 bp, were processed by RNAFold and then miRcheck to ascertain if they could form hairpin structures and have characteristics associated with the miRNA biogenesis pathway in plants with a read coverage profile. All candidate miRNA hairpin sequences were classified into one of eight categories (A-H, where A has a read coverage profile matching our expectations for a true miRNA) using three Boolean metrics based on their read coverage profile. Putative miRNA hairpins were further characterised by identifying if their sequence contained any perfect matches to the 35,828 mature miRNAs from miRBase v21 to determine novel miRNA hairpins. Please see Methods, Liu et al.(2015) for details.

organism: Triticum turgidum subsp. durum

source_name: Tjilkuri,developing head,water deficit stress treatment,season 1

growth_protocol: Please see Methods, Liu et al.(2015)

extract_protocol:
Total RNA was isolated using the TriPure reagent. Small RNA was excised and purified  from TBE urea polyacrylamide gel.
Small RNA libraries were constructed using NEB Next Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, UK) following the manufacturer’s instructions.

treatment_protocol: Please see Methods, Liu et al.(2015)

tag: variety name

value: Tjilkuri

tag: water deficit stress tolerance

value: Sensitive

tag: treatment group

value: Water deficit stress treatment group (WG)

value: Developing head (H)

tag: growing season

value: Season 1

tag: plant id number


title: Tjilkuri-H-WG-1-c


title: sub064


title: Tjilkuri-H-WG-2-b

source_name: Tjilkuri,developing head,water deficit stress treatment,season 2

value: Season 2


title: Tjilkuri-H-CG-1-c

source_name: Tjilkuri,developing head,control treatment,season 1

value: Control Group (CG)


title: sub065


title: Tjilkuri-H-WG-1-b


title: Tjilkuri-H-CG-2-b

source_name: Tjilkuri,developing head,control treatment,season 2


title: sub060


title: sub058


title: sub056


title: Tjilkuri-H-CG-2-a


title: Tjilkuri-H-CG-1-b


title: sub067


title: sub055


title: sub072


title: sub054


title: Tjilkuri-H-WG-2-c


title: Tjilkuri-FL-WG-2-c

source_name: Tjilkuri,flag leaf,water deficit stress treatment,season 2

value: Flag leaf (FL)


title: sub050


title: Tjilkuri-H-WG-2-a


title: sub047


title: sub045


title: Tjilkuri-FL-WG-2-a


title: Tjilkuri-FL-WG-1-b

source_name: Tjilkuri,flag leaf,water deficit stress treatment,season 1


title: Tjilkuri-H-CG-1-a


title: Tjilkuri-FL-WG-1-a


title: Tjilkuri-H-CG-2-c


title: sub042


title: sub034


title: sub039


title: Tjilkuri-FL-CG-2-b

source_name: Tjilkuri,flag leaf,control treatment,season 2


title: Tjilkuri-FL-CG-2-c


title: sub031


title: sub028


title: Tjilkuri-FL-CG-1-c

source_name: Tjilkuri,flag leaf,control treatment,season 1


title: Tjilkuri-FL-WG-2-b


title: Tjilkuri-FL-CG-1-b


title: sub025


title: sub022


title: Tjilkuri-FL-CG-1-a


title: Yawa-H-WG-2-b

source_name: Yawa,developing head,water deficit stress treatment,season 2

value: Yawa

value: Tolerant


title: sub019


title: sub016


title: Yawa-H-WG-2-a


title: Tjilkuri-FL-WG-1-c


title: PARP-1 ChIP-seq MDA-MB231

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

data_processing: PARP-1 SOLiD output files were converted to fastq using custom script. Mapped PARP-1 reads to the Human genome (Hg19) using BWA v0.6.1. Estimated the mean PARP1 fragment length of each replicate by computing the offset that gave the highest covariation of read depth between the forward and reverse strands. Estimated PARP1 nucleosome midpoint locations as the read start plus the offset (or minus the offset for those that mapped to the reverse strand. Genome_build: hg19. Supplementary_files_format_and_content: wig files containing counts of mapped fragment midpoints at each genomic position

growth_protocol: MCF7 and MDA-MB231 cells were obtained from ATCC

extract_protocol:
GSM1517305
Libraries were prepared according to Applied Biosystems protocol for SOLiD fragment paired-end sequencing. Briefly, DNA was end-repaired and 5’-phosphorylated by incubation in DNATerminator end-repair kits, as recommended by the manufacturer (Lucigen Corp., Middleton, WI). SOLiD adapters were ligated and the DNA molecules PCR amplified (very low cycle number) and sequenced by using the Applied Biosystems protocol for SOLiD fragment paired-end sequencing. After adapter ligation DNA was PCR amplified with SoLiD primers for less than 12 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 a SoLid flow cell for cluster generation.

value: Breast cancer

value: Active motif-39559


title: sub037


title: Yawa-H-WG-1-c

source_name: Yawa,developing head,water deficit stress treatment,season 1


title: PARP-1 ChIP-seq MCF-7

source_name: MCF7 cells

extract_protocol:
MNase digested nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Applied Biosystems protocol for SOLiD fragment paired-end sequencing. Briefly, DNA was end-repaired and 5’-phosphorylated by incubation in DNATerminator end-repair kits, as recommended by the manufacturer (Lucigen Corp., Middleton, WI). SOLiD adapters were ligated and the DNA molecules PCR amplified (very low cycle number) and sequenced by using the Applied Biosystems protocol for SOLiD fragment paired-end sequencing. After adapter ligation DNA was PCR amplified with SoLiD primers for less than 12 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 a SoLid flow cell for cluster generation.


title: Yawa-H-WG-1-b


title: sub010


title: 35S-DCL1RDD/dcl234

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

institute: INRA

data_processing:
Removed adaptor “AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATG” using fastx_clipper
Mapped with bowtie, kept unique matches with no mismatch (-v 0 -a --best --strata -S -m 1)
Retrieve the sequence
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited: sequence, count

source_name: floral tissue

growth_protocol: standard long-day conditions (16h of light and 8 h of dark at 20°C)

extract_protocol:
Frozen tissue was homogenized in a buffer containing 0.1 M NaCl, 2% sodium dodecyl sulphate (SDS), 50 mM Tris–HCl (pH 9.0), 10 mM ethylenediaminetetraacetic acid (pH 8.0) and 20 mM β-mercaptoethanol, and RNAs were extracted two times with phenol and recovered by ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: Col

tag: genotype

value: RTL1 with 35S promoter and dcl2 dcl3 dcl4 triple mutant

value: flower


title: Tjilkuri-FL-CG-2-a


title: 35S-RTL1-2

value: RTL1 with 35S promoter


title: 35S-RTL1-1


title: sub009

value: Peripheral blood mononuclear cells (PBMCs)


title: Yawa-H-CG-2-c

source_name: Yawa,developing head,control treatment,season 2


title: dcl234-3

value: dcl2 dcl3 dcl4 triple mutant


title: sub026


title: sub007


title: Yawa-H-WG-2-c


title: Yawa-H-CG-2-b


title: dcl234-2


title: sub002


title: dcl234-1


title: Yawa-H-CG-1-c

source_name: Yawa,developing head,control treatment,season 1