title: 999b_HIC

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
The pipeline for processing of each data-set was assembled around the library (see https://bitbucket.org/mirnylab).  Briefly, each read of the sample was treated separately for alignment purposes and the information was then put together to make the HiC contact maps.  The bowtie2 aligner was used to align each reads from each end.  Only uniquely mapping reads were considered for further analysis.
The mapping is interative and starts with first 25 bases of each read, this length is extended by 5 bases till 75 bases to look for a unique mapping.
The assembled fragments are then filtered at the restriction fragment level and all the reads that span more than 4 restrction sites are discarded.  All the double sided reads  are discarded.  All the reads right next to the restriction site (possible dangling ends) are discarded.  All the duplicates are discarded.  All the fragments with very high or very low counts are discarded (these are usually possible PCR artefacts).  Very large and very small fragments are discarded.  All the interactions separated by very few restriction fragments are also discarded.  These data is then binned at 10 kB resolution
The bins with lowest 3% coverage are discarded (in addition to bins with zero counts).  Remove the diagonal and neighboring diagonal (i.e. interactions < 20kB).  Remove the standalone bins.  Do the iteractive correction.   Interpolate the singleton bins (singleton bins are the filtered out bins that are flanked by non-filtered out bins).  Normalize the sum = 1 along each row and column.
For replicate samples, an average matrix was used.
Genome_build: S. pombe Sept 2007 version from PomBase.
Supplementary_files_format_and_content: Each file contains a square matrix.  Each row and column has three parts, the
Supplementary_files_format_and_content: bin number, the number of a 10 kB bin.  Each bin number begins with number of
Supplementary_files_format_and_content: the chromosome on which that bin belongs.  Then there is name of the organism,
Supplementary_files_format_and_content: and finally the genomic coordinates of the regions represented by that bin.
Supplementary_files_format_and_content: Each cell in the matrix denotes score of interaction between the bins denotes by
Supplementary_files_format_and_content: the defining row and column.  The NA and NANs are the values that were discarded
Supplementary_files_format_and_content: during the process of generation of the interaction scores. See GSM1379427 for the supplementary file which contains averages of the two replicates represented in GSM1379427 and GSM1379428.

organism: Schizosaccharomyces pombe

source_name: Asynchronously growing cells

growth_protocol: The Cells were grown on YEA at optimal temperature (30 C).  Wherever temperature sensitive mutatnts were used, the cells were incubated at elevated temperatures (33 C) for 4 - 6 hours before library preparation.

extract_protocol:
A total of 500 ml of cells (OD at 600nm ~ 0.5) was fixed in 3% formaldehyde (Sigma) for 20 min at 26 C, and quenched with glycine for 5 min at 26 C.  Cells were poured into liquid nitrogen using 1x NEB2, disrupted by nitrogen grinding.  Cell lysate was treated with 0.1% SDS for 10 min at 65 C, and then quenched with 1% TritonX-100.  Cell lysate was digested overnight with 100 U HindIII at 37 C.  The 5' overhang from the HindIII digestion was filled in using Klenow fragment in presence of biotin-14-dCTP and dATP, dGTP, and dTTP at 37 C for 45 min.  The reaction was terminated with 1.5% SDS.  The DNA fragments were ligated by T4 DNA ligase in diluted conditions that favor the ligation between cross-linked DNA fragments in 16 C for 8 hours (Hi-C DNA).
The HiC-DNA was reverse cross-linked at 65 C overnight in the presence of proteinase K and purified by phenol/chrolorom extraction.  Purified Hi-C DNA was treated with 1 mg/ml Rnase A for 30 min at 37 C.  Un-ligated biotin lablelled DNA was selectively removed by T4 DNA plymerase and reaction were purified by phenol/chloroform extraction.  Hi-C DNA was then sheared by ultrasonication (Covaris) in the size range of <500 bp.  The sheared Hi-C DNA was subjected to end-repair and 3' end adenylation.  Hi-C DNA between 150 - 300 bp was selected with AMPure XP (Beckman-Coulter).  The biotin-labled Hi-C DNA was selectively captured by Dynabeads Myone Streptavidin C1 (Invitrogen) and used for Illumina PE adapter ligation.  Streptavidin beads containing bounds Hi-C DNA were used for the template for library amplification by PE-PCR primers (Illumina).

treatment_protocol: The temperature was shifted in the temperature sensitive mutants.


title: Degradome_B73_ear_I

status: Public on Oct 22 2014

type: SRA

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

country: China

institute: Sichuan Agricultural University

library_source: transcriptomic

data_processing:
Small RNA reads and degradome reads were both generated from an Illumina Genome Analyzer II. The raw data were preprocessed by the Fastx-toolkit pipeline to remove low quality reads and clip adapter sequences. As for the small RNA library, small RNAs ranging from 18-25 nt were collected and mapped to the maize genome (B73 RefGen_v2 (release 5b. 60 in February 2011)) reference sequences by SOAP2. Sequences with perfect match were retained for further analysis. To further analyze the RNA secondary structures comprising matched Solexa reads, a 250-nt genomic sequence flanking each side of these sequences were extracted, and secondary structure modeling of the DNA fragment was performed mFold 3.5 [62] and analyzed by MIREAP (https://sourceforge.net/projects/mireap/) under default settings. Segments that could potentially form the canonical stem-loop signature of a precursor miRNA were marked as candidate miRNAs. This candidate list was further trimmed based on the following criteria [51]: (1) mature miRNAs are present in one arm of the hairpin precursors, which lack large internal loops or bulges, (2) secondary structures of the hairpins are steady, with the free energy of hybridization lower than -20 kcal/mol, (3) hairpins are located in intergenic regions or introns, (4) overlapping loci were reduced to non-redundant representations, (5) loci that overlapped transposable and other repetitive elements were removed, (6) loci in which the matched mature miRNA was in the wrong orientation were removed, (7) each predicted secondary structure was curated manually and those with spurious stem-loop structures were removed, and (8) miRNA families that had no evidence of expression in the small RNA libraries. The final refined list of predicted miRNAs consisted of 132 individual miRNAs from 43 miRNA families. Based on the hairpin structure of the pre-miRNA, the mature miRNA and corresponding miRNA* sequence were identified for each.
As for the degradome library, only 20-21 nt sequences with high quality were collected for subsequent analysis. The raw sequences were first normalized to “reads per 10 million” (RP10M). The distinct reads that perfectly matched maize cDNA sequences remained. The 15 nt of sequence upstream and downstream of the 5’ end of matched reads were extracted to constitute 30-nt sequence tags for searching corresponding miRNA. The CleaveLand pipeline [49] was used to align the 30 nt sequence to maize known miRNAs from miRBase and our newly identified miRNAs. All alignments with scores up to 7 and no mismatches at the cleavage site (between the 10th and 11th nucleotides) were considered candidate targets.
Genome_build: n/a
Supplementary_files_format_and_content: abundance

molecule: total RNA

organism: Zea mays

source_name: Zea mays L.B73

extract_protocol:
All the samples were harvested and immediately frozen in liquid nitrogen and stored at -80°C. The total RNA from each sample was then isolated using Trizol (Invitrogen) according to the manufacturer’s instructions.
Small RNA library preparation and sequencing: the total RNAs from four developmental stages were pooled for Solexa sequencing. After small RNA cloning, the sequencing procedures were conducted as described previously. In brief, the sequencing was performed as follows: approximately 100 ug of total RNA was purified by polyacrylamide gel electrophoresis (PAGE), to enrich for molecules in the range of 18–30 nt, and ligated with proprietary adapters to the 5’ and 3’ termini of the RNA. The small RNA molecules samples were used as templates for cDNA synthesis. The cDNA was amplified with 18 PCR cycles and fragments of around 90 nt (small RNA + adaptors) were isolated from agarose gels. The purified DNA was used directly for cluster generation and Solexa sequencing analysis performed by the Illumina platform. The image files generated by the sequencer were then processed to produce digital-quality data. After masking of adaptor sequences and removal of contaminated reads, clean reads were processed for computational analysis. Degradome library construction: Small cDNA libraries using the sliced ends of polyadenylated transcripts from maize ears of four developmental stages were constructed according to previous report. In brief, poly(A) RNA was extracted from 200 μg of total RNA using the Oligotex kit (Qiagen), and it’s possessing 5’ monophosphates were ligated to an RNA adapter consisting of a MmeI recognition site in its 3’ end. After ligation, first-strand cDNA was generated using oligo d(T) and the PCR product was amplified using five PCR cycles. The PCR product was purified and digested with MmeI. The digested PCR product was then ligated to a double-stranded DNA oligo with degenerate nucleotides at the 5’ or 3’ end. The ligation product was further gel purified and amplified using 10 PCR cycles. The final PCR product was purified and sequenced using SBS sequencing technology.

tag: tissue

value: ears (female inflorescences)

tag: developmental stage

value: ears at the growth point elongation phase

tag: cultivar


title: clr4D_HIC

city: Bethesda

state: MD

country: USA

library_source: genomic

data_processing:
The pipeline for processing of each data-set was assembled around the library (see https://bitbucket.org/mirnylab).  Briefly, each read of the sample was treated separately for alignment purposes and the information was then put together to make the HiC contact maps.  The bowtie2 aligner was used to align each reads from each end.  Only uniquely mapping reads were considered for further analysis.
The mapping is interative and starts with first 25 bases of each read, this length is extended by 5 bases till 75 bases to look for a unique mapping.
The assembled fragments are then filtered at the restriction fragment level and all the reads that span more than 4 restrction sites are discarded.  All the double sided reads  are discarded.  All the reads right next to the restriction site (possible dangling ends) are discarded.  All the duplicates are discarded.  All the fragments with very high or very low counts are discarded (these are usually possible PCR artefacts).  Very large and very small fragments are discarded.  All the interactions separated by very few restriction fragments are also discarded.  These data is then binned at 10 kB resolution
The bins with lowest 3% coverage are discarded (in addition to bins with zero counts).  Remove the diagonal and neighboring diagonal (i.e. interactions < 20kB).  Remove the standalone bins.  Do the iteractive correction.   Interpolate the singleton bins (singleton bins are the filtered out bins that are flanked by non-filtered out bins).  Normalize the sum = 1 along each row and column.
For replicate samples, an average matrix was used.
Genome_build: S. pombe Sept 2007 version from PomBase.
Supplementary_files_format_and_content: Each file contains a square matrix.  Each row and column has three parts, the
Supplementary_files_format_and_content: bin number, the number of a 10 kB bin.  Each bin number begins with number of
Supplementary_files_format_and_content: the chromosome on which that bin belongs.  Then there is name of the organism,
Supplementary_files_format_and_content: and finally the genomic coordinates of the regions represented by that bin.
Supplementary_files_format_and_content: Each cell in the matrix denotes score of interaction between the bins denotes by
Supplementary_files_format_and_content: the defining row and column.  The NA and NANs are the values that were discarded
Supplementary_files_format_and_content: during the process of generation of the interaction scores.

molecule: genomic DNA

source_name: Clr4D cells

tag: strain


title: rad21-K1_HIC

source_name: Cells with mutation in cohesin


title: 10 somite stage, sectioned from dorsal to ventral end

status: Public on Oct 23 2014

city: Utrecht

first: Jan Philipp

last: Junker

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript (Table S1). The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
Genome_build: mm10 and zv9 (with improved 3' annotation)
Supplementary_files_format_and_content: text files: read count matrices in which rows correspond to genes and columns to sections

organism: Danio rerio

source_name: whole embryo

extract_protocol:
RNA was isolated by TRIzol extraction
mRNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)

treatment_protocol: Unfixed samples (zebrafish embryos or mouse forelimbs) were embedded in tissue freezing medium. Blocks were cryosectioned, and individual slices were transferred to Eppendorf tubes on dry ice.

tag: Stage

value: 10 somites

tag: sectioning direction

value: dorsal-ventral

tag: section thickness

value: 18 µm

tag: embedding strategy

value: intact embryo


title: G1-arrested_HIC

source_name: G1 arrested cells in Cdc10 mutants


title: SKM1

city: Seattle

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

institute: Fred Hutchinson Cancer Research Center

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) as part of the HiSeq Control Software
Reads were trimmed using trim_galore (version 0.2.2) with the option “-q 20 –A AGATCGGAAGAGC” to remove adaptor sequences and low quality base calls, and then mapped to human (hg19) genome using BSMAP (version 2.74). Methylation calls were performed by “methylation.py” in the BSMAP package. The methylation ratio was calculated as the number of methylation counts over the total number of mapped reads for each CpG.
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, the number of methylation calls at a given site (.m columns) and the total number of reads covering the CpG site (.t columns) were generated using BSMAP (version 2.74) using the methratio.py script.

organism: Homo sapiens

source_name: adult skeletal muscle biopsy

growth_protocol: The human rhabdomyosarcoma cell line RD was grown in DMEM + 10% bovine calf serum and 1% penicillin/streptomycin. The human primary myoblast cell line NR135 was maintained in F-10 nutrient media, 20% fetal bovine serum, 1% penicillin/streptomycin, 10 ng/ml bFGF and 1 µM dexamethasone.

extract_protocol:
Genomic DNA from all sources was isolated using the DNeasy Blood and Tissue Kit (Qiagen).
EpiQuest libraries were prepared from 500 ng genomic DNA. The DNA was digested with 60 units of TaqI and 30 units of MspI (NEB) sequentially. Size-selected TaqI-MspI fragments (40–120bp and 120–350bp) were filled-in and 30-terminal-A extended, extracted with Zymo Research DNA Clean and Concentrator(tm) kit. Ligation to pre-annealed adaptors containing 50-methyl-cytosine instead of cytosine (Illumina) was performed using the Illumina DNA preparation kit and protocol. Purified, adaptor-ligated fragments were bisulphite treated using the EZ DNA Methylation-Direct(tm) Kit (Zymo Research). Preparative-scale PCR was performed and DNA Clean and Concentrator-purified PCR products were subjected to a final size selection on a 4% NuSieve 3:1 agarose gel. SYBR-green-stained gel slices containing adaptor-ligated fragments of 130–210 or 210–460bp in size were excised. Library material was recovered from the gel (Zymoclean(tm) Gel DNA Recovery Kit) and sequenced on an Illumina GAIIx genome analyzer.

treatment_protocol: RD cells were transfected with a construct containing a MyoD~E12 forced heterodimer (Yang Z, et al. Genes Dev. 2009 Mar 15;23(6):694–707) and differentiated by switching cells to low serum differentiation media consisting of DMEM with 1% horse serum, 1% penicillin/streptomycin, 0.1% insulin, and 0.1% transferrin. NR135 primary human myoblasts were differentiated by transferring cells to low serum differentiation media consisting of F-10 media with 1% horse serum, 1% penicillin/streptomycin, 0.1% insulin, and 0.1% transferrin.

tag: sample type

value: adult skeletal muscle biopsy


title: 999a_HIC


title: RMS11

source_name: rhabdomyosarcoma

value: rhabdomyosarcoma patient sample


title: RMS9


title: RMS12


title: SKM2


title: RMS13


title: RMS14


title: RMS7


title: RMS10


title: RMS6


title: RMS8


title: RMS5


title: RMS4


title: Honeysuckle Decoction

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequence were trimed by our Perl scripts.
Clean Reads were then aligned to known miRNA seqeunces obtained from miRBase 14.0 with no more than one mismatches.
Profiles of two RNA samples were generated from the alignment results.
Supplementary_files_format_and_content: tab-delimited text files including miRNA ID，Read No., Sequence, Other Names(same sequence).

organism: Lonicera japonica

source_name: Honeysuckle

extract_protocol: Total RNA was isolated from 1g HS or 5ml HS decoction using the Universal Plant MicorRNA Kit (Bioteke, Beijing, China) according to the manufacturer's instructions.

treatment_protocol: HS decoction was prepared by boiling 10g HS in 100 ml water for 30 mins.

tag: treatment

value: HS Decoction


title: RMS3


title: RMS1


title: RD_MDE

source_name: rhabdomyosarcoma cell line

tag: cell line

value: RD

tag: cell type

value: rhabdomyosarcoma cell line


title: RD


title: o-vanillin

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Stationary phase cells were diluted to 1.0 X 10^6 cells in 50 ml of YPD medium. The cells were incubated with o-vanillin (0.125mg/ml, dissolved in DMSO)  at 30°C for 3 hrs, and total RNA was extracted.

data_processing:
Base-calling: CASAVA v1.8
Alignment: CLC Genomics Workbench 4.5
Generation of normalized abundance measurement: CLC Genomics Workbench 4.5
Genome_build: Cryptococcus neoformans var. grubii H99 Sequencing Project, Broad Institute of Harvard and MIT (http://www.broadinstitute.org/)
Supplementary_files_format_and_content: txt

organism: Cryptococcus neoformans H99

source_name: microorganisms

growth_protocol: Stationary phase wild-type cells were diluted to 1.0 X 10^6 cells in 50 ml of YPD medium. The cells were then incubated with or without o-vanillin at 30°C for 3 hrs

extract_protocol: Total RNA was extracted with the RiboPure-Yeast Kit (Ambion, AM1926). Sequencing library was constructed by using Illumina TruSeq RNA Sample Preparation Kits v2 following manufacturer's instructions.

treatment_protocol: Each sample was treated with or without 0.125mg/ml of o-vanillin for 3 hours.

tag: genotype

value: wild type

value: 0.125mg/ml of o-vanillin


title: NR135_MB

source_name: myoblast cell line

value: primary myoblast cell line


title: DMSO

description: Stationary phase cells were diluted to 1.0 X 10^6 cells in 50 ml of YPD medium. The cells were incubated only with DMSO (no drug control) at 30°C for 3 hrs, and total RNA was extracted.

value: no drug control


title: NR135_MT

source_name: myotube cell line


title: FSKM

source_name: fetal skeletal muscle biopsy

value: fetal skeletal muscle biopsy


title: jc379_MCF_input_rep3_CRI01

status: Public on Oct 21 2014

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-Seq reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.6, March 2008) using bwa 0.6.1 with default settings.
Reads mapped with MAPQ < 15 were filtered out. Reads overlapping regions producing aspecific binding were also removed (regions(obtained from http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/wgEncodeDukeRegionsExcluded.bed).
Peak were identified with MACS 1.4.1 using as control file the input library matched by the same cell line as the treatment library.
Genome_build: hg18
Supplementary_files_format_and_content: Text files produced by MACS reporting peak positons and statistics. File description from MACS manual (http://liulab.dfci.harvard.edu/MACS/00README.html):  NAME_peaks.xls is a tabular file which contains information about called peaks. You can open it in excel and sort/filter using excel functions. Information include: chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region (e.g. pvalue =1e-10, then this value should be 100), fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage. Coordinates in XLS is 1-based which is different with BED format.

source_name: Breast adenocarcinoma

growth_protocol: Human MCF7, MDA-MB-231 cell lines were obtained from the ECACC (European Collection of Animal Cell Cultures) and grown in DMEM supplemented with 10% FBS.

extract_protocol: 6 x15cm2 plates used per IP protocol, IP carried out as described in Schmidt et al (2009). In brief, cells were cross-linked using 1% formaldehyde for 10 min at RT, reaction quenched with 1/20th volume 2.5M Glycine and cell pellets collected after scrapping plates. Nuclear lysates were prepared by lysing with LB1 (50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X plus PI) 10 min at 4°C, LB2 (10mM Tris-HCl, pH8.0, 200mM NaCl, 1mM EDTA, 0.5M EGTA plus PI) 5 min at 4°C followed by sonication in LB3 (10mM Tris-HCl, pH8.0, 100mM NaCl, 1mM EDTA, 0.5M EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine plus PI) using a diagnode sonicator to give a fragment size of ~200-300bp. Sonicated lysate combined with 100ul protein-A magnetic beads preloaded with 10ug anti-FOXM1 antibody (Santa Cruz Biotechnology, USA; cat no. sc-502; lot no. D0110) O/N at 4°C. Beads washed X6 in RIPA buffer (50mM HEPES pH7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and DNA eluted for 16 hr at 65°C in elution buffer (50mM Tris-HCl, pH8.0, 10mM EDTA, 1%SDS). Extracted DNA treated with RNase A for 30 min at 37°C followed by Proteinase K for 1 hr at 55°C and DNA purified by phenol-chloroform extraction. DNA prepared for Illumina library construction by repair with Klenow and T4 polymerase, A-tailing with Klenow exo polymerase and attachment of adapters (diluted 1:20) using DNA ligase. Adapter ligated fragments amplified by PCR using phusion polymerase (12 cycles) and ~200-300 bp fragments extracted by gel purification. Library size and quantity determined by bioanalyser.

treatment_protocol: Cells were grown to 60% confluence then treated with Thiostrepton (10μM) or DMSO (0.1%) for 4 hr.

value: input


title: control for compound C3 replicate 2

city: Basel

first: Friedrich

last: Metzger

address: Grenzacherstr.

country: Switzerland

institute: F. Hoffmann-La Roche

data_processing:
Real time image analysis and base calling were performed on the the HiSeq 2500 instrument using the HiSeq Sequencing Control Software (HCS).
CASAVA software version 1.8 was used for de-multiplexing and production of FASTQ sequence files
Sequenced reads were mapped to humanRefSeq transcripts and hg19 whole genome using bowtie2
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample (first column=entrezgene id, second column=rpkm value)

source_name: SMA type I fibroblasts_control for compound C3

extract_protocol:
RNA was purified with the RNeasy Mini Kit (Qiagen)
Template DNA molecules suitable for cluster generation were prepared from 1 ug of total RNA samples using the TruSeq RNA Sample Preparation Kit v2. Libraries were quantified using the KAPA Library Quantification Kit (KK4824, Kapa Biosystems, Boston, MA). The libraries were pooled at equimolar concentrations and diluted prior to loading onto the flow cell of the HiSeq 2500 (Illumina Inc., San Diego, CA) for both clustering and sequencing. The libraries were extended and bridge-amplified to create single sequence clusters using the TruSeq Rapid PE Cluster Kit - HS (Illumina Inc., San Diego, CA). Amplified clusters in the flow cell were then sequenced with 50-bp paired-end reads using the TruSeq Rapid SBS Kit - HS (Illumina Inc., San Diego, CA) in rapid run mode.

treatment_protocol: Fibroblast cells derived from type 1 SMA patients were treated with SMN-C3 at 500 nM for 24 hours (cell line PNN 1-46 ), or SMN-C1 at 100nM for 24 hours (cell line GM03813).

value: SMA type I fibroblasts

tag: treated with

value: 0.5% dimethyl sulfoxide (DMSO) for 24hrs


title: compound C3 replicate 1

source_name: SMA type I fibroblasts_compound C3

value: 500nM SMN-C3 for 24hrs


title: control for compound C1 replicate 2

source_name: SMA type I fibroblasts_control for compound C1


title: compound C1 replicate 2

source_name: SMA type I fibroblasts_compound C1

value: 100nM SMN-C1 for 24hrs


title: compound C1 replicate 1


title: control for compound C3 replicate 1


title: Ls174T_DMSO_IgG_ChIPseq

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the human genome (hg19) with BOWTIE v0.12.8 using default parameters.
For RNAseq, differential expression and statistical inference was done using EdgeR.
For ChIPseqs, generation of wiggle files was performed with MACS v1.4.2 with default parameters, but the --keep-dup parameter was set to 5 (Miz1) or 3 (Myc, IgG).
Genome_build: hg19
Supplementary_files_format_and_content: For RNAseq, the txt-files contain tables showing the differential expression (as FoldChange, in column) of all ensemble annotated genes (ensemble gene ids, in rows) between each two samples (=experimental conditions) and the calculated p-value and adjusted p-value for each FoldChange.  .wig files for ChIPseq experiments were generated with MACS using a resolution of 10bp.

source_name: Ls174T cells

growth_protocol: Ls174T were grown in RPMI 1640 (Sigma) supplemented with 10% FBS (Biochrom AG) and 1% penicillin/streptomycin (Sigma).

extract_protocol:
For ChIPseq cells were crosslinked with 1% formaldehyde at 37°C for 10min. Cells were lysed and after centrifugation nuclei were re-suspended in RIPA buffer. DNA was sonicated with a Branson sonifier to obtain DNA fragments ≤ 500 bp. Chromatin was pre-cleared with protein A- or protein G-sepharose beads (blocked with BSA) and immunoprecipitated with indicated antibodies. Chromatin/protein complexes were collected by incubation with Protein A- or Protein G-sepharose beads for 6 hrs. After several washings chromatin was eluted with 1 % SDS/0.1 M NaHCO3 and  crosslinking was reverted overnight. DNA was purified by Phenol/Chloroform extraction. For RNAseq total RNA was extracted using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion. Poly-A RNA was isolated from total RNA using the NEBNext Poly(A)mRNA Magnetic Isolation Module (E7490).
Libraries for ChIP-seq samples were contructed following manufactor's intructions using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240). Briefly, ChIP DNA was end repaired,  A-tailed  and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Size-selected DNA was amplified with 18 PCR cycles. Libraries for the RNA-seq samples were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (E7530) or the NEBNext mRNA Library Prep Master Mix Set for Illumina (E6110) following the instruction manual. Depending on the kit used for sample preparation, DNA libraries were size selected using Agencourt AMPure XP Beads (Beckman Coulter) followed by amplification with 12 PCR cycles or by excision of 250 bp fragments from 2 % agarose gels and amplification with 13 cycles of PCR. For the resulting ChIP-seq and RNA-seq libraries, amplicon sizes and quantitiies were determined using the Biorad Experion system. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufactor's instructions.

treatment_protocol: Ls174T cells were treated with HUWE1 inhibitor BI8622 (20µM) for 16hrs. For HUWE1 knockdown Ls174T cells were infected lentivirally with shRNA targeting HUWE1 and selected with Puromycin. Inducible deletion of MIZ1 was achieved by treatment with 1µg/ml Doxycycline for 4 days.

tag: antibody


title: RMS2


title: Ls174T_DMSO_Miz1_ChIPseq


title: jc168_231-Input_CRI01


title: Ls174T_BI8622_IgG_ChIPseq


title: Ls174T_BI8622_Myc_ChIPseq

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog number

tag: antibody lot number


title: Ls174T_BI8622_Miz1_ChIPseq


title: Ls174T_pIND-shMiz1_+Dox_BI8622_replicate 2_RNAseq


title: Ls174T_DMSO_Myc_ChIPseq


title: Ls174T_pIND-shMiz1_+Dox_BI8622_replicate 1_RNAseq


title: control for compound C1 replicate 3


title: control for compound C1 replicate 1


title: control for compound C3 replicate 3


title: compound C3 replicate 3


title: Ls174T_pIND-shMiz1_+Dox_DMSO_replicate 1_RNAseq


title: Ls174T_pIND-shMiz1_-Dox_BI8622_replicate 2_RNAseq


title: Ls174T_pIND-shMiz1_-Dox_BI8622_replicate 1_RNAseq


title: Ls174T_pIND-shMiz1_-Dox_DMSO_replicate 2_RNAseq


title: Ls174T_pLKO-shHUWE1_BI8622_replicate 2_RNAseq


title: compound C1 replicate 3


title: Ls174T_pLKO-shHUWE1_BI8622_replicate 1_RNAseq


title: Ls174T_pLKO-empty_BI8622_replicate 2_RNAseq


title: Ls174T_pLKO-shHUWE1_DMSO_replicate 2_RNAseq


title: Ls174T_pLKO-shHUWE1_DMSO_replicate 1_RNAseq


title: Ls174T_pLKO-empty_DMSO_replicate 1_RNAseq


title: Ls174T_pIND-shMiz1_+Dox_DMSO_replicate 2_RNAseq


title: Ls174T_pLKO-empty_DMSO_replicate 2_RNAseq


title: Egr2CKO CD4+ T 16h RNASeq

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: TCR stimulated

data_processing:
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8 (HiSeq2000)
Raw reads were aligned to the mm9 mouse genome assembly using Bowtie 0.12.7
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts
For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm9 refseq database
Genome_build: mm9
Supplementary_files_format_and_content: BED files are generated using BEDTOOLS and unpublished python scripts, rpkm (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts

organism: Mus musculus

source_name: T cells

growth_protocol: Naïve CD4+ T cells from spleen and lymph nodes were purified from 6 week old mice using a CD4+CD62+ T cell Isolation Kit II (Miltenyi). Cells were activated with 2 μg/ml plate-bound anti-CD3 + 1 μg/ml soluble anti-CD28 (PharMingen)

extract_protocol: For RNA-Seq, total RNA was extracted from 5x10^6 cells per sample using Rneasy Mini kit (QIAGEN) and the quality and concentration were determined by Nanodrop ND-1000 spectrophotometer. Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor. After repairing ends, adaptor (Illumina) was added using T4 DNA ligase (New England Biolabs), and 250-450 bp fragments were isolated using 2% E-Gel (Invitrogen) and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).

treatment_protocol: For RNA-Seq,naïve CD4+ T cells, not stimulated or stimulated with anti-TCR for 1, 4, and 16 h

value: T cells

tag: tissue

value: Spleen


title: Egr2CKO CD4+ T 4h RNASeq

description: TCR stimulated


title: WT CD4+ T 4h RNASeq

description: TCR stimulated


title: WT CD4+ T 0h RNASeq

description: TCR stimulated


title: Egr2CKO CD4+ T 1h RNASeq

description: TCR stimulated


title: Total T EGR2 16h

description: ChIP against EGR2

data_processing:
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8 (HiSeq2000)
Raw reads were aligned to the mm9 mouse genome assembly using Bowtie 0.12.7
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts
For ChIP-Seq, peaks are called using MACS 1.3.7.1
Genome_build: mm9
Supplementary_files_format_and_content: BED files are generated using BEDTOOLS and unpublished python scripts, rpkm (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts

extract_protocol: For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.

treatment_protocol: For ChIP-Seq,Total T cells were stimulated with TCR for indicated time.

tag: chip antibody

value: Anti-EGR2 (Covance, PRB-236P D13BF00486)


title: WT CD4+ T 16h RNASeq

description: TCR stimulated

tag: strain


title: Egr2CKO CD4+ T 0h RNASeq

description: TCR stimulated


title: Total T EGR2 4h

description: ChIP against EGR2


title: Total T EGR2 0h

description: ChIP against EGR2


title: WT CD4+ T 1h RNASeq

description: TCR stimulated


title: Total T IgG

description: ChIP against IgG

value: Rabbit IgG (R&D systems.)


title: Ls174T_pLKO-empty_BI8622_replicate 1_RNAseq


title: Oral Cancer Poor 5-year survival Y017

city: New York

first: Angela

last: Yoon

state: NY

address: 630 West 168th Street, PH15W-1562

institute: Columbia University Medical Center

description: Oral Cancer Poor 5-year survival Y017

data_processing:
3'end adapters were clipped with fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit)
Clipped reads were processed with miraligner (Pantano. NAR 2010)
Genome_build: miRBase v20
Supplementary_files_format_and_content: counts

source_name: Oral cancer tissue

extract_protocol:
Ten 10-mm sections were obtained from archived FFPE tumor tissue samples for all subjects. Total RNA was isolated from tissues using RNeasy FFPE kit (Qiagen Inc., Valencia, CA) following the manufacturer’s protocol and yield was quantitated by Nanodrop, and stored at -80o C.
Total RNA (minimum of 2 mg) ranging from 18 to 30 nt were gel-purified and ligated to 3’ adaptor and 5’adaptor. Ligation products were reverse transcribed, then amplified for 16 cycles using the adaptor primers, and the fragments around 150 bp were isolated from PAGE-gel using TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA).

value: oral mucosa

tag: survival

value: Poor 5-year survival

tag: disease state

value: oral cancer


title: Oral Cancer Poor 5-year survival Y019

description: Oral Cancer Poor 5-year survival Y019


title: Oral Cancer Poor 5-year survival Y014

description: Oral Cancer Poor 5-year survival Y014


title: Oral Cancer Poor 5-year survival Y018

description: Oral Cancer Poor 5-year survival Y018


title: Oral Cancer Poor 5-year survival Y013

description: Oral Cancer Poor 5-year survival Y013


title: Oral Cancer Poor 5-year survival Y020

description: Oral Cancer Poor 5-year survival Y020


title: Oral Cancer Favorable 5-year survival Y010

value: Favorable 5-year survival


title: Oral Cancer Poor 5-year survival Y016

description: Oral Cancer Poor 5-year survival Y016


title: Oral Cancer Poor 5-year survival Y011

description: Oral Cancer Poor 5-year survival Y011


title: Oral Cancer Favorable 5-year survival Y008


title: Oral Cancer Favorable 5-year survival Y009


title: Oral Cancer Favorable 5-year survival Y007


title: Oral Cancer Poor 5-year survival Y015

description: Oral Cancer Poor 5-year survival Y015


title: Oral Cancer Favorable 5-year survival Y006


title: Oral Cancer Favorable 5-year survival Y004


title: Oral Cancer Favorable 5-year survival Y003


title: Oral Cancer Favorable 5-year survival Y001


title: Oral Cancer Favorable 5-year survival Y002


title: Oral Cancer Favorable 5-year survival Y005


title: WT-Pat-rep1

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

data_processing:
RRBS sequencing reads were mapped to the mouse genome (mm9) using Bismark v0.10.1 (Babraham Bioinformatics) after adapter trimming by Trim Galore (Babraham Bioinformatics). The methylation level of each covered cytosine in CpG context was calculated as the number of reported C divided by the total number of reported C and T.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are the coverage files generated by Bismark (chr, start, end, methylation%, number of reported C, number of reported T)

source_name: WT-Pat

growth_protocol: When collecting pronuclei of zygotes, 7-10 week-old CKO (Zp3-Cre, f/-) or WT (f/f) females were superovulated. MII oocytes were collected from the mice, transferred into HTF medium supplemented with 10 mg/ml bovine serum albumin (BSA; Sigma-Aldrich), and inseminated with activated spermatozoa obtained from the caudal epididymides of adult C57BL/6J male mice. Spermatozoa capacitation was attained by 1 h incubation in HTF medium. Zygotes were cultured in a humidified atmosphere of 5% CO2/95% air at 37.8°C. Five hours after fertilization, zygotes were cultured in KSOM (Millipore). Twelve hours post-fertilization (hpf), zygotes were transferred into M2 media containinig 5 µM cytochalasin B. Zona pellucidae were cut by a Piezo impact-driven micromanipulator (Prime Tech Ltd., Ibaraki, Japan) and pronuclei of the zygotes were isolated. The parental pronuclei were distinguished by (1) the distance from the second polar body and (2) the pronuclear size. The isolated paternal and maternal pronuclei were frozen at 13 hpf in -80°C. For aphidicolin treatment, zygotes were transferred into KSOM containing 3 µg/ml aphidicolin (Sigma-Aldrich) at 5 hpf.

extract_protocol:
5 µl of lysis buffer (20 mM Tris-EDTA [pH 8.0], 20 mM KCl, and 0.3% Triton X-100, 1 mg/ml QIAGEN Protease) was directly added to the frozen samples (in < 1µl PBS) followed by 3 hours of incubation at 50 ℃ and 30 minutes of inactivation at 75 ℃. Then to the same tube, 13 µl of MspI digestion master mix containing 10 units of MspI (Thermo Scientific) and 1.8 µl 10x Buffer Tango (Thermo Scientific) was added followed by 3 hours of incubation at 37 ℃ and 20 minutes of inactivation at 80 ℃.
The digested DNA was then filled-in and tailed with an extra A to the 3’ end by adding 2 µl of end-preparation master mix containing 5 units of Klenow Fragment (exo-; Thermo Scientific), 1.8 µl of 10x Buffer Tango, 0.4 mM dATP, and 0.04 mM each of dGTP and dCTP (Thermo Scientific), followed by 40 minutes of incubation at 37 ℃ and 15 minutes of inactivation at 75 ℃. Adaptor ligation was then performed by adding 5 µl of ligation master mix, which contains 30 Weiss Units of T4 DNA Ligase (HC, Thermo Scientific), 0.5 µl of 10x Buffer Tango, 5mM ATP (Thermo Scientific), and 150 nM of methylated custom adaptor (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where * indicates phosphorothioate bond). After three incubation steps (16 ℃ for 30 min, 4 ℃ overnight, and 65 ℃ for 20 min), the reaction mix was subjected to EpiTect Fast Bisulfite Conversion Kit (QIAGEN) following manufacturer’s low-concentration protocol. The bisulfite converted DNA was immediately subjected to PCR amplification using KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems) and NEBNext Primers for Illumina (New England Biolabs). Typically, 21 PCR cycles were required when starting with ~20 pronuclei. After amplification, final libraries were obtained by size selection of 150-500 bp DNA fragments using SPRIselect beads (Beckman Coulter).

value: WT

tag: parent-of-origin

value: paternal

value: mock


title: WT-Pat-rep2


title: Oral Cancer Poor 5-year survival Y012

description: Oral Cancer Poor 5-year survival Y012


title: WT-Pat-Aphi-rep2

source_name: WT-Pat-Aphi

value: aphidicolin


title: WT-Mat-rep2

source_name: WT-Mat

value: maternal


title: WT-Mat-rep1


title: WT-Mat-Aphi-rep2

source_name: WT-Mat-Aphi


title: WT-Mat-Aphi-rep1


title: Sperm-rep1

source_name: Sperm


title: CKO-Pat-rep2

source_name: CKO-Pat

value: CKO


title: CKO-Pat-rep1


title: Oocyte-rep1

source_name: Oocyte


title: CKO-Pat-Aphi-rep1

source_name: CKO-Pat-Aphi


title: Oocyte-rep2


title: CKO-Mat-Aphi-rep1

source_name: CKO-Mat-Aphi


title: CKO-Mat-rep1

source_name: CKO-Mat


title: Blast-CKO-rep2

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) with TopHat v2.0.10 coupled with Bowtie v2.1.0. The mapped reads were subjected to Cufflinks v2.2.0 with the reference annotation (UCSC gene models) to calculate the FPKM values of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: the processed data files contain the FPKM values of each gene (gene id, FPKM value)

source_name: blastocysts derived from Tet3-null oocytes

growth_protocol: MII oocytes were collected from superovulated CKO (Zp3-Cre, f/-) or WT (f/f) females. The oocytes were transferred into the HTF medium and fertilized in vitro with sperms from adult CAST/EiJ males. Zygotes that had 2 pronuclei were cultured in KSOM (Millipore). Ten of 2-cell embryos and seven of blastocysts at 30 or 96 hours after fertilization, respectively, were washed with PBS containing 0.03% BSA. They were then transferred into 0.2 ml tubes and stored at -80°C until use.

extract_protocol: To prepare RNA-Seq libraries, frozen 2-cell embryos and blastocysts were directly lysed and used for cDNA synthesis using SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech) following manufacturer’s instructions. After amplification, the cDNA samples were fragmented to an average size of 150 bp using a Covaris M220 sonicator (Covaris). Fragmented DNA was subjected to standard Illumina sequencing library preparation using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions.

tag: genotype/variation

value: CKO; Tet3-null

tag: developmental stage

value: blastocyst


title: Blast-CKO-rep1


title: Blast-WT-rep1

source_name: blastocysts derived from wildtype oocytes

value: wild type


title: WT-Pat-Aphi-rep1

tag: treatment


title: 2C-WT-rep2

source_name: 2-cell embryos derived from wildtype oocytes

value: 2-cell embryo


title: 2C-WT-rep1


title: Ls174T_pIND-shMiz1_-Dox_DMSO_replicate 1_RNAseq

tag: cell line


title: 2C-CKO-rep1

source_name: 2-cell embryos derived from Tet3-null oocytes


title: DMSO_input

first: Thomas

last: De Raedt

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Harvard Medical School -  Brigham Women's Hospital

data_processing:
Alignment used the BWA package.
Peak calling used the HOMER software package with the false discovery rate set to 0.001.
peak files in txt; Mapped tags were analyzed using a statistical method that fits a Poisson distribution to the data and calculates a global false discovery rate (FDR) for peak detection. Peak calling was performed using the HOMER software package with the FDR set to 0.001. Peak calling in this setting is differential because the algorithm requires that the number of tags mapped to an identified peak region is 4-fold higher in the test sample as compared to the Input sample. A background filter was applied by analyzing a 10kb region surrounding each peak. Peaks were removed unless tag density within each peak is at least 4-fold higher than in the surrounding region. Peaks were only  called in regions of the genome that are not masked by standard repeat element filters. Although repeat areas are removed, some regions of the genome still have low mappability due to undetected repeats or genome duplications. Accordingly, a final filter removed peaks in such poorly mappable regions.
Genome_build: hg19
Supplementary_files_format_and_content: peak files in txt

source_name: MPNST cells 90-8TL_DMSO

growth_protocol: 10% DMEM media

extract_protocol:
ChIPed following the Agilent Mammalian ChIP-on-chip protocol. Cells were cross- linked for 15 min at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution to the growth media.
NEBNext ChIP Master Mix Kit for Illumina following manufacturers instructions.

treatment_protocol: 24h treatment with DMSO or PD-032901 (2uM) + JQ1 (100nM) in 10% DMEM media

value: MPNST cell line 90-8TL

value: DMSO for 24hrs


title: PDJQ_BRD4_ChIPseq

source_name: MPNST cells 90-8TL_PDJQ

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat. #


title: PDJQ_H3K27Ac_ChIPseq

tag: treated with

value: Abcam


title: CKO-Mat-rep2

tag: genotype


title: DMSO_H3K27Ac_ChIPseq


title: DMSO_BRD4_ChIPseq


title: CKO-Pat-Aphi-rep2


title: mPB_CD34plus_UM171-78_1nM

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: mobilized peripheral blood_UM171

growth_protocol: Cells were cultured in serum free media supplemented with Flt3L  [100ng/ml], SCF  [100ng/ml], TPO [50ng/ml] and LDL [10ug/ml]

extract_protocol:
Trizol
TruSeq RNA (Illumina)

treatment_protocol: Cells were treated in a dose response with UM171 [11.9nM, 19nM, 30.5nM, 48.8nM, 78.1nM and 125nM], SR1 [500nM] and combination of UM171  [48.8nM]+SR1 [500nM])

tag: cell type

value: mobilized peripheral blood cells

tag: modulating agent

tag: growth time

value: 16 hour culture


title: CB_CD34+_DMSO

source_name: Cord blood CD34+_DMSO

value: Cord blood CD34+ cells

value: DMSO


title: Blast-WT-rep2


title: mPB_CD34plus_UM171-48_8nM


title: mPB_CD34plus_UM171-125nM


title: CKO-Mat-Aphi-rep2


title: degradome-orange-Fr

city: Wuhan

first: Liu

last: Yuanlong

address: Shizishan street NO.1

institute: Huazhong agriculture university

description: Sample 3

data_processing:
Illumina Casava software used for basecalling.
Raw datas about 35nt length obtained from Solexa sequencing, go through steps likely adaptor, pollution, low quality trimmed to obtain clean sequence
Mapped to sweet orange genome
Genome_build: Sweet orange genome sequence, http://citrus.hzau.edu.cn/orange/index.php
Supplementary_files_format_and_content: Tab-delimited text files include length, count and sequence for each sample

organism: Citrus sinensis

growth_protocol: The sweet orange was planted at the Institute of Citrus Research located in Guilin, Guangxi Province, China.

extract_protocol:
All samples were collected and frozen in liquid nitrogen immediately after collection and kept at -80℃ until use.Total RNA was extracted using Trizol reagent.
The 3’ fragment generated by RISC (RNA-induced silencing complex), which contains a 5’-monophosphate, was ligated to a 5’ RACE adaptor. Reverse transcription is then performed using oligo(dT) as a 3’ adaptor and the cDNAs were formed by second strand synthesis.

tag: tissue

value: Fruit

value: 170 days after flowering


title: mPB_CD34plus_UM171-30_5nM


title: degradome-orange-F

description: Sample 2

value: Flower

value: Samples in all stages mixed


title: mPB_CD34plus_UM171-11_9nM


title: mPB_CD34plus_SR1-500nM

source_name: mobilized peripheral blood_SR1


title: 2C-CKO-rep2


title: mPB_CD34plus_DMSO

source_name: mobilized peripheral blood_DMSO


title: Sperm-rep2

value: WT

value: paternal

value: mock


title: PDJQ_input

tag: chip antibody


title: CB_CD34plus_UM171-30_5nM

source_name: Cord blood CD34+_UM171


title: CB_CD34plus_UM171-78_1nM


title: mPB_CD34plus_d0

source_name: mobilized peripheral blood_uncultured

value: uncultured


title: CB_CD34plus_UM171-19nM


title: degradome-orange-L

description: Sample 1

value: wild type

value: Leaf


title: CB_CD34plus_UM171-125nM


title: CB_CD34plus_UM171-11_9nM


title: CB_CD34plus_SR1-500nM

source_name: Cord blood CD34+_SR1


title: CB_CD34plus_SR1-500nMplusUM171-48_8nM

source_name: Cord blood CD34+_SR1+UP171


title: CB_CD34plus_d0

source_name: Cord blood CD34+_uncultured


title: mPB_CD34plus_UM171-19nM


title: CB_48hr_SR1

source_name: CD34+ human cord blood-derived cells

growth_protocol: CD34+ human cord blood-derived cells was cultured in serum free media supplemented with LDL (10μg/ml)  and the following cytokine: FLT3L (100ng/ml), SCF (100ng/ml), TPO(50ng/ml)

extract_protocol:
RNA extration using Trizol reagent
TruSeq RNA (Illumina)

treatment_protocol: Cells were treated upon culture with DMSO (vehicle), UM171 [35nM], SR1[500nM] or combination of UM171 [35nM]+SR1[500nM]


title: CB_72hr_DMSO


title: CB_72hr_SR1


title: CB_Fresh


title: CB_72hr_UM171


title: CB_72hr_Combi


title: CB_48hr_DMSO


title: CB_3hr_UM171


title: CB_48hr_UM171


title: CB_30min_SR1


title: CB_3hr_Combi


title: CB_48hr_Combi


title: CB_30min_UM171


title: CB_24hr_UM171


title: Orange-L

description: Sample 1

data_processing:
Illumina Casava software used for basecalling.
Get rid of the 5' adaptor, contaminant and low quality reads from the original 35nt reads to obtain clean reads
Mapped to sweet orange genome
Genome_build: Sweet orange genome sequence, http://citrus.hzau.edu.cn/orange/index.php
Supplementary_files_format_and_content: Tab-delimited text files include length, count and sequence for each sample

extract_protocol:
All samples were collected and frozen in liquid nitrogen immediately after collection and kept at -80℃ until use.Total RNA was extracted using Trizol reagent.
Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing.

value: leaf

value: samples in all stages mixed


title: CB_24hr_DMSO


title: CB_3hr_SR1


title: CB_3hr_DMSO


title: Scc2-4 -break input

city: Stockholm

first: Lena

last: Ström

address: Berzelius väg 35

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
SOLiD raw data were converted to csfasta and qaul files and mapped with bowtie.
Basecalls performed using Corona
mapped to S. cerevisiae whole genome using bowtie v0.12.2 with parameters -n3 -m10
The result files were formatted sam type with the option --sam.
Then, sam files were converted to wig files with the script “bed2wig.py”(https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py)
Data were visualized using Cairo
Genome_build: sacCer1
Supplementary_files_format_and_content: wig files

organism: Saccharomyces cerevisiae

source_name: Scc2-4 -break input

growth_protocol: YEP media supplemented with 2% raffinose

extract_protocol:
Lysates were clarified from sonicated nuclei and Scc1 flag tagged DNA complexes were isolated with anti-flag antibody (Sigma F3165)
The 5500 SOLiD™ Fragment Library Core Kit

treatment_protocol: Log phase yeast cells were arrested in G2/M. The temperature was raised and 30 minutes later galactose was added to induce one DSB in cells containing the recognition site for the HO enzyme. Ninety minutes later, cells were harvested.

tag: strain

tag: condition

value: no break Chr. VI


title: CB_24hr_Combi


title: CB_30min_Combi


title: WT +break input

source_name: WT +break input

value: WT W303

value: break Chr. VI


title: Orange-F

description: Sample 2

value: flower


title: Scc2-4 -break IP

source_name: Scc2-4 -break IP

value: anti-flag antibody

value: Sigma


title: WT -break IP

source_name: WT -break IP


title: Scc2-4 +break IP

source_name: Scc2-4 +break IP


title: PH Yak Rep2

status: Public on Oct 20 2014

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

country: France

institute: Institute de Génétique Humaine

description: processed data file: dYak_binned_profiles.txt

data_processing:
Mapping - For each ChIP-seq experiment, we mapped short reads (36/50 bps) to the appropriate reference genome using Bowtie-0.12.2 by specifying ‘-a –m 1 -best -strata’ options. Our reference genomes included the heterochromatic fraction of chromosomes and non-assembled contigs, and any read that could be mapped to more than one genomic locus was filtered from further processing.
Pile-up - Mapped tags were extended to 140bp and coverage statistics for 20bp bins over each of the genomes were computed. This was done following analysis of the correlation between coverage in the forward and reverse strands, which indicated peak correlation between the two at an offset of 140bp, suggesting the empirical fragment length assayed by ChIP-seq was 140bp.
Normalizing per-species' mappability - Each species genome contains regions that are non-unique and therefore cannot be profiled using short read tags. We generated a control profile for each species by applying the mapping and binning procedure as described above for all possible 36/50bp subsequences in each of the genomes. We derived mappability tracks for each species, indicating the fraction of fragments covering each 20bp genomic bin that could be mapped uniquely to the respective genome. We then normalized the coverage score of each experiment by dividing it with this mapability value. Regions with mappability lower than 50% were filtered out and marked as Not Mapable in subsequent analysis. Note that unmappable regions were different between the species due to duplications and deletions.
Coverage normalization - To control for ChIP-seq coverage and variable ChIP-seq specificity, we transformed raw coverage values to minus log2 of its (1 - quantile) value For example, a normalize value of 9 indicates coverage is in the top 1-2-9 quantile (e.g. – in the top (1/512)th of the distribution).
Genome_build: dm3,droSim1,droYak2,dp4,droVir3
Supplementary_files_format_and_content: For each species we have a tab-delimited file. Each row represents a position in the appropriate genome (1 value for each 20bp bin). The first and second columns are chromosome and position respectively. Columns 3 on represent different ChIP-Seq experiments. Values represent normalized coverage as described in the data processing step.

organism: Drosophila yakuba

source_name: D. Yakuba_PH

extract_protocol:
Chromatin prepared from Drosophila embryos was immunoprecipitated with specific antibodies and precipitated DNA was isolated (see mat and methods for details)
Libraries were prepared according to Illumina's instructions

value: embryos

tag: age

value: none (input)

tag: chip antibody ref.

value: Schuettengruber et al, Plos Biol 2009


title: WT -break input

source_name: WT -break input

tag: genotype/variation


title: Scc2-4 +break input

source_name: Scc2-4 +break input


title: PHO Yak Rep2

source_name: D. Yakuba_PHO

value: PHO

value: Klymenko et al, 2006


title: CB_24hr_SR1


title: compound C3 replicate 2

source_name: SMA type I fibroblasts_compound C3

value: SMA type I fibroblasts

value: 500nM SMN-C3 for 24hrs


title: DSP1 Yak Rep1

source_name: D. Yakuba_DSP1

value: wild type


title: CB_12hr_UM171


title: WT +break IP

source_name: WT +break IP


title: PC Yak Rep1

source_name: D. Yakuba_PC

value: PC


title: CB_12hr_SR1


title: CB_12hr_DMSO

value: DMSO


title: CB_12hr_Combi


title: PHO Yak Rep1


title: Input Yak Rep2

source_name: D. Yakuba_Input


title: H3K4me3 Yak Rep1

source_name: D. Yakuba_H3K4me3

value: H3K4me3, Millipore  #07-473


title: CB_30min_DMSO


title: CS-spike2-sRNAseq

city: Beijing

first: Mengdi

last: Liu

address: No.38 Xueqing Road, Haidian District

institute: Novogene institute

description: sRNA profiling

data_processing:
For small RNA-Seq data, raw sequence reads were processed into clean full-length reads using the BGI small RNA pipeline.
For small RNA-Seq data, all low-quality reads were removed from the raw sequence, and the 3' adapter reads, 5' adapter contaminants, sequences containing the polyA tail and those smaller than 18 nt were also discarded.
For mRNA RNA-Seq data, TopHat for mapping, HTSeq for estimating their abundances
Genome_build: Reference genome sequences and annotations were downloaded from the wheat genome website (A genome: ftp://climb.genomics.cn/ pub/10.5524 /100001_101000/100050 /A/Assembly/; D genome ftp://climb.genomics.cn /pub/10.5524 /100001_101000 /100054/D/Assembly/). To avoid bias toward D-specific gene models, we blasted A gene models against the D genome and used BLAST-aligned homologous regions as references for gene expression quantification. We also used these D genome regions as references to identify single nucleotide polymorphisms (SNPs) between homoeologous reads of the two progenitors.
Supplementary_files_format_and_content: The *rpkm.txt.gz files include abundance measurements (RPKM values) for each mRNA RNA-Seq sample. The *sRNA.txt.gz processed files contain clean tags and filtered, 18-30 nt, unique sequence reads of smallRNA with counts for each small RNA-Seq sample.

organism: Triticum aestivum

source_name: spike

growth_protocol: Seedlings were grown in 18–20°C day and 14–15°C night temperatures under a 16-h photoperiod.

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Invitrogen Corp., Carlsbad, CA, USA) and treated with RNase-free DNase I (New England Biolabs, Ipswich, MA, USA) to remove any contaminating genomic DNA.
mRNA extraction was performed using Dynabeads oligo(dT) (Dynal; Invitrogen Corp.). Double-stranded cDNAs were synthesized using reverse transcriptase (Superscript II; Invitrogen Corp.) and random hexamer primers. The cDNAs were then fragmented by nebulization, and the standard Illumina protocol was followed thereafter to create the mRNA-seq libraries. Small RNAs were prepared using a protocol published in Kasschau et al., (2007) and subjected to high-throughput sequencing.

tag: developmental stage

value: spike at heading date stage

tag: genome

value: AABBDD

tag: relationship

value: natural hexaploid wheat


title: CS-spike1-sRNAseq

description: sRNA profiling


title: S3-spike1-sRNAseq

description: sRNA profiling

value: progeny:S3 generation


title: S3-seed1-sRNAseq

description: sRNA profiling

source_name: seed

value: seed of 11 day after flowering (DAF)


title: S4-spike1-sRNAseq

description: sRNA profiling

value: progeny:S4 generation


title: CS-seed2-sRNAseq

description: sRNA profiling


title: H3K27me3 Yak Rep1

source_name: D. Yakuba_H3K27me3

value: embryos

value: H3K27me3, Millipore, #07-449


title: PH Yak Rep1

value: PH

value: Schuettengruber et al, Plos Biol 2009


title: CS-spike1-RNAseq

description: mRNA profiling


title: Input Yak Rep1

value: none (input)


title: S3-spike2-sRNAseq

description: sRNA profiling


title: S3-seed2-sRNAseq

description: sRNA profiling


title: S3-seedling1-sRNAseq

description: sRNA profiling

source_name: seedling

value: 7-day-old age seedling


title: S3-seedling2-sRNAseq

description: sRNA profiling


title: S2-seed1-sRNAseq

description: sRNA profiling

value: progeny:S2 generation


title: S1-spike1-sRNAseq

description: sRNA profiling

value: progeny:S1 generation


title: S1-seed1-sRNAseq

description: sRNA profiling


title: S3-spike2-RNAseq

description: mRNA profiling


title: CS-seed2-RNAseq

description: mRNA profiling


title: S3-seed1-RNAseq

description: mRNA profiling


title: CS-spike2-RNAseq

description: mRNA profiling


title: S3-seedling1-RNAseq

description: mRNA profiling


title: S1-spike1-RNAseq

description: mRNA profiling


title: S4-spike1-RNAseq

description: mRNA profiling


title: S3-seed2-RNAseq

description: mRNA profiling


title: S3-spike1-RNAseq

description: mRNA profiling


title: PHO Pse Rep2

description: processed data file: dPse_binned_profiles.txt

organism: Drosophila pseudoobscura

source_name: D. Pseudoobscura_PHO

value: wild type

value: PHO

value: Klymenko et al, 2006


title: S1-seed1-RNAseq

description: mRNA profiling


title: PH Pse Rep2

source_name: D. Pseudoobscura_PH


title: S3-seedling2-RNAseq

description: mRNA profiling


title: S2-seed1-RNAseq

description: mRNA profiling


title: H3K27me3 Pse Rep2

source_name: D. Pseudoobscura_H3K27me3


title: H3K4me3 Pse Rep2

source_name: D. Pseudoobscura_H3K4me3

value: H3K4me3, Millipore  #07-473


title: PHO Pse Rep1


title: PC Pse Rep2

source_name: D. Pseudoobscura_PC

value: PC


title: PC Pse Rep1


title: H3K27me3 Pse Rep1


title: DSP1 Pse Rep1

source_name: D. Pseudoobscura_DSP1


title: DSP1 Pse Rep2


title: PH Pse Rep1


title: CMV-Fny infection (degradome)

city: Hangzhou

first: Junli

last: Feng

address: Hangzhou, Jiaogong Road 149#

institute: Zhejiang Gongshang University

description:
Degradome-Seq
FJL_B

data_processing:
The raw small RNA sequencing data were firstly processed with an in-house program called LCS ACGT101-miR v4.2 (LC Sciences, Texas, USA), to filter out the adapter sequences. Then, the extracted small RNA sequences with 15-29 nt in length were subjected to mRNA, RFam, Repbase filters. Finally, the remaining unique sequences were compared to the miRNA database (ftp://mirbase.org/pub/mirbase/CURRENT/) and Solanum Genome network (http://solgenomics.net/) for miRNA and pre-miRNAs identification and novel miRNA prediction .
To identify potential novel miRNAs in tomato, the unmapped small RNA sequences were BLASTed against the tomato genome and folded into a secondary structure by Mfold software (http://mfold.rna.albany.edu/) and Vienna RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). Only the non-coding sequence which could form a perfect stem-loop structure and meet the criteria for miRNAs prediction were then considered to be a novel potential candidate miRNA (PC-miRNA).
The raw reads for each small RNA sequence were firstly normalized by the global normalization procedures, then the differentially expressed sequence counts in mock- and CMV-infected tomato were analyzed by the online service IDEG6 (http://telethon.bio.unipd.it/bioinfo/IDEG6_form/).
In degradome sequencing, raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software to remove adaptor sequences and low quality sequencing reads. The extracted sequencing reads with the length of 20 and 21 nt were then used to identify potentially cleaved targets by the CleaveLand pipeline. The degradome reads were mapped to tomato mRNA database (http://www.sgn.cornell.edu/about/tomato_sequencing.pl). Only the perfect matching alignment(s) for the given read would be kept and extend to 35-36 nt by adding 15 nt of upstream of the sequence. All resulting reads (t-signature) were reverse-complemented and aligned to the miRNA identified in our study.
Genome_build: solanum lycopersicum genome：http://solgenomics.net  ftp://ftp.solgenomics.net/est sequences/species/Tomato
Supplementary_files_format_and_content: All_Expressed_miRNA_output4.txt is the summary of small RNA sequences detected in this study (referred to miRbase 20.0).FJL01_short_outfile_1_anno.txt is the predict targets of all plant miRNAs identified in mock infected library and their GO analysis. FJL02_short_outfile_1_anno2.txt is the predict targets of all plant miRNAs identified in CMV-Fny infected library and their GO analysis.

organism: Solanum lycopersicum

source_name: Tomato micro-Tom

growth_protocol: The miniature tomato cultivar, micro-Tom, was used as host plants in our study. Tomato seedlings were grown in a greenhouse at 12 h day/12 h night (18-22°C) and light intensity of >8000 lx.

extract_protocol: Small RNA sequencing libraries were generated from Group A and group B. Firstly, small RNA fractions between 18-30 nt were isolated from 10 g total RNAs by 15% denaturing polyacrylamide gel electrophoresis. After recovering the isolated RNAs, the obtained short RNAs were then ligated to the 5'(GUUCAGAGUUCUACAGUCCGACGAUC) and 3'(P-UCGUAUGCCGUCUUCUGCUUG-UidT) chimeric oligonucleotide adapters, and reverse transcribed to single-stranded cDNAs with an RT primer (CAAGCAGAAGACGGCATACGA). Subsequently, the cDNAs were PCR amplified using primers that annealed to the ends of adapters. Finally, the amplification products were sequenced using High-seq 2000 sequencing platform (LC Sciences).Degradome sequencing libraries were constructed using mRNA isolated from total RNA samples used in small RNA sequencing. Library construction comprises the following steps: 1) Poly-adenylated RNA molecules are isolated ; 2) RNA adapter is added to the 5’ ends of the single-stranded RNA molecules; 3) Reverse transcriptase is used to generate the first strand of cDNA using an oligo (dT) with a 3’ adapter sequence; 4) A short PCR is used to amplify the cDNA to obtain sufficient quantities of template; 5) The product of the PCR reaction is then digested with MmeI ; 6) A 3’ adapter with degenerate nucleotides in the overhang region is ligated to the MmeI digestion products 7) The resulting material is PCR amplified, gel purified and used for sequencing.

treatment_protocol: CMV-Fny, a typical strain of CMV subgroup I, was reconstituted from infectious clones, and maintained on Nicotiana tabacum. Inoculation was carried out by mechanical inoculation on the first true leaves of 14-day old tomato seedlings, with sap prepared from systemically infected tobacco leaf tissues homogenized in 20 volumes of 100 mM sodium phosphate buffer, pH7.2. Mock-treated tomatoes were inoculated with sodium phosphate buffer only.

value: Micro-Tom

value: Tomato leaves

value: 20 days post inoculation

tag: infection

value: CMV-Fny


title: CMV-Fny infection (small RNA)

description:
miRNA-Seq
FJL_B


title: PI94655-seed2-sRNAseq

description: sRNA profiling

organism: Triticum turgidum

value: seed of 11 day after flowering (DAF)

value: AABB

value: maternal parent


title: Mock treated (degradome)

description:
Degradome-Seq
FJL_A

value: mock


title: Mock treated (small RNA)

description:
miRNA-Seq
FJL_A


title: PI94655-seed1-sRNAseq

description: sRNA profiling


title: PI94655-spike2-sRNAseq

description: sRNA profiling

value: spike at heading date stage


title: PI94655-seedling2-sRNAseq

description: sRNA profiling

value: 7-day-old age seedling


title: PI94655-seedling1-sRNAseq

description: sRNA profiling


title: Input Pse Rep2

source_name: D. Pseudoobscura_Input

value: embryos

value: none (input)


title: PI94655-spike2-RNAseq

description: mRNA profiling


title: PI94655-seed1-RNAseq

description: mRNA profiling


title: Input Pse Rep1

value: wild type


title: PI94655-spike1-RNAseq

description: mRNA profiling


title: H3K4me3 Pse Rep1


title: PI94655-seedling2-RNAseq

description: mRNA profiling


title: AS2404-seedling2-sRNAseq

description: sRNA profiling

organism: Aegilops tauschii

value: DD

value: paternal parent


title: PI94655-seedling1-RNAseq

description: mRNA profiling


title: AS2404-seed2-sRNAseq

description: sRNA profiling


title: AS2404-seed1-sRNAseq

description: sRNA profiling


title: AS2404-spike2-sRNAseq

description: sRNA profiling


title: PI94655-spike1-sRNAseq

description: sRNA profiling


title: AS2404-spike1-sRNAseq

description: sRNA profiling


title: AS2404-seedling2-RNAseq

description: mRNA profiling


title: AS2404-seedling1-sRNAseq

description: sRNA profiling


title: AS2404-spike2-RNAseq

description: mRNA profiling


title: AS2404-seed1-RNAseq

description: mRNA profiling


title: PI94655-seed2-RNAseq

description: mRNA profiling


title: AS2404-seedling1-RNAseq

description: mRNA profiling


title: AS2404-spike1-RNAseq

description: mRNA profiling


title: PC Phdel rep2

description: processed data file: dMel_binned_profiles.txt

organism: Drosophila melanogaster

source_name: D. Melanogaster_PC Phdel

value: PH del mutant

value: Schuettengruber et al, Plos Biol 2009


title: PC Phdel rep1

value: PC


title: Input WT Rep2

source_name: D. Melanogaster_Input WT


title: PHO Phdel rep1

source_name: D. Melanogaster_PHO Phdel

value: PHO


title: PC WT Rep1

source_name: D. Melanogaster_PC WT


title: Input WT Rep1


title: Input Phdel rep1

source_name: D. Melanogaster_Input Phdel


title: PC WT Rep2


title: PHO Mel Rep2

source_name: D. Melanogaster_PHO

value: Klymenko et al, 2006


title: Input Phdel rep2


title: AS2404-seed2-RNAseq

description: mRNA profiling

source_name: seed


title: H3K4me3 Mel Rep2

source_name: D. Melanogaster_H3K4me3

value: H3K4me3, Millipore  #07-473


title: Input Mel Rep2

source_name: D. Melanogaster_Input


title: PHO Mel Rep1


title: DSP1 Mel Rep2

source_name: D. Melanogaster_DSP1


title: PC Mel Rep2

source_name: D. Melanogaster_PC


title: PH Mel Rep2

source_name: D. Melanogaster_PH

value: PH


title: H3K27me3 Mel Rep2

source_name: D. Melanogaster_H3K27me3

value: H3K27me3, Millipore, #07-449


title: Input Mel Rep1


title: H3K4me3 Mel Rep1


title: PHO Phdel rep2


title: PHO WT Rep2

source_name: D. Melanogaster_PHO WT


title: DSP1 Mel Rep1


title: PH Mel Rep1


title: PC Mel Rep1


title: H3K27me3 Mel Rep1


title: PHO WT Rep1


title: HEK293T_ssRNase_digestion_control_rep3

city: Philadelphia

first: Ian

middle: M

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

description:
RNA is denatured and proteinase K treated and then digested with a ssRNase (RNaseOne)
HEK293T_Form_SSase_rep3.CSAR_PPS_FDR05.bed
HEK293T_Form_SSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed

data_processing:
Basecalls performed with Bustard 1.13.48.
3' adapter sequences were trimmed using cutadapt (version 0.9.5 with parameters -e 0.06 -O 6 -m 14)
Trimmed reads were aligned to the human genome (hg19) using Tophat (version 2.0.9 with parameters --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search --no-novel-juncs)
Protein-protected sites were identified using a modified version of the CSAR software package (Muino et al. 2011). Specifically, read coverages were calculated for each base position in the genome and a Poisson test was used to compute an enrichment score for ‘protected’ versus ‘unprotected’ libraries. PPSs were then called as described (Muino et al. 2011) with an FDR of 5%
Genome_build: hg19
Supplementary_files_format_and_content: BED format of protein protected sites (PPSs)

growth_protocol: HEK293T cells were seeded in 15-cm standard Corning tissue-culture treated culture dishes (Sigma, St Louis, MO), grown to 90% confluence (approximately 18 million cells) in DMEM media (Life Technologies, San Diego, CA) supplemented with L-glutamine, 4.5 g/L D-glucose, 10% fetal bovine serum (FBS (Atlanta Biologics, Atlanta, GA)) and Pen/Strep (Fisher Scientific, Waltham, MA).

extract_protocol:
We lysed the cell pellets using RIP buffer (25 mM Tris-HCl, pH = 7.4; 150 mM KCl, 5 mM EDTA, pH = 7.5; 0.5% NP40; 10 mM DTT; 1 tablet protease inhbitors/10mL) and manual grinding. The resulting cell lysate was treated with RNase-free DNase (Qiagen; Valencia, CA).  Subsequently, these DNA-depleted lysates were treated with either a single-stranded RNase (ssRNase) (RNaseONE (Promega; Madison, WI)) or double-stranded RNase (dsRNase) (RNaseV1 (Ambion; Austin, TX)) as previously described ((Zheng et al. 2010; Li et al. 2011), see Fig. 1A for a schematic description). Proteins were then denatured and digested by treatment with 1% SDS and 0.2ug/ml Proteinase K (Roche; Basel, Switzerland). It is worth noting for clarity that we had two cell lysates for these experiments: one treated with the ssRNase and the other with dsRNase. For formaldehyde cross-linking experiments, Proteinase digestion was followed by a 2-hour incubation at 65°C to reverse the crosslinks. To determine whether nuclease resistant regions in RNAs are due to protein binding or specific secondary structures, we also determined the digestion patterns of ds- and ssRNases in the absence of bound proteins. To do this, we performed the identical treatments as described directly above except that the cross-linked cellular lysates were treated with 1% SDS and 0.2 ug/ml Proteinase K (Roche; Basel, Switzerland) and ethanol precipitated prior to being treated with the two RNases. In this way, the SDS and Proteinase K solubilized and digested the proteins allowing us to deduce protein-protected sites within all detectable RNAs in the cells of interest. The digested RNA was then isolated using the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
(TruSeq small RNA sequencing kit [illumina, Valencia, CA]), as previously described (Zheng et al. 2010; Li et al. 2011), with the exception that we also include DSN library normalization per manufacturer instructions (Illumina; San Diego, CA).

treatment_protocol: A 37% formaldehyde solution (Sigma, St. Louis, MO) was added drop-wise with mixing directly to cell culture dishes to a final concentration of 1% and incubated at room temperature for 10 minutes. Next, 1M glycine (Sigma, St. Louis, MO) was added to a final concentration of 125 mM and incubated for an additional 5 minutes with mixing.  Then, cells were washed twice with ice cold PBS and collected.  Finally, cells were pelleted and frozen until the PIP-seq digestions were performed.

tag: cell line

value: ssRNase (RNase ONE)


title: HEK293T_dsRNase_digestion_control_rep1

description:
RNA is denatured and proteinase K treated and then digested with a dsRNase (Rnase V1)
HEK293T_Form_DSase_rep1.CSAR_PPS_FDR05.bed
HEK293T_Form_DSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed

value: dsRNase (RNase V1)


title: HEK293T_dsRNase_digestion_control_rep3

description:
RNA is denatured and proteinase K treated and then digested with a dsRNase (Rnase V1)
HEK293T_Form_DSase_rep3.CSAR_PPS_FDR05.bed
HEK293T_Form_DSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: HEK293T_ssRNase_footprint_rep3

description:
RNA is treated with ssRNase (RNaseOne)
HEK293T_Form_SSase_rep3.CSAR_PPS_FDR05.bed
HEK293T_Form_SSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: HEK293T_dsRNase_footprint_rep1

description:
RNA is treated with dsRNase (RNase V1)
HEK293T_Form_DSase_rep1.CSAR_PPS_FDR05.bed
HEK293T_Form_DSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: HEK293T_ssRNase_digestion_control_rep2

description:
RNA is denatured and proteinase K treated and then digested with a ssRNase (RNaseOne)
HEK293T_Form_SSase_rep2.CSAR_PPS_FDR05.bed
HEK293T_Form_SSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: HEK293T_dsRNase_footprint_rep3

description:
RNA is treated with dsRNase (RNase V1)
HEK293T_Form_DSase_rep3.CSAR_PPS_FDR05.bed
HEK293T_Form_DSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: HEK293T_dsRNase_footprint_rep2

description:
RNA is treated with dsRNase (RNase V1)
HEK293T_Form_DSase_rep2.CSAR_PPS_FDR05.bed
HEK293T_Form_DSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: HEK293T_ssRNase_digestion_control_rep1

description:
RNA is denatured and proteinase K treated and then digested with a ssRNase (RNaseOne)
HEK293T_Form_SSase_rep1.CSAR_PPS_FDR05.bed
HEK293T_Form_SSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: HEK293T_ssRNase_footprint_rep1

description:
RNA is treated with ssRNase (RNaseOne)
HEK293T_Form_SSase_rep1.CSAR_PPS_FDR05.bed
HEK293T_Form_SSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: Input Vir Rep2

description: processed data file: dVir_binned_profiles.txt

organism: Drosophila virilis

source_name: D. Virilis_Input


title: HEK293T_dsRNase_digestion_control_rep2

description:
RNA is denatured and proteinase K treated and then digested with a dsRNase (Rnase V1)
HEK293T_Form_DSase_rep2.CSAR_PPS_FDR05.bed
HEK293T_Form_DSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: Input Vir Rep1


title: H3K27me3 Vir Rep1

source_name: D. Virilis_H3K27me3


title: SCBI STAT B

city: Durham

first: Louis

middle: S

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

data_processing:
Illumina Casava1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to SCBI whole genome using CLC workstation
Genome_build: CP003424 and CP003425
Supplementary_files_format_and_content: tab-delimited text files include the locus tags of genome and RPKM values for each Sample.

organism: Serratia sp. SCBI

source_name: culture

growth_protocol: LB medium 28C for 18h

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

value: Wild type control

tag: growth state

value: stationary phase

tag: culture condition


title: H1B T0 input

city: Los Angeles

first: Jinkai

last: Wang

state: CA

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

description: Sample 2

data_processing:
50bp single-end RNA-Seq reads were mapped to hg19 genome using Tophat.
bam files were converted to bedgraphs using genomeCoverageBed, which were in turn converted to bigwigs using bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs show number of reads uniquely mapped to the genome

molecule: polyA RNA

source_name: ES cell, no IP (input RNA)

extract_protocol:
Cells well harvested by direct addition of TRIzol reagent (Ambion Cat.#15596018) to the cell culture plate after removal of the media and extracted using Trizol reagent protocol. Subsequently, the total RNA was DNAse treated using DNAse I (Promega Cat.# M610A) for 20 minutes at 37ºC followed by acid phenol/chloroform extraction, chloroform extraction and overnight NaCl2 precipitation. The precipitated RNA was washed with 70ºC ethanol and re-suspended in ultra pure H2O. RNA concentration and purity were verified by nanodrop followed by BioAnalyzer for quality control. Double polyA+ RNA selection was performed using twice Invitrogen Dynabeads mRNA Purification Kit (Cat. #610.06) protocol. RNA concentration and purity were once again verified by nanodrop followed by BioAnalyzer for quality control.
For the input and post m6A-RNA IP fraction (i.e. m6A positive fraction), 100ng of RNA was used for library construction using TrueSeq Stranded mRNA Sample Preparation Guide, entering the protocol by adding the Fragment, Prime, Finish Mix, skipping the elution step and proceeding directly to synthesis of the First Strand cDNA. From that point on, the exact steps of the Illumina TruSeq Stranded mRNA sample Preparation Guide were followed to the end.

tag: cell type

value: embryonic stem (ES) cell


title: H1A T48 input

description: Sample 3

source_name: Endoderm cells, no IP (input RNA)

value: Endoderm


title: H1A T0 input

description: Sample 1


title: H1A T0 eluate

description: Sample 1

source_name: ES cell, RNA IP against m6A


title: H1A T48 eluate

description: Sample 3

source_name: Endoderm cells, RNA IP against m6A


title: 22-F6-b

value: pin mutant


title: SCBI STAT A


title: H1B T48 input

description: Sample 3


title: H1B T0 eluate (new run)

description:
Sample 3
This is additional sequencing run


title: H1A T0 eluate (new run)


title: H1B T48 eluate

description: Sample 3


title: H1B T0 input (new run)


title: H1A T0 input (new run)


title: 22-F6-A


title: LN229-control

city: hangzhou

first: jie

last: liu

address: yuhangtang road 866

institute: zcni

description: the last five nucleotides of raw reads were index"CGTAT"

data_processing:
Basecalls performed using OLB1.8.0 with default parameters
raw reads were separated into two parts according to different index(the last five nucleotides).TCGAT represented LN229-SOX4,and CGTAT represented LN229-control.
ChIP-seq reads were aligned to the hg19 genome database using bowtie version 0.12.7 with the following configurations: -S -l 26 -n 2 -e 70 --phred64-quals -m 1 --best --strata -X 1000
peaks were called using MACS version 1.4.0alpha2 with the following setting: effective genome size = 2.70e+09 band width = 300 model fold = 10,30 pvalue cutoff = 1.00e-05
Genome_build: hg19
Supplementary_files_format_and_content: SOX4_peaks.bed: peaks of reads (.bed format), peaks were called using MACS version 1.4.0alpha2 with the following setting: effective genome size =2.70e+09 band width = 300 model fold = 10,30 pvalue cutoff = 1.00e-05.
Supplementary_files_format_and_content: MACS_treat.tar.gz: (.wig format), when we do peakcalling using MACS with parameter -w(-w, --wig    Whether or not to save extended fragment pileup at every WIGEXTEND bps into a wiggle file.), we will get these files.
Supplementary_files_format_and_content: MACS_control.tar.gz: (.wig format), when we do peakcalling using MACS with parameter -w, we will get these files.

source_name: LN229 human glioblastoma cell line with GFP  overexpression

extract_protocol:
Lysates were clarified from sonicated nuclei and SOX4-DNA complexes were isolated with anti-Flag antibody. The negative control experiment used LN229-GFP cell and anti-Flag antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: LN229 cells were transfected with Flag-SOX4-HA or GFP-Flag-HA plasmid

value: LN229 glioblastoma cell line

value: control

value: anti-Flag (Sigma, Catalog# F3165)


title: LN229-SOX4

description: the last five nucleotides of raw reads were index"TCGAT"

source_name: LN229 human glioblastoma cell line with SOX4 overexpression


title: HEK293T_ssRNase_footprint_rep2

description:
RNA is treated with ssRNase (RNaseOne)
HEK293T_Form_SSase_rep2.CSAR_PPS_FDR05.bed
HEK293T_Form_SSase.CSAR_PPS_FDR05.bed
HEK293T_Form.CSAR_PPS_FDR05.bed


title: 22-C7-B

value: gidA mutant


title: 16-D2-A

value: aprE mutant


title: 22-C7-A


title: 16-D2-B


title: H1B T0 eluate

description: Sample 2


title: PHO Sim Rep2

description: processed data file: dSim_binned_profiles.txt

organism: Drosophila simulans

source_name: D. Simulans_PHO

value: wild type

value: embryos

value: PHO


title: PH Sim Rep3

source_name: D. Simulans_PH

value: PH

value: Schuettengruber et al, Plos Biol 2009


title: Ly6C_Lo_Mono

city: Ridgefield

first: Jonathan

middle: Daryl

last: Hill

state: CT

address: 900 Ridgebury Road

department: Computational Biology

institute: Boehringer Ingelheim Pharmaceuticals Inc

data_processing:
Libraries were sequenced using an Illumina HiSeq2000 platform and 50bp, single or paired-end sequencing data was obtained with approximately 15-20 million reads per sample.
Alignment to mouse genome using STAR version 2.3
FPKM calculations with Cufflinks 2.1
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are Cufflinks output with FPKMs provided for each gene.  The files themselves are tab-delimited text.

source_name: Sorted mouse CNS and blood cells

growth_protocol: Isolation and analysis of CNS cells: Female C57BL/6 mice (6–10 wk of age) were purchased from The Jackson Laboratory. Animals were fed and watered ad libitum under 12-h light/dark cycles. All studies were performed in accordance with Institutional Animal Care and Use Committee guidelines. Mice were placed under anesthesia and were perfused intracardially with PBS until the liver became blanched. The brain and spinal cord were isolated and homogenized in a dounce homogenizer with 7 ml of Hank’s Balanced Salt Solution. 3 ml of Percoll solution (9 parts of Percoll PLUS (GE) with 1 part of 10X DPBS) was added to make a 30% Percoll solution. This mixture was then overlayed onto a 70% percoll solution followed by centrifugation at 18°C for 20 minutes at 500 × g. After centrifugation, the top layer of debris was removed and the cellular layer at the 30%/70% interphase was collected and washed. The pellet was resuspended in cell staining buffer and prepared for flow cytometry. Isolation of peritoneal macrophages  C57BL/6 mice were anesthetized by inhaled isoflurane, sacrificed by cervical dislocation, and the peritoneal space lavaged with 7 ml of cold phosphate saline buffer with 1% fetal bovine serum albumin (Invitrogen) and 1 uM sodium EDTA (Sigma, St. Louis).  The recovered lavage fluid was placed on ice, centrifuged at 4 ºC and 500 × g, the supernatant decanted and resuspended in Buffer RLT (Qiagen) and the lysates was stored at -80°C before subsequent RNA isolation and library preparation for RNA-Seq as performed by Covance Laboratories.

extract_protocol:
Sorted populations were washed and centrifuged, followed by resuspension in Buffer RLT (Qiagen). Cell lysates were frozen at -80˚C. RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s directions.
Library preparation was performed using the Nugen Ovation kit for low abundance RNA according to the manufacturer’s instructions .

treatment_protocol: C57BL/6 mice were subcutaneously injected with 100 μg of MOG35-55 (myelin oligodendrocyte glycoprotein; AnaSpec) in incomplete Freund's adjuvant (Difco) containing 250 μg of Mycobacterium tuberculosis (Difco). On the same day and again 48 hours later, mice received an intraperitoneal injection of 200 ng of pertussis toxin (List Biological Laboratories). Mice were scored as follows: 0, no symptoms; 1, limp tail; 2, limp tail and inability to right itself when placed on its back; 3, partial hind limb paralysis; 4, complete hind limb paralysis; 5, complete hind limb paralysis with forelimb involvement or moribund (Lewis et al. , 2013).  CNS and blood cells were isolated and pooled from 10 naive mice, 10 mice with an EAE score of 0 on day 7 post-immunization (due to lower cell numbers early in disease course), and 6 mice with an EAE score of 3 on day 14 post-immunization. Microglia   and monocytes were sorted with a FACSAria (BD Biosciences) utilizing the gating scheme in Fig. 1. Sorted populations were washed and centrifuged, followed by resuspension in Buffer RLT (Qiagen). Cell lysates were frozen at -80˚C and shipped to Covance Genomics Laboratories (Seattle, WA) for all remaining steps.

tag: gender

value: female

tag: timepoint

tag: celltype

value: Monocyte


title: Ly6C_Hi_Mono


title: PHO Sim Rep1

tag: tissue

tag: chip antibody

value: Klymenko et al, 2006


title: Input Sim Rep2

source_name: D. Simulans_Input

value: none (input)


title: Mi_00

tag: strain

value: Microglia


title: Mi_08


title: PH Sim Rep2

tag: age


title: Mi_14


title: Mo_08


title: PH Sim Rep1

tag: chip antibody ref.


title: Mo_00


title: H3K4me3 Sim Rep1

source_name: D. Simulans_H3K4me3

tag: genotype/variation

value: H3K4me3, Millipore  #07-473


title: Mo_14


title: DSP1 Sim Rep1

source_name: D. Simulans_DSP1


title: PM_5

value: Peritoneal Mac


title: p_mac


title: PM_4


title: PM_1


title: PM_2


title: PM_Mix


title: PM_3


title: WT rep1

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

description: library strategy: Hi-C

data_processing:
Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the bowtie program with parameters (-t -a -m 1 --best).  Unmapped or non-unique mapped reads were discarded.
We then divided read pairs into four groups: SS (reads mapping to the same restriction fragment, or to two adjacent restriction fragments); S2 (reads in which both ends mapped precisely on the DpnII site); S1 (reads in which one of the ends mapped precisely on the DpnII site); S0 (reads in which both ends did not map precisely to a DpnII site). SS, S2 and S1 pairs were discarded from subsequent analysis.
Mapped reads were then associated with the first restriction fragment end encountered when moving from the mapped position in the appropriate strand.
All subsequent analysis was done in the space of fragment end pairs. The Drosophila genome contains 464,246 restriction fragments. After discarding low mappability fragments 301,687 fragments are left (and each defines two fragment ends).
A model accounting for systematic biases in contact probability was constructed as previously (Yaffe and Tanay; Nature Genetics, 43, p.1059-65). Briefly, we used the local G+C content of up to 200 bp from the restriction site (agc, bgc), and the DpnII restriction fragment lengths (alen, blen), to correct for systematic biases in Hi-C coverage by modeling: P(Xa,b) = Pprior x Flen(alen,blen) x Fgc(agc,bgc).
We estimated maximum likelihood model parameters (the matrices Flen and Fgc) through application of an iterative algorithm as described, using 20 bins for G+C content and 20 bins for fragment length.
Genome_build: dm3
Supplementary_files_format_and_content: 50_200_top5.domains: a list of the physical domains  index - unique ID for domain  chrom - chromosome  start - start co-ordinate of domain  end - end co-ordinate of domain  cluster - a number from 1 to 4 to identify the epigenetic nature of the domain. 1 = null, 2 = active, 3 = PcG, 4 = HP1/centromeric
Supplementary_files_format_and_content: *.bins: the real genomic co-ordinates of the involved bins  cbin - the identity of the bin  chr - chromosome  from.coord - start co-ordinate of bin  to.coord - end co-ordinate of the bin  count - the number of fends contained within the bin
Supplementary_files_format_and_content: *.n_contact: give the contact score maps  cbin1 - the identity of the first bin  cbin2 - the identity of the second bin  expected_count - the number of counts expected for this pairwise bin combination, based on the technical normalisation  observed_count - the number of tags counted from the Hi-C dataset for this pairwise bin combination

source_name: 16-18 hr embryo

growth_protocol: Oregon-R w1118 flies were raised in standard cornmeal yeast extract media at 25°C. Egg laying was performed on plates with standard vinegar medium and yeast. Embryos were collected in 0.03% Triton-X100, 0.4% NaCl 16-18 hr after egg laying.

extract_protocol: ~3000-4000 embryos were dechorionated for 5 min in fresh bleach, before douncing in 5 ml fix buffer (2% formaldehyde, 15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 0.1% Triton-X100, 0.5 mM DTT, protease inhibitor cocktail (Roche)) and fixed for a total of 10 min at 25°C, 750 rpm on a shaker. After quenching with 5 ml 2 M glycine, nuclei were collected by centrifugation for 5 min at 4500 g, 4°C, then washed once with 5 ml fix buffer (without formaldehyde) and once with 1.25 x NEB3 buffer (New England Biolabs), with centrifugation for 5 min at 4500 g, 4°C each time. Nuclei were resuspended in 300 µl 1.25 x Dpn II buffer (New England Biolabs) plus 0.3% SDS and incubated for 1 hr at 37°C, 1000 rpm on a shaker. Triton-X100 was added to a final concentration of 2% and the nuclei were incubated for a further 1 hr at 37°C, 1000 rpm, before overnight digestion with 1500 U Dpn II (New England Biolabs) at 37°C, 1000 rpm. The restriction enzyme was inactivated by incubation for 20 min at 65°C, 1000 rpm with SDS at a final concentration of 1.3%, before dilution of the chromatin in 10 ml 1x T4 DNA ligase buffer (New England Biolabs) plus 1% Triton-X100 and incubation for 1 hr at 37°C, 750 rpm. The chromatin was ligated for 4 hr at 25°C, 750 rpm with 40,000 U T4 DNA ligase (New England Biolabs) then crosslinks were reversed overnight at 65°C, 750 rpm in the presence of 150 µg/ml proteinase K. The 3C DNA was then purified by 1 hr treatment with 40 µg/ml RNase A at 37°C, 750 rpm, phenol extraction, phenol/chloroform extraction and ethanol precipitation. The DNA was quantified with the Qubit dsDNA assay (Invitrogen). Aliquots of 5 µg 3C DNA were sonicated in a Bioruptor (Diagenode) in 50 µl volumes in sonication buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS) to obtain a smear between 500-1500 bp. The sonicated 3C DNA was then purified by phenol/chloroform extraction and ethanol precipitation and quantified with the Qubit dsDNA assay (Invitrogen). Libraries for paired-end sequencing were made from 500 ng aliquots of sonicated 3C DNA using Illumina reagents and protocols, with size selection for products of ~800 bp.

tag: developmental stage

value: Embryo

tag: genotype

value: w1118 (wild-type white)


title: WT rep2

description: library strategy: Hi-C


title: M63 0.4 B2 TEX pos L1 HS2

status: Public on Oct 18 2014

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (TRAPL)
Read mapping using segemehl version 0.13 (TRAPL)
Coverage calculation and normalisation (TRAPL)
Genome_build: NC_000913.2
Supplementary_files_format_and_content: wiggle

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655 cells

growth_protocol: To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution.

extract_protocol:
Hot phenol (Sharma et al. 2010, Bloomberg 1990, EMBO J)
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

treatment_protocol: Samples were mixed, incubated on ice for 10 min after which cells were collected by centrifugation at 4150 rpm at 4˚C for 10 min.  Cell pellets were snap frozen in an ethanol/dry ice slurry and stored at -80°C until total RNA could be extracted.

tag: medium

tag: growth phase

value: exponential


title: M63 0.4 B2 TEX pos L1 HS1


title: M63 0.4 B2 TEX neg L1 HS2


title: Input Sim Rep1


title: LB 2.0 B2 TEX pos L1 HS1

value: LB

value: stationary


title: LB 2.0 B2 TEX pos L1 HS2


title: PC Sim Rep1

source_name: D. Simulans_PC

value: wild type

value: PC


title: LB 2.0 B2 TEX neg L2 HS2


title: LB 2.0 B2 TEX neg L1 HS2


title: M63 0.4 B2 TEX neg L1 HS1


title: H3K27me3 Sim Rep1

source_name: D. Simulans_H3K27me3

value: embryos

value: H3K27me3, Millipore, #07-449


title: M63 0.4 B1 TEX pos L1 GA


title: LB 2.0 B1 TEX neg L2 HS2


title: M63 0.4 B1 TEX neg L1 GA


title: LB 2.0 B1 TEX pos L2 HS2


title: LB 0.4 B2 TEX pos L1 HS2


title: LB 0.4 B2 TEX pos L1 HS1


title: LB 0.4 B2 TEX neg L1 HS1


title: LB 0.4 B1 TEX neg L1 GA


title: LB 2.0 B1 TEX neg L1 GA


title: LB 0.4 B2 TEX neg L1 HS2