title: anaerobic INPUT DNA

description: Antibodies for beta of RNAP - NeoClone, Cat Number: W0002, Lot Number: 2008L10-001; Antibodies for sigma70 of RNAP - NeoClone, Cat Number: W0004, Lot Number: 2008K12-001; All other antibodies (FNR, H-NS, IHF) were produced in this study and are not commercially available.

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome Build:
INPUT_ChIP-seq_Anaerobic_WIG.wig: U00096.2

extract_protocol:
Antibodies for beta of RNAP - NeoClone, Cat Number: W0002, Lot Number: 2008L10-001  Antibodies for sigma70 of RNAP - NeoClone, Cat Number: W0004, Lot Number: 2008K12-001  All other antibodies (FNR, H-NS, IHF) were produced in this study and are not commercially available.
10 ng of DNA were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation.  Samples were sheared to 200-500 nt during the IP process to facilitate library preparation.  All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting either 275 bp fragments (s70 libraries) or 400 bp fragments (FNR libraries).  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  A single read, 36 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx.  A paired read, 100 bp runs were used for one replicate of each s70 aerobic and anaerobic growth conditions, using standard SBS kits (v4) and SCS 2.6 on an Illumina HiSeq.  Basecalling was performed using the standard Illumina Pipeline version 1.6.


title: WT_116HG_ChIRP-seq rep1

status: Public on Jun 20 2013

type: SRA

city: Davis

first: Weston

last: Powell

state: CA

address: 3426 Tupper Hall

department: MMI

country: USA

institute: UC Davis

description: Sample 1

library_source: genomic

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2-2.0.0-beta6 with default settings and option -p 2.
Peaks were called using MACS14 v.1.4.2 with options -f BAM --bw 1000 -s 50 -g mm.
Output peak file from MACS was filtered using Excel sort on FDR to exclude peaks with FDR >1, and Excel sort on fold enrichment to exclude peaks with fold enrichment <20.  Excel spreadsheet was converted to .bed file using command line $ tr '\r' '\n' <excel_peaks.txt >peaks.bed.
RNA-seq reads were aligned to the mm9 genome assembly using TopHat v2.0.5 with options --library-type fr-firststrand -p 2 -G Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf
Differential transcript abundance was called using cuffdiff v2.0.2 with options -p 2 -L WT,Snord116del --FDR 0.015  -u --library-type fr-firststrand Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf.
Genome_build: mm9
Supplementary_files_format_and_content: .bed files represent peaks called using MACS14 and filtered for FDR and fold enrichment from input for samples WT_116HG_ChIRP-seq_1, WT 116HG_ChIRP-seq_2, WT_NSC_ChIRP-seq, Snord116del_116HG_ChIRP-seq, Snord116del_NSC_ChIRP-seq.
Supplementary_files_format_and_content: RNAseq.txt is automatic output from cuffdiff gene level.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: B6(Cg)-Snord116tm1.1Uta/J (Snord116del) and WT C57BL/6J mice were obtained from Jackson Labs (Bar Harbor, ME) and housed in a 24-hour light/dark cycle (6am-6pm light, 6pm-6am dark), temperature controlled room and fed a standard diet of Picolab mouse chow 20 (PMI international, St. Louis, MO).

extract_protocol:
Tissue was crosslinked in 1% formaldehyde, homogenized, and lysates clarified by sonication. lncRNA:DNA was isolated using biotin oligo probes and streptavidin beads. DNA was purified with phenol:chloroform extraction and resuspended in H2O.
Libraries were prepared according to Nugen's protocol accompanying the Ovation Ultralow DR Multiplex System 1-8 (Part# 0330). The libraries were analyzed on a Bioanalyzer, and submitted to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries were sequenced on the Hi-Seq 2000 following the manufacturer's protocols.

tag: strain

tag: genotype/variation

value: wild type

tag: age

value: adult

tag: tissue

value: brain

tag: oligo set

value: custom 116HG oligos


title: aerobic INPUT DNA

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome Build:
INPUT_ChIP-seq_Aerobic_WIG.wig: U00096.2

organism: Escherichia coli str. K-12 substr. MG1655star

source_name: Aerobic Cultures

growth_protocol: Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

tag: antibody

value: INPUT

value: Wild Type K-12

tag: growth condition

value: Aerobic Cultures


title: Suz12_Restko

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
High quality reads (Chastity score .= 0.6) were aligned to the mouse genome (mm9) using Eland (Illumina) allowing up to two mismatches within the first 32 bases. Reads not aligning uniquely to the mouse genome were removed.
Aligned datasets were filtered for multiple reads at the same position occurring after PCR amplication. Where more than one read mapped to the same position and at the same strand duplicates were removed.
The reads were extended to 200 bp length, and the number of reads at a given position was counted and saved as a fixedStep wig file with 100 bp resolution.
Peak calling was done in CisGenome 1.2 using IgG samples as negative controls. Lists of peaks and further descriptions can be found here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002494
Genome_build: mm9
Supplementary_files_format_and_content: aln: list of aligned reads. wig: fixedStep Wiggle file containing densities with 100 bp resolution of aligned and filtered reads.

source_name: Mouse embryotic stem cells

growth_protocol: Mouse embryonic stem (mES) cells were cultured on 0.1% (w/v)  gelatin-coated plates in Glasgow medium (Sigma) supplemented  with glutamax-1 (Gibco), non-essential amino acids (Gibco),  50 mM 2-mercaptoethanol–PBS, 15% ES-cell-qualified FBS  (Gibco) in the presence of 1,000 U/ml of LIF (Millipore), and 1% (v/v) pen/strep. In addition, the Rest2/2 and Wt control mES cells were cultured in the presence of feeder cells (Mitomycin C treated primary mouse embryonic fibroblasts). The mES Eed2/2 and Rnf22/2 mES cells were provided by Dr. Anton Wutz. The Rest2/2 and Wt control mES cells were provided by Dr. Zhou-Feng Chen and Dr. Helle Færk Jørgensen.

extract_protocol:
Cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as in Dietrich  et al. (2007) EMBO J 26: 1637–1648.
DNA from three parallel ChIPs were pooled and 10 ng was used for making ChIP-seq libraries. Libraries were generated according to Illumina recommendations and sequencing was done on a Genome Analyzer II (Illumina).

tag: genotype

value: Rest-/-

tag: cell type

value: mESC

tag: chip antibody

value: rabbit anti-SUZ12 (Cell signaling)

tag: chip antibody manufacturer

value: Cell Signaling


title: Suz12_Ctrl

value: wt (ctrl for Rest)


title: σ70 IP ChIP-seq Anaerobic A

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome Build:
Sigma70_IP_ChIP-seq_Anaerobic_A_SET_WIG.wig: U00096.2

source_name: Anaerobic Cultures

value: RNA Polymerase σ70 monoclonal antibody from NeoClone (W0004)

value: Anaerobic Cultures


title: σ70 IP ChIP-seq Aerobic B

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome_build: U00096.2

extract_protocol: DNA were submitted to the Joint Genome Institute for ChIP-seq library preparation.  Samples were sheared to 200-500 nt during the IP process to facilitate library preparation.  All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting either 275 bp fragments (s70 libraries).  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  A single read, 36 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. Basecalling was performed using the standard Illumina Pipeline version 1.6.


title: Ring1B_Ctrl

value: rabbit anti-RNF2/Ring1B (NAST; antigen sequence:NASTHSNQEAGPSNKRTKT)

value: NAST


title: Ring1B_Restko


title: FNR IP ChIP-seq Anaerobic A

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome Build:
FNR_IP_ChIP-seq_Anaerobic_A_WIG.wig: U00096.2

value: Affinity purified FNR polyclonal antibody


title: σ70 IP ChIP-seq Aerobic A

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome Build:
Sigma70_IP_ChIP-seq_Aerobic_A_SET_WIG.wig: U00096.2


title: K27me3_Ctrl

value: rabbit anti-H3K27Me3 (Cell Signalling, C36B11)

tag: chip antibody catalog #


title: Rest_Restko

value: rabbit anti-REST (Millipore, 07-579)

value: Millipore


title: IgG_Ctrl

value: Rabbit IgG (DAKO)

value: DAKO


title: FNR IP ChIP-seq Anaerobic B

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome Build:
FNR_IP_ChIP-seq_Anaerobic_B_WIG.wig: U00096.2

value: Wild Type K-12


title: K27me3_Restko


title: Jarid2_Restko

value: rabbit anti-Jarid2 (Novus Biologicals)

value: Novus


title: NMuMG_day20_H3K27me3, biological replicate 2

city: Basel

first: Piotr

middle: Jan

last: Balwierz

address: Klingelbergstrasse 50-70

country: Switzerland

institute: University of Basel

data_processing:
Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads).
Alignments to the M. musculus genome (mm9) were performed by the software Bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BED files represent mapped reads. Scores can be ignored.

source_name: NMuMG cells, TGFβ, day 20

growth_protocol: NMuMG cells were cultured as previously described (Maeda et al., Journal of Cell Sciences (2007)).

extract_protocol:
ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of H3K27me3 antibody (Millipore, cat# 07-449).
The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions and sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

treatment_protocol: NMuMG cells were treated with 2ng/ml TGFβ for 1, 4, 7, 10 and 20 days to induce EMT into them. TGFβ was changed every alternative day.

tag: cell line

value: NMuMG

tag: treatment

value: TGFβ

tag: time point

value: day 20


title: NMuMG_day10_H3K27me3, biological replicate 1

source_name: NMuMG cells, TGFβ, day 10

value: day 10


title: IgG_Restko

value: Rest-/-

value: mESC


title: NMuMG_day04_H3K27me3, biological replicate 2

source_name: NMuMG cells, TGFβ, day 4

value: day 4


title: NMuMG_day20_H3K27me3, biological replicate 1


title: NMuMG_day04_H3K27me3, biological replicate 1


title: NMuMG_day10_H3K27me3, biological replicate 2


title: NMuMG_day07_H3K27me3, biological replicate 2

source_name: NMuMG cells, TGFβ, day 7

value: day 7


title: NMuMG_day07_H3K27me3, biological replicate 1


title: NMuMG_day00_H3K27me3, biological replicate 1

source_name: NMuMG cells, TGFβ, day 0

value: day 0


title: NMuMG_Input_DNA

source_name: NMuMG cells, input


title: NMuMG_day00_H3K27me3, biological replicate 2


title: NMuMG_day01_H3K27me3, biological replicate 2

source_name: NMuMG cells, TGFβ, day 1

value: day 1


title: DOL

city: Zhengzhou

first: ZhongJun

last: Gong

state: Henan

address: HuaYuan Road 116

department: Institute of plant protection

country: China

institute: Henan academy of agricultural sciences

description: Sitodiplosis mosellana-orange blossom wheat midge

library_source: transcriptomic

data_processing:
The original image data were transferred into sequence data by base calling and was defined as raw data. To obtain clean reads, all dirty raw reads were removed before data analysis. Dirty raw reads were defined as (1) reads with adaptors, (2) reads with more than 10 % unknown bases and (3) low quality reads with more than 50 % low quality bases with quality value ≤5.
Clean reads were mapped to reference sequences (unigenes from transcriptome data of different developmental stages; the reference sequences are available at the NCBI Short Read Archieve (SRA) with the accession number: SRR787284; public identifiers for the genes can be traced in NCBI BioProject:PRJNA192921) using SOAPaligner/soap2 . No more than two base mismatches were allowed in the alignment. The gene expression level was calculated using the RPKM method (Reads Per kb per Million reads) . If there were more than one transcript for a gene, the longest one was then used to calculate its expression level and coverage.
To identify differentially expressed genes between two samples, the false discovery rate (FDR) method was used to determine the threshold of P-value in multiple tests. The significance of gene expression difference was judged using a threshold FDR ≤ 0.001 and an absolute value of log2 Ratio ≥ 1. The genes that were expressed at different levels across samples were further annotated by GO functional analysis and KEGG pathway analysis.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample with columns: Gene ID, Uniq_reads_num, length, coverage, RPKM, TSA accession number.  For Gene IDs lacking TSA accession numbers, please see the fasta file (linked as a supplementary file on the Series record)  containing the corresponding sequences.

molecule: total RNA

organism: Sitodiplosis mosellana

source_name: larvae, DOL

extract_protocol:
Total RNA was extracted separately from DOL and NDOL using Trizol Reagent following manufacturer’s instructions. Approximately 10μg RNA from each sample was used to construct individual DGE libraries.
After extracting the total RNA from the samples, mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads and mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.

tag: developmental stage

value: diapause owbm larvae

value: whole body


title: Macrophages from flu-treated mice

status: Public on Jun 19 2013

city: New York

first: Brian

last: Brown

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were filtered for low quality and mapped to the mm9 genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following the protocol from Mortazavi et al, Nat Methods, 2008. Briefly, all reads falling in the exons of a given gene were counted and normalized by the length of the gene and the total reads of the run.
Supplementary_files_format_and_content: RPKM abundance

source_name: lung

extract_protocol: CD103+ dendritic cells and alveolar macrophages were cell-sorted from lungs of untreated and flu-treated mice. Total RNA was extracted from sorted cells following Qiazol protocol.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Mice were treated with 106 pfu of NS1-GFP flu virus and sacrificed 12h later

value: Macrophages

value: lung

value: flu-treated


title: Rest_Ctrl

value: wt (ctrl for Rest)

value: rabbit anti-REST (Millipore, 07-579)

value: Millipore


title: Jarid2_Ctrl

value: rabbit anti-Jarid2 (Novus Biologicals)

value: Novus


title: Macrophages from untreated mice

value: untreated


title: CD103+ dendritic cells from flu-treated mice

value: CD103+ dendritic cells


title: CD103+ dendritic cells from untreated mice


title: Fermentation 1, 51 hr

status: Public on Jun 18 2013

city: St Lucia

first: Esteban

last: Marcellin

state: QLD

address: Corner college and Coopers Rd

department: AIBN

country: Australia

institute: The University of Queensland

data_processing:
The initial image processing and base calling was done by a standard Software pipeline provided by Illumina.
Reads were aligned to the S. erythraea genome using Burrows-Wheeler Aligner BWA  and Bowtie requiring no more than 2 mismatches.
Only reads that aligned to one genomic location were retained unless specified for the analysis.
We employed CuffDiff to determine gene expression using SAM files resulting from alignment, annotated gene file, upper quantile normalization and masking of rRNA sequences.
For expression of non-standard features, such as transcriptional macro-domains, read alignment was summed over genomic annotations. Hierarchal clustering of gene expression was performed by persons pair-wise complete linkage using Cluster3
Gene expression was normalized  between the seven libraries for total alignable reads.
Genome_build: Saccharopolyspora erythraea NRRL2338/NRRL23338 ASM6288v1
Supplementary_files_format_and_content: tab-delimited text files include normalised expression (RPKM) values for each Sample

organism: Saccharopolyspora erythraea

source_name: cells cultured in Bioreactors

growth_protocol: S. erythraea was grown on minimal  media.

extract_protocol: Seven libraries were prepared after duplex-specific thermostable (DSN) treatment. All sequencing was performed on the Illumina Genome Analyzer IIx.

treatment_protocol: RNA isolation was performed after 8h incubation at 4°C in RNA-later (Ambion). Total RNA was extracted using two cycles of cellular lysis in RNAse-free zirconia beads. RNA was purified using RNeasy midi kit (Qiagen) with on column DNase treatment. Ribosomal RNA was removed with duplex-specific thermostable nuclease enzyme from kamchatka crab (DSN) as described in the Illumina’s protocol.

value: NRRL 2338

tag: growth protocol

value: fermentation (cells cultured in Bioreactors)

tag: time


title: Fermentation 1, 93 hr

tag: strain


title: Fermentation 1, 57 hr


title: Fermentation 1, 72 hr


title: Fermentation 1, 40 hr


title: Fermentation 1, 48 hr


title: IgG_ChIP-seq

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

data_processing:
Libraries were sequenced on the Illumina GA2 and HiSeq 2000 platforms. After barcode removal, 32 bp reads were aligned uniquely to the C. elegans WS190 genome using bowtie.
MACS (version 1.4) was used to call peaks and create pileups with DPY-27 ChIP as the treatment and random IgG ChIP as the control.
To account for read depth, ChIP signal was normalized to the total number of reads that uniquely aligned to the genome.
To correct for non-specific binding, IgG signal was subtracted from DPY-27 signal.
The resulting ChIP-seq signal from two biological replicates was averaged at each base pair genome-wide.
Genome_build: Wormbase WS190
Supplementary_files_format_and_content: wiggle files of the average at 10 bp averaging

organism: Caenorhabditis elegans

source_name: Wild-type embryos

growth_protocol: Wild-type N2 animals were grown on NG agar plates with HB101 bacteria. Mixed-stage embryos were harvested from gravid hermaphrodites

extract_protocol:
The mixture was ground under liquid nitrogen by mortar and pestle. Chromatin was sheared by the Covaris S2 (20% duty factor, power level 8, 200 cycles per burst) for a total of 30 min processing time (60 sec ON, 45 sec OFF, 30 cycles).
To perform the ChIP reactions, extract containing approximately 2 mg of protein was incubated in a microfuge tube with 6.6 mg of anti-DPY-27 or random IgG antibodies overnight at 4°C. A 25 mL bed volume of protein A sepharose beads was added to the ChIP for 2 hr. ChIPs were washed for 5 min at room temperature twice with FA Buffer (150 mM NaCl), once with FA Buffer (1 M NaCl), once with FA Buffer (500 mM NaCl), once with TEL buffer (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE Buffer. Protein and DNA were eluted twice with 1% SDS, 250 mM NaCl, 1mM EDTA at 65°C for 15 min. After elution, sequencing libraries were prepared as published in Zhong et al. (2010) with minor changes: sequencing adapters were as described in Lefrancois et al. (2009) and adapters were ligated using NEB Quick Ligation Kit (M2200).

treatment_protocol: Embryos were cross-linked with 2% formaldehyde for 30 min. Cross-linked embryos were resuspended in 3 ml of FA Buffer (150 mM NaCl, 50 mM HEPES-KOH (pH 7.6), 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM DTT, protease inhibitor cocktail) for every 1 gram of embryos. This mixture was frozen on liquid nitrogen

value: Embryo

value: wild type

tag: genetic background

value: Rabbit IgG from Santa Cruz Biotechnology (sc-2027, Lot # A2609)


title: GRO-cap_N2_StarvedL1 TAP-

data_processing:
Libraries were sequenced with Illumina’s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further.
To remove reads containing the RT-PCR adapter, we used cutadapt version 0.9.5 (http://code.google.com/p/cutadapt/) with the following command (cutadapt -a TGGAATTCTCGGGTGCCAAGG -a AAAAAAAAAAAAAAAAAAAA -z -O 15 -e .1 --minimum-length=30).
The remaining reads were trimmed to 30 bp in length and aligned uniquely to the C. elegans WS230 genome using bowtie’s default settings (version 0.12.7), which permit 2 mismatches in the first 28 bp.
Because the 5’ base in each read identifies the 5'-cap, we created pile-ups using only the first base of each read. The pile-up of reads mapping to both strands was normalized by the number of millions of reads that mapped uniquely to the genome (reads per million).
GRO-cap data from the TAP+ libraries, TAP- control libraries, and TAP+ with TAP- subtracted are included
Genome_build: WormBase WS230
Supplementary_files_format_and_content: wig files of the GRO-seq data split into the plus and minus strands

source_name: Wild-type starved L1s

growth_protocol:
sdc-2 and the negative control L4440 RNAi feeding bacteria were prepared by growing HT115 bacteria bearing the RNAi plasmid overnight in TB and ampicillin, inducing for 2 hours with 1 mM IPTG, pelleting, and resuspending in 1 vol (w/v) of LB with 20% glycerol. For samples that were to be treated with RNAi, embryos were harvested from gravid hermaphrodites and allowed to hatch off for 24 hr. NG Agar plates supplemented with 1 mM IPTG and 100 mg/ml Carbenicillin were spotted with super-induced RNAi bacteria and allowed to induce further overnight at 25°C. Hatched off L1 larvae were spotted on the RNAi plates and grown at 20°C until gravid.
For wild type samples, embryos were harvested from gravid hermaphrodites grown at 20°C on concentrated HB101. Embryos were allowed to hatch off and starve for 24 hr at 20°C. Worms were fed and grown to L3 stage under liquid culture (1 worm/ml; 10 mg/ml HB101) for 34 hr at 20°C.

extract_protocol:
Starved L1 and L3 samples were ground under liquid nitrogen by mortar and pestle. Larval samples, post-grinding, and embryo samples were dounced with a Kontes 2 ml glass dounce to release nuclei. Douncing and collection of nuclei was performed for up to 6 rounds as follows: dounce with 10X pestle A, 10X pestle B, 5 min centrifugation at 100xg, removal of nuclei-containing supernatant, and addition of an equal volume of Nuclear Isolation Buffer to the pellet. Nuclear isolation was monitored each round to determine effectiveness and when it was complete. The pooled supernatant was centrifuged for 5 min at 1000xg to pellet nuclei. The nuclear pellet was washed with Nuclear Freezing Buffer (40% Glycerol, 50 mM Tris-HCl (pH 8.3), 0.1mM EDTA, 5 mM MgCl2, 1 mM DTT, protease inhibitors, 4 units/ml SUPERaseIn). Approximately 1x108 nuclei were resuspended in 100 ul Nuclear Freezing Buffer and stored at -80°C until GRO-seq reactions were performed.
All NRO-reactions and bead enrichment steps for GRO-cap were carried out as described above, with the exception that the RNA for GRO-cap was not base hydrolyzed. After the first bead binding, the TruSeq RNA 3’ Adapter (RA3), (Illumina part # 15013207) was ligated to the 3’-end of the NRO RNA. First, 50 pmoles of the 3’-adapter were mixed with NRO RNA, and 2 ml 50% PEG 8000, brought to 14 ml with DEPC water, incubated at 70°C for 3 min and put on ice for 2 min. Then, 2 ml of 10X T4 RNA Ligase I buffer, 2 ml 10 mM ATP, 1 ml SUPERaseIN, and 1.5 ml T4 RNA Ligase I (NEB, M0204) were added and reaction incubated at 22°C for 4-6 hr. The reaction was then brought to 100 ml with binding buffer and subjected to a second round of bead enrichment.
After the second bead enrichment, 5’ mono-phosphate RNAs were selected against in two successive steps.  First, to selectively degrade RNAs with a 5’-mono-phosphate, NRO RNA was resuspended in 16.5 ml DEPC water, mixed with 0.5 ml SUPERaseIN, 2 ml 10X Terminator reaction buffer A, and 1 ml of Terminator 5’-phosphate-dependent exonuclease (Epicentre, TER51020), and incubated at 30°C for 1 hr. The reaction was extracted and precipitated using the standard method (above), and resupended in 10 ml DEPC water.  Second, 5’-mono-phospate RNAs were deposphorylated to prevent their participation in subsequent ligation reactions. For this, the RNA was then mixed with 1 ml SUPERaseIN, 14.5 ml DEPC water, 10X Antarctic Phosphatase buffer, 1.5 ml of Antarctic Phosphatase (NEB, M0289S), and incubated at 37°C for 30 min. The reaction was brought to 200 ml with 10 mM Tris-HCl (pH 7.5), 5 mM EDTA, and heat inactivated at 65°C for 5 min. The reaction was then extracted and precipitated using the standard extraction method and resuspended in 10 ml DEPC water.
The 5’-capped RNAs then were prepared for ligation and the final library preparation steps.  The NRO RNAs were then split in half and the experimental sample was treated with Tobacco Acid Pyrophosphatase (TAP): 1 ml SUPERaseIN, 15 ml DEPC water, 3 ml 10X TAP buffer, and 1 ml TAP (Epicentre, T19500), incubation at 37°C for 1 hr. The control reaction was treated identically except for the addition of TAP. The reaction was brought to 200 ml and then extracted and precipitated using the standard method. The TruSeq RNA 5’ Adapter (RA5), (Illumina part # 15013205) was ligated to the 5’-end of the NRO RNA. First, 50 pmoles of the 5’-adapter were mixed with NRO RNA, and 2 ml 50% PEG 8000, brought to 14 ml with DEPC water, incubated at 70°C for 3 min and put on ice for 2 min. Then, 2 ml of 10X T4 RNA Ligase I buffer, 2 ml 10 mM ATP, 1 ml SUPERaseIN, and 1.5 ml T4 RNA Ligase I (NEB, M0204) were added and reaction incubated at 22°C for 4-6 hr. The reaction was then brought to 100 ml with binding buffer and subjected to a third round of bead enrichment. After the third enrichment, samples were reverse transcribed, amplified and PAGE purified as described in (Core, Waterfall, and Lis, 2008), and quantified before submission for sequencing.

treatment_protocol: Animals were collected from whichever stage was desired. After washing twice with M9 buffer, animals were washed with cold Nuclear Isolation Buffer (250 mM Sucrose, 10 mM Tris-HCl (pH 7.9), 10 mM MgCl2, 1 mM EGTA, 0.25% NP-40, 1 mM DTT, protease inhibitors, 4 units/ml SUPERaseIn (Ambion, AM2696). Animals were resuspended in Nuclear Isolation Buffer (embryos and starved L1 in 3 vol, L3 in 1 vol), and dripped into liquid nitrogen to freeze.

value: starved

tag: sample type

value: Wild-Type (N2)

tag: digestion

value: TAP-


title: GRO-cap_N2_L3

source_name: Wild-type L3s

value: TAP+


title: DPY-27_ChIP-seq

value: DPY-27 polyclonal rabbit antibody (#699) was generated in:"CHUANG, P. T., D. G. ALBERTSON and B. J. MEYER, 1994 DPY-27:a chromosome condensation protein homolog that regulates C. elegans dosage compensation through association with the X chromosome. Cell 79:459-474."


title: GRO-cap_N2_L3  TAP-


title: GRO-cap_N2_Emb


title: GRO-seq_N2_StarvedL1

data_processing:
Libraries were sequenced with Illumina’s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further.
To remove reads containing the RT-PCR adapter, we used cutadapt version 0.9.5 (http://code.google.com/p/cutadapt/) with the following command (cutadapt -a TGGAATTCTCGGGTGCCAAGG -a AAAAAAAAAAAAAAAAAAAA -z -O 15 -e .1 --minimum-length=30).
The remaining reads were trimmed to 30 bp in length and aligned uniquely to the C. elegans WS230 genome using bowtie’s default settings (version 0.12.7), which permit 2 mismatches in the first 28 bp.
Because the 5’ base in each read most closely identifies the location of transcriptionally engaged RNA Polymerase prior to the run-on, we created pile-ups using only the first base of each read. The pile-up of reads mapping to both strands was normalized by the number of millions of reads that mapped uniquely to the genome and was multiplied by 1000 to obtain RPKM (reads per kilobase per million).
GRO-seq data from two biological replicates was averaged at each base pair genome-wide.
Genome_build: WormBase WS230
Supplementary_files_format_and_content: wig files of the GRO-seq data split into the plus and minus strands, and at 1 bp resolution or averaged across 25 bp

extract_protocol:
Starved L1 and L3 samples were ground under liquid nitrogen by mortar and pestle. Larval samples, post-grinding, and embryo samples were dounced with a Kontes 2 ml glass dounce to release nuclei. Douncing and collection of nuclei was performed for up to 6 rounds as follows: dounce with 10X pestle A, 10X pestle B, 5 min centrifugation at 100xg, removal of nuclei-containing supernatant, and addition of an equal volume of Nuclear Isolation Buffer to the pellet. Nuclear isolation was monitored each round to determine effectiveness and when it was complete. The pooled supernatant was centrifuged for 5 min at 1000xg to pellet nuclei. The nuclear pellet was washed with Nuclear Freezing Buffer (40% Glycerol, 50 mM Tris-HCl (pH 8.3), 0.1mM EDTA, 5 mM MgCl2, 1 mM DTT, protease inhibitors, 4 units/ml SUPERaseIn). Approximately 1x108 nuclei were resuspended in 100 ul Nuclear Freezing Buffer and stored at -80°C until GRO-seq reactions were performed.
NRO reaction. Nuclei (100 ml) were mixed with an equal volume of reaction buffer (10 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 1 mM DTT, 300 mM KCL, 20 units of SUPERaseIn, 1% sarkosyl, 500 mM each of ATP, GTP, and Br-UTP, 2 mM CTP and 0.33 mM a-32P-CTP (3000Ci/mmole)). The reaction was allowed to proceed for 5 min at 30°C. The reaction was stopped by the addition of 2 ml (10X volume) of Trizol (Invitrogen). The phases were separated by addition of 400 ml of chloroform as per manufacturers instruction. An additional acid-phenol and then chloroform extraction were carried out, followed by precipitation with 2.5 volumes of ethanol. The pellet was washed in 75% ethanol before resuspending in 20 ml of DEPC-treated water. Base hydrolysis was performed on ice by addition of 5 ml 1 M NaOH and incubated on ice for 30 min. The reaction was neutralized by addition of 25 ml 1 M Tris-HCl (pH 6.8). The reaction was then run through a p-30 RNAse-free spin column (BioRad), according to the manufacturer’s instructions. The column flowthrough was brought to 100 ml with DEPC water and EDTA was added to a final concentration of 1 mM.
Bead pre-wash. All buffers used in bead enrichment steps were kept on ice and were supplemented with 4 units/ml of SUPERaseIN. Anti-deoxyBrU beads (Santa Cruz Biotech, #sc-32323-ac) were first washed three times with a pre-wash buffer: 0.25X SSPE, 500 mM NaCl, 1 mM EDTA, 0.05% tween for 5 min; washed twice in binding buffer: 0.25X SSPE, 37.5 mM NaCl, 1 mM EDTA, 0.05% tween for 5 min; blocked in bead blocking buffer: 0.25X SSPE, 1 mM EDTA, 0.05% tween, 0.1% PVP, and 1 mg/ml ultrapure BSA (Ambion, AM2618) for 1 hr; followed by one wash in binding buffer for 5 min. The ratio of beads to volume did not exceed 1:8 for any wash or blocking step. The beads were resuspended in a 25% slurry (original concentration).
Bead enrichment. NRO RNA was heat denatured at 70°C for 3 min and placed on ice for 2 min. 350 ml of binding buffer and 50 ml of bead slurry were added to the RNA, and the samples were incubated for 30 min on a rotating stand (8 rpm). The beads were washed once in binding buffer; once in low salt wash buffer: 0.2X SSPE, 1 mM EDTA, 0.05% Tween; once in high salt wash buffer: 0.25% SSPE, 137.5 mM NaCl, 1 mM EDTA, 0.05% Tween; and twice in TET: 10 mM Tris-HCl (pH 7.5), 1 mM EDTA, .05% Tween. The NRO RNA was eluted three times (2X 125 ml, 1X 250 ml) with elution buffer: 20 mM DTT, 150 mM NaCl, 5 mM Tris-HCl (pH 7.5), 1 mM EDTA, and 0.1% SDS. The NRO RNA was then isolated by a standard extraction-precipitation method: One acid-phenol extraction, one chloroform extraction, addition of NaCl to 300 mM and 1 ml of glycoblue (Ambion, AM9515) to the aqueous phase, precipitation with 2.5 volumes of cold ethanol, and a wash of the resulting pellet with 75% ethanol. The pellet was resupended in DEPC water at volumes appropriate for the subsequent step.
3’- end repair. NRO RNA was heated 70°C for 3 min, followed by incubation on ice for 2 min. 3 ml 10X T4 PNK buffer, 1 ml SUPERaseIn, and 2 ml of T4 Polynucleotide Kinase (NEB), were added and the reaction incubated for 30 min at 37°C. The reaction was brought to 100 ml with DEPC water and EDTA to a final concentration of 10 mM to stop the reaction. RNA was heat denatured as above and subjected to two more rounds of bead binding / elution as described above.
Poly-A tailing, reverse transcription and amplification. NRO RNAs were then polyadenylated as decribed in (Ingolia, NT, 2010). Poly-A tailed RNA (20 ml) was then reverse transcribed as follows:  2 pmol of reverse transcription primer (TruSeq_circ_RTP_pT: 5’- /5Phos/GATCGTCGGACTGTAGAACTCTGAAC / iSP18 / CACTCA  / iSP18 / GCCTTGGCACCCGAGAATTCCATTTTTTTTTTTTTTTTTTTTVN -3’), 1 ml 12.5 mM dNTPs and 3 ml of DEPC water were added the mixture incubated at 75°C for 3 min. The primer (note the low concentration) is allowed to anneal at 42° for 10 min. 1 ml, 0.1 mM DTT; 1 ml, 1M Tris-Cl, pH 8.3; 1 ml SUPERaseIN; and 1 ml SuperScript III reverse transcriptase (Invitrogen, 18080051) were added and the reverse transcription was carried out at 48°C for 5 min and 54°C for 30 min. The reaction was stopped by incubation at 70°C for 10 min. The reaction was extracted once with buffer saturated phenol-chloroform (pH 8.0), once with chloroform, supplemented with 2 ml glycoblue and 300 mM NaCl, and then precipitated with 2.5 volumes of ethanol.
The NRO-cDNA library was then PAGE purified away from excess RT primer on an 8% denaturing PAGE gel as described in Ingolia (Ingolia, NT).  The purified library was then circularized in an intra-molecular ligation reaction as follows: cDNA was resuspended in 15 ml of 10 mM Tris-HCl (pH 8.0) and mixed with 2 ml of 10X circLigase buffer, 1 ml 1 mM ATP, 1 ml of 50mM MnCl2, 1ml of circLigase (Epicentre).  The reaction was incubated at 60° C for 90 min, with a brief centrifugation every 15 min to bring down condensation.  The reaction was heat inactivated at 80° C for 10 min, extracted once with buffer saturated phenol-chloroform (pH 8.0), once with chloroform, supplemented with 2 ml glycoblue and 300 mM NaCl, and then precipitated with 2.5 volumes of ethanol.
The circularized NRO-cDNA library was resuspended in 10 ml of water and amplified and PAGE purified as described (Core et al., 2008) and quantified before submission for sequencing.  Amplification was achieved using the TruSeq miRNA cloning oligo set (RP1: 5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’, Illumina part # 15005505; and RPI-#: 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’, where the ‘#’ represents one of the 48 Illumina 6-base barcodes in the middle of the oligo, shown above as “NNNNNN”).


title: GRO-cap_N2_Emb TAP-


title: NDOL

source_name: larvae, NDOL

value: non diapause owbm larvae

tag: tissue

value: whole body


title: GRO-cap_N2_StarvedL1


title: GRO-seq_N2_L3


title: H9_RNase R treated

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: There are three technical replicates for control samples from Series GSE24399: GSM601403 for replicate 1, GSM601404 for replicate 2, and GSM601405 for replicate 3.

data_processing:
Basecalling using Illumina Casava1.8.2 software.
Five nucleotides were trimmed at both 5' and 3' end.
Map to human genome hg19 using Tophat(v 1.3.3)
Bam to Bedgraph using genomeCoverageBed_2.13.3
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html). The .bw file reports the abundance score at each genomic position if there is RNA-seq signal.

organism: Homo sapiens

source_name: hES h9 cells, RNase R treated

growth_protocol: hES H9 cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF)

extract_protocol:
Total RNAs were prepared using Trizol Reagent and treatment with DNase I. 20μg of total RNAs were separated into polyadenylated and nonpolyadenylated fraction by oligo(dT) magnetic beads (Invitrogen). Ribosomal RNAs were further depleted in nonpolyadenylated fraction by using RiboMinus kit (Invitrogen) to get the poly(A)-/ribo- RNA population. Poly(A)-/ribo- RNAs were further incubated with 5U of RNase R (Epicentre) for 3h at 37℃ and then were subjected to Trizol extraction (Invitrogen).
An aliquot of poly(A)-/ribo- enriched and RNase R digested RNA was used for library preparation with Illumina TruSeq Stranded Total RNA HT Sample Prep Kit (P/N 15031048), and then subjected to 1x100 deep sequencing with Illumina HiSeq 2000

value: human embryonic stem cells

tag: chromosome

value: diploid

tag: passages

value: RNase R


title: OKZ

first: Wenchao

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to sacCer3 whole genome using bowtie v0.12.7 with parameters -a -v 1 -m 1.
Genome_build: UCSC sacCer3
Supplementary_files_format_and_content: Tab-delimited text files include the positions of Okazaki fragments.

organism: Saccharomyces cerevisiae

source_name: budding yeast cells

growth_protocol: Cells were grown at 30 degrees in YEPD to O.D. 1.2.

extract_protocol:
Genomic and mitochondrial DNA were extracted using CsCl gradients according to a protocol from Gerbi SA et al., Methods, 1997. Then, a linear sucrose gradient was used to purify DNA fragments shorter than 300 nt. Finally, sequential reactions of phophorylation, RNA degradation and lambda exonuclease digestion were performed to enrich Okazaki fragments.
Double-stranded sequencing adaptors with N6 random overhangs were ligated to each end of extracted Okazaki fragments.After PCR amplification, the products were from agarose gels.


title: NMuMG_day01_H3K27me3, biological replicate 1

value: NMuMG

value: TGFβ

value: day 1


title: input DNA

city: Vienna

first: Gerhard

last: Duernberger

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM

description: All samples were sequenced with 50 basepair single-end reads and multiplexing using Illumina’s third-read barcoding scheme

data_processing:
Initial data processing and quality was performed using the CASAVA (v 1.8.2 Illumina) and FastQC
Sequencing reads were trimmed by clipping regions with low base-calling quality or adapter contamination
Resulting quality-filtered reads were aligned to the hg19/GRCh37 assembly of the human genome using Bowtie
UCSC Genome Browser WIG/bigWig tracks and peak calls were established using the MACS software with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: peaks txt, wig (peaks)

source_name: Human Embryonic Kidney cells

growth_protocol: HEK293 cells were cultivated in DMEM (PAA Laboratories) supplemented with 10% FCS (Invitrogen) and antibiotics (penicillin (100 U/ml) and streptomycin (100 μg/ml))

extract_protocol:
Nuclei were disrupted using LB3 buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDeoxycholate, 0.5% N-lauroylsarcosine)
Illumina TruSeq DNA Sample Preparation Kit v2 (Illumina, San Diego)


title: Fermentation 1, 23 hr

value: NRRL 2338

value: fermentation (cells cultured in Bioreactors)


title: GRO-seq_N2_Emb

value: Embryo

tag: genotype

value: wild type


title: GRO-seq_y93.sdc2RNAi_Emb

source_name: sdc-2(y93) mutant embryos fed with sdc-2(RNAi) bacteria

value: sdc-2(y93) fed with sdc-2(RNAi)

value: sdc-2 RNAi


title: GRO-seq_controlRNAi_Emb

source_name: Wild-type embryos fed with L4440 control RNAi bacteria

value: Wild-Type (N2) fed with L4440 Control RNAi

value: L4440 control siRNA


title: GRO-cap_y93.sdc2RNAi_Emb TAP-

value: TAP-


title: YB-1 ChIP

tag: chip antibody

value: anti-HA ChIP-grade (ab9110), Abcam

value: Abcam


title: GRO-cap_y93.sdc2RNAi_Emb

value: TAP+


title: H6 liver 2 RNA

status: Public on Jun 17 2013

city: shenzhen

first: zhiyong

last: huang

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

institute: BGI-Shenzhen, Shenzhen 518083, China

description: Sequenced reads were generated from liver of Myotis brandtii sample2 that hibernated for 6 months

data_processing:
use Myotis brandtii genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.4.1 with default parameters except  -I 50000 -r 20 --solexa1.3-quals
Genome_build: Myotis_brandtii_v1
Supplementary_files_format_and_content: bedGraph file, and the format is: scaffold or contig ID, start, end, transcrptome depth

organism: Myotis brandtii

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with  30  oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was  performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second  strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with  Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp  fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE  adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR  amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end  sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: state

value: 6 mo hibernation

value: liver


title: H6 kidney 1 RNA

description: Sequenced reads were generated from kidney of Myotis brandtii sample1 that hibernated for 6 months

value: kidney


title: H6 liver 1 RNA

description: Sequenced reads were generated from liver of Myotis brandtii sample1 that hibernated for 6 months


title: H6 kidney 2 RNA

description: Sequenced reads were generated from kidney of Myotis brandtii sample2 that hibernated for 6 months


title: A liver 1 RNA

description: Sequenced reads were generated from liver of summer active Myotis brandtii sample1

value: active


title: A kidney 1 RNA

description: Sequenced reads were generated from kidney of summer active Myotis brandtii sample1


title: H2 brain 2 RNA

description: Sequenced reads were generated from brain of Myotis brandtii sample2 that hibernated for 2 months

value: 2 mo hibernation

value: brain


title: A brain 1 RNA

description: Sequenced reads were generated from brain of summer active Myotis brandtii sample1


title: A kidney 2 RNA

description: Sequenced reads were generated from kidney of summer active Myotis brandtii sample2


title: H2 liver 2 RNA

description: Sequenced reads were generated from liver of Myotis brandtii sample2 that hibernated for 2 months


title: H2 kidney 2 RNA

description: Sequenced reads were generated from kidney of Myotis brandtii sample2 that hibernated for 2 months


title: H2 brain 1 RNA

description: Sequenced reads were generated from brain of Myotis brandtii sample1 that hibernated for 2 months


title: H2 kidney 1 RNA

description: Sequenced reads were generated from kidney of Myotis brandtii sample1 that hibernated for 2 months


title: H2 liver 1 RNA

description: Sequenced reads were generated from liver of Myotis brandtii sample1 that hibernated for 2 months


title: Eblast_input

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description: Used as a background for calling TF binding peaks only

data_processing:
Sequenced reads were mapped to the mouse genome (UCSC genome browser assembly mm9, NCBI build 37) using the Eland V2 short-read alignment program. An ungapped local alignment against the reference genome allowed no more than 2 mismatches when aligning a read. Any alternative alignments (ie, nonunique hits to the genome) are also reported. We aligned reads using the maximum allowable seed length and only considered unique genomic alignments for downstream analyses.
We used the Model-based Alignment of ChIP-Seq (MACS) program35 to call peaks of EKLF occupancy. MACS compares the number of EKLF-enriched sequence tags in a given window with the number of tags in surrounding windows and with the number of tags in the same region of the control library. Peaks are defined based on a user-selected significance level. The algorithm empirically models the length of ChIP-Seq fragments from the sequence data, considering local genomic biases for analysis of distribution of mapped reads. The following parameters were used: macs, t, treatment_bedfile; c, control_bedfile; tsize _ 36; wig; P _ 10_5 also with P _ 10_06.
We performed a comprehensive genome-wide RNA-Seq analysis of mRNA levels in biologic replicates of sorted progenitor cells and erythroblasts (Figure 4A). Sequenced reads were mapped to the UCSC mouse mm9 assembly to determine expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: The peaks.bed files are in the "ENCODE broadPeak: Broad Peaks (or Regions) format" format, which is a "BED 6+3 format" (https://genome.ucsc.edu/FAQ/FAQformat.html#format13).  Column headers are: chrom, start, end, name, score, strand, signalValue, pValue, qValue.
Supplementary_files_format_and_content: KLF1_RPKM.txt (linked as supplementary file on the Series record) is an RNA abundance file.
Supplementary_files_format_and_content: The bigwig files were used for browser shots.

source_name: Fetal Liver

growth_protocol: None -- Primary cells

extract_protocol:
Library construction was performed using the Illumina ChIP-Seq library preparation kit according to the standard protocol. ChIP-Seq fragments were separated on an agarose gel, and fragments of approximately 200 bp were ligated to Illumina-specific adapters to generate libraries. Six cycles of PCR amplification were used to select for fragments containing both Illumina-specific adapters before bead-based elimination of unligated adapters.
ChIP enrichment of HA-EKLF-bound chromatin obtained from fetal liver progenitors and erythroblasts was performed as previously described.9,27,34 Chromatin was processed using the Magna ChIP A kit (#17-610; Millipore) according to the manufacturer’s instructions. Chromatin was immunoprecipitated with monoclonal antibodies against HA (F-7, sc-7329X, Santa Cruz Biotechnology). As a background genomic control, sheared chromatin from E13.5 HA-EKLF fetal liver cells was processed in parallel, minus incubation with the antibodies.
Fetal livers were dissociated to single- cell suspension and stained with anti-CD71–FITC and anti-Ter119–PE antibodies (BD Biosciences PharMingen). Cell populations were isolated using a FACSAria flow cytometer running FACSDiva 6.1.3 software (BD Biosciences). Cells were collected as erythroid progenitors (Ter119-CD71- and Ter119-CD71+) or erythroblasts (Ter119+CD71+). At least 3 indepen- dent cell sorts for each population were performed.

treatment_protocol: None -- Primary cells

tag: genotype/variation

value: hemagglutinin-Klf1 (KLF1 is hemagglutinin-tagged)

tag: cell markers

value: none (input)

tag: cell type

value: erythroblast


title: Progenitor_input

value: Ter119-CD71- and and Ter119-CD71+

value: erythroid progenitor


title: Erythroblast_RNA_R2

description: cDNA from mRNA

extract_protocol:
RNA was extracted from sorted fetal liver progenitor cells and erythroblasts. RNA-Seq libraries were generated and sequenced using Illumina adapters for paired-end 51-bp sequencing on the Illumina Genome Analyzer IIxplatform.
Fetal livers were dissociated to single- cell suspension and stained with anti-CD71–FITC and anti-Ter119–PE antibodies (BD Biosciences PharMingen). Cell populations were isolated using a FACSAria flow cytometer running FACSDiva 6.1.3 software (BD Biosciences). Cells were collected as erythroid progenitors (Ter119-CD71- and Ter119-CD71+) or erythroblasts (Ter119+CD71+). At least 3 indepen- dent cell sorts for each population were performed.


title: Erythroblast_RNA_R1

description: cDNA from mRNA


title: Erythroid_Progenitor_RNA

description: cDNA from mRNA


title: Erythroid_Progenitor_EKLF

value: HA (Santa Cruz Biotechnology, sc-7329X, F-7)


title: AD sample 47

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

data_processing:
Demultiplexing of the raw sequencing data and generation of the fastq files was done using CASAVA v.1.8.2
The raw reads were preprocessed by cutting the 3' adapter sequence using the program fastx_clipper from the FASTX-Toolkit
mirbase v18 counts and counts for novel predicted miRNAs  were collected using the miRDeep2 pipeline
miRNAs with less than 50 read counts summed up across all samples of each group (ad or control) were excluded from further analysis
the counts were normalized by quantile normalization
Genome_build: hg19
Supplementary_files_format_and_content: Excel table containing the raw mirbase and novel mirna counts and the quantile normalized counts

source_name: whole blood

extract_protocol:
Total RNA including miRNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) following the manufacturer’s recommendations.
For the library preparation, 200 ng of total RNA was used per sample. Preparation was performed following the protocol of the TruSeq Small RNA Sample Prep Kit (Illumina). Libraries were then pooled in batches of six samples in equal amounts and clustered with a concentration of 9 pmol in one lane each of a single read flowcell using the cBot (Illumina).

tag: group

value: alzheimer patient

tag: gender

value: male

tag: age


title: AD sample 45


title: AD sample 44


title: AD sample 43

value: female


title: AD sample 40


title: AD sample 41


title: AD sample 42


title: AD sample 46


title: A liver 2 RNA

description: Sequenced reads were generated from liver of summer active Myotis brandtii sample2


title: AD sample 38


title: AD sample 36


title: AD sample 35


title: control sample 21

value: control


title: AD sample 37


title: Muscle larvae_rep1

city: Changchun

first: Xiaolei

last: Liu

address: 5333 Xian Road

institute: Key Laboratory of Zoonosis, Jilin University

data_processing:
Basecalls performed using phred/phrap software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Trichinella spiralis whole genome with SOAP2, allowing for no more than one nucleotide mismatch.
Genome_build: Trichinella spiralis genome 3.7.1
Supplementary_files_format_and_content: tab-delimited text files include count for each sequence.

organism: Trichinella spiralis

source_name: Muscle larvae_polypide

growth_protocol: Muscle larvae (ML) of T. spiralis (strain ISS534) were obtained from rats 35 days post infection by digestion of minced skeletal muscle in 1% pepsin, 1% HCl for 3 h at 37°C with agitation as previously described [PMID:840494]. To purify adult worms and newborn larvae, Wistar rats at 6 weeks of age were inoculated with T. spiralis (strain ISS534) orally with a dose of 8000 larva per rat. At 30 h or 6 days post infection, all rats were executed and the entire intestines were removed, opened longitudinally and cut into pieces (about 0.5-1 cm). The fragmented intestine was put on a layer of gauze which was immersed into 37 °C 0.9% sodium chloride solution and incubated for 3 h. Adult T. spiralis worms would migrate into the liquid phase, which were harvested by centrifugation. To obtain new-born larvae, adult worms collected at 6 days post infection were incubated in IMDM in 75-cm2 cell culture plate at 37 °C, the newborn larvae were harvested every 12 h.

extract_protocol: Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent. 6 μg of total RNA from each preparation was treated with Oligo-(dT) conjugated magnetic beads to purify mRNA. Double-strand cDNA was synthesized guided by the Oligo-(dT) as a primer and then digested with the endonuclease NlaⅢ that recognizes the CATG sites. The Illumina adaptor 1, containing a MmeI restriction site, was added to the cDNAs attached to the magnetic beads, which was further digested with MmeI. Following MmeI digestion and dephosphorylation, cDNA fragments were purified and the Illumina adaptor 2 was ligated to the 3’ends of the tags to create tag library with different adapters at both ends. After15 cycles of linear PCR amplification, 95 bp fragments were purified from 6% TBE PAGE gels and attached to the Illumina sequencing chip for sequencing.

tag: developmental stage

value: Muscle larvae

value: polypide


title: AD sample 39


title: AD sample 34


title: Adult larvae_rep1

source_name: Adult larvae_polypide

tag: strain

value: Adult larvae


title: Newborn larvae_rep1

source_name: Newborn larvae_polypide

value: Newborn larvae


title: control sample 18


title: control sample 20


title: control sample 14


title: control sample 16


title: control sample 12


title: control sample 17


title: control sample 15


title: control sample 19


title: control sample 13


title: control sample 11


title: control sample 7


title: control sample 8


title: control sample 9


title: control sample 10


title: control sample 2


title: control sample 5


title: control sample 3


title: control sample 4


title: control sample 6


title: AD sample 32


title: control sample 0


title: AD sample 31


title: AD sample 28


title: control sample 1


title: AD sample 33


title: AD sample 30


title: AD sample 27


title: AD sample 24


title: AD sample 22


title: AD sample 25


title: AD sample 26


title: AD sample 21


title: AD sample 20


title: AD sample 19


title: AD sample 17


title: AD sample 16


title: AD sample 15


title: AD sample 13


title: AD sample 29


title: AD sample 7


title: AD sample 10


title: AD sample 11


title: AD sample 5


title: AD sample 8


title: Dre_48h_silver_bulk

city: Exeter

first: Ronny

last: van Aerle

state: Devon

address: Stocker Road

department: Biosciences, College of Life and Environmental Sciences

country: United Kingdom

institute: University of Exeter

data_processing:
FASTQ/A Barcode splitter from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/download.html) was used to separate the samples from each lane using the 4 base barcode.
FASTQ-to-FASTA from the FASTX-Toolkit was used to convert the fastq files to fasta files.
FASTQ/A trimmer from the FASTX-Toolkit was used to remove the barcodes (the first 4 bases) from the sequence.
A Perl script was used to remove all bases after the last occurence of CATG (NlaIII restriction site, used for sequence tag preparation) in each of the sequences
FASTX_collapser was used to collapse the sequences and calculate the frequency of unique sequence tags (unitags) in each library
Supplementary_files_format_and_content: tabulated text files include frequency of all unitags in the treatment library

molecule: polyA RNA

organism: Danio rerio

growth_protocol: Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al., 2008 Aquat Toxicol. 87(2):115-26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers, approximately 1 hour post-fertilisation (hpf). Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.

extract_protocol: High throughput (HT)-SuperSAGE libraries were prepared as described in Matsumura et al 2010, PLoS ONE 5(8):e12010. Samples were multiplexed on each lane of the Illumina flow-cell.

treatment_protocol: Stock solutions for Ag NP, Ag Bulk and silver nitrate were made up in ultrapure water, and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers, at 28+/- 1°C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures, glass chambers received 400 mL of ISO water, prepared according to OECD guidelines for zebrafish embryo experiments (http://www.oecd.org/), containing 5 µg/L of 10nm Ag NP, 5  µg/L of Ag Bulk or 0.25  µg/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period, and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h, 3 pools of 50 embryos were removed from each exposure tank, immediately frozen in liquid nitrogen and stored at -80°C for analysis of gene expression. The experiment was terminated at 48 hpf.

value: wild-type WIK strain

value: whole embryos

value: 48 hpf

tag: treatment

value: silver bulk (0.6-1.6µm; 5 µg/L)

tag: barcode

value: GCGC


title: Dre_48h_silver_ions

value: silver ions (0.25 µg/L of silver nitrate)

value: GCGA


title: AD sample 4


title: AD sample 12


title: AD sample 6


title: Dre_48h_control

value: GCTT


title: AD sample 23


title: Erythroblast_EKLF

value: hemagglutinin-Klf1 (KLF1 is hemagglutinin-tagged)

value: HA (Santa Cruz Biotechnology, sc-7329X, F-7)

value: liver

value: erythroblast


title: AD sample 18

value: alzheimer patient

value: male


title: AD sample 1


title: AD sample 2


title: Dre_24h_silver_NP

value: 24 hpf

value: silver nanoparticles (10nm; 5µg/L)

value: GCAG


title: Dre_24h_silver_bulk

value: wild-type WIK strain

value: GCTC


title: Dre_24h_silver_ions

value: whole embryos

value: GCTA


title: AD sample 0

value: female


title: Selected AHR DIFFD14 PURO+TCDDCONT Rep 2

status: Public on Jun 15 2013

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

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

source_name: Embryonic Stem Cells

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell group

value: Selected AHR+ Cells

value: Treated

tag: day


title: AD sample 14


title: AD sample 9


title: Selected AHR DIFFD8 PURO+TCDDCONT Rep 2

description: Selected AHR DIFFD8 PURO+TCDDCONT Rep 2


title: Selected AHR DIFFD11 PURO Rep 2

description: Selected AHR DIFFD11 PURO Rep 2

value: Ctrl


title: Selected AHR DIFFD5 PURO Rep 2

description: Selected AHR DIFFD5 PURO Rep 2


title: Selected AHR DIFFD11 PURO+TCDDCONT Rep 2


title: Selected AHR DIFFD5 PURO+TCDDCONT Rep 2

description: Selected AHR DIFFD5 PURO+TCDDCONT Rep 2


title: AD sample 3


title: Unselected DIFFD8 0TRT Rep 2

description: Unselected DIFFD8 0TRT Rep 2

value: Unselected Differentiated ESCs


title: Selected AHR DIFFD14 PURO+TCDDCONT Rep 1


title: Dre_48h_silver_NP

tag: tissue

value: 48 hpf

value: GCTG


title: Unselected DIFFD8 0TRT Rep 1

description: Unselected DIFFD8 0TRT Rep 1


title: Selected AHR DIFFD14 PURO Rep 1

description: Selected AHR DIFFD14 PURO Rep 1


title: Selected AHR DIFFD8 PURO Rep 2

description: Selected AHR DIFFD8 PURO Rep 2


title: Unselected DIFFD5 0TRT Rep 1

description: Unselected DIFFD5 0TRT Rep 1


title: Selected AHR DIFFD11 PURO Rep 1

description: Selected AHR DIFFD11 PURO Rep 1


title: Selected AHR DIFFD11 PURO+TCDDCONT Rep 1


title: Selected AHR DIFFD8 PURO+TCDDCONT Rep 1

description: Selected AHR DIFFD8 PURO+TCDDCONT Rep 1


title: Unselected DIFFD14 0TRT Rep 2

description: Unselected DIFFD14 0TRT Rep 2


title: Selected AHR DIFFD8 PURO Rep 1

description: Selected AHR DIFFD8 PURO Rep 1


title: Unselected DIFFD11 0TRT Rep 1

description: Unselected DIFFD11 0TRT Rep 1


title: Selected AHR CIFFD14 PURO Rep 2

description: Selected AHR CIFFD14 PURO Rep 2


title: Selected AHR DIFFD5 PURO+TCDDCONT Rep 1

description: Selected AHR DIFFD5 PURO+TCDDCONT Rep 1


title: Unselected DIFFD14 0TRT Rep 1

description: Unselected DIFFD14 0TRT Rep 1


title: T47D RNA-Seq

city: St. Louis

first: Nathan

last: VanderKraats

state: MO

address: 660 S. Euclid Ave

department: Center for Pharmacogenomics

institute: Washington University in St. Louis, School of Medicine

description: replicates: 2

data_processing:
RNA-Seq reads were mapped to hg18 using Tophat v1.3.3
Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats according to RepeatMasker: snRNA, scRNA, srpRNA, tRNA, and RNA.
htseq-count 0.5.3p3 was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method
Genes mapping to ribosomal and mitochondrial proteins were filtered
A floor of 10 counts per million (cpm) was applied to avoid artificially high fold changes resulting from one sample having a very small number of counts.  This also effectively filters genes that were not expressed in either sample.
Genes with an expression change less than two-fold are discarded.
Differentially expressed genes (FDR=0.05) were identified using edgeR 2.6.12 with TMM normalization and tagwise dispersion.
Ensembl gene annotations were mapped to RefSeq IDs and Gene Symbols using the corresponding UCSC Genome Browser tables
Genome_build: hg18
Supplementary_files_format_and_content: 5-column tab-delimited (ENSG ID, Gene Symbol, RefSeq ID, CPM1, CPM2), where each row represents a gene after the filtering above, and CPM1, CPM2 are the expression values for sample MCF7, T47D, respectively

source_name: human breast cancer cell line

growth_protocol: MCF7 and T47D cell lines were maintained in RPMI 1640 medium supplemented with 5% fetal bovine serum, 10 mmol/L HEPES, 4.5 g/L glucose, 2 mmol/L L-glutamine, 1 mmol/L sodium pyruvate, and 50 µg/ml gentamicin in a humidified 37°C incubator containing 5% carbon dioxide.

extract_protocol:
Total RNA (10 ug) was isolated from MCF7 and T47D cells, DNase treated, and twice oligo(dT) selected using the Dynabeads mRNA purification kit (Invitrogen).
RNA-seq libraries were constructed using the NEBNext Kit from New England Biolabs. MCF7_1 and T47D_1 libraries were constructed with custom 4 bp barcodes and sequenced with an Illumina GAIIx (32 bp single-end reads).  MCF7_2 and T47D_2 libraries were constructed with standard Illumina indexed primers and sequenced using Illumina HiSeq 2000 (42 bp single-end reads).

tag: cell line

value: human breast cancer


title: MCF7 RNA-Seq

description: replicates: 2


title: WCE_CM_Rep_1

city: Cambridge

first: Laurie

middle: A

last: Boyer

state: MA

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Short reads were aligned to the mm9 mouse genome using Bowtie (2 bp mismatch)
Sequences were extended +200 bp for histone marks and RNAPser5 and allocated in 25-bp bins. Extended sequences were also processed into Wiggle format for visualization.
Biological replicate whole cell extracts were sequenced for each time point and combined for use as background model. A Poissonian model was used to determine statistically enriched bins with a p value threshold set at 1 X 10^9 as described previously (Marson et al., 2008) and a 5-fold enrichment over input cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: .wig files,representing read density across the genome, were generated after extending aligned sequences by 200 nt.
Supplementary_files_format_and_content: *_ENRICHED_REGIONS.txt files are encoded in bed format and contain genomic regions corresponding to enriched ChIP-Seq regions.

source_name: CM stage cultures, Whole cell extract

growth_protocol: Embryonic stem cells were differentiated as EBs for two days in serum-free media (3 parts IMDM (Cellgro #15-016-CV): 1 part Ham’s F12 (Cellgro #10-080-CV), 0.05% BSA, 2 mM GlutaMax (GIBCO), B27 supplement (GIBCO #12587010), N2 supplement (GIBCO #17502048)) supplemented with 50 mg/ml ascorbic acid and 4.5 3 10^4 M monothioglycerol. Embryoid bodies were dissociated and reaggregated for 40 hr in the presence of 5 ng/mL human VEGF (R&D #293-VE) and human Activin A (R&D #338-AC) and human BMP4 (R&D #314-BP) at concentrations empirically determined depending on lot. EBs were dissociated and plated at 470,000 cells/cm2 in StemPro-34 (GIBCO #10639011) supplemented with 5 ng/mL VEGF, 10 ng/mL human basic FGF (R&D #233-FB) and 25 ng/mL FGF10 (R&D #345- FG).

extract_protocol:
Chromatin immunoprecipitation of histone modifications were performed according to the Young lab protocol (Lee et al., 2006) with minor modification. Briefly, frozen pellets of cross-linked cells (10 3 106) were thawed in cold lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 3 protease inhibitors) and gently rocked at 4  C for 10 min in 14 ml conical tubes. Cells were pelleted at 1350 x g at 4 C in a clinical centrifuge and resuspended in cold lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 3 protease inhibitors) and gently rocked at 4 C for 10 min in 14 ml conical tubes. Cells were pelleted at 1350 x g at 4C in a table top centrifuge and resuspended in 2 ml cold lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1 3 protease inhibitors) and sonicated to 200-600 bp fragments using a Diagenode Bioruptor (3 3 10 min cycles, 30 s ON / 30 s OFF at 4 C). Soni- cated lysates were cleared by pelleting insoluble material at 20,000 x g at 4  C followed by incubation with antibody bound Protein A/G magnetic beads (2.5 mg Ab / 50uL beads / IP) in 1 ml of 0.5% BSA/PBS overnight at 4 C. Magnetic beads were washed 3 times with block (0.5% BSA/PBS), incubated for approximately 4 hr at 4 C with antibody in block and then washed 3 times with block prior to addition of cleared cell lysates. Immunoprecipitated material was washed five times with cold wash buffer (RIPA: 50 mM HEPES-KOH, pKa 7.55, 500 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate) and one time with TE plus NaCl, followed by elution and uncrosslinking in 210 uL of 1% SDS in TE overnight at 65  C. 200 uL of uncrosslinked material was treated with RNase A for 2 hr, proteinase K for 2 hr and extracted 2 times with phenol chloroform isoamyl alcohol, followed by ethanol precipitation with a glycogen coprecipitant, 80% ethanol wash and final resuspension in TE.
Illumina sequencing libraries were generated (Schmidt et al., 2009), with minor modi- fication. Briefly, 5-50 ng of immunoprecipitated nucleic acid was end repaired, a-tailed and ligated to Illumina single end adapters using an NEB Next kit (New England Biolabs).  200-300 bp adaptor ligated nucleic acid was gel purified and enriched via 19 cycles of PCR amplification with Phusion High-Fidelity DNA Polymerase, followed by sequencing on an Illumina HiSeq 2000 system

tag: time point

value: Differentiation Day 10

value: cardiomyocytes (CM)

tag: antibody

value: None (Whole cell extract)


title: WCE_CM_Rep_3


title: Unselected DIFFD5 0TRT Rep 2

description: Unselected DIFFD5 0TRT Rep 2


title: Unselected DIFFD11 0TRT Rep 2

description: Unselected DIFFD11 0TRT Rep 2


title: WCE_CP_Rep_3

source_name: CP stage cultures, Whole cell extract

value: Differentiation Day 5.3

value: cardiac precursors (CP)


title: WCE_CP_Rep_1


title: WCE_MES_Rep_3

source_name: MES stage cultures, Whole cell extract

value: Differentiation Day 4

value: mesodermal cells (MES)


title: WCE_MES_Rep_1


title: RNAP_Ser5_Phos_CM_Rep_2

source_name: CM stage cultures, RNA Polymerase II

extract_protocol:
Altered sonication and wash buffers used for this sample as described in Rahl et al., 2010
Chromatin immunoprecipitation of histone modifications were performed according to the Young lab protocol (Lee et al., 2006) with minor modification. Briefly, frozen pellets of cross-linked cells (10 3 106) were thawed in cold lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 3 protease inhibitors) and gently rocked at 4  C for 10 min in 14 ml conical tubes. Cells were pelleted at 1350 x g at 4 C in a clinical centrifuge and resuspended in cold lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 3 protease inhibitors) and gently rocked at 4 C for 10 min in 14 ml conical tubes. Cells were pelleted at 1350 x g at 4C in a table top centrifuge and resuspended in 2 ml cold lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1 3 protease inhibitors) and sonicated to 200-600 bp fragments using a Diagenode Bioruptor (3 3 10 min cycles, 30 s ON / 30 s OFF at 4 C). Soni- cated lysates were cleared by pelleting insoluble material at 20,000 x g at 4  C followed by incubation with antibody bound Protein A/G magnetic beads (2.5 mg Ab / 50uL beads / IP) in 1 ml of 0.5% BSA/PBS overnight at 4 C. Magnetic beads were washed 3 times with block (0.5% BSA/PBS), incubated for approximately 4 hr at 4 C with antibody in block and then washed 3 times with block prior to addition of cleared cell lysates. Immunoprecipitated material was washed five times with cold wash buffer (RIPA: 50 mM HEPES-KOH, pKa 7.55, 500 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate) and one time with TE plus NaCl, followed by elution and uncrosslinking in 210 uL of 1% SDS in TE overnight at 65  C. 200 uL of uncrosslinked material was treated with RNase A for 2 hr, proteinase K for 2 hr and extracted 2 times with phenol chloroform isoamyl alcohol, followed by ethanol precipitation with a glycogen coprecipitant, 80% ethanol wash and final resuspension in TE.
Illumina sequencing libraries were generated (Schmidt et al., 2009), with minor modi- fication. Briefly, 5-50 ng of immunoprecipitated nucleic acid was end repaired, a-tailed and ligated to Illumina single end adapters using an NEB Next kit (New England Biolabs).  200-300 bp adaptor ligated nucleic acid was gel purified and enriched via 19 cycles of PCR amplification with Phusion High-Fidelity DNA Polymerase, followed by sequencing on an Illumina HiSeq 2000 system

value: RNA Polymerase II (phospho S5) (Abcam ab5131)


title: RNAP_Ser5_Phos_CM_Rep_1


title: WCE_ESC_Rep_3

source_name: ESC stage cultures, Whole cell extract

value: Differentiation Day 0

value: embryonic stem cells (ESC)


title: WCE_ESC_Rep_1


title: RNAP_Ser5_Phos_CP_Rep_2

source_name: CP stage cultures, RNA Polymerase II


title: Selected AHR DIFFD5 PURO Rep 1

description: Selected AHR DIFFD5 PURO Rep 1

value: Selected AHR+ Cells


title: RNAP_Ser5_Phos_CP_Rep_1


title: RNAP_Ser5_Phos_MES_Rep_2

source_name: MES stage cultures, RNA Polymerase II


title: RNAP_Ser5_Phos_MES_Rep_1


title: H3K4me3_CM_Rep_2

source_name: CM stage cultures, H3K4me3

value: H3K4me3 (Millipore 07-473)


title: RNAP_Ser5_Phos_ESC_Rep_2

source_name: ESC stage cultures, RNA Polymerase II


title: H3K4me3_CP_Rep_1

source_name: CP stage cultures, H3K4me3


title: H3K4me3_CM_Rep_1


title: H3K4me3_MES_Rep_2

source_name: MES stage cultures, H3K4me3


title: H3K4me3_MES_Rep_1


title: H3K4me3_CPs_Rep_2


title: H3K4me3_ESC_Rep_2

source_name: ESC stage cultures, H3K4me3


title: H3K4me3_ESC_Rep_1


title: H3K27me3_CM_Rep_3

source_name: CM stage cultures, H3K27me3

value: H3K27me3 (Millipore 07-449)


title: ai rep 2

city: Saint Louis

first: Jianqing

last: Li

address: 660 S Euclid Ave.

department: Molecular Microbiology

data_processing:
Illumina 1.8
Sequenced reads are aligned to human hg19 transcriptome with Tophat v2.0.7 with parameter tophat –no-novel-juncs -G ~/hg19/genes.gtf
FPKM are calculated from alignment with Cufflinks v2.0.2 with parameters -G ~/hg19/genes.gtf
Differential expression analysis is done with Cuffdiff v2.0.2 with parameter -b ~/hg19/genome.fa -u ~/hg19/genes.gtf
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: HeLa cells transduced with anti-ASCC3 shRNA

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma) supplemented with 10% fetal bovine serum (FBS) (Omega Scientific), 100 IU/ml penicillin, 100 μg/ml streptomycin, 10 mM HEPES (pH 7.3), and 10 mM nonessential amino acids (Cellgro) at 37°C and 5% CO2

extract_protocol:
Total RNA was harvested using RNeasy Mini Kit (Qiagen) followed by mRNA extraction using Dynal mRNA Direct kit. mRNA was then fragmented and reverse transcribed to double stranded cDNA. Sequencing was performed in a single lane with Illumina HiSeq 2000 sequencing instruments at 1x50 single read run.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HeLa cells were transduced with lentiviral vectors carrying either scrambledn shRNA or shRNA targeting ASCC3

tag: passages

tag: cell types

value: Anti-ASCC3 shRNA


title: ai rep 3

value: HeLa cells transduced with anti-ASCC3 shRNA


title: H3K27me3_CM_Rep_2


title: H3K27me3_CM_Rep_1


title: H3K27me3_CP_Rep_2

source_name: CP stage cultures, H3K27me3


title: H3K27me3_CP_Rep_3


title: ai rep 1


title: H3K27me3_CP_Rep_1


title: ni rep 3

source_name: HeLa cells transduced with scrambled shRNA

value: Scrambled shRNA


title: H3K27me3_MES_Rep_3

source_name: MES stage cultures, H3K27me3


title: H3K27me3_MES_Rep_1


title: H3K27me3_MES_Rep_2


title: ni rep 2

value: HeLa cells transduced with scrambled shRNA


title: H3K27me3_ESC_Rep_3

source_name: ESC stage cultures, H3K27me3


title: H3K27me3_ESC_Rep_2


title: ni rep 1


title: RNA_CM_Rep_2_JW-H8B

data_processing:
Paired-end RNA-Seq 36 base pair reads were aligned to mm9 (Mus musculus assembly July 2007) using novoalign V2.07.00 (http:// novocraft.com) with default options, except that no repeats were reported (-r None) and the fragment length and standard deviation were set at 176 and 11, respectively (-i PE 176,11).
The RNA-Seq application in USeq 7.0 (Nix et al., 2008) was used to generate gene-level read counts and estimate RPKM (reads per kilobase of exon per million reads mapped). Only genes with expression values >1 RPKM in at least one cell type are included.
Genome_build: mm9
Supplementary_files_format_and_content: .bw files represent BigWig browser tracks.  Tracks display mapped reads per base pair.
Supplementary_files_format_and_content: Tab-delimited file with RPKM values for all genes at each stage expressed >1 RPKM in at least one timepoint

source_name: CM stage cultures

extract_protocol:
RNA was extracted using TRIzol reagent according to the manufacturer's instructions.
10 ug RNA was used for library construction according to Illumina RNA-seq library kit with minor modifications.  Briefly, mRNA was isolated using Dynabeads mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation. First and second strand synthesis were performed followed by end repair, A-tailing, paired end adaptor ligation and size selection on a Beckman Coulter SPRI TE nucleic acid extractor. 200-400 bp dsDNA was enriched by 15 cycles of PCR with Phusion High-Fidelity DNA Polymerase (NEB) followed by gel purification of 250 bp fragments from the amplified material. Amplified libraries were sequenced on an Illumina GAIIx sequencer.

value: Differentiation Day 10


title: H3K27ac_CM_Rep_2

source_name: CM stage cultures, H3K27ac

value: H3K27ac (Abcam ab4729)


title: RNA_CM_Rep_1_JW-H7B

value: cardiomyocytes (CM)


title: H3K27ac_CM_Rep_1


title: RNA_CP_Rep_2_JW-H6B

source_name: CP stage cultures

value: Differentiation Day 5.3


title: RNA_CP_Rep_1_JW-H5B

value: cardiac precursors (CP)


title: Dre_24h_control

value: wild-type WIK strain

value: whole embryos

value: 24 hpf

value: control

value: GCAT


title: H3K27ac_CP_Rep_2

source_name: CP stage cultures, H3K27ac


title: H3K27ac_CP_Rep_1


title: H3K27ac_MES_Rep_2

source_name: MES stage cultures, H3K27ac

value: Differentiation Day 4

value: mesodermal cells (MES)


title: H3K27ac_MES_Rep_1


title: RNA_MES_Rep_2_JW-H4B

source_name: MES stage cultures


title: H3K27ac_ESC_Rep_2

source_name: ESC stage cultures, H3K27ac

value: Differentiation Day 0

value: embryonic stem cells (ESC)


title: H3K27ac_ESC_Rep_1


title: RNA_ESC_Rep_2_JW-H10B

source_name: ESC stage cultures


title: H3K4me1_CP_Rep_3

source_name: CP stage cultures, H3K4me1

value: H3K4me1 (Abcam ab8895)


title: RNA_MES_Rep_1_JW-H3B


title: H3K4me1_CM_Rep_1

source_name: CM stage cultures, H3K4me1


title: RNA_ESC_Rep_1_JW-H9B


title: H3K4me1_CP_Rep_2


title: H3K4me1_CM_Rep_2


title: H3K4me1_MES_Rep_2

source_name: MES stage cultures, H3K4me1


title: H3K4me1_MES_Rep_3


title: H3K4me1_CP_Rep_1


title: H3K4me1_ESC_Rep_1

source_name: ESC stage cultures, H3K4me1


title: H3K4me1_ESC_Rep_3


title: H3K4me1_ESC_Rep_2


title: RS RNA replicate1

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing:
Low-complexity reads were filtered out on the basis of dinucleotide entropy.
Read are aligned by using Bowtie.
Tab and wig files were generated in the same way as described in Stadler et al., Nature 2011, pubmed ID: 22170606
Genome_build: mm9
Supplementary_files_format_and_content: Wig files show the average coverage per base in 100 bp windows in the genome.

source_name: Round spermatids

extract_protocol:
Mouse spermatozoa were collected by swim-up procedure5 from C57BL/6J mice. Round spermatids were isolated by FACS sorting using 28 day old BL6 mice. Mono-nucleosomal chromatin samples were prepared by MNase treatment. ChIP experiments for histone variants, H3.1/H3.2, H3.3, and histone modifications H3K4me3 and H3K27me3 were performed on native chromatin.
ChIP-seq and MNase-seq libraries were produced using the Illumina ChIP-seq DNA Sample Prep Kit (Cat# IP-102-1001).Before preparing RNA-seq libraries, rRNA from RNA  was depleted by using the Ribo-Zero rRNA removal kit (Epicentre Biotechnologies). Bisulfite libraries were prepared as described in Stadler et al., Nature 2011, pubmed ID: 22170606  Strand specific RNA-seq libraries were prepared by following the Illumina directional  mRNA-seq library preparation pre-release protocol.

value: Round spermatids


title: RS H3K27me3 replicate1

value: Millipore 07-449


title: RS H3K4me3 replicate1

value: Millipore 17-614


title: KO2_MeRIP

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

description: processed data file: KO.fjfs.peaks.bed

data_processing:
library strategy: MeRIP-Seq
Reads aligned to genome using BWA 0.6.2-r126 with default parameters
filtered using samtools 0.1.18 with MAPQ < 20
Peaks were found using MeRIPPeR 0.9.1 software.
Genome_build: mm9
Supplementary_files_format_and_content: peak files (bed format)

source_name: Fto KO_midbrain_striatum_MeRIP

extract_protocol:
Tissue was microdissected and RNA was extracted using TRIzol
Total RNA was isolated from adult mouse midbrain and striatum and then subjected to RiboMinus treatment to remove rRNAs.  RNA was then subjected to 2 rounds of m6A RNA immunoprecipitation (MeRIP) using an antibody that recognizes m6A

tag: strain background

tag: genotype/variation

value: global Fto knockout

value: adult

value: neural tissue (midbrain and striatum)

tag: sample type

value: RNA IP against m6A

tag: merip antibody

tag: merip antibody vendor

value: Synaptic Systems (SYSY)

tag: merip antibody cat. #

tag: rna subtype

value: RiboMinus RNA


title: KO1_No IP

description: processed data file: KO.fjfs.peaks.bed

source_name: Fto KO_midbrain_striatum_MeRIP_input

tag: age

value: no IP (input RNA)


title: KO3_No IP

description: processed data file: KO.fjfs.peaks.bed


title: KO3_MeRIP

description: processed data file: KO.fjfs.peaks.bed


title: Sperm H3K27me3 replicate1

source_name: Sperm

value: Sperm

tag: strain


title: KO1_MeRIP

description: processed data file: KO.fjfs.peaks.bed


title: KO2_No IP

description: processed data file: KO.fjfs.peaks.bed


title: WT3_MeRIP

description: processed data file: WT.fjfs.peaks.bed

value: wild-type littermate


title: WT2_No IP

description: processed data file: WT.fjfs.peaks.bed


title: H3K4me1_CM_Rep_3

value: Differentiation Day 10

tag: cell type

value: cardiomyocytes (CM)


title: WT1_No IP

description: processed data file: WT.fjfs.peaks.bed


title: WT2_MeRIP

description: processed data file: WT.fjfs.peaks.bed


title: WT1_MeRIP

description: processed data file: WT.fjfs.peaks.bed


title: H3K4me1_MES_Rep_1

value: Differentiation Day 4

value: mesodermal cells (MES)


title: RS RNA replicate2


title: Sperm H3.3 replicate2

extract_protocol:
Mouse spermatozoa were collected by swim-up procedure from C57BL/6J mice. Round spermatids were isolated by FACS sorting using 28 day old BL6 mice. Mono-nucleosomal chromatin samples were prepared by MNase treatment. ChIP experiments for histone variants, H3.1/H3.2, H3.3, and histone modifications H3K4me3 and H3K27me3 were performed on native chromatin.
ChIP-seq and MNase-seq libraries were produced using the Illumina ChIP-seq DNA Sample Prep Kit (Cat# IP-102-1001).Before preparing RNA-seq libraries, rRNA from RNA  was depleted by using the Ribo-Zero rRNA removal kit (Epicentre Biotechnologies). Bisulfite libraries were prepared as described in Stadler et al., Nature 2011, pubmed ID: 22170606  Strand specific RNA-seq libraries were prepared by following the Illumina directional  mRNA-seq library preparation pre-release protocol.

value: Millipore 09-838


title: Sperm Nucleosome replicate3


title: RS H3K27me3 replicate2

value: Round spermatids


title: RS H3.1/H3.2

value: Van Der Heijden et al. Nature Genetics, 2007, pubmed ID:17237782


title: RS H3.3

value: Millipore 17-10245


title: Sperm H3K4me3 replicate1

value: Millipore 17-614


title: Sperm sonicated genomic DNA

data_processing:
Low-complexity reads were filtered out on the basis of dinucleotide entropy.
Read are aligned by using Bowtie.
Tab and wig files were generated in the same way as described in Stadler et al., Nature 2011, pubmed ID: 22170606
Genome_build: mm9
Supplementary_files_format_and_content: Tab file show the total and methylated alignments overlapping individual CpGs.


title: Sperm H3K27me3 replicate2

value: Millipore 07-449


title: Sperm Nucleosome replicate1


title: sfl2-CaEXP-SFL1-HA_2

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

data_processing:
1-FASTQ Groomer
2-Adaptor trimming
3-Mapping using Bowtie
4-Peak finding using MACS version 1.4
Genome_build: Candida albicans Assembly 21
Supplementary_files_format_and_content: Wiggle files generated by MACS version 1.4-Wiggle tracks with tag counts for every 10 bp segment

organism: Candida albicans

growth_protocol: Two independent cultures of strains sfl1-CaEXP or sfl2-CaEXP (untagged; control strains) and sfl1-CaEXP-SFL1-HA or sfl2-CaEXP-SFL2-HA (triple-HA tagged strains) were grown overnight in 2 ml YPD at 30°C.

extract_protocol: Cultures were treated with 1% formaldehyde (cross-linking) and snap-frozen in liquid nitrogen. Total cell extracts were prepared by bead beating using a FastPrep-24 instrument (MP Biomedicals) with 6 runs during 1 minute each at 6.0 m/sec and 1 minute on ice in between (these settings led to efficient breakage of hyphal cells). Preparation of soluble chromatin fragments was performed by sonicating the extracts 6 times during 20 sec at power 8 (knob position) for an output signal amplitude of 15 (Microns, Peak to Peak) using a probe sonicator (MSE), yielding ~200-bp DNA fragments on average. The extracts were then incubated at 4°C overnight with a mouse monoclonal anti-HA antibody (F-7) (Santa Cruz Biotech, sc-7392) coupled to magnetic beads (pan-mouse immunoglobulin G Dynabeads; Dynal Biotech, Brown Deer, WI). Beads were then washed twice with lysis buffer, twice with lysis buffer supplemented with 360 mM NaCl, twice with wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na deoxycholate, 1 mM EDTA), and once with TE buffer (10 mM Tris, pH 8.0, 1 mM EDTA). The cross-links were reversed by incubating the washed beads overnight in 50 μl of TE-1% SDS at 65°C. The eluted material was then treated with proteinase K and RNase A and extracted twice with phenol:chloroform:isoamyl alcohol (25:24:1), and the DNA was precipitated with 100% ethanol and resuspended in 50 μl of TE.The concentration of the purified immunoprecipitated DNA was ranging between 0.2 ng/ml and 1.5 ng/ml in 50 ml TE.

treatment_protocol: Cells were diluted to an OD600 of 0.3 in Lee’s medium deprived of methionine and cysteine (to induce the MET3 promoter) and grown during 4 hours at 37°C (hyphae-inducing conditions).

tag: developmental stage

value: Hyphal development


title: Sperm H3.3

city: Basel

tag: tissue


title: WT3_No IP

description: processed data file: WT.fjfs.peaks.bed

value: adult

value: neural tissue (midbrain and striatum)


title: Sperm H3.1/H3.2 replicate2


title: s1

city: Guangzhou

first: Zhumei

last: He

address: 135 Xingangxi Street

department: School of Life Sciences

institute: Sun Yat-sen University

description: read of an average length 115 bp

data_processing: After removing the artificial reads, reads adapters and reads that were shorter than 50 bp after removing the end-sequence with low quality, the remaining reads were mapped to the A. flavus genome , A. flavus EST sequencing , and rRNA sequencing  using multiple tools including TopHat(1.3.1) and Bowtie. Cufflinks(1.2.0)was used to assembles transcripts, estimates their abundances, discovery of novel transcripts, identification of alternative splicing and tests for differential expression in our two A. flavus RNA-Seq samples. The expression level of gene was normalized by calculating the number of fragments per kilobase of exon region per million mapped reads (FPKM).

organism: Aspergillus flavus

source_name: RNA from A. flavus cultured with PDB medium

growth_protocol: Conidia of A. flavus NRRL 3357 were collected from plates using 0.05% Triton X-100. Then 3.3×107 CFU conidia medium was inoculated in 250-ml conical flasks containing 100 ml 2.4% (w/v) potato dextrose broth (PDB, purchased from Difco) and cultured in a shaker at 200 rpm and kept at 30°C.

extract_protocol: Total RNA was extracted from the fungal mycelia using a modified hot acid phenol method. A total of 2 g of the fine powder was promptly scraped into a 50-ml pre-cooled tube containing 15 ml extraction buffer (10 mM Tris-HCl, pH 8.0; 10 mM EDTA, pH 8.0; 0.5% (w/v) SDS) and 15 ml acid phenol. After incubation in the water bath at 65°C for 15 min, the tube was vortexed thoroughly and centrifuged at 11,000 rpm at 4°C for 10 min. The aqueous phase was then transferred into a pre-cooled tube with 15 ml acid phenol:chloroform:isoamylol (25:24:1, v/v/v), vortexed, and centrifuged at 10,000 rpm at 4°C for 10 min. This step was repeated several times to completely remove the impurities. Finally, only the aqueous phase was transferred to a new pre-cooled tube, and isopropanol (100%) was added to the tube at 1:1 (v/v) to precipitate RNA at -20°C overnight. The mixture was centrifuged at 10,000 rpm at 4°C for 15 min to collect the RNA. After washing with 70% ethanol twice, RNA was resuspended in DEPC-treated water. Each RNA sample was composed of three independent original samples with equal weight. The integrity of total RNA was checked using an Agilent Technologies 2100 Bioanalyzer, and all original samples and final samples had a RNA integrity number (RIN) value greater than six. The cDNA libraries were prepared using an Illumina ® TruSeq™ RNA Sample Preparation Kit according to the TruSeq™ RNA Sample Preparation guide. The first step in the workflow was purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces (380±50 bp) using divalent cations under elevated temperatures. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then went through an end repair process, an addition of a single ‘A’ base, and then ligation of the sequencing adapters using the Illumina TruSeq DNA sample preparation kit.

treatment_protocol: The 5-AC treated samples were cultured in PDB containing 1 mM 5-AC. The GA treated samples were cultured in PDB containing 1% GA (w/v).

value: mycelium cells

tag: treatment

value: PDB medium


title: s3

description: read of an average length 115 bp

source_name: RNA from A. flavus cultured with PDB+GA medium

value: PDB+GA medium


title: sfl2-CaEXP_2


title: sfl1-CaEXP-SFL1-HA_2


title: sfl2-CaEXP_1


title: sfl2-CaEXP-SFL2-HA_1


title: sfl1-CaEXP-SFL1-HA_1


title: sfl1-CaEXP_2


title: RS H3K4me3 replicate2


title: sfl1-CaEXP_1