title: ddm1_drd1

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads were divided in half and 50 base reads were processed as single reads.  Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.
RNA-seq: Illumina reads from cDNA libraries were aligned to genomic DNA. The file lists the log2 of the number of reads (first base) matching each 50-bp window, normalized to the total number of aligned reads in each library.
Mnase-seq: We aligned 36-base Illumina paired ends reads to genomic DNA. To measure nucleosome occupancy, we counted the number of sequenced molecules corresponding to each nucleotide of the genome. To reduce the size of the file we collapsed all adjacent positions with equal scores to one window.
Genome_build: TAIR8

source_name: AT roots 3 weeks Columbia-0

extract_protocol: For bisulfite sequencing (Bisulfite-Seq) About 500 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec. The enriched libraries were either gel-purified (~300 bp band) or purified with solid phase reversible immobilization (SPRI) method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). For RNA-Sequencing, approximately 30 ug total RNA was isolated from 21 days roots using the RNEasy Plant Extraction Kit (Qiagen) with the optional on-column DNAse treatment.  mRNA was purified from total RNA by two treatments of poly-A enrichment using the Oligotex kit (Qiagen #72022), followed by a rRNA removal step using the RiboMinus Plant Kit for RNA-sequencing (Invitrogen #A1083702). Precipitated mRNA samples were eluted with 9 μl of RNase free water and fragmented with 1 μl of 10X fragmentation buffer (Ambion, #AM8740) at 70oC. Reactions were stopped after 5 minutes by adding 1 μl Stop buffer and RNA was purified by ethanol precipitation. cDNA was synthesized from 100-300 ng of mRNA using Superscript III reverse transcriptase (Invitrogen #18080-051). Double-stranded DNA was synthesized as described (3). DNA was cleaned with a QIAquick PCR spin column (Qiagen, #28106), sequencing adapters were ligated according to the Illumina protocol and library was amplified by 18 cycles of PCR using Phusion DNA polymerase (NEB, #F-530). Bands around 300 bp were gel-purified and cloned for validation. Traditional sequencing confirmed that the libraries were properly constructed, showing high percentage of mRNA over rRNA. The libraries were sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating single ends (SE) 36 base reads. For MNase-sequencing, Arabidopsis roots (1 g) were ground in liquid nitrogen, resuspended in 20 ml of HBM buffer (25mM Tris, pH 7.6, 0.44M Sucrose, 10 mM MgCl2, 2 mM spermine and 0.1% Triton X-100), homogenized, filtered through miracloth, transferred to a 30 ml round bottom glass tube, centrifuged at 2000g (40C) for 10 min and resuspended in 1 ml HBB buffer (25mM Tris, pH 7.6, 0.44M Sucrose, 10 mM MgCl2 and 0.1% Triton X-100). Nuclei were further spun down at 200g, 40C for 2 min and resuspended in 1 ml of TNE buffer (10 mM Tris, pH 8.0, 100 mM NaCl and 1 mM EDTA). MNase digestion was done with 4 ul of 1M CaCl2 and 1 ul of diluted (1/20) MNase (200ul/ml; Sigma #N-3755) per 100 ul of pellet nuclei. Nuclei were then divided to several tubes and digestion was stopped at 45 sec intervals with 10mM EDTA. Digested nuclei were spun down at maximum speed for 5 min at 40C, and released soluble nucleosomes were collected from the supernatant. Following RNase A and proteinase K digestion, DNA was purified using phenol/chloroform. Purified DNA samples were run on a 2% agarose gel, digested samples with most enriched intact mononucleosomes were chosen and bands corresponding to ~150 bp were cut and purified with a Gel Purification kit (Qiagen). Illumina libraries were constructed and sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating paired ends (PE) 36 base reads. For MNase sequencing, we aligned 36 bases Illumina paired reads to the TAIR8 Arabidopsis genomic scaffold, allowing up to two mismatches per read. We subsequently used a Perl script to insure that paired reads mapped to opposite strands within 300 bp of each other. To measure nucleosome occupancy, we summed the aligned reads (all bases between both paired reads got a score of 1) for every single nucleotide throughout the genome.

value: roots 3 weeks


title: wt_exp2

status: Public on Apr 17 2013

type: SRA

city: Berkeley

first: Toshiro

last: Nishimura

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

country: USA

institute: University of California at Berkeley

library_source: transcriptomic

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown according to one of the following methods: 1) For shoot tissues, seeds were planted on 1x Murashige and Skoog Media with micronutrients and 1.5% Sucrose (Caisson Laboratories) and grown under 16h light/ 8h dark for 14 or 21 days in a growth chamber.  2) For roots, seeds were grown in Gamborg's B-5 liquid Media with 1.5% Sucrose (Caisson Laboratories) and grown shaking under 16h light/ 8h dark for 21 days.

tag: ecotype

tag: developmental stage

tag: genotype

value: wt


title: rdr2-1

library_source: genomic

molecule: genomic DNA

tag: function

value: RdDM


title: drd1_exp1

value: methylase/RdDM


title: drd1_exp2


title: ddm1rdr2

source_name: AT shoots 3 weeks Columbia-0

value: shoots 3 weeks


title: drm2-3

source_name: AT shoots 2 weeks Columbia-0

value: shoots 2 weeks

value: methylase


title: ddm1_exp2


title: ddm1_exp1


title: cmt2-5

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads were divided in half and 50 base reads were processed as single reads. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNA-seq: Illumina reads from cDNA libraries were aligned to genomic DNA. The file lists the log2 of the number of reads (first base) matching each 50-bp window, normalized to the total number of aligned reads in each library.
Mnase-seq: We aligned 36-base Illumina paired ends reads to genomic DNA. To measure nucleosome occupancy, we counted the number of sequenced molecules corresponding to each nucleotide of the genome. To reduce the size of the file we collapsed all adjacent positions with equal scores to one window.
Genome_build: TAIR8
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

growth_protocol: Arabidopsis plants were grown according to one of the following methods: 1) For shoot tissues, seeds were planted on 1x Murashige and Skoog Media with micronutrients and 1.5% Sucrose (Caisson Laboratories) and grown under 16h light/ 8h dark for 14 or 21 days in a growth chamber. 2) For roots, seeds were grown in Gamborg's B-5 liquid Media with 1.5% Sucrose (Caisson Laboratories) and grown shaking under 16h light/ 8h dark for 21 days.

extract_protocol:
For bisulfite sequencing (Bisulfite-Seq) About 500 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec. The enriched libraries were either gel-purified (~300 bp band) or purified with solid phase reversible immobilization (SPRI) method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). For RNA -Sequencing, approximately 30 ug total RNA was isolated from 21 days roots using the RNEasy Plant Extraction Kit (Qiagen) with the optional on-column DNAse treatment. mRNA was purified from total RNA by two treatments of poly-A enrichment using the Oligotex kit (Qiagen #72022), followed by a rRNA removal step using the RiboMinus Plant Kit for RNA-sequencing (Invitrogen #A1083702). Precipitated mRNA samples were eluted with 9 μl of RNase free water and fragmented with 1 μl of 10X fragmentation buffer (Ambion, #AM8740) at 70oC. Reactions were stopped after 5 minutes by adding 1 μl Stop buffer and RNA was purified by ethanol precipitation. cDNA was synthesized from 100-300 ng of mRNA using Superscript III reverse transcriptase (Invitrogen #18080-051). Double-stranded DNA was synthesized as described (3). DNA was cleaned with a QIAquick PCR spin column (Qiagen, #28106), sequencing adapters were ligated according to the Illumina protocol and library was amplified by 18 cycles of PCR using Phusion DNA polymerase (NEB, #F-530). Bands around 300 bp were gel-purified and cloned for validation. Traditional sequencing confirmed that the libraries were properly constructed, showing high percentage of mRNA over rRNA. The libraries were sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating single ends (SE) 36 base reads. For MNase-sequencing, Arabidopsis roots (1 g) were ground in liquid nitrogen, resuspended in 20 ml of HBM buffer (25mM Tris, pH 7.6, 0.44M Sucrose, 10 mM MgCl2, 2 mM spermine and 0.1% Triton X-100), homogenized, filtered through miracloth, transferred to a 30 ml round bottom glass tube, centrifuged at 2000g (40C) for 10 min and resuspended in 1 ml HBB buffer (25mM Tris, pH 7.6, 0.44M Sucrose, 10 mM MgCl2 and 0.1% Triton X-100). Nuclei were further spun down at 200g, 40C for 2 min and resuspended in 1 ml of TNE buffer (10 mM Tris, pH 8.0, 100 mM NaCl and 1 mM EDTA). MNase digestion was done with 4 ul of 1M CaCl2 and 1 ul of diluted (1/20) MNase (200ul/ml; Sigma #N-3755) per 100 ul of pellet nuclei. Nuclei were then divided to several tubes and digestion was stopped at 45 sec intervals with 10mM EDTA. Digested nuclei were spun down at maximum speed for 5 min at 40C, and released soluble nucleosomes were collected from the supernatant. Following RNase A and proteinase K digestion, DNA was purified using phenol/chloroform. Purified DNA samples were run on a 2% agarose gel, digested samples with most enriched intact mononucleosomes were chosen and bands corresponding to ~150 bp were cut and purified with a Gel Purification kit (Qiagen).
Illumina libraries were constructed and sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating paired ends (PE) 36 base reads. For MNase sequencing, we aligned 36 bases Illumina paired reads to the TAIR8 Arabidopsis genomic scaffold, allowing up to two mismatches per read. We subsequently used a Perl script to insure that paired reads mapped to opposite strands within 300 bp of each other. To measure nucleosome occupancy, we summed the aligned reads (all bases between both paired reads got a score of 1) for every single nucleotide throughout the genome.


title: MNase


title: ddm1drd1


title: wt_exp1


title: met1_exp2


title: wt_shoots


title: cmt2-3


title: cmt3-12


title: met1_exp1


title: ESC NPA RNA-seq

city: Jerusalem

first: Ilana

last: Livyatan

address: Silberman Bldg. Room 2-542 Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

description: Non-polyadenylated RNA

data_processing:
Reads of 50nt were aligned to the mm9 genome using Bowtie (Langmead et al. 2009). Seed sequence length was set at 45nt which had median phred quality score consistently above 15 (base-calling accuracy > 97%). A maximum of two mismatches in the seed were allowed. Uniqueness of alignment was not enforced and reads that mapped to more than one genomic location were dealt with via the "best" option, which chooses the best mapping based on lowest number of mismatches and highest read quality scores.
In order to be comparative with the tiling array platform, we filtered out reads that mapped to the mitochondrial chromosome (chrM), to an index of murine ribosomal sequences, or intersected with Repeat Masker regions including both rRNA and tRNA gene regions
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain mapped reads after filtering as mentioned above. Each mapped read has 5 fields - chrom, start, end, strand, and sequence.

organism: Mus musculus

source_name: Embryonic Stem Cells (R1)

growth_protocol: Mouse R1 male ESCs were grown and differentiated into 7 day ESC-derived NPCs (Meshorer et al. 2006; Efroni et al. 2008): ESCs were grown on a feeder layer of Mitomycin C treated MEFs on 0.2% gelatin-coated cell culture dishes. Culture medium consisted of DMEM, 15% ES-grade fetal calf serum (FCS, Biological Industries), 1 mM sodium pyruvate (Biological Industries), 0.1 mM nonessential amino acids (Biological Industries), 0.1 mM β-mercaptoethanol (Sigma), 100 U/ml penicillin and 0.1 mg/ml streptomycin and 1000 U/ml leukemia inhibitory factor (LIF). ESCs were maintained at 37°C, 5% CO2, and fed with fresh media every day. For differentiation, ESCs were plated on bacterial culture dishes without LIF for 4 days to allow for embryoid body (EB) formation. EBs were replated on tissue culture plates coated with poly-L-ornithine (PLO, Sigma) and fibronectin (R&D systems), in DMEM/F12 medium (Sigma) supplemented with ITS (5 mg/ml insulin, 50 mg/ml transferrin, 30 nM selenium chloride, Gibco) and 5 mg/ml fibronectin. Media was changed on day 6 and NPCs gathered on day 7. The R1 ESC differentiation system has previously been extensively characterized (Lee et al. 2000; Meshorer et al. 2006).

extract_protocol: Library was constructed from 2ug RNA starting material using the SOLiD™ Whole Transcriptome Analysis Kit (PN 4425680). Briefly, Ribosomal RNA was removed using one round Life technologies’ RiboMinus Eukaryote kit (A1083708). RNA was fragmented by RNase III (10 minutes, 37oC). Adaptors were hybridized and ligated directly to the fragmented RNA, and reverse transcription was performed on the ligation product. Size selection was done on 4% agarose gels: 150-250 bp fragments were excised and purified using QiagenMinElute Gel extraction Kit (28604). Library was then amplified by 15 cycles of PCR. 1400 pmole of each library were amplified on magnetic beads (ePCR) and sequenced on 1/8 sequencing slide, on SOLiD 3 machine.

tag: cell type

value: Embryonic Stem Cells

tag: passages

tag: strain


title: drd1-7


title: NPC NPA RNA-seq

description: Non-polyadenylated RNA

source_name: ESC-derived Neuronal Progenitor Cells

value: ESC-derived Neuronal Progenitor Cells


title: wt_roots


title: ASF1a ChIP

status: Public on Apr 18 2013

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

description: ChIP-seq of histone chaperone ASF1a

data_processing:
Basecalls performed using CASAVA 1.6
Sequenced reads were mapped to hg18 whole genome using bowtie v0.12.7 with parameter -p 8 -m 1 --best and remaining default settings
Aligned reads normalised by library size, extended to 150bp and converted to bigWig format
USeq 7.1.2 was used to perform peak finding with the following steps. BED files converted to Useq Point Format (Tag2Point). Satellite Repeat regions were removed from the dataset (FilterPointData). ScanSeqs used to identify enriched windows (-w 200 -p 150 -f). Enriched Regions Extracted (EnrichedRegionMaker) with 5% FDR and 2 fold change (-i 2,4 -s 13,1)
Genome_build: hg18
Supplementary_files_format_and_content: bed files represent aligned reads (one line per read) in UCSC bed format.  bigWig files represent pileups of the reads at each base.  bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.  peak files were generated with USeq and thresholded at 5% FDR and 2 fold change cutoffs

organism: Homo sapiens

source_name: ASF1a ChIP

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS, 2 mM L-Glutamine, 50 U Pen-Strep and incubated at 37°C in a humidified 5% CO2 atmosphere. Every 3-4 days the cells were passaged to maintain 40-90% confluence level

extract_protocol:
Cross-linked cells were solubilized by ultrasound treatment (Bioruptor Diagenode) to generate DNA fragmentation in 150-300 bp range. Protein-DNA complexes were isolated using corresponding antibody pre-immobilized on Dynabeads (Invitrogen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and PCR-amplified using Illumina primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Adherent cells were washed with PBS and cross-linked using sequential treatment with EGS and formaldehyde. Cells were incubated in 1.5mM EGS (Sigma, E3257), PBS for 45 min at room temperature, then formaldehyde (Sigma, 252549) was added to the media to 1% final concentration and cells were incubated for 15 more minutes. Cross-linking was quenched by adding 1/10 of volume of 1.25 M glycine (125mM final) and incubating for 5 min at room temperature. Media was aspirated and cells were rinsed twice with PBS, scraped into ice-cold PBS supplemented with protease inhibitors (Sigma, P8340) and collected by centrifugation (5 min at 200g, 4°C). Cell pellets were snap frozen in dry ice with ethanol and kept at -70°C before use.

value: HeLa

tag: chip antibody

value: equimolar mixture of Ms mAbs MPH7, MPB1, MPD5 (Ambagala et al., 2009)


title: met1-6


title: Adx_liver_dex_RNAPII_rep1

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description:
GH540
Adx_liver_dex_RNAPII_rep1

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Areas of enrichment were identified using DNase2Hotspots software(htrceforge.net/projects/dnase2hotspots/) software with FDR 0%.   Peaks with the maximum tag density lower than 10 were eliminated.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Genome_build: mm9 (NCBI 37)
Supplementary_files_format_and_content: tab-delimited  peak text files include genomic locations (Chromosome, start,  end ).

source_name: Male C57BL/6, adrenalectomized

growth_protocol: Male C57BL/6 mice, eight weeks old

extract_protocol: Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.

treatment_protocol: Bilateral adrenalectomy was carried out via a dorsal approach under ketamine/xylazine anesthesia. Mice were intraperitoneal injection of dex-cyclodextrine complex, containing 65 mg/g of dex (1 mg/kg), or vehicle (1 mg/kg cyclodexitrine) in a total volume of 300 ul of sterile saline.

tag: genetic background

tag: gender

value: male

tag: tissue

value: liver

tag: treatment

value: dex

tag: replicate

value: RNAPII, Abcam, ab5131

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #


title: Adx_liver_dex_RNAPII_rep2

description:
GH541
Adx_liver_dex_RNAPII_rep2


title: Adx_liver_veh_RNAPII_rep2

description:
GH539
Adx_liver_veh_RNAPII_rep2

value: veh


title: ddm1-2

value: roots 3 weeks


title: Adx_liver_veh_RNAPII_rep1

description:
GH538
Adx_liver_veh_RNAPII_rep1


title: Adx_liver_veh_input_rep2

description:
GH262
Adx_liver_veh_input_rep2

value: input


title: Adx_liver_dex_input_rep1

description:
GH220
Adx_liver_dex_input_rep1


title: Adx_liver_veh_input_rep1

description:
GH219
Adx_liver_veh_input_rep1


title: Adx_adDN-C/EBP_liver_dex_GR_ChIP_rep2

description:
GH505
Adx_adDN-C/EBP_liver_dex_GR_ChIP_rep2

value: dex adDN-C/EBP

value: cocktail of PA-510A and PA-511A from Affinity BioReagents and sc-1004 from Santa Cruz


title: Adx_adDN-C/EBP_liver_dex_DNase_rep3

description:
GH503
Adx_adDN-C/EBP_liver_dex_DNase_rep3

value: DNase


description:
GH498
Adx_adDN-C/EBP_liver_dex_CEBPbeta_ChIP_rep1

value: C/EBPbeta sc-150, santa cruz


title: Adx_adGFP_liver_dex_DNase_rep3

description:
GH502
Adx_adGFP_liver_dex_DNase_rep3

value: dex adGFP


title: Adx_adGFP_liver_dex_GR_ChIP_rep2

description:
GH504
Adx_adGFP_liver_dex_GR_ChIP_rep2


title: Adx_adDN-C/EBP_liver_dex_GR_ChIP_rep1

description:
GH496
Adx_adDN-C/EBP_liver_dex_GR_ChIP_rep1


title: Adx_adGFP_liver_dex_CEBPbeta_ChIP_rep1

description:
GH497
Adx_adGFP_liver_dex_CEBPbeta_ChIP_rep1


title: Adx_adGFP_liver_dex_GR_ChIP_rep1

description:
GH495
Adx_adGFP_liver_dex_GR_ChIP_rep1


title: Adx_adGFP_liver_dex_DNase_rep2

description:
GH485
Adx_adGFP_liver_dex_DNase_rep2


title: Adx_adDN-C/EBP_liver_dex_DNase_rep1

description:
GH466
Adx_adDN-C/EBP_liver_dex_DNase_rep1


title: Adx_liver_dex_CEBPbeta_ChIP_rep2

description:
GH430
Adx_liver_dex_CEBPbeta_ChIP_rep2

value: Santa Cruz


title: Adx_liver_veh_CEBPbeta_ChIP_rep2

description:
GH429
Adx_liver_veh_CEBPbeta_ChIP_rep2


title: Adx_liver_dex_CEBPbeta_ChIP_rep1

description:
GH396
Adx_liver_dex_CEBPbeta_ChIP_rep1


title: Adx_liver_dex_DNase_rep2

description:
GH308
Adx_liver_dex_DNase_rep2


title: Adx_liver_veh_DNase_rep1

description:
GH305
Adx_liver_veh_DNase_rep1


title: Adx_liver_veh_DNase_rep2

description:
GH306
Adx_liver_veh_DNase_rep2


title: Adx_liver_Dex_GR_ChIP_rep2

description:
GH335
Adx_liver_Dex_GR_ChIP_rep2


title: Adx_liver_dex_DNase_rep1

description:
GH307
Adx_liver_dex_DNase_rep1


title: Adx_liver_dex_input_rep2

description:
GH263
Adx_liver_dex_input_rep2


title: Adx_liver_dex_GR_ChIP_rep1

description:
GH215
Adx_liver_dex_GR_ChIP_rep1


title: Adx_liver_veh_GR_ChIP_rep2

description:
GH334
Adx_liver_veh_GR_ChIP_rep2


title: Adx_liver_veh_GR_ChIP_rep1

description:
GH216
Adx_liver_veh_GR_ChIP_rep1


title: C. dubliniensis_WS-2

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

data_processing:
Basecalls for both sequencing technologies performed using standard softwares supplied by either Roche for FLX sequencing or by Illumina for GAIIx sequencing.
For FLX reads the barcodes at the 5’-end (C. albicans: 5’-CGAGAC-3’ and C. dubliniensis: 5’- CGTCGT-3’) and the remaining sequences from the B adapter at the 3’-end (5’-CTGAGACTGCCAAGGCACACAGGGGATAGG-3’) were trimmed. The processed reads were then blasted with BLASTN (ncbi-blast-2.2.23). Only unique and non-spliced reads with at least 90% identities over the whole length of the reads has passed the quality filter. For intron spanning reads we also performed BLAT alignments (BLAT Suite 0.34).
GAIIx reads were mapped with their full length of 75 sequenced bases with SOAP2 (version 2.20) using a seed length of 40 bp allowing 5 mismatches with the exception for sample "C.dubliniensis_GAIIx_YPS_blastospores-2.fastq" where the first base of each sequence was trimmed resulting in 74 bp reads. As SOAP2 is not compatible with intron-spanning reads we performed another mapping with the remaining unmapped reads with TOPHAT (version 1.3.1).
Genome_build: C. albicans: Assembly21 at CGD (latest update 2010-06-15, http://www.candidagenome.org/download/sequence/Assembly21); C. dubliniensis: Assembly CD36 at NCBI (latest update 2010-04-09, ftp://ftp.ncbi.nih.gov/genomes/Fungi/Candida_dubliniensis_CD36)
Supplementary_files_format_and_content: BLASTN/BLAT output files were generated as table formats, then piped (shell script) into *.gff3  and finally  into *.bedGraph. Standard SOAP output files were converted similarly. Standard TOPHAT output files were converted with BEDtools (bam-to-bed) into *.bed file format. Scores represent coverage of raw mapped reads.

organism: Candida dubliniensis

source_name: hyphal cells

growth_protocol: Cells were grown in water supplemented with 10% fetal calf serum at 37°C for 4 hours.

extract_protocol:
The cDNA libraries for GAIIx-sequencing were performed according Illumina’s mRNA-Seq Sample Prep Kit protocol. Each of the six samples was loaded on one lane. Thus, the sequencing run was performed on a fully loaded flow cell with single-end 76bp reads and resulted in approximately 30 mio. reads per sample.
After 4h of incubation under the corresponding conditions, C. dubliniensis and C. albicans cells were harvested by centrifugation and immediately frozen with liquid nitrogen. Disruption was carried out using a Mixer Mill MM 200 (RETSCH) with a shaking frequency of 30/s. The resulting powder was resuspended in lysis buffer RLT (QIAGEN, Hilden, Germany) supplemented with 0.01% v/v of ß-mercaptoethanol. The extraction of total RNA was performed according to QIAGEN’s Mechanical Disruption Protocol for the isolation of total RNA from yeast using the RNeasy Midi Kit. After precipitation of the RNA by addition of 0.1 volume of 3M NaAc pH 5.3 and 2.5 volume of 100% EtOH, the concentration and integrity of total RNA was analyzed using the Agilent 2100 Bioanalyzer using the RNA Nano kit.

tag: morphology

value: hyphae


title: Soybean Early Maturation Seed Coat Palisade-Biological Replicate 3

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-SCPS-3

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file. The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (v1.1) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140).
Genome_build: Glycine max V1.1
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample.

organism: Glycine max

source_name: Soybean Early Maturation-Seed Coat Palisade

growth_protocol: Soybean plants were grown at the UC Davis Greenhouses with a 16:8 day:night cycle at 22°C-30°C. Seeds were germinated in Modified UC Mix (equal parts of ground canadian sphagnum, horticultural grade sand, white pumice, redwood compost) for 10 days.  Individual seedlings were transfered to 1 gallon pots where they were grown for an additional 3 weeks before being transplanted to 3 gallon pots.  Plants were watered as needed with water containing 190 ppm Nitrogen, 40 ppm Phosphorus and 140 ppm Potassium and micronutrients.

extract_protocol:
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg  C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific compartments of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with one microgram of double-stranded cDNA using Illumina TruSeq DNA Sample prep kit (Hayward, CA), according to manufacturer's instructions except for the PCR enrichment step where Agilent Pfu Turbo Cx hotstart DNA polymerase was used for 15 cycles of amplification.  Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

tag: tissue source

value: seeds ranging 6.0-7.0mm in length

tag: seed compartments/tissue


title: C. dubliniensis_YPS-2

source_name: blastospore cells

growth_protocol: Cells were grown in YPD supplemented with 10% fetal calf serum at 37°C for 4 hours.

value: blastospores


title: Soybean Early Maturation Root Tip-Biological replicate 2

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-RT-2

source_name: Soybean Early Maturation Stage-Root Tip

value: Soybean Early Maturation Stage-Root Tip


title: Soybean Early Maturation Seed Coat Hilum-Biological Replicate 3

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-HI-3


title: Adx_adDN-C/EBP_liver_dex_DNase_rep2

description:
GH486
Adx_adDN-C/EBP_liver_dex_DNase_rep2

value: male

value: liver


title: Soybean Early Maturation Seed Coat Hourglass-Biological Replicate 1

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-SCHG-1

source_name: Soybean Early Maturation-Seed Coat Hourglass Cells


title: Soybean Early Maturation Root Tip-Biological replicate 3

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-RT-3


title: C. dubliniensis_YPS-1


title: Adx_adGFP_liver_dex_DNase_rep1

description:
GH465
Adx_adGFP_liver_dex_DNase_rep1


title: Soybean Early Maturation Seed Coat Palisade-Biological Replicate 1

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-SCPS-1

value: Soybean Early Maturation-Seed Coat Palisade


title: Soybean Early Maturation Cotyledon Vasculature-Biological replicate 2

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Cot-VS-2

source_name: Soybean Early Maturation Stage-Cotyledon Vasculature


title: Soybean Early Maturation Seed Coat Hourglass-Biological Replicate 3

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-SCHG-3

value: Soybean Early Maturation-Seed Coat Hourglass Cells


title: Adx_liver_veh_CEBPbeta_ChIP_rep1

description:
GH395
Adx_liver_veh_CEBPbeta_ChIP_rep1

value: veh


title: Soybean Early Maturation Seed Coat Hilum-Biological Replicate 1

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-HI-1

source_name: Soybean Early Maturation Stage-Seed Coat Hilum


title: Soybean Early Maturation Cotyledon Vasculature-Biological replicate 1

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Cot-VS-1

value: Soybean Early Maturation Stage-Cotyledon Vasculature


title: Soybean Early Maturation Cotyledon Abaxial Epidermis-Biological replicate 3

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Cot-ABEPD-3

source_name: Soybean Early Maturation Stage-Cotyledon Abaxial Epidermis


title: Soybean Early Maturation Seed Coat Hilum-Biological Replicate 2

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-HI-2


title: C. dubliniensis_WS-1


title: Soybean Early Maturation Cotyledon Abaxial Epidermis-Biological replicate 2

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Cot-ABEPD-2

value: Soybean Early Maturation Stage-Cotyledon Abaxial Epidermis


title: Soybean Early Maturation Axis Parenchyma-Biological replicate 4

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Ax-PY-4

source_name: Soybean Early Maturation Stage-Axis Parenchyma


title: C. dubliniensis mix

description: pooled mRNA out of two different conditions for qualitative purposes

source_name: hyphal and blastospore cell mixture

growth_protocol: Blastospore cells were grown in YPD supplemented with 10% fetal calf serum at 37°C for 4 hours while hyphal cells were induced in water supplemented with 10% fetal calf serum at 37°C for 4 hours.

extract_protocol:
For the normalized cDNA libraries for FLXTitanium-sequencing, equal amounts of approximately 25 µg of total RNA per condition were pooled together per species. To get rid of genomic contaminants another purification step was performed using QIAGEN’s RNeasy Mini Plus Kit. From the pooled total RNA poly(A)+-RNA was prepared according to standard protocols (Ref.). First-strand cDNA synthesis was carried out with a N6 randomized primer. Then 454 adapters A (5’-CCATCTCATCCCTGCGTGTCTCCGACTCAG-3’) and B (5’-CTGAGACTGCCAAGGCACACAGGGGATAGG-3’) were ligated to the 5' and 3' ends of the cDNAs, respectively, to obtain strand-specificity of the transcripts. Additionally, the C. albicans and the C. dubliniensis samples were barcoded at the 5’-end of the fragments with 5’-CGAGAC-3’ and 5’- CGTCGT-3’, respectively. The cDNAs were amplified with 16 cycles of PCR. Normalization was carried out by one cycle of denaturation and reassociation of the cDNA. Reassociated ds-cDNA was separated from the remaining ss-cDNA (normalized cDNA) by passing the mixture over a hydroxylapatite column. After hydroxylapatite chromatography, the ss-cDNA was amplified by 9 PCR cycles. For Titanium sequencing the cDNA in the size range of 500 – 700 bp was eluted from preparative agarose gels. Aliquots of the size fractionated cDNAs were analyzed by capillary electrophoresis with the Shimadzu MultiNA microchip system. The two normalized and barcoded cDNA libraries were pooled at equal amounts and were sequenced on a full flow cell with the Titanium chemistry resulting in about 500.000 reads per species.
After 4h of incubation under the corresponding conditions, C. dubliniensis and C. albicans cells were harvested by centrifugation and immediately frozen with liquid nitrogen. Disruption was carried out using a Mixer Mill MM 200 (RETSCH) with a shaking frequency of 30/s. The resulting powder was resuspended in lysis buffer RLT (QIAGEN, Hilden, Germany) supplemented with 0.01% v/v of ß-mercaptoethanol. The extraction of total RNA was performed according to QIAGEN’s Mechanical Disruption Protocol for the isolation of total RNA from yeast using the RNeasy Midi Kit. After precipitation of the RNA by addition of 0.1 volume of 3M NaAc pH 5.3 and 2.5 volume of 100% EtOH, the concentration and integrity of total RNA was analyzed using the Agilent 2100 Bioanalyzer using the RNA Nano kit.

value: blastospores and hyphae


title: Soybean Early Maturation Cotyledon Abaxial Epidermis-Biological replicate 1

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Cot-ABEPD-1


title: Soybean Early Maturation Axis Vasculature-Biological replicate 3

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Ax-VS-3

source_name: Soybean Early Maturation Stage-Axis Vasculature


title: C. albicans_YPS-2

organism: Candida albicans


title: Soybean Early Maturation Axis Vasculature-Biological replicate 2

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Ax-VS-2

value: Soybean Early Maturation Stage-Axis Vasculature


title: Soybean Early Maturation Seed Coat Parenchyma-Biological Replicate 1

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-SCPY-1

source_name: Soybean Early Maturation-Seed Coat Parenchyma


title: C. albicans mix

growth_protocol: Blastospore cells were grown in YPD at 30°C for 4 hours while hyphal cells were induced in YPD supplemented with 10% fetal calf serum at 37°C for 4 hours.


title: Soybean Early Maturation Axis Parenchyma-Biological replicate 2

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Ax-PY-2

value: Soybean Early Maturation Stage-Axis Parenchyma


title: Soybean Early Maturation Seed Coat Hourglass-Biological Replicate 2

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-SCHG-2


title: C. albicans_YPS-1


title: Soybean Early Maturation Axis Parenchyma-Biological replicate 1

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-Ax-PY-1


title: Input Control_ChIPSeq

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: inguinal white adipose tissue (iWAT)-derived adipocytes

data_processing:
Sequence reads from each ChIP-seq library were trimmed to 40 bases, and each library was collapsed using FastX (http://hannonlab.cshl.edu/fastx_toolkit)
Each collapsed library was aligned to the genome (mm9) using Bowtie (Langmead B, et al., Genome Biol. 10:R25) with the following parameters: -m 3 –best –strata, with all other parameters set at default.
Regions enriched for PPARγ binding were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) with the “-factor” setting and a false-discovery rate (FDR) cutoff of_0.1%. Moreover, only peaks with >4-fold tag count enrichment compared to both input control and local tag density (10-kb region around putative peak) were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files generated using HOMER

source_name: iWAT-derived adipocytes

growth_protocol: Outbred, male (NMRI) mice at the age of 4 to 5 weeks, mice were deprived of food for 2 h and killed between 9 and 11 a.m. by cervical dislocation. BAT was isolated from the interscapular, cervical, and axillary depots and pooled, and WAT was isolated from the epididymal (eWAT) and inguinal/dorsolumbar (iWAT) depots. The pooled adipose tissues were carefully minced and treated with collagenase (typeII, Sigma). to separate the SVF from mature adipocytes. SVFs were cultured under differentiation- inducing conditions in a medium consisting of Dulbecco modified Eagle medium (DMEM) (Sigma), 10% newborn calf serum (NCS) (HyClone), 30 nM insulin, 25 ug/ml sodium ascorbate, 10 mM HEPES pH7.4, at 37°C, 4mML-glutamine (Invitrogen), 100_g/ml streptomycin, 62.5  ug/ml penicillin, and 1 uM rosiglitazone (Novo Nordisk). Cells of SVF were cultured at 37°C and 8% CO2. Medium was changed 1 day after seeding and subsequently every second day.

extract_protocol: eWAT-, iWAT-, and BAT-derived adipocytes were cross-linked using 0.5 M disuccinimidyl glutarate (DSG) (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min. Cross-linking was stopped by the addition of glycine to a final concentration of 0.125 M for 10 min, followed by addition of ChIP lysis buffer (1% Triton X-100, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, and 20 mM Tris, pH 8.0). Samples were sonicated using the Diagenode Bioruptor twin (3 x14 cycles, 30 s on/off, maximum level). Chromatin IP was performed using anti-PPARγ (sc-7196; Santa Cruz). ChIPed DNA was sequenced according to the manufacturer’s instructions (Illumina).

tag: antibody

value: none (input)

tag: animal model

value: NMRI


title: Soybean Early Maturation Endosperm-Biological replicate 3

description:
Compartments collected from seeds ranging 6.0-7.0mm in length
EM-ES-3

source_name: Soybean Early Maturation Stage-Endosperm


title: 1hr DMSO treated HCT116

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: GRO-seq nascent RNA from HCT116 DMSO treated cells

data_processing:
Library strategy: GRO-Seq
GRO-seq data analysis: Unless otherwise noted all data processing was carried out using custom Python scripts (Python version 2.6). The reads from three biological replicates were combined into a single file comprising 425,379,448 total reads which were mapped to the reference human genome (GRCh37/hg19) using Bowtie 0.12.7, allowing for at most 2 mismatches (Langmead et al., 2009). Using this strategy 309,772,394 (73%) of the reads mapped to the genome. The resulting SAM file was then processed by SAMtools (version 0.1.16) to create a sorted BAM file.
The sorted BAM files mentioned above were used to make a Bedgraph by running genomeCoverageBed –bg on each strand separately (v2.12.0). The negative strand values were assigned negative values in the BedGraph. The BedGraph values were then divided by the number of million mapped (309,772,394) reads to give values of reads per million per bp (rpm/bp) for each position in the genome and the two files (strands) were concatenated back together.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedgraph file of reads per bp per million mapped for positive and negative strand from all three replicates

source_name: colorectal cancer cells

growth_protocol: Hct116 cells were plated in McCoys 5A medium supplemented with 10% fetal calf serum 24hrs prior to treatment as indicated

extract_protocol: GRO-seq library preparation and Illumina sequencing: Nuclear run-on and sequencing library preparation were performed essentially as described in Wang et al. (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390–394. for a total of three biological replicates.  HCT116 cells were plated at a concentration of 1 x 107 on 15 cm plates in McCoy’s 5A medium and allowed to grow 24 hr before harvesting. Cells were washed three times with ice cold PBS and then treated with 10 ml per plate of ice-cold lysis buffer (10  mM Tris-Cl pH 7.4, 2  mM MgCl2, 3  mM CaCl2, 0.5% IGEPAL, 10% glycerol, 1 mM DTT, 1x Protease Inhibitor Cocktail (Roche 11 836 153 001), 4U / ml SUPERase-In RNase inhibitor) and collected by scraping. Cells were then centrifuged at 1000x g for 7 min at 4ºC and re-suspended in 1.5 ml lysis buffer by pipetting 20-30 times. A further 8.5 ml of lysis buffer was added and the suspension centrifuged at 1000x g for 7 min at 4ºC to collect nuclei. Nuclei were washed in 1 ml lysis buffer and re-suspended in 500 µl freezing buffer (50  mM Tris pH 8.3, 40% glycerol, 5  mM MgCl2, 0.1  mM EDTA, 4U / ml SUPERase-In), pelleted again (2000x g for 2 min at 4ºC), and finally re-suspended in 100 µl freezing buffer. To determine concentration, nuclei were counted and diluted with freezing buffer before 100 µl aliquots of 5 x 106 nuclei were snap-frozen in liquid Nitrogen and stored at -80ºC. Nuclear run-on was performed by adding 100 µl aliquots of nuclei to 100 µl reaction buffer (10  mM Tris pH 8.0, 5  mM MgCl2, 1  mM DTT, 300  mM KCl, 20 units SUPERase-In, 1% Sarkosyl, 500  μM each of ATP, GTP, CTP and Bromo-UTP) and incubating for 5 min at 30 °C. Reactions were stopped by adding 1 ml Trizol to the reaction and vortexing to homogeneity. Samples were split in half and another 500 µl Trizol added to each half. To isolate RNA, 220 µl chloroform was added to each half sample and samples were centrifuged at 12,000x g for 15 min. The aqueous phase was transferred to a new tube and 22.5 µl 5M NaCl added. Samples were extracted twice with phenol-chloroform (pH 4.5), then once with chloroform. Finally, RNA was co-precipitated with 1 µl glyco-blue (Ambion) by adding three volumes of ice cold ethanol and incubating at -20°C for at least 20 min. Pellets were washed with 70% ethanol, air-dried 2 min and dissolved in 20 µl DEPC-treated water. RNA was base-hydrolyzed with 5 µl 1M NaOH on ice for 30 min (creating an average fragment size of ~150 bp). Reactions were neutralized with 25 µl 1M Tris-Cl pH6.8 and passed through a BioRad P-30 column as per the manufacturer’s protocol. Samples were then DNAse treated in 1x RQ1 DNase buffer with 3 µl RQ1 DNaseI (Promega) at 37ºC for 10 min and again passed through BioRad P-30 columns. To remove 5’ phosphates, 8.5 μl 10x   phosphatase buffer, 5  μl of antarctic phosphatase (New England Biolabs) and 1  μl of SUPERase-In was added to each RNA sample followed by incubation for 1 hr at 37 °C. Samples were passed through a third BioRad P-30 column and the final volume of each RNA solution was brought up to 100 µl with DEPC-treated H2O and 1 µl 500 mM EDTA. To prepare beads for immunopurification of Br-UTP-labeled nascent RNA, 60 μl anti-BrdU agarose beads (Santa Cruz Biotech) per sample were washed in 500  μl blocking buffer (0.5x  SSPE, 1  mM EDTA, 0.05% Tween-20, 0.1% PVP, and 1  mg/ml BSA), incubated in 500  μl blocking buffer for 1 hr at 4 °C, washed twice for 5 min each in binding buffer (0.5x  SSPE, 1  mM EDTA, 0.05% Tween-20) and finally re-suspended in 400 µl binding buffer. Total RNA samples (100 µl) were heated to 65 °C for 5 min, chilled on ice and then incubated with blocked anti-BrdU beads in 400 µl binding buffer for 1 hr at room temperature with rocking. Beads were washed (3 min with rocking) once in binding buffer, once in low salt buffer (0.2x  SSPE, 1  mM EDTA, 0.05% Tween-20), once in high salt buffer (0.5% SSPE, 1  mM EDTA, 0.05% Tween-20, 150  mM NaCl) and twice in TET buffer (TE pH 7.4, 0.05% Tween-20). Nascent RNA was eluted four times with 125  μl elution buffer (5  mM Tris pH 7.5, 300  mM NaCl, 20  mM DTT, 1  mM EDTA, 0.1% SDS). Pooled RNA elutions were then extracted once with phenol/chloroform (pH 4.5), once with chloroform and precipitated by the addition of 1 µl glyco-blue, 300 mM NaCl, three volumes of ethanol at 20ºC for at least 20 min. The precipitated RNA was washed with 70% ethanol and re-suspended in 50  μl PNK reactions (45 μl DEPC-treated water, 5.2  μl T4 PNK buffer, 1  μl SUPERase-In, 1  μl T4 PNK, New England Biolabs), incubated at 37ºC for 1 hr and RNA was recovered as above. Poly-A tails were added to PNK-treated RNA fragments (in 5 μl water) by adding 0.8 μl poly-A polymerase buffer, 0.8 μl 10 mM ATP, 0.5 μl SUPERase-In and 0.75 μl poly-A polymerase (New England Biolabs) and incubating 10 min at 37ºC. Reactions were stopped by adding by adding 8 μl 500 mM EDTA, 12 μl 5M NaCl and 184 μl DEPC-water. The RNA was then recovered by phenol/chloroform extraction and ethanol precipitation and subjected to a second round of immunopurification with anti-BrdU bead binding and washes as above.  Reverse transcription was performed as follows: RNA fragments, in 8 µl water, were added to reactions with 1 µl dNTPs (10mM each), 2.5 µl 12.5uM oNTI223HIseq primer (5′-pGATCGTCGGACTGTAGAACTCT;CCTTGGCACCCGAGAATTCCATTTTTTTTTTTTTTTTTTTTVN-3’) where p indicates 5′ phosphorylation, ‘;’ indicates a furan modification that introduces a stable abasic site and VN indicates degenerate nucleotides. This mix was heated for 3 min at 75°C, chilled briefly on ice, followed by the addition of 0.5 µl SuperRase-In, 3.75 µl 0.1 M DTT, 2.5 µl 25 mM MgCl2, 5 µl 5x reverse transcription buffer, and 2 µl Superscript III reverse transcriptase (Life Technologies) and incubation at 48°C for 30 min. Excess oNTI223HIseq primer was removed by adding 3.2 µl 10X Exonuclease I buffer and 4 µl Exonuclease I (Fermentas) and incubating at 37°C for 1 hr. RNA was removed by adding 1.8 µl 1 M NaOH and incubating for 20 min at 98°C. The reaction was then neutralized with 2 µl 1 M HCl and cDNA was recovered by phenol/chloroform (pH 8) extraction and recovered by precipitation with 300 mM NaCl and three volumes of ethanol. cDNA was dissolved in 8 µl of water and added to 20 µl FLB (80% Formamide, 10 mM EDTA, 1 mg/ml Xylene Cyanol, 1 mg/ml Bromophenol Blue) and loaded on an 8% polyacrylamide TBE-urea gel. cDNA fragments of 200-650 nucleotides were excised and eluted from shattered gel slices by soaking overnight in 1x TE with 150 mM NaCl and 0.1% Tween-20. Eluates were passed through 0.22 µm spin X columns (Costar) at 10,000 rpm for 2 min at room temperature. Samples were snap frozen in liquid nitrogen and volume was reduced to <500 µl in a speed-vac and cDNA was recovered by phenol/chloroform extraction and ethanol precipitation as above. Circularization was carried out by dissolving cDNAs in 8 µl water with 1 µl CircLigase buffer, 0.5 µl mM ATP, 0.5 µl 50 mM MnCl2 and 0.5 µl CircLigase (Epicentre) and incubating at 60ºC for 1 hr, followed by heat inactivation at 80ºC for 20 min. To each reaction, 3.8 µl of 4x re-linearization supplement (100 mM KCl, 2 mM DTT) and 1.5 µl ApeI (New England Biolabs) was added and the reactions incubated at 37°C for 1hr. Re-linearized cDNA fragments were recovered by ethanol precipitation as above. To amplify single-stranded DNA fragments with adapter sequences on each end, each sample was dissolved in 15 µl water and added to 10 µl 5x Phusion HF buffer, 0.5 µl 25 µM HighSeq fwd primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’), 0.5 µl 25 µM HighSeq rev primer index 1 (5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’), 2.5 µl 10

treatment_protocol: 20 ml McCoys 5A medium supplemented with 10% fetal calf serum with 20 ul DMSO for 1 hour

value: DMSO

tag: cell line


title: root-wt

data_processing:
For Bisulfite Sequencing, we used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads were divided in half and 50 base reads were processed as single reads.  Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNA-seq: Illumina reads from cDNA libraries were aligned to genomic DNA. The file lists the log2 of the number of reads (first base) matching each 50-bp window, normalized to the total number of aligned reads in each library.
Mnase-seq: We aligned 36-base Illumina paired ends reads to genomic DNA. To measure nucleosome occupancy, we counted the number of sequenced molecules corresponding to each nucleotide of the genome. To reduce the size of the file we collapsed all adjacent positions with equal scores to one window.
Genome_build: TAIR8
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

source_name: AT root 4 weeks in sterile media Columbia-0

extract_protocol: For bisulfite sequencing (BS-seq) About 500 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec. The enriched libraries were either gel-purified (~300 bp band) or purified with solid phase reversible immobilization (SPRI) method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). For RNA -Sequencing, approximately 30 ug total RNA was isolated from 21 days roots using the RNEasy Plant Extraction Kit (Qiagen) with the optional on-column DNAse treatment.  mRNA was purified from total RNA by two treatments of poly-A enrichment using the Oligotex kit (Qiagen #72022), followed by a rRNA removal step using the RiboMinus Plant Kit for RNA-sequencing (Invitrogen #A1083702). Precipitated mRNA samples were eluted with 9 μl of RNase free water and fragmented with 1 μl of 10X fragmentation buffer (Ambion, #AM8740) at 70oC. Reactions were stopped after 5 minutes by adding 1 μl Stop buffer and RNA was purified by ethanol precipitation. cDNA was synthesized from 100-300 ng of mRNA using Superscript III reverse transcriptase (Invitrogen #18080-051). Double-stranded DNA was synthesized as described (3). DNA was cleaned with a QIAquick PCR spin column (Qiagen, #28106), sequencing adapters were ligated according to the Illumina protocol and library was amplified by 18 cycles of PCR using Phusion DNA polymerase (NEB, #F-530). Bands around 300 bp were gel-purified and cloned for validation. Traditional sequencing confirmed that the libraries were properly constructed, showing high percentage of mRNA over rRNA. The libraries were sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating single ends (SE) 36 base reads. For MNase-sequencing, Arabidopsis roots (1 g) were ground in liquid nitrogen, resuspended in 20 ml of HBM buffer (25mM Tris, pH 7.6, 0.44M Sucrose, 10 mM MgCl2, 2 mM spermine and 0.1% Triton X-100), homogenized, filtered through miracloth, transferred to a 30 ml round bottom glass tube, centrifuged at 2000g (40C) for 10 min and resuspended in 1 ml HBB buffer (25mM Tris, pH 7.6, 0.44M Sucrose, 10 mM MgCl2 and 0.1% Triton X-100). Nuclei were further spun down at 200g, 40C for 2 min and resuspended in 1 ml of TNE buffer (10 mM Tris, pH 8.0, 100 mM NaCl and 1 mM EDTA). MNase digestion was done with 4 ul of 1M CaCl2 and 1 ul of diluted (1/20) MNase (200ul/ml; Sigma #N-3755) per 100 ul of pellet nuclei. Nuclei were then divided to several tubes and digestion was stopped at 45 sec intervals with 10mM EDTA. Digested nuclei were spun down at maximum speed for 5 min at 40C, and released soluble nucleosomes were collected from the supernatant. Following RNase A and proteinase K digestion, DNA was purified using phenol/chloroform. Purified DNA samples were run on a 2% agarose gel, digested samples with most enriched intact mononucleosomes were chosen and bands corresponding to ~150 bp were cut and purified with a Gel Purification kit (Qiagen). Illumina libraries were constructed and sequenced at the UC Berkeley Genomic Sequencing Laboratory, generating paired ends (PE) 36 base reads. For MNase sequencing, we aligned 36 bases Illumina paired reads to the TAIR8 Arabidopsis genomic scaffold, allowing up to two mismatches per read. We subsequently used a Perl script to insure that paired reads mapped to opposite strands within 300 bp of each other. To measure nucleosome occupancy, we summed the aligned reads (all bases between both paired reads got a score of 1) for every single nucleotide throughout the genome.

value: root

value: 4 weeks in sterile media

tag: genotype

value: WT


title: root-h1

source_name: AT root 4 weeks in sterile media h1


title: 22 h

city: Wuhan

first: Wang

last: Jieping

address: Shizishan Street No. 1

country: China

institute: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to the CT-43 genome using BlastN in Blastall version 2.2.25 with the following parameters: e-value, 0.0001 and the ‘‘-F F’’.
The gene expression level of each ORF was normalized by converting the number of reads per gene into RPKM value (Reads Per Kilo bases per Million reads).
Genome_build: NC_017208.1
Supplementary_files_format_and_content: Excel files include RPKM values of all ORFs (encoding by chromosome and plasmids) at 7 h, 9 h, 13 h and 22 h.

organism: Bacillus thuringiensis

source_name: Bacterial cells

growth_protocol: The strain CT-43 was grown at 28C with shaking at 200 rpm in liquid GYS medium , comprising of (NH4)2SO4, 2 g; MgSO4·7H2O, 0.3 g; ZnSO4·7H2O, 0.005 g; MnSO4·4H2O, 0.05 g; CaCl2, 0.08 g; CuSO4·5H2O, 0.005g; FeSO4·7H2O, 0.0005g; K2HPO4, 0.5g; glucose, 1.0 g; and yeast extract 2.0 g/L (pH 7.4).

extract_protocol: Double-stranded cDNA was synthesized using RNA-Seq Library Preparation Kit (Gnome Gen).

treatment_protocol: Two biological replicate cell samples were collected at time points of 7 h, 9 h, 13 h and 22 h, respectively. Total RNA was isolated using TRIzol reagent (Invitrogen, USA) following the standard protocol. The final total RNA was dissolved in 200 μL RNase-free water. The concentration of total RNA was determined by NanoDrop (Thermo Scientific, USA), and the RNA integrity value (RIN) was checked using RNA 6000 Pico LabChip of Agilent 2100 Bioanalyzer (Agilent, USA). Total RNA was incubated with 10 U DNase I (Ambion) at 37C for 1 h, and then nuclease-free water was added to bring the sample volume to 250 μL. Messenger RNA was further purified by depleting ribosomal RNA and tRNA with TerminatorTM 5’-phosphate-dependent exonuclease (Epicentre) digestion. The resulted RNA samples were quantified by the spectrophotometer DU800 (Beckman Coulter, USA) and resolved on agarose gel to verify its integrity.

tag: growth phase

value: late-stationary growth phase

tag: strain


title: 13 h

value: mid-stationary growth phase


title: 9 h

value: early-stationary growth phase


title: HH18 AVC

status: Public on Apr 16 2013

city: Nashville

first: Daniel

last: DeLaughter

state: TN

address: Preston Research Building Room 460

department: Cell and Developmental Biology

institute: Vanderbilt University Medical School

data_processing:
HiSeq 2000 reads are aligned by TOPHAT2 (http://tophat.cbcb.umd.edu/) to produce bam files.
Gene expression profiles were generated using a Bayesian p-value
Genome_build: galGal3
Supplementary_files_format_and_content: tab-delimited text files include expression values (normalized reads to total per million)

organism: Gallus gallus

source_name: Heart tube

extract_protocol:
HH18 chick (n=200) and E11.0 ICR (n=160, in duplicate) mouse hearts were dissected into AVC, OFT, and VEN and the samples were pooled.  Standard phenol-chloroform extraction of RNA was performed.  RNA integrity was checked with Agilent 2100 Bioanalyzer
RNAseq libraries were generated without normalizations or RNA/cDNA fragmentation

value: Cobb-Cobb broiler line

tag: developmental stage

value: Heart atrioventricular canal


title: HH18 OFT

value: Heart outflow tract


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 4, techical replicate 2

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 4, techical replicate 2

data_processing:
The base-calling step was performed by Illumina HiSeq 2000 instrument control software's Real Time Analysis (RTA, version 1.12). The Multiplexed samples were demultiplexed using Illumina CASAVA 1.8.2.
RNA-Seq data analysis was completed in CLC Genomics Workbench 5.1 (http://www.clcbio.com/index.php?id=1240, CLC bio, Cambridge, MD) using methods described by Baggerley et al. [2003]. The data analyses included sequence data filtering, read mapping, transcript and gene identification, differential expression analysis, and functional annotation and analysis.
Twenty-four short read sequencing samples (across the 3 sequencing schemes) were de-multiplexed and imported into the CLC Genomics Workbench 5.1 separately. Several quality control trimming methods were used within the CLC Genomics Workbench 5.1 including quality trimming, ambiguity trimming and adapter trimming with default settings applied before mapping to the reference genome.
The reference genome for the chicken (Gallus gallus, build 2.1) was downloaded (ftp://ftp.ensembl.org/pub/release-64/fasta/gallus_gallus/dna/) in FASTA format along with the corresponding annotation file (ftp://ftp.ensembl.org/pub/release-64/gtf/) in GTF format. In total, 17,934 genes and 22,298 transcripts are annotated in Gallus gallus build 2.1. Two hundred flanking upstream and downstream residues around known genes were included in the analysis. The short read sequences (101 base pairs) were mapped to the reference genome. Mapping parameters enforced a maximum of two mismatches and that reads must map with  e 90% of the bases aligned to the reference sequence with e 80% similarity. Non-specific matches (reads mapped to multiple places in the reference genome) were not included in the analysis.
The unique exon reads count (including the exon-exon and exon-intron junctions) for the reads mapped to a gene and its flanking regions were used as the raw expression value for that gene. This raw expression value was normalized to the median of the total mapped reads across the 24 samples to account for variation in original library concentration and multiplexing number. The 24 sequencing samples (4 individuals x 2 genotype x 3 replicates) were analyzed together. Samples were grouped by treatment (FL and LL), resulting 12 sequencing replicates in each group. Normalized expression values were analyzed as a beta-binomial model Baggerley et al. [2003] to detect differential expression. The samples were weighted and estimated based on total number of normalized reads assuming a beta distribution on the proportions in a group. The two-sided P-value was false discovery rate (FDR) corrected to deal with the issue of multiple testing (Benjamini 1995). Genes with a FDR adjusted P-value (P²0.05) and fold change of  e 1.2 were considered to be differentially expressed.
Genome_build: The reference genome for the chicken (Gallus gallus, build 2.1) was downloaded (ftp://ftp.ensembl.org/pub/release-64/fasta/gallus_gallus/dna/) in FASTA format

growth_protocol: Standard broiler chicken growth protocol

extract_protocol:
Total RNA was extracted using a RNeasy Midi kit according to the manufacturer’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE). RNA integrity was examined using a RNA 6000 Nano Assay kit and the Model 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA).
Paired-end sequencing libraries were made from 5 µg of total adipose RNA with the Illumina RNA Sample Prep Kit v3 following standard Illumina protocols. Individual RNA samples were indexed (bar-coded) after the fragmentation step to enable multiplexing of libraries within sequencing lanes.
Bar-coded libraries were pooled and sequenced using an Illumina HiSeq 2000 Sequencing System (http://www.illumina.com/systems/hiseq_2000.ilmn, Illumina, InC., San Diego, CA) at Delaware Biotechnology Institute, University of Delaware. Three separate sequencing schemes were employed to determine depth of coverage with varying numbers of multiplexed libraries. In the first scheme, all 8 libraries (4 FL and 4 LL) were multiplexed together and sequenced in two replicate lanes. In Scheme 2, 4 libraries (2 FL and 2 LL) were multiplexed and sequenced across 2 lanes using four different birds per sequencing lane. In the third scheme, one library from the FL and one library from the LL were each sequenced alone in two sequencing lanes.

treatment_protocol: Divergently selected on abdominal fat weight (FL genotype) for seven generations.

tag: line

value: LL cockerel

tag: age

value: 7 week

value: Abdominal adipose


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 4, techical replicate 3

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 4, techical replicate 3

tag: tissue


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 4, techical replicate 1

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 4, techical replicate 1


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 2, techical replicate 1

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 2, techical replicate 1


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 1, techical replicate 3

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 1, techical replicate 3


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 3, techical replicate 3

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 3, techical replicate 3


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 3, techical replicate 2

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 3, techical replicate 2


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 4, techical replicate 1

value: FL cockerel


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 4, techical replicate 3


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 2, techical replicate 3

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 2, techical replicate 3


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 2, techical replicate 2

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 2, techical replicate 2


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 3, techical replicate 3


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 1, techical replicate 2

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 1, techical replicate 2


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 3, techical replicate 2


title: HH18 VEN

value: Heart ventricles


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 3, techical replicate 1


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 1, techical replicate 1

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 1, techical replicate 1


title: 7 h

value: mid-exponential growth phase


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 2, techical replicate 1


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 2, techical replicate 2


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 2, techical replicate 3


title: Nr31 Rotenone 20day rep2

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava1.7 software used for extraction of FASTQ files
FASTQ files were mapped using TopHat (v1.4.1, parameters: --butterfly-search -g 1) vs. the C. elegans genome assembly WS220 (Ensembl release 66)
Gene counts were obtained using the Python package HTSeq and the respective Ensembl annotation GTF file (parameters: –stranded=no --idattr=gene_id --mode=union)
HTSeq result files were processed using the R programming language and RPKM values were calculated
Genome_build: WS220 (ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.WS220.genomic.fa.gz)/WBcel235
Supplementary_files_format_and_content: raw counts and RPKM values for each sample

organism: Caenorhabditis elegans

source_name: total RNA from whole animals

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at −80°C until use.
Total RNA was inspected for degradation using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). For library preparation an amount of 2μg of total RNA per sample was processed using Illumina's TruSeq™ RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer's instruction. Each library includes its own index sequence.

treatment_protocol: Treatment of C. elegans was carried out on NGM agar plates containing respective complex I inhibitors. All agar plates were prepared from the same batch of NGM agar, whereas treatment plates were supplemented with the respective compound and control plates with the respective solvent

value: whole animal

value: 20 days after L4

value: Adult (20 days after L4)

tag: treatment

value: 100nM rotenone


title: Chicken Abdominal fat, lean line (LL), 7 week of age, biological replicate 3, techical replicate 1

description: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 3, techical replicate 1


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 1, techical replicate 2


title: Nr29 DMSO 20day rep2

value: control plate


title: Nr28 DMSO 20day rep1


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 4, techical replicate 2


title: Nr22 Rotenone 10day rep1

value: 10 days after L4

value: Adult (10 days after L4)


title: Nr23 Rotenone 10day rep2


title: Nr24 Rotenone 10day rep3


title: Nr21 DMSO 10day rep3


title: Nr20 DMSO 10day rep2


title: Nr19 DMSO 10day rep1


title: Nr10 DMSO 5day rep1

value: 5 days after L4

value: Adult (5 days after L4)


title: Nr06 Rotenone 1day rep3

value: 1 days after L4

value: Adult (1 days after L4)


title: Nr12 DMSO 5day rep3


title: Nr13 Rotenone 5day rep1


title: Nr05 Rotenone 1day rep2


title: Nr04 Rotenone 1day rep1


title: Nr02 DMSO 1day rep2


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 1, techical replicate 3


title: Nr11 DMSO 5day rep2


title: Nr01 DMSO 1day rep1


title: E11.0 VEN rep2

data_processing:
HiSeq 2000 reads are aligned by TOPHAT2 (http://tophat.cbcb.umd.edu/) to produce bam files.
Gene expression profiles were generated using a Bayesian p-value
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include expression values (normalized reads to total per million)

value: ICR


title: Chicken Abdominal fat, fat line (FL), 7 week of age, biological replicate 1, techical replicate 1

value: 7 week


title: E11.0 OFT rep1

value: Heart outflow tract


title: E11.0 VEN rep1


title: E11.0 AVC rep1

value: Heart atrioventricular canal


title: Nr30 Rotenone 20day rep1


title: E11.0 OFT rep2


title: Nr14 Rotenone 5day rep2


title: hst 3,4 D H2A.Z ChIP

status: Public on Apr 15 2013

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
1. Liu CL, Schreiber SL, Bernstein BE (2003) Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 4: 19.
2. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
H2A.Z ChIP in Hst3,4 delete

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
reads were mapped to the yeast S288C genome using BLAT
genome wide cross correlation between the reads mapping to the Watson and Crick strands was determined and the length of the reads were extended by this value to count the number of reads present at each base pair
the average read count value was calculated and the data were normalized to one
S288C (S. cerevisiae)
Genome_build: SacCer_May2010
Supplementary_files_format_and_content: tab-delimited text files of the normalized read counts showing -500bp to end of gene coding sequence surrounding the transcription start site

organism: Saccharomyces cerevisiae W303

source_name: yeast with hst3 and hst4 deletions

growth_protocol: WT and H3K56Q were grown to log phase in YPD media at 30°C and Hst 3,4 D was gorn at 23C in YPD

extract_protocol:
Cells were washed in water, cell walls were broken with bead beating and spheroplasts were treated with micrococcal nuclease.  Immunoprecipitations were performed with extract equivalent to 100 ml of cell culture in the following volume: 6μl anti-Htz1 (Active Motif). Immunoprecipitation, washing, protein degradation, and DNA isolation were performed as previously described [1].
ChIP DNA, was treated with calf intestinal phosphatase (NEB), was blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors, and the final library was amplified via PCR and size selected by gel purification (BioRad)

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: ChIP

value: Hst3,4 delete


title: rve8_mock_3

city: Durham

first: Polly

middle: Yingshan

last: Hsu

state: NC

address: Duke University

department: Biology

institute: Duke University

description: Sample 12

data_processing:
Illumina Casava version 1.8 was used for basecalling.
Quality filtering (-q 20 -p 85, minimum quality score to keep: 20, minimum percent of bases that must satify the quality score cut-off: 85) using FASTX-toolkit (command-line)
Remove adaptor contamination using a perl script
De-multiplexing (allow one mis-match in the index sequnce) using "FASTX Barcode Splitter" included in FASTX-toolkit and removed the index sequnce from the reads
The reads were mapped to Arabidopsis cDNA representative_gene_model (TAIR 10) using BWA (aln -l 20, -t 4, using the first 20 subsequnce as seeds, tread number: 4)
Used samtools to combine bam files from the two lanes together and convert to sam files
Separated the reads mapped to forward or reverse strands using command-line
Summarized from the sam files to counts using R
Genome_build: TAIR10 cDNA representative_gene_model
Supplementary_files_format_and_content: sam2counts_RV.txt: COUNTS from reads mapped to the reversed strand in the 12 samples; suitable for edgeR analysis

source_name: Arabidopsis seedlings

growth_protocol: Arabidopiss rve8-1 RVE8::RVE8:GR and rve8-1 seeds (~30 seeds/ per sample) were sterilized and stratified on fine nylon mesh on MS +3% sucrose at 4 degree in the dark for 2 days. Seedlings were grown in 12 hours light (~50 micro Ei white light)/ 12 hours dark for 7 days.

extract_protocol: Total RNA was isolated using trizol and then purified by Qiagen mini-elute column. A customized Illumina-based strand-specific multiplex library construction protocol was used (modified from Wang et al., A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq, 2011)

treatment_protocol: At ZT4 (4 hourse after lights on), meshes with the seedlings were transferred to liquid MS+3% sucrose media containing 30 mM dexamethasone (DEX) or the same volume of solvent (mock). After four hours incubation with gentle agitation, plants were harvested and quickly frozn in liquid nitrogen.

value: 7 days old

value: whole seedlings

tag: genotype/variation

value: mock


title: rve8_DEX_3

description: Sample 9

value: dexamethasone


title: rve8_DEX_1

description: Sample 7


title: rve8_mock_1

description: Sample 10


title: wt H2A.Z ChIP

description:
1. Liu CL, Schreiber SL, Bernstein BE (2003) Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 4: 19.
2. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
H2A.Z ChIP in wt cells

source_name: wt yeast derived from W303

value: wildtype


title: rve8_DEX_2

description: Sample 8


title: RVE8:GR_DEX_3

description: Sample 3

value: rve8-1 RVE8::RVE8:GR


title: RVE8:GR_mock_1

description: Sample 4


title: RVE8:GR_DEX_2

description: Sample 2


title: RVE8:GR_DEX_1

description: Sample 1


title: Prostate  FFPE

city: Columbus

first: wei

last: meng

state: Ohio

address: 400 W12 street

department: Radiation Oncology

institute: The Ohio State University

data_processing:
The linker sequences of small RNA libraries were removed using cutadapt software (http://code.google.com/p/cutadapt/) under default parameters.
After removing linker sequences and filtrating by different small RNA databases, reads were mapped with miRBase V16.
All reads of each sample were aligned against miRBase and the hg19 reference genome using SOLiD™ small RNA Analysis pipeline (http://solidsoftwaretools.com), and were normalized as reads per million (RPM).
Sequences with expression value below 5 RPMs were considered not detected.
Genome_build: miRBase version 16
Supplementary_files_format_and_content: txt file contained 250 microRNA expression information

source_name: Prostate

extract_protocol:
RNA from FFPE samples were extracted using Recover All Total Nucleic Acid Isolation Kit (Life Technologies Corporation, Carlsbad, CA). The microRNA samples from the fresh frozen samples were extracted using PureLink™ miRNA Isolation Kit (Life Technologies Corporation, Carlsbad, CA).
Small RNAs from FFPE and fresh frozen samples were prepared for SOLiD sequencing as follows: the total RNA samples were processed by the flashPAGE fractionator (Ambion) and flashPAGE Clean-Up Kit (Ambion). The enriched small RNA was then processed according to the SOLiD Small RNA Expression Kit protocol (Applied Biosystems). The purified small RNAs were ligated with 5' and 3' adapter mix using RNA ligase. The ligated products (40–60 bases in length) were reverse transcribed and purified on Novex 10% TBE-Urea gel. Subsequently, 15–18 cycles of PCR were performed by amplifying the purified cDNA with barcoded PCR primer sets provided in the kit, which differed by a unique 6-nucleotide sequence. The amplified products were loaded on Novex 6% TBE gel (Invitrogen) and the gel bands containing 110 to 130bp fragments were excised. The amplified products were purfied from excised gel band, amplified by emulsion PCR, then loaded on Applied Biosystems SOLiD 4 next generation high throughput sequencing system for data acquisition.  The quality of the samples and libraries were verified on the Agilent Bioanalyzer.

treatment_protocol: Eight paired human malignant tissue samples were received.  Remnant surgical tissues were taken after diagnostic samples were secured from patients.Surgical specimens were transported from the operating rooms to Tissue Procurement, examined under a pathologist’s supervision and preserved within 5 to 57 recorded minutes. Paired tissue samples selected for research were either immediately snap frozen in liquid nitrogen and placed in a -80 °C freezer for monitored storage or fixed in 10% buffered formalin for up to 24 hours and then processed into a paraffin embedded block and stored at room temperature .

tag: tissue storage

value: FFPE

value: Prostate

tag: histology

value: Adenocarcinoma

tag: Sex

value: M


title: Lung  FFPE

source_name: Lung

value: Lung


title: Thigh, left posterior  FFPE

source_name: Thigh, left posterior

value: Thigh, left posterior

value: Sarcoma


title: Kidney FFPE 2

source_name: Kidney

value: Kidney

value: Clear Cell Carcinoma

value: F


title: Kidney FFPE 1


title: Prostate  Frozen

value: Frozen


title: Breast FFPE 1

source_name: Breast

value: Breast

value: Invasive ductal carcinoma


title: Breast  Frozen 2


title: Lung  Frozen


title: rve8_mock_2

description: Sample 11

value: 7 days old

value: whole seedlings

value: mock


title: Pelvis Frozen

source_name: Pelvis

value: Pelvis

value: Metastatic Melanoma


title: Breast Frozen 1


title: Kidney Frozen 1


title: RVE8:GR_mock_2

description: Sample 5

value: rve8-1 RVE8::RVE8:GR


title: Human microvascular endothelial cell

status: Public on Apr 14 2013

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: HMVEC

data_processing:
Trimmed sequences were generated as fastq outputs and analyzed based on the TopHat/Cufflinks pipeline based on reference annotations produced by the Ensembl Gencode project. Differential and significant gene expression analysis was carried out using gene-level FPKM (fragments per kilobase of gene locus summarized mRNA per million reads) expression levels.
Gene-level expression was normalized and baselined to the 80th percentile of that sample's overall expression in GeneSpring v7.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Each sample has a corresponding .txt file with normalized FPKM

source_name: Human microvascular endothilial cell

growth_protocol: Cultured with endothelial cell growth medium-2MV (EGM-2, Lonza)

extract_protocol:
Using RNeasy Mini Kit (Qiagen), total RNA was extracted and quantitative polymerase chain reaction was performed using Taqman gene expression assays (Applied Biosystems)
RNA-Seq–based expression analysis was carried out using RNA samples converted into individual cDNA libraries using Illumina (San Diego, CA).  TruSeq methods employed single reads of 50 base-lengths sequenced at 20-30 million read depths using the Illumina HiSeq 2500 instrument.

tag: cell type

value: Human Dermal Microvascular Endothelial Cells (Lonza)


title: iEC: Rep1

description: iECa

source_name: Induced endothelial cell

growth_protocol: Fibroblasts were treated with Poly I:C (30ng/ml) and the medium changed to DMEM with 7.5% FBS and 7.5% knockout serum replacement (KSR).  With daily treatments of Poly I:C for 7 days, the medium was gradually transitioned to contain 10% KSR. Cells were treated with transdifferentiation medium containing 20ng/ml bone morphogenetic protein-4 (BMP-4, Peprotech), 50ng/ml vascular endothelial growth factor (VEGF, Peprotech) and 20ng/ml basic fibroblast growth factor (bFGF, BD Bioscience) for another 7 days, with new medium every 2 days. For maintenance of transdifferentiation, the cells were cultured another 2 weeks in the presence of bFGF, VEGF and 0.1mM 8-bromoadenosine-3’:5’-cyclic monophosphate sodium salt (8-Br-cAMP, Sigma), with the medium changed every 2 days

value: Induced endothelial cells from cultured foreskin fibroblast cells (Stegment)


title: Fibroblast

description: Fibro

source_name: Fibroblast

growth_protocol: Cultured in DMEM with 10% FBS and 1% penicillin/streptomycin (5% CO2, 37°C)

value: Cultured foreskin fibroblast cells (Stegment)


title: iEC: Rep2

description: iECb


title: Breast  FFPE 2

value: FFPE


title: ChIP:cdk7_081312

status: Public on Apr 13 2013

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against cdk7

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Multiple myeloma

growth_protocol: RPMI medium containing 10% FCS, 2x10^8 MM1.S cells in exponential growth phase

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: No

tag: chip antibody

tag: antibody catalog number

value: Bethyl A300-405A


title: WCL_050212_ChipSeq

growth_protocol: Cells were grown to appr. 80% confluency in DMEM supplemented with 10% FCS.

treatment_protocol: Untreated

value: Bethyl A301-985A

value: Melanoma


title: WCL_061412_ChipSeq

description: Chromatin IP against WCL_061412

treatment_protocol: No cell treatment


title: CDK7_061912_ChipSeq

description: Chromatin IP against CDK7

treatment_protocol: No treatment


title: Input for cdk7 ChIP

description: WCE

tag: sample type

value: input


title: IP:BRD4_061412_ChipSeq

description: Chromatin IP against BRD4_061412


title: AD-MV4;11 WCE_ChipSeq

description: AD-MV4;11 WCE

source_name: Leukemia

growth_protocol: RPMI, 10% FBS. Pen step


title: AD-MV4;11_K9-K14ac_ChipSeq

description: Chromatin IP against AD-MV4;11_K9-K14ac

growth_protocol: RPMI, 10% FBS, Pen strep

value: Millipore 06-599


title: AD-5-Med1-3x10*6-0.1-20s_ChipSeq

description: Chromatin IP against AD-5-Med1-3x10*6-0.1-20s

growth_protocol: Most common:    MM1.S cells were grown in RPMI + 10% FBS. Treated with indicated compound. Crosslinked with 1% formaldehyde for 20 min. Washed 4 times with PBS. Flash frozen.

treatment_protocol: bioruptor 20 cycles-3x10*6 cells, 12 min fix

value: Bethyl A303-876A


title: Mz-0

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Bioscope version 1.3 was used to align .csfasta and .qual files to SNP-substituted reference genomes for each accession using default parameters which allows up to 10 locations per sequenced read.
Cufflinks version 1.1 was used to quantify gene expression values using the following parameters: -F 0 –b –N –library-type fr-secondstrand –G TAIR10.gtf.
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression values for all genes in the TAIR10 reference annotation as defined by Cufflinks version 1.1

molecule: polyA RNA

source_name: leaf

extract_protocol:
RNA was isolated using the Qiagen Plant RNeasy kit (Qiagen) following the manufacturer’s instructions.
RNA-Seq libraries were prepared according to the described methods in Li, L. et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev 26, 785-790 (2012).

value: leaf

tag: cultivar


title: Kidney Frozen 2

value: Frozen

value: Kidney

value: Clear Cell Carcinoma

value: F


title: Bd_0


title: rhr2_comp (replicate 2)

status: Public on Apr 12 2013

city: Pittsburgh

first: Jigar

middle: V

last: Desai

state: PA

address: 4400 Fifth Avenue

institute: Carnegie Mellon University

description: planktonic growth condition, 8h, Spider medium, 37°C

data_processing:
The sequencing reads were aligned to the C. albicans reference genomes (SC5314 or WO-1) using TopHat allowing up to two mismatches per 30bp segment and removing reads that aligned to more than 20 locations.
The alignment files from TopHat were then utilized to generate read counts for each gene and a statistical analysis of differential gene expression was performed using the DESeq package from Bioconductor (PMID: 20979621)
Genome_build: SC5314 (Genbank assembly ID GCA_000182965.1) and WO-1 (Genbank assembly ID GCA_000149445.2) genomes for alignment
Supplementary_files_format_and_content: tab-delimited text file containing ORF names and their corresponding normalized average read count across replicates, along with the relative abundance values across samples

extract_protocol:
For RNA extraction, the biofilms were harvested by scraping the bottoms of the flasks using a cell scraper and filtering the cell slurry on a vacuum manifold. The planktonic cells (wild-type strains-48h/ rhr2 mutant and complement strains-8h) were harvested similarly by vacuum filtration. The filters were flash frozen immediately after harvesting each sample. The cells were kept frozen on filters at -80°C until RNA extraction. RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions
For comparison of biofilm and planktonic growth in the wild type strains, the RNA-seq libraries (strand-specific, single read) were prepared as described by Bruno et al. (PMID: 20810668). For the comparison of rhr2Δ/Δ and complemented strains, the RNA-seq libraries (non-strand-specific, paired end) were prepared with the TruSeq RNA Sample Prep kit (Illumina, San Diego, CA) per manufacturer’s protocol

tag: genotype

value: rhr2-delta/delta + pRHR2

value: DAY185 (derived from an SC5314 derivative, BWP17)


title: rhr2_comp (replicate 1)

tag: strain


title: IP:BRD4_050212_ChipSeq

description: Chromatin IP against IP:BRD4_050212

growth_protocol: Cells were grown in DMEM supplemented with 10%FCS to appr. 80% confluency.


title: rhr2Δ/Δ (replicate 2)


title: rhr2Δ/Δ (replicate 1)


title: WO1_white_plan (replicate 2)

description: planktonic growth condition, 48h, Spider medium, 37°C

value: wild-type


title: WO1_opaque_plan (replicate 1)


title: SC5314_plan (replicate 2)


title: WO1_opaque_plan (replicate 2)


title: AD-2-WCE-3X10*6_ChipSeq

treatment_protocol: Bioruptor 20 cycles-fix12 min


title: WO1_white_plan (replicate 1)


title: SC5314_bio (replicate 2)

description: biofilm growth condition, 48h, Spider medium, 37°C


title: WO1_opaque_bio (replicate 2)


title: WO1_opaque_bio (replicate 1)


title: E11.0 AVC rep2

source_name: Heart tube

value: ICR

tag: developmental stage

value: Heart atrioventricular canal


title: SC5314_plan (replicate 1)


title: WO1_white_bio (replicate 2)


title: WO1_white_bio (replicate 1)


title: SC5314_bio (replicate 1)


title: Nr03 DMSO 1day rep3

source_name: total RNA from whole animals

value: whole animal

value: 1 days after L4

value: Adult (1 days after L4)

value: control plate


title: Chop-/- Mock-RNA-seq

status: Public on Apr 11 2013

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

description: CHOP KO Control

data_processing:
ERANGE was used to create .rds database files and then wig files with -raw option turned on.
ChIP-Seq peaks were identified using ERANG with default settings
rpkm files: mm9

source_name: Mouse embronic fibroblast

growth_protocol: Mouse embryonic fibroblast cells were rountinely subcultured in high-glucose DMEM supplemented with 10% FBS, Pen/Strep, NEAA (all invitorgen) on cell culture dishes.

extract_protocol: unknown

treatment_protocol: MEFs were treated with tunicamycin for 10hr. After treatment, chromatin immunoprecipitation or RNA isolation were performed.

value: Mouse embryonic fibroblast

value: Chop-/-

value: mock


title: Chop+/+ Tm ChIP-seq

description: CHOP WT ChIP-Seq

data_processing:
ERANGE was used to create .rds database files and then bedgraph files with -raw option turned on.
ChIP-Seq peaks were identified using ERANG with default settings
Genome Build:
CHOP_WT.bedgraph: mm9

tag: antibody

value: anti-CHOP

value: WT

value: Tunicamycin


title: rdr6-15 mutant total small RNA

middle: Keith

last: Slotkin

address: 318 West 12th Ave.

department: Molecular Genetics

description: library strategy: small-RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads de-multiplexed and were trimmed for adaptor sequence
Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, then mapped to the genome using bowtie with parameters --best --strata -M1
tRNA and rRNA-matching reads were removed
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced

source_name: Inflorescence tissue

growth_protocol: Plants were grown on soil in 18 hour per day light at 23C. All plants used in this study were grown side-by-side.

extract_protocol:
Total RNA was extracted using Trizol reagent, and small RNAs were purified using mirVana microRNA isloation kit.
Cloning of small RNAs was performed using the Illumina TruSeq Small RNA Sample Preparation Kit

tag: background strain

value: unopened flower buds

tag: growth conditions

value: 18 hour light, 23C


title: S288C_TLSeq2

first: Joshua

last: Arribere

address: 31 Ames St

institute: MIT

description:
Biological replicate of TL-seq.
TL-Seq, +pyrosphosphatase

data_processing:
Library strategy: TL-Seq
Reads mapped to genome with Bowtie.
Reads assigned to genes. Intergenic reads were assigned to the closest gene, regardless of strand. Antisense reads were ignored for subsequent analyses.
Peaks were called assuming a uniform background distribution, using Poisson distribution to identify regions of high read density.
Genome_build: Scer downloaded from yeastgenome.org on May 26, 2010.
Supplementary_files_format_and_content: Tab-delimited file of monopeak TL genes giving TL length.

organism: Saccharomyces cerevisiae

source_name: S288C yeast, TLSeq

growth_protocol: Yeast cultures (Sigma 1278b MAT a ura3 leu2 trp1 his3 and BY4742 Mat α his3∆1 leu2∆0 lys2∆0 ura3∆0) were grown to mid-log (OD600~0.5-1.0) phase in YPAD (1% yeast extract, 2% peptone, 0.01% adenine hemisulfate, 2% glucose) at 30°C in flasks with vigorous shaking.

extract_protocol: 200-1000 µg RNA was subjected to poly(A) selection using oligo dT cellulose as described previously (Sambrook et al.). Poly(A)-selected RNA was fragmented by alkaline hydrolysis (2 mM EDTA, 100mM NaCO3, pH 9.3) for one hour at 95°C. RNA fragments were gel purified and dephosphorylated with 30 U Calf-Intestinal Phosphatase (CIP, NEB) in 50 ml reactions containing 100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.9 at 37°C for 60 min, followed by phenol:chloroform extraction and isopropanol precipitation. Purified CIP-treated fragments were treated (or mock-treated) with 25 U Tobacco Acid Pyrophosphatase (TAP, Epicentre) in 50 ml at 37°C for two hours, then precipitated. Next a 5’RNA adaptor (AAUGAUACGGCGACCACCGACAGGUUCAGAGUUCUACAGUCCGACG) was added via ligation in a 20 ml reaction with 20 U of T4 RNA Ligase (NEB) for one hour at 37°C. Gel purification of a higher molecular weight species yielded the ligated RNA, which was then 3’end captured via poly(A) tailing (TL-Seq, as previously described in (Ingolia et al., 2009)) or ligation with preadenylated adaptor (TATL-Seq, as previously described in (Mayr and Bartel, 2009)). cDNA was prepared from ligated RNA (Superscript III, Invitrogen), amplified by 10-12 cycles of PCR (Phusion, Finnzymes), and sequenced on an Illumina HiSeq 2000.

treatment_protocol: Total RNA was isolated from yeast cell pellets by hot phenol extraction as described (Clarkson et al., 2010). Polysome gradients were prepared and RNA was extracted from gradient fractions as described (Arribere et al., 2011).


title: S288C_TLSeq1


title: Atf4-/- Tm-RNA-seq

description: ATF4 KO Treatment

tag: treatment


title: Atf4-/- Mock-RNA-seq

description: ATF4 KO Control


title: ddm1/rdr6 double mutant total small RNA

description: library strategy: small-RNA-seq

tag: tissue


title: Chop-/- Tm-RNA-seq

description: CHOP KO Treatment

tag: genotype/variation


title: RVE8:GR_mock_3

description: Sample 6

source_name: Arabidopsis seedlings

tag: age

value: 7 days old

value: whole seedlings

value: rve8-1 RVE8::RVE8:GR


title: Wild-type mock-RNA-seq

description: WT Control


title: Wild-type Tm-RNA-seq

description: WT Treatment


title: Atf4+/+ Tm ChIP-seq

description: ATF4 WT ChIP-Seq Replicates

data_processing:
ERANGE was used to create .rds database files and then bedgraph files with -raw option turned on.
ChIP-Seq peaks were identified using ERANG with default settings
Genome Build:
run48_s_1.bedgraph: mm9
run58_s_4.bedgraph: mm9
run58_s_6.bedgraph: mm9