title: U-2932_RNASeq

description: Sample 9

data_processing:
Base calls performed using Illumina ELAND
RNA-Seq reads were aligned to hg19 using BowTie v0.9.9.3, with parameters "--best -k 2 --unfa".  The top two best mappings were kept, tolerating two or fewer mismatched bases per read. Then a custom script was used to select the better of these two unique mappings.
Filtered out reads that mapped to human ribosomal RNAs
Filtered reads were intersected with the RefSeq transcriptome
Replicates were normalized using DESeq: The effective library size of each sample was estimated based on the pooled count data. First, a reference sample was defined in which the reference count of each transcript is its geometric mean over all samples. Second, for each sample, a vector was calculated as the ratios of the read counts over the reference counts for all the transcripts. Third, the median of these ratios across all the transcripts was defined as the “size factor” of each sample. Lastly, each sample was normalized by dividing the real counts by its size factor.
Collapsed the replicates by summing the read counts of two replicates for each cell line, because of the high degree of similarity between RNA-Seq replicates
Applied the negative binomial model in DESeq to assess the significance levels of differential gene expression.  The dispersion parameter in the model is estimated from the data by examining the relationship between the mean and variance of read counts across all the transcripts.  To contrast two conditions, we used the parameterized negative binomial model for each gene and obtained the p-values. To correct for multiple comparison, we adjusted the p-values with the Benjamini-Hochberg procedure which controls false discovery rate.
Genome_build: hg19
Supplementary_files_format_and_content: mRNA_ReadCountsByLine.txt: Abundance measurements.  The total fragment count for 22,156 RefSeq genes in each of the 8 cell lines, after normalization.  Linked as supplementary file on Series record.
Supplementary_files_format_and_content: mRNA_StatisticalResults.txt: Mean fragment count for 22,156 RefSeq genes in each subtype (ABC, GCB) after normalization; calculated fold change; p-value and FDR for differential gene expression between the two subtypes.  Linked as supplementary file on Series record.

source_name: B cells

value: diffuse large B cell lymphoma (DLBCL)

value: ABC


title: GM16234

status: Public on Dec 16 2013

type: SRA

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: genomic

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling. The reads were demultiplexed, allowing no mismatches in the index sequence.
Sequencing reads were mapped to hg19 genome using bowtie-0.12.7 with parameters -p 16 -r 100.
Analysis specific to 3C-Seq was performed using r3CSeq Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: bed format files were created by obtaining the normalized values in the form of reads per million per restriction fragment size.

molecule: genomic DNA

organism: Homo sapiens

source_name: EBV lymphoblastoid cell line

growth_protocol: Epstein Barr virus (EBV)-transformed lymphoblastoid cells were purchased from the National Institute of General Medical Sciences (NIGMS) Human Genetic Cell Repository at the Coriell Institute, Camden, New Jersey, USA. Lymphoblastoid cell lines were grown in RPMI 1640 (PAA) medium with 2 mM L-glutamine and 10% fetal calf serum (PAA) and supplemented with 1x penicillin/streptomycin solution (GIBCO) at 37 °C in 5% CO2

extract_protocol:
The 3C protocol was adapted from Hagege et al. (2007) with some modifications. 1x107 cells was cross-linked with 1% formaldehyde in 10ml culture medium for 10 minutes at room temperature. The reaction was quenched by the addition of glycine to 0.125M. Nuclei were harvested by lysis of the cells in 1ml ice-cold lysis buffer (150mM NaCl, 50mM Tris-HCl (pH 7.5), 5mM EDTA, NP-40 (0.5% v/v), Triton-X-100 (1.0% v/v)) with 1x protease inhibitor cocktail solution (Sigma) plus 0.5mM PMSF. Nuclei were resuspended in 0.5ml EcoRI restriction buffer (NEB) with 0.3% SDS and incubated for 1 hour at 37°C with agitation. Triton X-100 was added to 2% (v/v) and incubated for 1 hour at 37°C with agitation. Cross-linked nuclei were digested overnight at 37°C with 400U EcoRI. Addition of SDS to 1.6% to stop restriction and further incubated at 65°C for 20 minutes with agitation. The reaction was diluted with 7ml ligation buffer with Triton-X-100 and incubated for 1 hour at 37°C prior addition of 100U of T4 DNA ligase (Fermentas) for 4 hours at 16°C and then 30 minutes at RT. Reverse cross-linking was done by adding 600mg Proteinase K and incubated at 65°C overnight. After RNase A digestion, DNA was purified by phenol/ chloroform extraction. The DNA pellet was resuspended in 150 ml 10 mM Tris-Cl (pH7.5).
3C-seq templates were generated as for 3C by using EcoRI. After ligation and purification, the restriction fragments ligated to the anchor region (containing FXN exon 1) were amplified by inverse PCR as described (Simonis et al., 2006). 1 µg of template was amplified per reaction by using Phusion High-Fidelity PCR kit (Finnzymes; Cat.# F-553S) and primers incorporated with different indexes. Primer sequences were listed in Supplementary Table 1. The libraries were processed according to manufacturer’s instructions (Illumina Inc.).

tag: tissue

value: PBMC

tag: group

value: FRDA affected individual

tag: cell line


title: Hi-C, RAD21cv HEK293, TEV treated, replicate one

city: La Jolla

first: Jesse

middle: R

last: Dixon

state: CA

address: 10010 N. Torrey Pines Rd.

country: USA

institute: Salk Institute for Biological Studies

data_processing:
Library strategy: Hi-C
fastq:  Illumina's HiSeq Control Software
Hi-C reads were aligned as single end reads using BWA with default parameters.  Uniquely mapping reads were manually paired using in an in house pipeline.  PCR duplicate reads were removed using Picard MarkDuplicates.
RNA-seq data were mapped as paired-end reads using tophat with the following parameters: -g 1 -p 12 --solexa1.3-quals --library-type fr-firststrand --segment-length 25 --bowtie1
RNA-seq bigWig files were generated through an in house pipeline that includes performing trimmed mean of M (TMM) normalization (Robinson et al. Genome Biology 2010)
ChIP-seq data were mapping with bowtie using the following parameters: -v 3 -m 1 --best --strata -S --time -p 8.  Data was filtered for uniquely mapping reads.  PCR duplicates were removed using Picard MarkDuplicates
ChIP-seq bigWig files were generated through an in house pipeline
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq and RNA-seq processed files are in bigWig format.  As the RNA-seq experiment was strand specific, bigWig files for both the positive and negative strands are included
Supplementary_files_format_and_content: Hi-C processed files are in a modified bed format.  Each row lists the chromosome and the start and end coordiates of two interacting bins as well as the normalized interaction frequency between these two bins
Supplementary_files_format_and_content: Processed mRNA-seq data include information for each gene and its count and rpkm values.  Each line includes chromosome, start position, end position, strand, gene name, read counts, and rpkm values
Genome Build:
TEV_r1_cis.index.txt: hg18

source_name: Hi-C, RAD21cv HEK293, TEV treated

growth_protocol: Cells were grown in DMEM supplemented with 0.2mM L-glutamine, 100 U/mL penicillin, 100 mg/mL streptomycin, and 10% fetal calf serum at 37°C and 5% CO2

extract_protocol:
Hi-C experiments were conducted using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).
Sequencing libraries were constructed according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

treatment_protocol: A stably integrated transgene in the RAD21cv HEK293T cells was activated for 3 days with 2µg/mL of doxycycline.  Cells were then transfected with a plasmid expressing TEV protease using Lipofectamine 2000 (Invitrogen) for 24 hours before harvesting

value: HEK293T RAD21cv


title: GM15851

value: Healthy individual


title: GM15850


title: RBP7 (Tb927.10.12100) over-expressor minus dox rep 1

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

library_source: transcriptomic

data_processing:
The quality of raw sequence data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).   No additional processing of the primary data was required.
Paired end sequences were aligned to the Tbb genome (obtained from ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/ ) using bowtie2 (parameters: --very-sensitive-local; version: 2.0.2), piped through samtools (parameters: -bhS; version: 0.1.18), and stored in indexed BAM format.
The annotated Tbb genome was viewed using Artemis software (http://www.sanger.ac.uk/resources/software/artemis/ ; http://ukpmc.ac.uk/abstract/MED/11120685), and coding segment (CDS) region coordinates extracted prior to conversion to bedtools bedfile format.  Bedtools (paramters: multicov -bams ; version: bedtools 2.15.0) was used to generate coverages for each CDS for each sample replicate.  RPKM-like values were calculated by dividing coverage by CDS size.
Statistical analyses of the sample groups were undertaken in the R environment (www.R-project.org) using Bioconductor (www.bioconductor.org) packages.  Differential expression was explored using linear models and empirical Bayes methods, using the limma package (Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3. (Online, Tech Report PDF)).  RPKM-like values were offset by 1, logged, and quantile normalised prior to group-wise comparison.  Data were filtered to remove loci whose mean RPKM-like values across all samples were below the 10% quantile.
Genome_build: ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/
Supplementary_files_format_and_content: Annotated, normalised RPKM values (log2)

molecule: total RNA

organism: Trypanosoma brucei brucei

growth_protocol: RBP7 (Tb927.10.12100) RNAi  and over-expressor lines were grown in mice.

extract_protocol:
RNA was isolated from AnTat1.1 cells grown in mice with or without doxycycline and from RBP7 RNAi or over-expressor lines grown in mice with or without doxycycline.  The method used for RNA extraction was RNAeasy (Qiagen).
Library construction and sequencing was carried out by BGI-Hong Kong using the Illumina® TruSeq™ RNA Sample Preparation Kit.

treatment_protocol: RBP7 over-expressor and RNAi lines were grown in mice with or without doxycycline.

tag: Stage

value: Pleomorphic slender

tag: strain

tag: days after infection


title: OCI-Ly7_ChIPSeq

city: Stanford

first: Jennifer

middle: Marion

last: Hardee

state: California

address: 300 Pasteur Dr., M-344

institute: Stanford University

description: Sample 4

data_processing:
Base calls performed using Illumina ELAND
ChIP-Seq reads were aligned to hg19 using BowTie v0.12.5, parameters "-p 8 -S -q -v 2 -m 1 --best --strata encodeHg19Male" (or encodeHg19Female).
The SPP peak caller v1.10.1 was used with a relaxed peak calling threshold (FDR = 0.9) to obtain a large number of peaks (maximum of 300,000) that span true signal as well as noise (false identifications).
Used the Irreproducible Discovery Rate (IDR) framework in order to identify high confidence and reliable regions of enrichments (peaks) in the ChIP-seq datasets. Specifically, we followed the ENCODE uniform processing pipeline as outlined at http://anshul.kundaje.net/projects/idr. The number of peaks with IDR scores better than 0.02 (2%) was used as the cross-replicate peak rank threshold.
Overlapping or abutting high confidence STAT3 peaks were merged into broader “binding regions” to facilitate comparison between cell lines (output file: ChIPSeq_STAT3BindingRegions.txt).  The ChIP-Seq data for each line was then rescored to determine how many fragments mapped to each binding region.  Binding regions that occurred in only one cell line were eliminated from further analysis.
Replicates were normalized using DESeq: The effective library size of each sample was estimated based on the pooled count data. First, a reference sample was defined in which the reference count of each binding region is its geometric mean over all samples. Second, for each sample, a vector was calculated as the ratios of the read counts over the reference counts for all the binding regions. Third, the median of these ratios across all the binding regions was defined as the “size factor” of each sample. Lastly, each sample was normalized by dividing the real counts by its size factor.
Applied the negative binomial model in DESeq to assess the significance levels of differential STAT3 binding.  The dispersion parameter in the model is estimated from the data by examining the relationship between the mean and variance of read counts across all the BRs. To contrast two conditions, we used the parameterized negative binomial model for each gene and obtained the p-values. To correct for multiple comparison, we adjusted the p-values with the Benjamini-Hochberg procedure which controls false discovery rate.  We compared 24 GCB replicates versus 11 ABC replicates.  Cell line OCI-Ly19 was excluded from the analysis: RNA-Seq data showed that its gene expression clustered in between the subtypes, probably due to its EBV+ status.
STAT3 binding regions (BRs) were associated with genes that they might regulate via the Genomic Regions Enrichment of Annotations Tool v2.0.2 using its default settings (http://great.stanford.edu).  To determine whether a BR and a given gene are linked, GREAT first determines a putative regulatory domain for every gene.  This consists of a basal regulatory domain (BRD) from 5 kb upstream to 1 kb downstream, plus an extended domain calculated by elongating the BRD both upstream and downstream for 1000 kb or until reaching another gene’s BRD, whichever occurs first.  Once this set of extended regulatory domains is established, GREAT associates the list of ChIP-Seq STAT3 binding regions with all of the genes whose regulatory domains they overlap.
Genome_build: hg19
Supplementary_files_format_and_content: *ChIPSeq_STAT3_IDRpeaks.bed: BED files were generated using the IDR pipeline (http://anshul.kundaje.net/projects/idr).  Files are in the UCSC-supported ENCODE narrowPeak format (http://genome.ucsc.edu/FAQ/FAQformat.html#format12).  NOTE:  BED column 4 reports ranks, as the IDR analysis pipeline uses rank as an important measurement of peak significance.
Supplementary_files_format_and_content: ChIPSeq_STAT3BindingRegions.txt: File was generated by a custom script. "IDRpeaks.bed" files for all 9 cell lines were concatenated.  Any overlapping or abutting regions were merged together to form one larger "binding region" (BR). Regions that occurred in only one cell line were discarded.  Headers are "chr/start/end/numCellLines", where "numCellLines" is "number of cell lines in which this peak is found".  Linked as supplementary file on Series record.
Supplementary_files_format_and_content: ChIPSeq_ReadCountsByReplicate.txt: Abundance measurements.  The total fragment count for 10,337 STAT3 binding regions in each of the 35 replicates, after normalization.  Linked as supplementary file on Series record.
Supplementary_files_format_and_content: ChIPSeq_StatisticalResults.txt: Mean fragment count for 10,337 STAT3 binding regions in each subtype (ABC, GCB) after normalization; calculated fold change; p-value and FDR for differential gene expression between the two subtypes.  Linked as supplementary file on Series record.
Supplementary_files_format_and_content: ChIPSeq_AssociatedGenes.txt: Location-based association between 10,337 STAT3 binding regions and annotated RefSeq genes (analyzed via GREAT).  In many cases, STAT3 BRs fall in regions where the regulatory domains of two genes overlap; consequently, GREAT associates these BRs with both genes.  For purposes of downstream comparison, we treated these multiple associations as separate table entries, to allow the greatest sensitivity in detecting associations with gene expression data.  Linked as supplementary file on Series record.

growth_protocol: Cell lines OCI-Ly7, OCI-Ly19, SU-DHL2, SU-DHL4, SU-DHL6, SU-DHL10, and U-2932 were cultured in suspension in RPMI 1640, supplemented with 15% heat-inactivated FBS.  Cell lines OCI-Ly3 and OCI-Ly10 were cultured in suspension in IMDM, supplemented with 15% heat-inactivated FBS and 55 uM beta-mercaptoethanol.

extract_protocol:
Crosslinked cell pellets were dounce homogenized to collect nuclei.  Nuclear lysate was sonicated, then immunoprecipitated.  Antibody-protein-DNA complexes were collected using Protein A agarose beads.
Libraries were prepared according to Illumina's instructions using non-Illumina enzymes and kits.  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 (End-It Repair Kit, Epicenter-Illumina). The blunt 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. DNA was then gel purified and size selected for 150-300 bp fragments to exclude unligated adapters, PCR amplified with Illumina primers using Phusion high-fidelity DNA polymerase for 15 cycles, and size selected again from an agarose gel for 150-300 bp fragments. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: Cells were suspended in their growing media at 1e6 per mL and crosslinked with formaldehyde at a final concentration of 1% for 10 minutes at room temperature, followed by quenching with glycine in PBS at a final concentration of 125 mM for 5 minutes.

tag: disease state

tag: dlbcl subtype

value: GCB

tag: chip antibody

value: STAT3 (Santa Cruz, sc-482X)


title: GM14664


title: HeLa_mIgG_CLIP

city: Winnipeg

first: Geoffrey

last: Hicks

state: Manitoba

address: BMSB 669, 745 Bannatyne Avenue

department: Biochemsity & Medical Genetics

country: Canada

institute: University of Manitoba, Manitoba Institue of Cell Biology

data_processing:
Library strategy: CLIP-Seq
Illumina default workflow (Casava1.4 software) was used for sequence basecalling.
CLIP-seq reads were trimmed to remove apator sequences. Reads with identical sequence were collapsed into a signle read. Reads were aligned to the GRCh37 genome assembly using BlastN, with default parameters.
Peaks were determined using CisGenome V2 with the following parameters: Window Size W=150 bp; Cutoff C>=12 reads; Step Size S=25 bp; Max Gap=50 bp; Min Peak Length=100 bp.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited BED files include chr name, chr start, chr end, name of the BED line, score (set 1 to all), and strand.

extract_protocol:
After UV crosslinking, FUS-RNA complexes were immunoprecipitated with antibodies. The immunoprecipiated FUS-RNA complexes were radiolabled, size purified, and RNA was extracted using phenol chloroform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: passage

tag: cell type

value: HeLa cells


title: HeLa_FUS_CLIP


title: Barcode1: AMP selected

data_processing:
Primer sequences were removed from the raw sequences using cutadapt (parameters: -O 10 -m 25 -n 3 -q 20; version 1.0), partitioning processed reads into terminal (primer-containing, thus trimmed) and internal (untrimmed) datasets.
Sequences were aligned to the Tbb genome (obtained from ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/ ) using bowtie2 (parameters: --very-sensitive; version: 2.0.2), piped through samtools (parameters: -bhS; version: 0.1.18), and stored in indexed BAM format.
The annotated Tbb genome was viewed using Artemis software (http://www.sanger.ac.uk/resources/software/artemis/ ; http://ukpmc.ac.uk/abstract/MED/11120685), and read depth values were extracted from the BAM files and/or viewed directly in Artemis.
master_list.txt
genome build: ftp.sanger.ac.uk/pub4/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_WGS_24_08_2012/chromosomes/
processed data files format and content: Annotated read depth summary

source_name: Whole organism

extract_protocol:
Three cAMP-selected and five AMP-selected populations outgrew and were subject to DNA isolation and RNAi fragment insert amplification. The method used for RNA extraction was RNAeasy (Qiagen).  Amplicon populations from the cAMP and AMP selections were analysed by ion torrent sequencing.
PCR amplicon primers (Forward primer: 5' TAGCCCCTCGAGGGCCAGT 3', Reverse primer: 5' GGAATTCGATATCAAGCTTGGC 3') were used to generate PCR fragments, which ranged in size up to about 2kk.  These were subsequently fragmented to 250-200nt sized fragments before barcoding and sequencing.

treatment_protocol: An RNAi library population of 2x107 cells (~5 fold genome coverage) was selected in the presence of 100µM 8-pCPT-2’-O-Me-cAMP or 10µM 8-pCPT-2’-O-Me-5’-AMP22 in several replicate flasks either induced, or not, to activate RNAi.

value: monomorphic slender

value: Lister 427

tag: treatment

value: AMP selected


title: Barcode2: cAMP selected

value: cAMP selected


title: A549 Input

city: Tampa

first: Jonathan

last: Nguyen

state: FL

department: Tumor Biology

institute: Moffitt Cancer Centre & Research Institute

description: input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome (hg19; Feb, 2009 assembly) using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: hg19

source_name: A549 Input

growth_protocol: Human NSCLC cell line A549 was maintained in Ham’s F-12K (Cellgro) supplemented with 10% FBS (Cellgro).

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.  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 (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 200-250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: The cells were rendered quiescent by serum starvation for 36 hours and stimulated with 1 µM nicotine for 24 hours. Cells were then fixed with 1% formaldehyde under gentle agitation for 15 minutes at room temperature. Fixation was stopped by adding 1/20th volueme of 2.5M glycine and the cells were scrapped off from the plate, pelleted by centrifugation and washed with PBS three times. Finally, the pellets were snap frozen and sent to GENpathway for further analysis.

value: NSCLC

tag: passages


title: A549 Serum starved

description: Chromatin IP against Beta arrestin 1

source_name: A549 Serum starved

value: Beta arrestin-1 Ab


title: A549 Nicotine

description: Chromatin IP against Beta arrestin 1

source_name: A549 Nicotine stimulated


title: Vitro 60C

status: Public on Dec 15 2013

city: Cambridge

first: Silvi

last: Rouskin

state: MA

address: 455 Main Street

institute: Whitehead Institute

description:
Sample 15
processed data files: WIGv60ALL_plus.wig, WIGv60ALL_min.wig

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignments were performed with bowtie using the first 25 nt of each read
Reads were first aligned to the ribosomal RNA and the unaligned reads were then aligned to the genome
reads were filtered for unique map to the genome and no mismatches
reads were filtered for reverse transcriptase stops at As and Cs only
Genome_build: Saccharomyces cerevisiae assembly R61 (UCSC: sacCer2).
Supplementary_files_format_and_content: The position number directly indicates the DMS modified position starting at 1. Raw reads for each replicates were combined together in wiggle format. Separate files are provided for positive and negative strand maching reads.
Supplementary_files_format_and_content: For the ribosomal RNA, processed wig files are aligned to the ribosomal RDN locus (RDN18 is 18S rRNA and RDN25 is 25S rRNA).

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: in vitro 60C

growth_protocol: WT yeast were grown to exponential phase at 30C

extract_protocol:
Total RNA was extracted using hot acid phenol. mRNA was extracted with Dynal beads(invitrogen)
mRNA was randomly fragmented using Ambion fragmentatin reagents, followed by PNK, and ligation using T4  K227Q truncated RNA ligase. Superscript III was used for reverse trancription , and circ ligase (epicentre) for circularization. Illumina adapters were introduced by 8-10 cycles of PCR.

treatment_protocol: For in vivo samples, DMS was added directly to the  growing yeast culture at 2-4% for 2-3 min. 25%BME, 30% isoamyl alcholol was used to quench the DMS. Cells were lyzed with SDS and RNA was isolated with hot acid phenol. For in vitro samples, total RNA was extracted from yeast cells , polyA mRNA was selected, denatured at 95C, refolded in RNA folding buffer for 30min at 30C, and then probed with DMS at 2-5% for 3-5min.

tag: culture condition

value: in vitro 60C


title: Vitro 30C 4%DMS, 5min

description:
Sample 13
processed data files: Feb13_VitroAll_1_15_Plus.wig,
Feb13_VitroAll_1_15_Minus.wig,
4pDMSvitro5min_CAGATC_sc-rRNA.align18sRNAnoMiss.wig

source_name: in vitro 30C 4%DMS, 5min

value: in vitro 30C 4%DMS, 5min


title: Hi-C, HEK293 siRNA Control, replicate one

data_processing:
Library strategy: Hi-C
fastq:  Illumina's HiSeq Control Software
Hi-C reads were aligned as single end reads using BWA with default parameters.  Uniquely mapping reads were manually paired using in an in house pipeline.  PCR duplicate reads were removed using Picard MarkDuplicates.
RNA-seq data were mapped as paired-end reads using tophat with the following parameters: -g 1 -p 12 --solexa1.3-quals --library-type fr-firststrand --segment-length 25 --bowtie1
RNA-seq bigWig files were generated through an in house pipeline that includes performing trimmed mean of M (TMM) normalization (Robinson et al. Genome Biology 2010)
ChIP-seq data were mapping with bowtie using the following parameters: -v 3 -m 1 --best --strata -S --time -p 8.  Data was filtered for uniquely mapping reads.  PCR duplicates were removed using Picard MarkDuplicates
ChIP-seq bigWig files were generated through an in house pipeline
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq and RNA-seq processed files are in bigWig format.  As the RNA-seq experiment was strand specific, bigWig files for both the positive and negative strands are included
Supplementary_files_format_and_content: Hi-C processed files are in a modified bed format.  Each row lists the chromosome and the start and end coordiates of two interacting bins as well as the normalized interaction frequency between these two bins
Supplementary_files_format_and_content: Processed mRNA-seq data include information for each gene and its count and rpkm values.  Each line includes chromosome, start position, end position, strand, gene name, read counts, and rpkm values
Genome Build:
CTRL_r1_cis.index.txt: hg18

source_name: Hi-C, HEK293 siRNA Control

treatment_protocol: HEK293T cells were transfected with control siRNA oligos using Lipofectamine 2000 according to manufacterure's instructions.  Cells were harvested 48hrs later.


title: Vitro 45C

description:
Sample 14
processed data files: WIGv45ALL_plus.wig, WIGv45ALL_min.wig

source_name: in vitro 45C

value: in vitro 45C


title: Vitro 30C 2.5%DMS, 5min

description:
Sample 12
processed data files: Feb13_VitroAll_1_15_Plus.wig,
Feb13_VitroAll_1_15_Minus.wig,
2p5perDMSvitro3min_ATCACG_sc-rRNA.align18sRNAnoMiss.wig

source_name: in vitro 30C 2.5%DMS, 5min

value: in vitro 30C 2.5%DMS, 5min


title: Vitro 30C 2.5%DMS, 3min

description:
Sample 11
processed data files: Feb13_VitroAll_1_15_Plus.wig,
Feb13_VitroAll_1_15_Minus.wig,
2p5perDMSvitro3min_ATCACG_sc-rRNA.align18sRNAnoMiss.wig

source_name: in vitro 30C 2.5%DMS, 3min

value: in vitro 30C 2.5%DMS, 3min


title: Vitro 30C rep3

description:
Sample 10
processed data files: Feb13_DenaturedAll_1_15_Plus.wig,
Feb13_DenaturedAll_1_15_MINUS.wig,
ACden1_LateJune12res_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACden1_LateJune12res_sc-rrna.align.wigFiveCount.wig

source_name: in vitro 30C

value: in vitro 30C


title: Vitro 30C rep2

description:
Sample 9
processed data files: Feb13_DenaturedAll_1_15_Plus.wig,
Feb13_DenaturedAll_1_15_MINUS.wig,
ACden1_LateJune12res_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACden1_LateJune12res_sc-rrna.align.wigFiveCount.wig


title: Denatured (95C) rep3

description:
Sample 7
processed data files: Feb13_DenaturedAll_1_15_Plus.wig,
Feb13_DenaturedAll_1_15_MINUS.wig,
ACden1_LateJune12res_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACden1_LateJune12res_sc-rrna.align.wigFiveCount.wig


title: Vitro 30C rep1

description:
Sample 8
processed data files: Feb13_VitroAll_1_15_Plus.wig,
Feb13_VitroAll_1_15_Minus.wig, GCvitro2_LateJune12res_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_GCvitro2_LateJune12res_sc-rrna.align.wigFiveCount.wig


title: GM16798

value: PBMC

value: FRDA affected individual


title: Denatured (95C) rep1

description:
Sample 5
processed data files: Feb13_DenaturedAll_1_15_Plus.wig,
Feb13_DenaturedAll_1_15_MINUS.wig,
ACden1_LateJune12res_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACden1_LateJune12res_sc-rrna.align.wigFiveCount.wig


title: Vivo rep4

description:
Sample 4
processed data files: Feb13_VivoAllextra_1_15_PLUS.wig,
Feb13_VivoAllextra_1_15_Minus.wig,
ACviv1mset1mag_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACviv1mset1mag_sc-rrna.align.wigFiveCount.wig

source_name: in vivo

value: in vivo


title: Vivo rep1

description:
Sample 1
processed data files: Feb13_VivoAllextra_1_15_PLUS.wig,
Feb13_VivoAllextra_1_15_Minus.wig,
ACviv1mset1mag_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACviv1mset1mag_sc-rrna.align.wigFiveCount.wig


title: Vivo rep2

description:
Sample 2
processed data files: Feb13_VivoAllextra_1_15_PLUS.wig,
Feb13_VivoAllextra_1_15_Minus.wig,
ACviv1mset1mag_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACviv1mset1mag_sc-rrna.align.wigFiveCount.wig


title: Vivo rep3

description:
Sample 3
processed data files: Feb13_VivoAllextra_1_15_PLUS.wig,
Feb13_VivoAllextra_1_15_Minus.wig,
ACviv1mset1mag_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACviv1mset1mag_sc-rrna.align.wigFiveCount.wig


title: Vitro 75C

description:
Sample 16
processed data files: WIGv75ALL_plus.wig, WIGv75ALL_min.wig

source_name: in vitro 75C

value: in vitro 75C


title: mgIs30(rol-6(su1006)::lin-14; col-10::lacZ::lin-14; lim-6::gfp::unc-54)

city: Boston

first: Sylvia

middle: E. J.

last: Fischer

address: 185 Cambridge Street, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Sample 6
small RNA profiling

data_processing:
Raw datasets are fastq files generated using Illumina software.
Small RNA sequences were parsed using a custom Python program, then mapped to corresponding nematode reference genomes (Wormbase release WS230) allowing 0 mismatch using Bowtie software.
Genome_build: WS230
Supplementary_files_format_and_content: Tab-delimited text file includes Sequence and read count

organism: Caenorhabditis elegans

source_name: adult

growth_protocol: Animals were grown at 20 °C on E. coli strain OP50

extract_protocol:
Total RNA was isolated from synchronized animals, and 18-28 nt small RNAs were size-selected.
Small RNAs were treated with Tobacco Acid Phosphatase, then ligated to 3' and 5' adapters,  reverse transcribed and PCR amplified. PCR amplicons were extracted from gel prior to sequencing.

value: wt; mgIs30

value: 69 hrs post L1 arrest at 20°C

value: whole organism


title: arl-8(tm2472) 4x backcrossed

description:
Sample 5
small RNA profiling


title: eri-6(mg379); mgIs30(rol-6(su1006)::lin-14; col-10::lacZ::lin-14; lim-6::gfp::unc-54)

description:
Sample 1
small RNA profiling


title: eri-6(mg379) 6x backcrossed

description:
Sample 4
small RNA profiling


title: eri-6(mg379); Is(sur-5::gfp)

description:
Sample 2
small RNA profiling


title: DS22968 DNaseI-seq Tsu-1, 7 day old seedling

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to A. thaliana reference TAIR10 with bowtie version 0.12.7 with the following parameters: bowtie -p 8  --mm -n 2 -m 1 --best --phred33-quals
Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration except that peak thresholding was set to 95 percentile.
Genome_build: TAIR10
Supplementary_files_format_and_content: Dnase bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent per base Dnase cleavages in a 150bp window at 20bp steps across the genome.
Supplementary_files_format_and_content: peak bed files were generated with Hotspot and represent DnaseI hypersensitive sites

organism: Arabidopsis thaliana

source_name: Tsu-1, 7 day old seedling

growth_protocol: Seedlings were planted on 1XMS, 0.8% agar and stratified for 2-4 days before being placed in an incubator with LD (16hr light, 22°C; 8hr dark, 20°C) conditions for 7 days.

extract_protocol:
DNaseI: Nuclei were extracted and isolated with biotin-capture methods. Nuclei were then treated with 45u of DNase I for 3 minutes at 25°C. Resulting genomic DNA was size fractionated and small (double cut) fragments were sequenced using Illumina technology.
Illumina TruSeq v2

tag: intact line

value: seedling

tag: genetic background

tag: experiment

value: DNaseI-seq


title: Is(sur-5::gfp)

description:
Sample 3
small RNA profiling

value: wt; sur-5::gfp

tag: tissue


title: DS23077 DNaseI-seq Bur-0, 7 day old seedling

source_name: Bur-0, 7 day old seedling


title: DS22974 DNaseI-seq Est-1, 7 day old seedling

source_name: Est-1, 7 day old seedling


title: DS21954 RNA-seq 7 day old Seedling Dark 3hr light

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to A. thaliana reference TAIR10 with bowtie version 0.12.7 with the following parameters: bowtie -p 8  --mm -n 2 -m 1 --best --phred33-quals
For Light/Dark DNaseI data, reads where subsampled to a uniform level of 24 million reads all subsequent processing used the subsampled set
For Heat shock DNaseI data, reads where subsampled to a uniform level of 74 million reads all subsequent processing used the subsampled set
Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration except that peak thresholding was set to 95 percentile.
Footprints were called using the method described in PMID:   22955618
RNA-seq reads where aligned with eland_rna as part of CASAVA-1.8.2 (eland version ELANDv2e)
Genome_build: TAIR10
Supplementary_files_format_and_content: Dnase bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent per base Dnase cleavages in a 150bp window at 20bp steps across the genome.
Supplementary_files_format_and_content: RNA bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent RNA-seq read pileups
Supplementary_files_format_and_content: peak bed files were generated with Hotspot and represent DnaseI hypersensitive sites
Supplementary_files_format_and_content: footprint bed files where generated with the pipeline described in PMID 22955618 and represent transcription factor binding events

source_name: 7d Seedling

growth_protocol: LD (16hr light, 22°C; 8hr dark, 20°C); Dark (16hr 22°C; 8hr 20°C)

extract_protocol:
DNaseI: Nuclei were extracted and isolated with biotin-capture methods. Nuclei were then treated with 45u of DNase I for 3 minutes at 25°C. Resulting genomic DNA was size fractionated and small (double cut) fragments were sequenced using Illumina technology. RNA-seq 100-200mg of tissue was ground in liquid nitrogen and total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma), RNA was treated with DNase I and Ribo-Zero Plant leaf kit (Epicentre) and libraries were prepared using the TruSeq kit v2 (Illumina).
Illumina TruSeq v2

treatment_protocol: Light treatments: dark grown 7 day old seedlings were moved to light conditions for the specified amounts of time. Spray control: plates were un-wrapped and lightly sprayed with 0.5% EtOH and left for 3hrs

value: Dark 3hr light

value: RNA-seq


title: DS21955 RNA-seq 7 day old Seedling Dark 24hr

value: Dark 24hr LD


title: DS21959 RNA-seq 7 day old Seedling Heat Shock

value: Heat Shock (30min at 45°C) (LD)


title: DS21952 RNA-seq 7 day old Seedling Dark

value: Dark


title: DS21956 RNA-seq 7 day old Seedling Control

value: Control (LD)


title: DS22973 DNaseI-seq Bay-0, 7 day old seedling

source_name: Bay-0, 7 day old seedling


title: DS20423 SE DNaseI-seq 7 day old seedling Heat Shock

source_name: 7 day old seedling


title: DS21094 PE DNaseI-seq 7 day old seedling Control


title: DS21953 RNA-seq 7 day old Seedling Dark 30min light

value: Dark 30min light


title: SU-DHL2_ChIPSeq

description: Sample 6

source_name: B cells

value: diffuse large B cell lymphoma (DLBCL)

value: ABC

value: STAT3 (Santa Cruz, sc-482X)


title: DS19992 PE DNaseI-seq 7 day old seedling Control

value: Control (LD, light spray with 0.5% EtOH, 3hr wait)


title: DS20423 PE DNaseI-seq 7 day old seedling Heat Shock


title: DS22138 PE DNaseI-seq 7 day old seedling Dark


title: DS22138 SE DNaseI-seq 7 day old seedling Dark


title: DS21094 SE DNaseI-seq 7 day old seedling Control


title: DS22140 PE DNaseI-seq 7 day old seedling Dark 30min light


title: DS20412 PE DNaseI-seq 7 day old seedling Dark 3hr light


title: DS20412 SE DNaseI-seq 7 day old seedling Dark 3hr light


title: Denatured (95C) rep2

description:
Sample 6
processed data files: Feb13_DenaturedAll_1_15_Plus.wig,
Feb13_DenaturedAll_1_15_MINUS.wig,
ACden1_LateJune12res_sc-rrna.align18sRNAnoMiss.wig,
r25sDMS_ACden1_LateJune12res_sc-rrna.align.wigFiveCount.wig


title: DS22140 SE DNaseI-seq 7 day old seedling Dark 30min light


title: DS20968 SE DNaseI-seq 7 day old seedling Dark 24hr


title: DS20968 PE DNaseI-seq 7 day old seedling Dark 24hr


title: WT_H3K9me2_LJ_ChIP

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
ChIP-seq: Reads were mapped to the TAIR10 genome by allowing up to 2 mismatches, and only retaining uniquely mapping reads using Bowtie (Langmead et al., 2009). Reads mapping to identical locations were collapsed in to one read.
supplementary_files_format_and_content: ChIP-seq: Column 1 is chromosome. Column 2 is the genomic strand(+/-) the read mapped to. Column 3 is the genomic coordinate the read mapped to.
Genome_build: TAIR10

source_name: 3 wk leaves

growth_protocol: Plants were grown under continuous light

extract_protocol: ChIP-seq:One gram of tissue was ground in liquid nitrogen, and ChIP was performed as previously described (Law et al., 2013) using the following antibodies: H3K9me2 (Abcam 1220), H3 (Abcam 1791), H3K9me1 (Upstate 07-450), and H3K23ac (Millipore 07-355). Libraries were generated and sequenced following manufacturer instructions (Illumina).

tag: ecotype

tag: age

value: 3 weeks

value: leaves


title: suvh456_smRNA

description: Small RNA

data_processing:
smRNA-seq: Sequencing adapters were clipped off and reads were mapped to the TAIR10 genome by allowing no mismatches, and only retaining uniquely mapping reads using Bowtie (Langmead et al., 2009).
supplementary_files_format_and_content: smRNA-seq: Column 1 is chromosome. Column 2 is the genomic strand(+/-) the read mapped to. Column 3 is the genomic coordinate the read mapped to. Column 4 is the length of the read.
Genome_build: TAIR10

source_name: Flowers

extract_protocol: smRNA-seq: Total RNA was extracted from 0.2 g of flowers using Trizol (Invitrogen). siRNAs were purified as previously described (Lu et al. 2007) with the following modifications. To precipitate high molecular weight RNAs, 25% PEG was added to a final concentration of 12.5% instead of 5% PEG. For small RNA purification from LMW RNA, SYBR® Gold was used to stain the gel. The gel was crushed using Gel Breaker Tubes (IST Engineering Inc), and the debris was filtered using 5 µm Filter tubes (IST Engineering Inc). The final elution of the RNA was done in 5 µL of nuclease-free H2O for subsequent generation of libraries for high throughput sequencing. Libraries were generated and sequenced following manufacturer instructions (Illumina TruSeq Small RNA Sample Preparation Kits).

value: flowers


title: cmt2_smRNA

description: Small RNA


title: drm12cmt3_smRNA

description: Small RNA


title: WT_smRNA

description: Small RNA


title: DS19992 SE DNaseI-seq 7 day old seedling Control

value: seedling


title: drm12cmt23_BS

data_processing:
Bisulfite-seq: Analyzed exactly as previously described (Stroud et al., 2013), by allowing up to 2 mismatches using BS seeker (Chen et al., 2010).
supplementary_files_format_and_content: Bisulfite-seq:  Column 1 is chromosome (1..5).  Column 2 is the coordinate of the genomic cytosine. Column 3 is genomic strand (+/-) of the cytosine. Column 4 is context (CG, CHG, or CHH) of the genomic cytosine. Column 5 is the #Cs. Column 6 is the #Ts.
Genome_build: TAIR10

extract_protocol: Bisulfite-seq: 0.1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated and sequenced as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).


title: cmt2-3_BS


title: cmt23_BS


title: WT_BS


title: suvh456_H3K23ac_ChIP


title: suvh456_H3K9me2_ChIP


title: suvh456_H3_ChIP


title: drm12cmt23_H3K23ac_ChIP


title: drm12cmt23_H3_ChIP


title: drm12cmt23_H3K9me2_ChIP


title: WT_H3K23ac_ChIP


title: suvh456_mRNA_rep2

data_processing:
mRNA-seq: Reads were mapped using Bowtie (Langmead et al., 2009) allowing up to 2 mismatches, and uniquely mapping reads were retained.
supplementary_files_format_and_content: mRNA-seq: Wiggle format files with normalized read densities calculated in 25 bp bins. Normalized reads were calculated by # reads/0.1kb/uniquely mapping readsx10^6.
Genome_build: TAIR10

extract_protocol: mRNA-seq: RNA-seq experiments were performed in two biological replicates for each genotype. Tissue was ground in Trizol (Invitrogen).  Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina Truseq).


title: WT_H3K9me2_ChIP


title: suvh456_mRNA_rep1


title: drm12cmt23_mRNA_rep2


title: drm12cmt23_mRNA_rep1


title: WT_H3K9me1_LJ_ChIP


title: WT_H3_ChIP


title: drm12cmt23_smRNA

description: Small RNA


title: drm12cmt2_mRNA_rep1


title: drm12cmt3_mRNA_rep1


title: drm12cmt3_mRNA_rep2


title: drm12cmt2_BS


title: cmt23_mRNA_rep2


title: cmt23_mRNA_rep1


title: cmt3_mRNA_rep2


title: Sample 2 (3794)

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

institute: University of Arkansas at Little Rock

description: replicate 1

data_processing:
Illumina Casava1.7 software was used for basecalling.
Due to low quality score (less than 30) 50 nt were trimmed from the 5' end of each read with fastx_clipper tool from fastx_toolkit v0.0.6
Trimmed reads were mapped to TAIR10 whole genome using TopHat v1.3.2 with parameters -g 1 -p 16 -r 200
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated and changes in gene expression were detected using the Cuffdiff program with default parameters, BAM files with alignments and TAIR10_GFF3_genes.gff file with genome annotation obtained from http://www.arabidopsis.org/.
Genome_build: TAIR10
Supplementary_files_format_and_content: expression.txt is a tab-delimited text file (linked as a supplementary file on the Series record) that includes gene and FPKM values for sample 1 and sample 2

source_name: leaves of Arabidopsis Atclb1-1 loss of function mutant

growth_protocol: Mutant and wild type Arabidopsis plants were grown in growth chamber with a 16-h photoperiod at 23/23 C (day/night).

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA). RNA quality was assessed by checking the integrity of 18S and 28S rRNA bands on 1% agarose gel and quantified using a nano-drop. One microgram from each RNA sample was then subjected to next generation sequencing in a Genome Analyzer
library was constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Two-week-old wild type (ecotype Colombia) as well as from a previously characterized homozygous T-DNA knockout (KO) mutant of AtCLB gene (Atclb1-1) of Arabidopsis were collected. Leaves of both lines were frozen in liquid nitrogen for future RNA isolation.

value: Columbia

tag: genotype/variation

value: Atclb1-1 loss of function mutant


title: cmt3_mRNA_rep1


title: cmt2_mRNA_rep2


title: WT_mRNA_rep2


title: cmt2_mRNA_rep1


title: drm12_mRNA_rep2


title: drm12_mRNA_rep1


title: yeast_sono_seq_2_(20121109_8_10)

status: Public on Dec 14 2013

city: Seattle

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: (Replicate 2) Log-phase S. cerevisiae cells were cross-linked in culture with 1% formaldehyde for 15 minutes at room temperature, nuclei were isolated, and subject to sonication.

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: Cross-linked and sonicated chromatin

extract_protocol: Sono-seq: PMID 19706456. Log-phase S. cerevisiae cells were cross-linked in culture with 1% formaldehyde for 15 minutes at room temperature, nuclei were isolated, and subject to sonication.

tag: strain

value: S. cerevisiae W1588-4C strain carrying Reb1-3XFLAG


title: Abf1_600mM_2_Inp_(20121109_8_6)

description: (Replicate 2) Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction.

source_name: Native input chromatin

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction.

value: S. cerevisiae W1588-4C strain carrying Abf1-3XFLAG


title: yeast_sono_seq_1_(20121109_8_9)

description: (Replicate 1) Log-phase S. cerevisiae cells were cross-linked in culture with 1% formaldehyde for 15 minutes at room temperature, nuclei were isolated, and subject to sonication.


title: drm12cmt2_mRNA_rep2


title: Abf1_600mM_1_Inp_(20121109_8_5)

description: (Replicate 1) Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction.


title: Abf1_600mM_2_IP_(20121109_8_8)

description: (Replicate 2) Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.

source_name: Native-ChIPped chromatin

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.

tag: antibody

value: M2 anti-FLAG


title: Abf1_600mM_1_IP_(20121109_8_7)

description: (Replicate 1) Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.


title: Abf1_80mM_Inp_(20120921_7_3)

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 80 mM salt by needle extraction.


title: Sample 1 (3785)

description: replicate 1

source_name: leaves of wild type Arabidopsis

value: wild type


title: Reb1_600mM_2_Inp_(20121109_8_2)

description: (Replicate 2) Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction.

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction.


title: Reb1_150mM_IP_(20120921_7_6)

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.


title: Reb1_600mM_1_Inp_(20121109_8_1)

description: (Replicate 1) Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction.


title: Reb1_600mM_2_IP_(20121109_8_4)

description: (Replicate 2) Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.


title: Reb1_150mM_Inp_(20120921_7_5)

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction.


title: WT_mRNA_rep1


title: Psq_80mM_2_(20130104_8_6)

description: (Replicate 2) Drosophila S2 cell nuclei were isolated and subjected to MNase digestion for 10 minutes prior to chromatin extraction in 80 mM salt and native ChIP with anti-Pipsqueak antibody.

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release 5.30 (Sep 2010) of the D.Melanogater genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .bedgraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

organism: Drosophila melanogaster

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Drosophila S2 cell nuclei were isolated and subjected to MNase digestion for 10 minutes prior to chromatin extraction in 80 mM salt and native ChIP with anti-Pipsqueak antibody.

tag: cells

value: S2 cells

value: anti-Pipsqueak


title: Psq_80mM_1_(20130104_8_5)

description: (Replicate 1) Drosophila S2 cell nuclei were isolated and subjected to MNase digestion for 10 minutes prior to chromatin extraction in 80 mM salt and native ChIP with anti-Pipsqueak antibody.


title: Reb1_80mM_IP_(20120921_7_10)

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 80 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.


title: Reb1_80mM_Inp_(20120921_7_9)

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 80 mM salt by needle extraction.


title: IPIrf8onWT

city: Saint Louis

first: Kenneth

middle: M

last: Murphy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned using Novoalign (Novocraft Technologies) to build version NCBI37/mm9 of the mouse genome. Alignments were carried out using the following parameter "-o SAM -r random -l 30 -e 100 -a AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG  -H."
Peaks were called with Model based analysis of ChIP-Seq (MACS v1.4.2) peak finding algorithm.  A maximum of 1 duplicate tag and a p-value cutoff of 1x10-9 was used for all data sets.  Background estimates were made using ChIP-Seq on Irf8-/- DCs as the control.
Peak annotation and de novo motif discovery was performed with Homer software package.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command and default settings.

organism: Mus musculus

source_name: Flt3 ligand derived dendritic cells

growth_protocol: Bone marrow cells were obtained by flushing femurs and tibias of mice.  After lysing red blood cells, whole bone marrow was cultured in 200 ng/mL Flt3 ligand (Peprotech) for 10 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and IRF8-DNA complexes were isolated with antibody.
ChIP DNA was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs, and underwent amplification for 15 cycles.

tag: genotype

value: ICSBP Antibody (Santa Cruz biotechnology inc., C-19)

value: DC


title: R-red

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

country: Japan

institute: Shinshu University

data_processing:
Basecalls performed using CASAVA version 1.7
Small RNA sequences (15-29nt) were extracted after adapter sequence  trimming and count using Small RNA analysis tool in CLC Genomics Workbench ver 5.5.1 software (CLC bio).
Supplementary_files_format_and_content: tab-delimited text files include small RNA sequences and count

organism: Petunia x hybrida

source_name: Petal tissues

extract_protocol:
Tissues were frozen with liquid nitrogen and extracted with RNA extraction buffer (Goto et al., 2003 Plant Mol Biol Rep, 21, 51-58). Low-molecular-weight RNA was isolated through precipitations with LiCl, PEG and ethanol.
Low-molecular-weight RNA was ligated to 5′- and 3′-RNA adapters, reverse transcribed, and amplified by PCR using a Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol except that we separated small RNAs by electrophoresis on a 3% agarose gel instead of an acrylamide gel.

tag: line

value: Red Star

value: Red petal

tag: Stage

value: Before flower buds open


title: Abf1_80mM_IP_(20120921_7_4)

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Abf1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 80 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.


title: IPIrf8onBatf3KO

tag: chip antibody

tag: cell type


title: IPIrf8onIrf8KO


title: Reb1_600mM_1_IP_(20121109_8_3)

description: (Replicate 1) Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.


title: Reb1_150mM_yeast_fly_mixed_2_IP_(20121214_7_3)

description: (Replicate 2) Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. We also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary files .bam) 2. We extracted properly paired reads that were only mapped to one organism (Supplementary files .bed).

organism:
Saccharomyces cerevisiae
Drosophila melanogaster

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.

value: Mixture of S. cerevisiae W1588-4C strain carrying Reb1-3XFLAG and Drosophila S2 cells


title: GAF_80mM_2_(20130104_7_5)

description: (Replicate 2) Drosophila S2 cell nuclei were isolated and subjected to MNase digestion for 10 minutes prior to chromatin extraction in 80 mM salt and native ChIP with anti-GAGA binding factor antibody.

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Drosophila S2 cell nuclei were isolated and subjected to MNase digestion for 10 minutes prior to chromatin extraction in 80 mM salt and native ChIP with anti-GAGA binding factor antibody.

value: anti-GAGA binding factor


title: J-white

value: J-type

value: White petal


title: InVitro_Chemseq_JQ1S_20

status: Public on Dec 13 2013

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chem-Seq with JQ1.20_062612
TAGCTT

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 treatment

tag: antibody catalog number

value: Chem-Seq


title: InVitro_Chemseq_JQ1S_80

description:
Chem-Seq with JQ1.80_062612
CTTGTA


title: Reb1_150mM_yeast_fly_mixed_1_IP_(20121214_7_12)

description: (Replicate 1) Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.


title: RNA-seq 256-cell

city: Shanghai

first: Yong

last: Zhang

address: 1239 Siping Road

country: China

institute: Tongji University

description: Sample 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to zv9 whole genome using tophat v1.1.4 with parameters --mate-inner-dist 200 --mate-std-dev=18 --solexa-quals --library-type fr-unstranded --no-novel-juncs.
RPKM were calculated using Cufflinks v1.1.0 with parameters --frag-bias-correct --multi-read-correct.
Genome_build: zv9
Supplementary_files_format_and_content: Tab-delimited text file include abundance measurements (RPKM values) and corresponding Ensembl gene IDs.

organism: Danio rerio

source_name: embryos

growth_protocol: Zebrafish were maintained and raised under standard conditions. Wild-type embryos were collected at the 1-cell stage, synchronized and allowed to develop to the desired stage at 28°C.

extract_protocol:
Total RNA was isolated using the standard Trizol (Invitrogen) protocol. Two rounds of PolyA+-RNA purification were performed for each sample, using the PolyA(Purist)TM-MAG kit (Ambion). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bioanalyzer. Strand-specific libraries for 76 bp paired-end sequencing were prepared according to a modified UTP-method (Parkhomchuk et al. 2009), as detailed in (Levin et al. 2010).
Libraries were prepared using the Illumina sequencing library preparation protocol.

tag: developmental stage

value: 2.5 hpf (256-cell stage)


title: GAF_80mM_1_(20130104_7_2)

description: (Replicate 1) Drosophila S2 cell nuclei were isolated and subjected to MNase digestion for 10 minutes prior to chromatin extraction in 80 mM salt and native ChIP with anti-GAGA binding factor antibody.


title: MM1S_WCE_forCDK8

description: Sonicated nuclear extract_CDK8

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For samples ChIPab_H3K27me3_MM1S_071713 and ChIPab_H4K20me3_MM1S_071713 reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
For samples CDK8_ChipSeq and Input_CDK8_ChipSeq 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.

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

tag: cell line

value: Input

tag: barcode removed

value: ACTTGA


title: MM1S_CDK8

description: Chromatin IP against CDK8

value: Santa Cruz

value: CAGATC


title: MM1S_H4K20me3

description: ChIP-seq with ab_H4K20me3_MM1S_071713

value: Abcam

value: ACAGTG


title: MM1S_BioPsoralen_forBioPsoralen

description: Chromatin IP against Chem.nu_2h.10uM.bPSO.px

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 -n 2 -e 70 -m 2 -k 2 --best -l 40. 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.

value: Multiple myeloma

tag: treatment

value: Biotinylated compound BIO-PSORALEN

value: AGTTCC


title: MM1S_DMSO_forBioPsoralen

description: Chromatin IP against Chem.nu_2h.DMSO.px

value: Bio-Psoralen BIO-PSORALEN

value: AGTCAA


title: Reb1_150mM_yeast_fly_mixed_2_Inp_(20121214_7_1)

description: (Replicate 2) Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction.

extract_protocol: See ORGANIC_profiling_protocol.rtf for protocol with references. Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction.

value: Mixture of S. cerevisiae W1588-4C strain carrying Reb1-3XFLAG and Drosophila S2 cells


title: MM1S_BRD3_rep2

description:
Chromatin IP against ChIP368_BRD3.2_MM1S_071713
08142013_C2C55ACXX_5.GATCAG

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.
Whole cell extracts were sonicated to solubilize the chromatin.

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat. #

value: GATCAG


title: MM1S_H3K27me3

description: Chromatin IP against ChIPab_H3K27me3_MM1S_071713

value: TTAGGC


title: MM1S_BRD3_AB367A

description:
Chromatin IP against BRD3
05012013_C22WBACXX_3.AGTTCC


title: MM1S_BRD3_rep3

description:
Chromatin IP against ChIP368_BRD3.3_MM1S_071713
08142013_C2C55ACXX_5.TAGCTT

value: TAGCTT


title: MM1S_WCE_forBRD3rep1-3

description:
Input for BRD3_071713
08142013_C2C55ACXX_5.AGTTCC


title: MM1S_WCE_forBRD2rep1-BRD3AB367A

description:
Input for BRD2/3_040213
05012013_C22WBACXX_3.GGCTAC

value: GGCTAC


title: MM1S_WCE_forBRD2rep2-3

description:
Input for BRD2.H3.H4_071713
08142013_C2C55ACXX_4.CAGATC


title: R-white

value: Red Star

tag: tissue

value: White petal

value: Before flower buds open


title: MM1S_BRD2_rep1

description:
Chromatin IP against BRD2
05012013_C22WBACXX_3.CTTGTA

value: Cell Signaling

value: CTTGTA


title: Reb1_150mM_yeast_fly_mixed_1_Inp_(20121214_7_7)

description: (Replicate 1) Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction.


title: MM1S_BRD2_rep2

description:
Chromatin IP against ChIPcs_BRD2.1_MM1S_071713
08142013_C2C55ACXX_4.ATCACG

value: ATCACG


title: J-purple

value: J-type

value: Purple petal


title: MM1S_BRD2_rep3

description:
Chromatin IP against ChIPcs_BRD2.2_MM1S_071713
08142013_C2C55ACXX_4.CGATGT

value: Multiple myeloma

value: CGATGT


title: InVivo_Chemseq_JQ1S_0mins

description: InVivoChem-Seq bio-JQ1 timecourse_0min

tag: sample type

value: In Vivo

tag: time

value: 0 min


title: InVitro_Chemseq_JQ1R

description: Chem-Seq with JQ1R

value: In Vitro


title: InVivo_Chemseq_JQ1S_30min

description: InVivoChem-Seq bio-JQ1 30min

treatment_protocol: Cells were treated with 5uM bio-JQ1 for 30 min before addition of Formaldehyde

value: 30 min


title: InVivo_Chemseq_JQ1S_20mins

description: InVivoChem-Seq bio-JQ1 timecourse_20min

treatment_protocol: Cells were treated with 5uM bio-JQ1 for 20 min before addition of Formaldehyde

value: 20 min


title: InVitro_Chemseq_Control_forAT7519

description: Chemseq against DMSO-treated MM1S Cells or 24 hours

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 precipitated using biotinylated compound that had been pre-bound to streptavidin beads (invitrogen). 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: DMSO

value: DMSO


title: InVitro_Chemseq_JQ1S

description: Chem-Seq JQ1S


title: InVivo_Chemseq_Control

description: InVivoChem-Seq bio-JQ1 timecourse_Untreated

value: control


title: InVitro_Chemseq_AT7519

description: Chemseq against 25uM CDK9i (AT7519)-treated MM1S Cells for 24 hours

growth_protocol: 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.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments were precipitated using streptavidin beads (invitrogen). 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.


title: InVitro_Chemseq_Control

description: Chem-Seq with DMSO


title: MM1S_RNAPol2_AT7519_ChipSeq

description: Chromatin IP against RNAPol2_MM1S_AT7519

treatment_protocol: Treated with AT7519 (2uM for 6 hours), Cdk9 inhibitor

value: RNA Pol II (Rpb1 N-terminus)

tag: chip antibody catalog number

tag: chip antibody manufacturer

value: Santa Cruz

tag: duration

tag: concentration

tag: drug

value: GTCCGC


title: MM1S_WCE

description: WCE

tag: chip antibody

value: None WCE

value: ACTTGA


title: MM1S_WCE_DMSO_forCdk9i

treatment_protocol: Treated with DMSO (for 6 hours), use with Cdk9 inhibitor studies

value: GTTTCG


title: MM1S_WCE_AT7519

value: CGTACG


title: MM1S_BRD4

description: Chromatin IP against BRD4

value: Bethyl

value: AGTTCC


title: MM1S_CTCF

description: Chromatin IP against MM1S_WT_CTCF_JL

value: CTCF

value: Upstate 07-729

value: ATCACG


title: MM1S_RNAPol2_DMSO_forCdk9i

description: Chromatin IP against RNAPol2_MM1S_DMSO_forCdk9i

value: CCGTCC


title: MM1S_BRD3_rep1

description:
Chromatin IP against ChIP368_BRD3.1_MM1S_071713
08142013_C2C55ACXX_5.ACTTGA

tag: cell type

value: Multiple myeloma


title: Day 55, rep a

city: Blacksburg

first: Delasa

last: Aghamirzaie

state: VA

address: 101L Price Hall, Virginia Tech

department: GBCB

institute: virginia Tech

data_processing:
Illumina TruSeq used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hard-masked genome using Tophat which internally uses bowtie. Tophat was run with all default parameters except -r = 60
Reads were concatenated using Cufflinks, and the assmblies were merged using Cuffmerge.
Cuffdiff2 was used for testing differential expression between samples.
Genome_build: G. max reference genome provided in Phytozome v8.0 (Gmax_109)
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each Sample during time course together with p-values comparing each time point with its previous time point.

organism: Glycine max

source_name: Embryo

growth_protocol: 11/13 hour day/night photoperiod, 28/22°C day/night temperatures with light intensities between 350 and 450 μE and the relative humidity 70%.

extract_protocol:
Embryos were harvested and immediately frozen in liquid nitrogen until extration for total RNA with Qiagen RNeasy Plant Mini kit (catalog # 74904) and eluted in 32 microliter water.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocol by sequencing facility at Genome Quebec, Quebec, Canada

treatment_protocol: Normal growth (irrigation every 2-3 days; fertilization with Peter's Professional 20-10-20 once at 3 weeks post potted and the other time 6 weeks post potted)

tag: strain

value: cultivar Williams 82

value: embryo

tag: age

value: 55 days post initial seed size of 3-4 mm long

tag: genotype

value: wild type


title: Day 45, rep c

value: 45 days post initial seed size of 3-4 mm long


title: Day 45, rep a


title: Day 40, rep c

value: 40 days post initial seed size of 3-4 mm long


title: Day 45, rep b


title: Day 35, rep a

value: 35 days post initial seed size of 3-4 mm long


title: Day 55, rep b


title: Day 40, rep b


title: Day 55, rep c


title: Day 30, rep c

value: 30 days post initial seed size of 3-4 mm long


title: Day 35, rep c


title: Day 30, rep a


title: Day 25, rep b

value: 25 days post initial seed size of 3-4 mm long


title: Day 25, rep c


title: Day 30, rep b


title: Day 20, rep c

value: 20 days post initial seed size of 3-4 mm long


title: Day 20, rep b


title: Day 25, rep a


title: Sample_264C45LB

city: Pullman

first: Devendra

middle: H

last: Shah

address: #402, Bustad Hall

department: Veterinary Microbiology and Pathology

institute: Washington State University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (single-end) were mapped to S. Enteirtidis  whole genome (AM933172) using CLC-Bio Workbench version 5.0 with following parameters: minimum of 75 bp wihth allowance up to two mismatches and >90% of the each reads length had to map to the reference sequence to be considred as mapped reads.
Genes with zero reads were removed and the total raw read counts were used for data analysis using EdgeR and DESeq statistical packages for differential gene expression analysis
Genome_build: GenBank: AM933172.1
Supplementary_files_format_and_content: Tab-delimited text file includes total raw read counts values for all samples

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: poultry-associated field strains of S. Enteritidis grown in laboratory media at avian body temperature (42°C)_LP

growth_protocol: S. Enteritidis strains were grown at avian bpdy temperature (42C) in luria bertani broth

extract_protocol:
Bacterial cells wer epelleted and RNA was extracted using Ribopure Bacterial Kit (Ambion, USA), DNAse treated and ribosomal RNA was removed using DNS protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment

tag: phenotype

value: Low-pathogenic (LP)

tag: phenotype id

tag: serovar

value: Enteritidis


title: Day 20, rep a


title: Sample_264BC8LB

source_name: poultry-associated field strains of S. Enteritidis grown in laboratory media at avian body temperature (42°C)_HP

value: High-pathogenic (HP)


title: Sample_264UK1LB


title: Day 15, rep b

value: 15 days post initial seed size of 3-4 mm long


title: Day 15, rep c


title: Sample_264C19LB


title: Day 15, rep a


title: Day 40, rep a


title: Day 35, rep b


title: Sample_264G1LB

value: UK


title: Day 10, rep a

value: 10 days post initial seed size of 3-4 mm long


title: Leaf (+3)

city: Brisbane

first: Peter

middle: Richard

last: Sternes

state: Queensland

address: John Hines Building, University of Queensland, St Lucia

department: School of Agriculture and Food Science

country: Australia

institute: University of Queensland

description: small RNA

data_processing:
Sequencing adapter primers (proprietary) were trimmed using UNIX shell scripting
Sense and antisense matches to known tRNA, rRNA and chloroplast sequences from Rfam, Genomic tRNA, EMBL release 95 and SILVA rRNA databases were removed using UNIX shell scripting
Sequences were counted and displayed as tab delimited files containing a count and the unique sequence per line, using UNIX shell scripting
Supplementary_files_format_and_content: Tab delimited text files containing counts of trimmed and filtered small RNA sequences

organism: Saccharum sp.

source_name: Pooled leaf tissue (third oldest leaf with a visible dewlap) from 3 indenpendent field grown sugarcane plants

extract_protocol:
Total RNA was isolated using TRIsure reagent (Bioline) as per the manufacturer's intstructions
Libraries were constructed using the TruSeq Small RNA kit (Illumina)

tag: cultivar

value: Leaf

tag: tissue type

value: vegetative


title: IN6 (Internode 6)

description: small RNA

source_name: Pooled internode 6 tissue from 3 independent field grown sugarcane plants

tag: tissue

value: internode 6


title: Day 10, rep b

value: cultivar Williams 82

value: embryo


title: Day 5, rep c

value: 5 days post initial seed size of 3-4 mm long

value: wild type


title: IN16 (Internode 16)

description: small RNA

source_name: Pooled internode 16 tissue from 3 independent field grown sugarcane plants

value: internode 16


title: Day 10, rep c


title: Apex

description: small RNA

source_name: Pooled stem apex tissue from 3 independent field grown sugarcane plants

value: stem apex


title: Reference Epigenome: ChIP-Seq Input from Human Psoas Muscle Tissue; renlab.Input.STL003PO.02.01

status: Public on Dec 12 2013

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY311
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17646
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: Psoas Muscle tissue; renlab.Input.STL003PO.02.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sra sample accession

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Psoas Muscle

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Right Atrium Tissue; renlab.H3K4me3.STL003RA.02.01

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Right Atrium Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY305
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17539
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11888
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Atrium tissue; renlab.H3K4me3.STL003RA.02.01

value: Right Atrium

value: Histone H3K4me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Psoas Muscle Tissue; renlab.H3K4me3.STL003PO.02.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY335
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17634
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; renlab.H3K4me3.STL003PO.02.01


title: Day 5, rep a

value: cultivar Williams 82

value: embryo

value: 5 days post initial seed size of 3-4 mm long

value: wild type


title: Day 5, rep b


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Bladder Tissue; renlab.H3K4me3.STL001BL.02.01

description:
sample_term_id: UBERON_0001255
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Bladder Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY329
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17640
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

tag: sample alias

value: Shin Lin, Stanford University

value: Primary Tissue

value: Bladder

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American


title: Reference Epigenome: ChIP-Seq Input from Human Adrenal Gland Tissue; renlab.Input.STL002AD.02.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY309
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17643
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13995
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Adrenal Gland tissue; renlab.Input.STL002AD.02.01

value: iron deficiency, bipolar

value: Adrenal Gland

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: ChIP-Seq Input

value: Biorupter

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Right Ventricle Tissue; renlab.H3K4me3.STL003RV.02.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY335
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17649
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.H3K4me3.STL003RV.02.01

value: Right Ventricle

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Histone H3K4me3

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Adrenal Gland Tissue; renlab.H3K4me3.STL003AD.02.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY301
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17524
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Adrenal Gland tissue; renlab.H3K4me3.STL003AD.02.01

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Ovary Tissue; renlab.H3K4me3.STL002OV.02.01

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY303
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17530
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Ovary

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Aorta Tissue; renlab.H3K4me3.STL003AO.02.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY302
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17527
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Aorta

value: Caucasian


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Psoas Tissue; renlab.H3K4me3.STL001PO.02.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Psoas Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY304
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17533
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; renlab.H3K4me3.STL001PO.02.01

value: Psoas Muscle

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American

value: Biorupter


title: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL002; methylC-seq_STL002SX-01b

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL002
Library name: methylC-seq_STL002SX-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18872
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14062
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Spleen tissue; methylC-seq_STL002SX-01b

extract_protocol: Library construction protocol: One ug of genomic DNA was extracted from frozen ground tissue using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA).  Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 25 ul 2x KAPA HiFi HotStart Uracil+ReadyMix, 2.5 ul Primer 1, 2.5 ul Primer 2 (50 ul final). The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 4-8 cycles of 98C 15 sec, 60C 30 sec and 72C 4 min, ending with one 72C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: Spleen

value: Female

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 ug

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 uM


title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL003; methylC-seq_STL003SB-01b

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL003
Library name: methylC-seq_STL003SB-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18873
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11844
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Small Intestine tissue; methylC-seq_STL003SB-01b

value: Shin Lin, Stanford University

value: Primary Tissue

value: Small Intestine

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)


title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL002; methylC-seq_STL002SB-01b

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL002
Library name: methylC-seq_STL002SB-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18871
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14055
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Small Intestine tissue; methylC-seq_STL002SB-01b

value: iron deficiency, bipolar

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 ug

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Adrenal Gland Tissue; renlab.H3K4me3.STL002AD.02.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY327
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17637
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13995
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Adrenal Gland tissue; renlab.H3K4me3.STL002AD.02.01

value: Shin Lin, Stanford University

value: Adrenal Gland

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Thymus Tissue; renlab.H3K4me3.STL001TH.02.01

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2500 platform.
Library name: CY306
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17536
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Primary Tissue

value: Thymus

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American