title: RNA-Seq_S1

city: Lausanne

first: Swapna

last: Uplekar

address: Station 19, EPFL-GHI-UPCOL

institute: EPFL

description: RNAseq in Stationary phase

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to M.tb H37Rv genome (NCBI accession NC_000962.2) using the Bowtie v0.11.3 with parameters -S -n 1 --best --strata --solexa1.3-quals -a -m 5
Genome_build: NC_000962.2
Supplementary_files_format_and_content: Wig files contain reads mapping to forward and reverse strands normalized to the total number of reads

organism: Mycobacterium tuberculosis

source_name: Stationary phase Mtb H37Rv cells

growth_protocol: Mycobacterium tuberculosis H37Rv was grown at 37°C in 7H9 broth (Difco) supplemented with 0.2% glycerol, 0.05% Tween 80 and 10% albumin-dextrose-catalase (ADC, Middlebrook) or on 7H10 plates supplemented with 0.5% glycerol and 10% oleic acid-albumin-dextrose-catalase (OADC, Middlebrook). Logarithmic-phase cultures (exponential phase) were harvested at an optical density (OD600) of 0.4-0.6, stationary phase cultures were collected four weeks later.

extract_protocol: 100 ng of total RNA from exponential and stationary phase were mixed with 5x Fragmentation buffer (Applied Biosystems), incubated for 4 minutes at 70°C and then transferred immediately on ice. RNA was purified using RNAClean XP beads (Beckman Coulter), according to the manufacturer’s recommendations, and subsequently treated with Antarctic phosphatase (New England Biolabs). RNA was then re-phosphorylated at the 5’-end with polynucleotide kinase (New England Biolabs) and purified with Qiagen RNeasy MinElute columns. In order to ensure strand-specificity, v1.5 sRNA adapters (Illumina) were ligated at the 5’- and 3’-ends using RNA ligase. Reverse transcription was carried out using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). Twelve cycles of PCR amplification using Phusion DNA polymerase were then performed and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions.

treatment_protocol: Forty milliliters of either exponential or stationary phase M. tuberculosis cultures were pelleted and cells were flash frozen in liquid nitrogen and stored at -80°C until use. Bacteria were re-suspended in 1 ml Trizol (Invitrogen) and added to a 2-ml screw-cap tube containing 0.5 ml zirconia beads (BioSpec Products). Cells were disrupted by bead-beating twice for 1 minute with a 2-minute interval on ice. The cell suspension was then transferred to a new tube, where chloroform-isoamylalcohol (24:1) extraction was performed. RNA was precipitated by adding 1/10 volume of sodium acetate (2 M, pH 5.2) and 0.7 volume of isopropanol, washed with 70% ethanol, air-dried and resuspended in DEPC-treated water. DNase treatment was carried out twice using RQ1 RNase-free DNase (Promega), following the manufacturer’s recommendations, and the reactions were subsequently cleaned up by phenol-chloroform extraction and ethanol precipitation.

tag: growth phase

value: stationary


title: Mp708 Treated Midgut Replicate E

status: Public on Dec 01 2012

type: SRA

city: University Park

first: Howard

middle: W

last: Fescemyer

state: PA

address: 208 Mueller Lab

department: Biology

country: USA

institute: The Pennsylvania State University

library_source: transcriptomic

data_processing:
Filtering and Trimming: SOLiD sequence reads were filtered using NextGENe® version 2.0 (SoftGenetics, State College, PA).  Reads accepted had a median score threshold ≥12, contained ≥25 bases and contained one or more bases with a score ≥14.
Reference preparation: The 138911 Sanger ESTs in SPODOBASE (http://bioweb.ensam.inra.fr/spodobase) were assembled into a reference transcriptome using SeqMan Pro version 8.0.2 (DNASTAR Lasergene®, Madison, WI) and default parameters for Sanger sequences as recommended by the manufacturer.  Preassembly involved a medium end trim, a vector scan and contaminant sequence screen that used a minimum of 5 mismatches; vector and contaminant sequence catalogs were those provided by the software.  Assembly parameters were match size of 25, minimum match of 85%, match spacing of 150, minimum sequence length of 100, gap penalty of zero, gap length of 0.7 and maximum mismatch end bases of 15.  Consensus calling used primary trace evidence of 50%, a majority of 75%, and quality weights of nine before and 400 after.  Calling conflicts and single nucleotide polymorphisms (SNPs) used a minimum coverage of four, minimum inconsistency of 25% and two bases, and no pairing was specified.  The assembled reference contained 7869 contigs (7,049,947 nt) that more correctly should be considered gene models.
Mapping: The reads from each library representing a replicate within a maize inbred treatment were mapped separately to the reference transcriptome using the Bowtie-like algorithm in NextGENe® with the requirement that 85% of 12 or more nucleotides comprising a read must match the reference.  A read was allowed to map only once (i.e., no ambiguous mapping).  The number of mapped reads per gene in each library, representing a replicate within a maize inbred treatment, were summed by NextGENe® as read counts per gene.  These data representing transcript abundance were subsequently used in differential expression analyses.
Differential expression: The R software package (v2.15.0) was used to confirm the overall data quality (frequency distribution histogram plots, hexagonal binning plots with R hexbin package v1.26.0, MA plots with R edgeR package v2.6.7, complete linkage cluster dendrogram plots, frequency histograms of Fisher’s exact test P-values with R SAGEnhaft package v1.22.0), filter low expressing genes, and normalize the read counts.  Low expressing genes were filtered by summing raw read counts per gene across replicate libraries within a maize inbred treatment; a gene was deleted when this sum for either treatment was less than 20.  The filtered read count data were normalized using the trimmed mean of M values (TMM) method as follows; a scaling factor was computed for each replicate library within a maize inbred treatment via the normFact routine in edgeR using filtered read count data and the A-replicate of the Tx601 treatment as a reference.  Filtered counts for each gene within a mapped library were divided by the product of the scaling factor multiplied by the library size. Normalized read counts were used to perform two-tailed paired t-tests for each gene.  Estimated P-values from each t-test and log2 fold change values for each gene were used to create a volcano plot.  False discovery rate for differentially expressed genes was set at an experiment-wide rate of 5% using the Q-value method (R qvalue package v1.18.0).
Orthologous functional annotation: Functional annotation of contigs in the reference used an approach that first obtained a full-length lepidopteran ortholog (BLASTx) against predicted proteins from the whole genome sequence of Bombyx mori [SilkDB version 2.0).  These protein orthologs were in turn used to search (BLASTp) and obtain functional orthologs from Drosophila melanogaster (predicted proteins in Flybase release FB2012_04).  Functional annotations of genes with significant differential expression were compared to those of all midgut genes in the filtered read count dataset using GO analysis (DAVID v6.7).
Genome_build: Not applicable
Supplementary_files_format_and_content: A tab delimited text file (Filtrd&NormalizdReadCountsSeqsAnnot.txt) contains processed data used to form conclusions in the published manuscript.  This file contains information about the reference contigs to which sequence reads were mapped (e.g., contig assembly data, contig sequence, best-hit BLAST annotation results) is given in the data table in addition to the final processed mRNA-seq data (e.g., raw and normalized read counts, t-test P-values, fold differences).  The file only contains data for contigs that passed the low expressing gene filter.
Supplementary_files_format_and_content: The matched.csfasta contain processed reads consisting of filtered and trimmed sequence reads that mapped to the reference transcriptome.

molecule: total RNA

organism: Spodoptera frugiperda

source_name: Midgut tissue from last instar larvae fed on resistant Mp708 maize

growth_protocol: Beginning as neonates, fall armyworm larvae used in the mRNA-seq experiment were reared on yellow-green midwhorl foliage from resistant Mp708 maize or susceptible Tx601 maize.  Old foliage and frass were removed every other day and replaced with fresh foliage.

extract_protocol:
Isolation of total RNA was performed separately for each midgut from an individual larva.  Nearly all RNAlater® was removed after centrifugation.  Several 2.3 mm diameter stainless steel beads were added to the concial tube containing a midgut and everything was frozen in liquid nitrogen.  Tubes were transferred to adapter blocks prechilled at -20°C and tissue was first disrupted (20 Hz, 45 sec) and then homogenized in TRIzol® reagent (20 Hz, 3 min) on a mixer milll.  Isolation of RNA from the homogenate followed the TRIzol manufacturer’s protocol (Invitrogen), except for additional acid phenol:chloroform:isoamyl alcohol (25:24:1, v:v:v) and chloroform phase separation steps prior to RNA precipitation to reduce DNA contamination.  Agilent Bioanalysis (RNA Nano Chip) indicated that the isolated total RNA had no detectable DNA contamination and RNA integrity numbers ranged from 8.3 to 9.7.  Equal amounts (3 µg) of total RNA from an individual MG were randomly pooled into three replicates per treatment (i.e., Mp708 or Tx601) such that each treatment replicate derived from 12-13 MGs.  Each pool of total RNA was separately enriched for poly(A+) RNA using the MicroPoly(A)Purist™ Kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions.  Enrichment involved two rounds of oligo(dT) selection with a fresh spin column used in each round.  The resulting poly(A+) RNA showed little degradation of the mRNA with a broad peak ranging from 200 nt to 5000 nt centered at about 1880 nt (Agilent Bioanalyzer RNA Pico Chip).  Estimated rRNA contamination ranged from 3.2% to 6.1%.
The Penn State Genomics Core Facility (University Park, PA) prepared transcriptome libraries and performed sequencing.  Libraries were separately prepared from each of the six poly(A+) RNA samples using the strand-specific SOLiD™ Total RNA-Seq Kit (Applied Biosystems) according to the manufacturer’s protocol.  Briefly, samples were fragmented with RNAse III and purified.  Fragmented RNA (100 ng) was ligated overnight to adaptors and subsequently reverse transcribed.  Purified cDNA was size selected and then amplified using barcoded primers.  The resulting material was purified and assessed for proper amplification using an Agilent Bioanalyzer DNA 1000 chip (Agilent Technologies).
Barcoded libraries were combined in equimolar quantities and prepared for sequencing according to the “Applied Biosystems SOLiD 3 Plus System Templated Bead Preparation Guide.”  Barcode sequencing and fragment library sequencing (50 bp) was performed on a full plate run of the SOLiD 3 Plus System according to the “Applied Biosystems SOLiD 3 Plus System Instrument Operation Guide.”

treatment_protocol: Larvae were reared in an environmental chamber at 27°C, 14:10 (light:dark) photoperiod, and 70% relative humidity.  Midguts were dissected from feeding larvae 2 d after molting to the last instar with masses between 300 and 400 mg.  Dissections were done with cold anesthetized larvae submerged in Bombyx saline.  After removing Malpighian tubules, foregut anterior to the stomodial valve, hindgut and food bolus, the midgut was transferred from the body cavity, rinsed well with cold saline, and preserved in RNAlater®.

tag: insect strain

value: Corn Strain

tag: tissue

value: midgut

tag: Stage

value: last instar larvae

tag: treatment

value: reared on susceptible Mp708 maize


title: RNA-Seq_E2

country: Switzerland

description: RNAseq in Exponential phase

source_name: Log phase Mtb H37Rv cells

tag: strain

value: exponential


title: Mp708 Treated Midgut Replicate F


title: Input_DNA1

description: input DNA

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to M.tb H37Rv genome (NCBI accession NC_000962.2) using the Bowtie v0.11.3 with parameters -S -n 3 --best --strata --solexa1.3-quals -a -m 10
Genome_build: NC_000962.2
Supplementary_files_format_and_content: Reads mapping to the forward and reverse strands were shifted by 80bp and merged to generate a single ChIP-seq profile, represented as a bedgraph file

molecule: genomic DNA

extract_protocol: Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with either anti-RpoB or anti-NusA antibodies. Libraries were prepared according to Illumina's instructions.

treatment_protocol: M. tuberculosis cultures, either in exponential or stationary phase, were cross-linked with 1% formaldehyde for ten minutes at 37°C.

tag: chip antibody

value: exponential phase


title: Input_DNA2

description: input DNA

source_name: Stat phase Mtb H37Rv cells

value: stationary phase


title: RNA-Seq_E1

description: RNAseq in Exponential phase


title: NusA_CS_Stat2

description: Chromatin IP against NusA

value: anti-NusA


title: NusA_CS_Exp2

description: Chromatin IP against NusA


title: NusA_CS_Stat1

description: Chromatin IP against NusA


title: RNAP_CS_Stat2

description: Chromatin IP against RNAP

value: anti-RpoB


title: NusA_CS_Exp1

description: Chromatin IP against NusA


title: RNAP_CS_Exp2

description: Chromatin IP against RNAP


title: RNAP_CS_Exp1

description: Chromatin IP against RNAP


title: Tc1 Mouse Brain

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

description: RNA-Seq performed on polyadenylated RNA

data_processing: The sequence reads were aligned to human (hg18) and mouse (mm8) genomic sequence using Bowtie (Langmead et al., Genome Biol. 2009 10).

molecule: polyA RNA

organism: Mus musculus

source_name: Tc1 mouse brain

extract_protocol: Illumina FastTrack mRNA-Seq library construction

tag: genotype/variation

value: aneuploid

value: brain


title: Tc0 Mouse Brain

description: RNA-Seq performed on polyadenylated RNA

source_name: Tc0 (wildtype) mouse brain

value: wildtype


title: Tc0 Mouse Liver

description: RNA-Seq performed on polyadenylated RNA

source_name: Tc0 (wildtype) mouse liver

value: liver


title: idn2-1 RNA replicate 1

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

data_processing:
Image analysis and base calling were performed using standard illumina pipelines.
RNA-Seq reads were aligned via the Tophat software.
Differential transcripts between wild-type and mutants were called by Cufflinks using TAIR10 annotations of genes and transposons.
Genome_build: TAIR10
Supplementary_files_format_and_content: csv with list of gene differentially expressed in nrpe1, swi3b, and idn2 compared to Col0

organism: Arabidopsis thaliana

source_name: 2-3 week seedlings

growth_protocol: Strains were grown under long day conditions for 2-3 weeks.

extract_protocol: Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen). rRNA depletion was performed using the RiboMinus Plant Kit (Invitrogen).


title: idn2-1 RNA replicate 2


title: idn2-1 RNA replicate 3


title: nrpe1 H3 rep 2

description: H3 ChIP-seq

data_processing:
Image analysis and base calling were performed using standard illumina pipelines.
ChIP-Seq reads were aligned to the TAIR10 genome via the Bowtie software.
Reads were overlapped with nucleosomes called in Mnase-seq.
Differential nucleosomes were kept with a poisson score less than 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: peak file with nucleosomes occuring in Col-0 or nrpe1

extract_protocol: H3 bound DNA was immunoprecipitated using abcam ab1791 antibody.

tag: antibody

tag: vendor/catalog#

value: abcam ab1791


title: nrpe1 H3 rep 1

description: H3 ChIP-seq


title: Tx601 Treated Midgut Replicate M

source_name: Midgut tissue from last instar larvae fed on susceptible Tx601 maize

value: reared on susceptible Tx601 maize


title: Col-0 H3 rep 1

description: H3 ChIP-seq


title: Col-0 H3 rep 2

description: H3 ChIP-seq


title: nrpe1 Mnase

description: mnase digested DNA

data_processing:
Image analysis and base calling were performed using standard illumina pipelines.
MNase-Seq reads were aligned to the TAIR10 genome via the Bowtie software.
Nucleosomes were called in each strain using the TemplateFilter software.
Nucleosomes in each strain were combined and quantile normalized while the highest 5% by read count were removed to alleviate sequencing bias.
Differential nucleosomes were called using a combination of 2 fold change and poisson score less than .001.
Genome_build: TAIR10
Supplementary_files_format_and_content: peak file with nucleosomes occuring in Col-0 or nrpe1

extract_protocol: Mnase digested DNA was size selected from an 2% agarose gel using the QIAEX II gel extraction kit (Qiagen).


title: Col-0 Mnase

description: mnase digested DNA


title: swi3b +/- RNA replicate 2

value: swi3b +/-


title: swi3b +/- RNA replicate 1


title: nrpe1 RNA replicate 2


title: nrpe1 RNA replicate 1


title: RNAP_CS_Stat1

description: Chromatin IP against RNAP


title: Col-0 RNA replicate 3


title: Col-0 RNA replicate 2


title: Tc1 Mouse Liver

description: RNA-Seq performed on polyadenylated RNA

source_name: Tc1 mouse liver


title: gastrula stage embryo 12C CA2_12

status: Public on Nov 30 2012

city: Durham

first: Daniel

last: Runcie

state: NC

department: Biology Department

institute: Duke University

data_processing:
Initial filtering by Corona
Reads were mapped to the S purpuratus genome with Bowtie v0.12.7. Mapping parameters were -C -n 2 -l 9 -e 100 -M 1 -t -best -trim3 15
Reads were counted in gene models using Htseq with the parameters --mode=intersection-nonempty --stranded=yes
Genome_build: Spur_3.1.LinearScaffold.fa from www.SpBase.org
Supplementary_files_format_and_content: SPU_counts.txt countains total counts of reads per gene model per sample, as generated by Htseq

organism: Strongylocentrotus purpuratus

source_name: gastrula stage embryo

growth_protocol: Adult urchins were spawned by injecting 0.5M KCl. Eggs and sperm were mixed, fertilization rates assessed, washed, and then moved to larger culture dishes for growth. Embryos were cultured at low density until they reached the mid-point of gastrulation in artificial sea water at 18C or 12C.

extract_protocol: 6.5 − 8.5μg of DNase-treated total RNA was used as the input sample. mRNA was isolated via two rounds of poly-A selection using 100μl of Dynabeads (Invitrogen). Bar- coded SOLiD libraries were prepared using the RNA-seq protocol for the SOLiD Total RNA-Seq kit and the SOLiD Transcriptome Multiplexing Kit (Applied Biosystems). Library quality was assessed using a 2100 Bioanalyzer (Agilent). Libraries were quantitated using qPCR, and prepared for standard stand-specific SOLiD sequencing in equimolar concentrations. 50bp single-end reads were generated on 2 slides by the IGSP Genome Sequencing and Analysis Core Resource at Duke University.

treatment_protocol: Growth chambers were set to either 12C or 18C, and water was equilibrated prior to adding the fertilized embryos.

tag: developmental stage

value: gastrula stage embryo

tag: female parent

value: C

tag: male parent

value: A

tag: temperature


title: gastrula stage embryo 12C CD1_12

value: D


title: gastrula stage embryo 18C XA1_18


title: gastrula stage embryo 18C AA2_18


title: gastrula stage embryo 18C AD1_18


title: FAP+ CD34+ cells biological replicate 2

city: Cambridge

first: Andrew

last: Deonarine

address: Hills Road

country: United Kingdom

institute: Laboratory of Molecular Biology

description:
cd34p2
FACS sorted FAP+ cells from pancreatic ductal adenocarcinoma

data_processing:
RNA-seq data was then mapped to the iGenomes mm9 reference genome using Bowtie2 and Tophat2 was used to map junction reads (the switches used to run Tophat2 were"--GTF mm9 --b2-very-sensitive --b2-D 500 --b2-R 500 --solexa1.3-quals").
To quantify transcriptome expression levels, Cufflinks2 was used to produced bias-adjusted FPKM values (using the switches "--GTF mm9--multi-read-correct --frag-bias-correct"), while RPKM values were calculated from count data produced by Htseq-count (using the switches "--quiet --stranded=no -a 30"). Fragments were also estimated from FPKM values.
Using counts, fragments, FPKM (bias-adjusted), and RPKM, correlations, clustering, PCA, and differential expression analysis (usingDESeq and edgeR) were then calculated for the Panst, VA, Skelm, and FAPN replicates against reference T-helper cell types (naive, Th1, Th2, and nTreg).
Genome_build: iGenomes mm9 reference genome
Supplementary_files_format_and_content: FPKM and RPKM

source_name: Pancreatic ductal adenocarcinoma

extract_protocol: Purelink (Invitrogen) RNA prep, amplification by MessageAmp (Ambion).

tag: cell type

value: FAP+ CD34+ cells

tag: disease state

value: spontaneous pancreatic ductal adenocarcinoma model

tag: genetic background


title: FAP+ CD34- cells biological replicate 1

description:
cd34n1
FACS sorted FAP+ cells from pancreatic ductal adenocarcinoma

value: FAP+ CD34- cells


title: FAP+ CD34+ cells biological replicate 1

description:
cd34p1
FACS sorted FAP+ cells from pancreatic ductal adenocarcinoma


title: FAP+ CD34- cells biological replicate 2

description:
cd34n2
FACS sorted FAP+ cells from pancreatic ductal adenocarcinoma


title: swi3b +/- RNA replicate 3


title: nrpe1 RNA replicate 3


title: MM.1S_WCE_JQ1_JL_ChipSeq1

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

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.

organism: Homo sapiens

source_name: Whole cell extract from MM.1S cells (500 nM JQ1)

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

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: 500nM JQ1 treatment for 24 hours

tag: diagnosis

value: Multiple myeloma

value: None WCE

tag: antibody catalog number

value: Plasma cell

tag: treatment duration

tag: treatment concentration

tag: treatment drug


title: Med1_2_MM1S_ChipSeq

source_name: Chromatin IP against Med1 in MM1S Rep2

value: Bethyl A300-793A


title: MM.1S_Med1_JQ1_JL_ChipSeq

source_name: Chromatin IP against Med1 in MM.1S (500 nM JQ1)

value: 24 hr

value: DMSO


title: Col-0 RNA replicate 1

tag: strain


title: MM.1S_Max_JQ1_JL_ChipSeq

source_name: Chromatin IP against Max in MM.1S (500 nM JQ1) for 12022011_B0A1WABXX*

tag: chip antibody

value: Max

value: Santa Cruz SC-197


title: MM.1S_H3K4me3_JQ1_JL_ChipSeq

source_name: Chromatin IP against H3K4me3 in MM.1S (500 nM JQ1) for 12022011_B0A1WABXX*

value: Millipore 07-473


title: MM.1S_Brd4_DMSO_JL_ChipSeq

source_name: Chromatin IP against Brd4 in MM.1S (DMSO)

treatment_protocol: DMSO treatment for 24 hours

value: Bethyl A301-985A


title: MM.1S_CDK9_DMSO_JL_ChipSeq

source_name: Chromatin IP against CDK9 in MM.1S (DMSO) for 12022011_B0A1WABXX*

value: Multiple Antibodies SC-8338,SC-484


title: MM.1S_c_Myc_JQ1_JL_ChipSeq

source_name: Chromatin IP against c-Myc in MM.1S (500 nM JQ1)

value: c-Myc

value: Santa Cruz SC-764


title: gastrula stage embryo 12C AD2_12

value: gastrula stage embryo

value: A

value: D


title: MM.1S_CDK9_JQ1_JL_ChipSeq

source_name: Chromatin IP against CDK9 in MM.1S (500 nM JQ1) for 12022011_B0A1WABXX*


title: MM.1S_Brd4_JQ1_JL_ChipSeq

source_name: Chromatin IP against Brd4 in MM.1S (500 nM JQ1)


title: SUZ12_ChIPSeq_LNCaP

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls performed using CASAVA 1.6.0
ChIP-Seq reads are aligned to hg18 using Eland with default configurations, only uniqly mapped reads are kept
Redundant reads (reads mapped to exactly the same location) are removed
All libraries are sampled down to 10 million reads
Peaks are called using MACS2 2.0.9
Genome_build: hg18
bigwig files are generated using MACS2+bedGraphToBigWig
Supplementary_files_format_and_content: peaks.bed files: These bed files are the ChiP enriched regions generated by MACS
Supplementary_files_format_and_content: .bw files: The bigwig files are generated from the pile up track of MACS. Files treat_pileup.bw, normalized_sorted-norm-10M.bw, treat_pileup-norm-10000000.bw are all generated in the same way (but the naming is not consistent).

source_name: prostate cancer cells

growth_protocol: LNCaP cells were routinely maintained in RPMI-1640 with 10% fetal bovine serum (FBS) plus 1% antibiotics (penicillin and streptomycin). LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for up to 18 cycles and library fragments of 250-400 bp range (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 Illumina GAII system following the manufacturer's protocols.

treatment_protocol: For the purpose of ChIP experiments, the cells were kept in androgen-depleted medium for 3 days and then treated with either 10 nM 5α-dihydrotestosterone (DHT, for LNCaP cells) or with ethanol only (for abl cells) for 24 hours before the cells were collected.

tag: cell line

value: LNCaP prostate cancer cells

tag: genotype/variation

value: androgen-dependent prostate cancer cells

tag: passages

value: anti-SUZ12 (Cell Signaling (3737))


title: gastrula stage embryo 18C CD1_18

tag: developmental stage

value: C


title: H3K27me3_ChIPSeq_LNCaP

value: anti-H3K27me3 (Millipore (07-449))


title: inputDNA_LNCaP


title: inputDNA_abl

value: LNCaP-abl (abl) prostate cancer cells

value: androgen-independent prostate cancer cells


title: H3K4me3_ChIPSeq_abl

value: anti-H3K4me3 (Abcam (ab8580))


title: MM.1S_RNAPII_JQ1_JL_ChipSeq

source_name: Chromatin IP against RNAPII in MM.1S (500 nM JQ1) for 12022011_B0A1WABXX*

value: Multiple myeloma

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

value: Plasma cell

value: 24 hr


title: MM.1S_WCE_JQ1_JL_ChipSeq2

source_name: Whole cell extract from MM.1S cells (500 nM JQ1) for 12022011_B0A1WABXX*

value: None WCE


title: EZH2_ChIPSeq_abl

value: anti-EZH2 (Active Motif (39639) and BD Biosciences (612666))


title: MM.1S_H3K27ac_JQ1_JL_ChipSeq

source_name: Chromatin IP against H3K27ac in MM.1S (500 nM JQ1) for 12022011_B0A1WABXX*

value: Abcam AB4729


title: H3K27me3_ChIPSeq_abl


title: SUZ12_ChIPSeq_abl


title: AR_ChIPSeq_abl

description: anti-AR

value: anti-AR (Santa Cruz (N-20))


title: PolII_ChIPSeq_abl

description: anti-PolII

value: anti-PolII (Santa Cruz (sc-9001) and (sc-56767))


title: elc1∆2

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

country: Germany

institute: EMBL Heidelberg

data_processing:
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
RNA-seq reads were aligned to the S288c reference R64 genome assembly using Novoalign V2.07.10 with default parameters.
wig files were generated using samtools depth.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64 downloaded from SGD (http://www.yeastgenome.org/).
Supplementary_files_format_and_content: wig files

organism: Saccharomyces cerevisiae

source_name: Yeast cells, elc1 deletion mutant

growth_protocol: YPD 30 °C to mid-log phase.

extract_protocol: RNA was extracted with the RNeasy Mini Kit (QIAGEN) and on-column DNase I digestion was performed. Samples were subjected to RiboZero and standard Illumina library preparation.

treatment_protocol: None.

value: W303 elc1-delta::URA3


title: IMR90 Cells Methylated DNA

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Read files of technical replicates were pooled.
Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed. When more than one read mapped to the same genomic position, only one read was kept at that position.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. Counts across the whole genome in windows 20 bases wide, per 1 million mapped reads.

growth_protocol: IMR90 DNA was donated by Ryan Lister.

extract_protocol: MethylMiner Methylated DNA Enrichment Kit (Invitrogen #ME10025) was used to isolate methylated DNA, as previously described (Nair, S.S., Coolen, M.W., Stirzaker, C., Song, J.Z., Statham, A.L., Strbenac, D., Robinson, M.W., and Clark, S.J. (2011). Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6: 34-44.). The DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.


title: WT3

source_name: Yeast cells, wild-type

value: W303 wild-type


title: elc1∆1


title: elc1∆1 Control

description: Non-specific binding control using same chromatin as elc1∆1 RNA Polymerase II ChIP.

data_processing:
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
ChIP-seq reads were aligned to the S288c reference R64 genome assembly using Novoalign V2.07.18 with default parameters.
wig files were generated using samtools depth.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64 downloaded from SGD (http://www.yeastgenome.org/).
Supplementary_files_format_and_content: wig files

source_name: Yeast cells, elc1 deletion mutant, control

extract_protocol: ChIP performed using standard techniques (Kristjuhan, A. & Svejstrup, J. Q. (2004). Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. Embo J 23, 4243-4252) except cell breakage and antibody binding were performed in 500 mM NaCl-containing buffer. Chromatin extract was divided in two, to one sample 4H8 antibody was added and to the second non-specific mouse IgG. Purified DNA was subjected to the Illumina ChIP-Seq DNA Sample Prep Kit for library production.

treatment_protocol: 1% formaldehyde cross-linked for 20 minutes at 25 °C, quenched for 5 minutes at 25 °C with 200 mM glycine.

value: mouse IgG

value: Sigma

tag: antibody lot#


title: WT1


title: elc1∆2 RNA Polymerase II ChIP

description: 4H8 antibody was produced by Cancer Research UK LRI in-house antibody service. Can be purchased from Abcam Cat. No. ab5408.

source_name: Yeast cells, elc1 deletion mutant, Rpb1 ChIP


title: elc1∆2 Control

description: Non-specific binding control using same chromatin as elc1∆2 RNA Polymerase II ChIP.


title: WT2


title: elc1∆1 RNA Polymerase II ChIP


title: elc1∆3


title: EZH2_ChIPSeq_LNCaP

value: LNCaP prostate cancer cells

value: androgen-dependent prostate cancer cells


title: WT2 Control

description: Non-specific binding control using same chromatin as WT2 RNA Polymerase II ChIP.

source_name: Yeast cells, wild-type, control


title: WT1 Control

description: Non-specific binding control using same chromatin as WT1 RNA Polymerase II ChIP.


title: WT2 RNA Polymerase II ChIP

source_name: Yeast cells, wild-type, Rpb1 ChIP


title: WT1 RNA Polymerase II ChIP


title: H3K4me2_ChIPSeq_abl

value: LNCaP-abl (abl) prostate cancer cells

value: androgen-independent prostate cancer cells

value: anti-H3K4me2 (Millipore (07-030))


title: Mod(mdg4)2.2 (alternate antibody)

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: Chip-seq of Mod(mdg4)2.2, second antibody

data_processing:
Aligned to dm3 using Bowtie 0.12.7, parameters –best –strata –sam -m1 -n2 –tryhard -k1
Removed duplicates using Picard 1.49 MarkDuplicates
Removed reads falling in RepeatMasked regions (bedtools intersect, v2.17.2)
Peak calling using spp using default parameters except srange=c(50,200) for get.binding.characteristics(); FDR=0.01 for find.binding.positions().  Final broad peak regions were merged with bedtools merge (v2.17.2)
BigWigs created using bedtools genomecov (v2.17.2) with the -scale parameter set to 1/(mapped reads /  1e6) to convert BAM to scaled bedGraphs, then UCSC's bedGraphToBigWig to convert to bigWig format
Genome_build: dm3, excluding chrUextra
Supplementary_files_format_and_content: BigWig: Conversion of BAM to bigWig format.  BED: Called peaks from spp.

organism: Drosophila melanogaster

source_name: BG3 cells

growth_protocol: BG3-c2 cells were grown in S2 medium (Sigma) supplemented with 10% fetal calf serum and 10 µg/mL insulin. Cells were maintained in monolayer at 25˚C.

extract_protocol:
Cells were fixed in 1% formaldehyde added directly to cells in culture medium for 10 min at RT with gentle agitation; formaldehyde was quenched by addition of glycine to 0.125 M with gentle agitation for 5 min at RT. 5 x 106 to 107 cells were used per IP. Cells were pelleted at 400 rcf and washed twice in ice cold PBS. Cells were resuspended in 1 mL ice cold cell lysis buffer (5 mM PIPES, pH 8, 85 mM KCl, 0.5% NP-40) supplemented with protease inhibitors, and nuclei were released by Dounce homogenization with the B pestle and pelleted by centrifugation at 9190 rcf for 5 min at 4˚C. Nuclei and chromatin were further processed as described (Moshkovich and Lei, 2010).
Libraries were constructed according to the Illumina standard ChIP-seq protocol (Part # 11257047 Rev. A) with TruSeq adapters and sequenced on an Illumina HiSeq multiplexed in a single lane.

tag: antibody

value: Mod(mdg4)2.2, guinea pig


title: Mod(mdg4)2.2

description: Chip-seq of Mod(mdg4)2.2

value: Mod(mdg4)2.2, rabbit


title: Su(Hw)

description: ChIP-seq of Su(Hw)

value: Su(Hw)


title: Shep

description: ChIP-seq of Shep

value: Shep, guinea pig


title: Input

description: Input for ChIP-seq


title: SP70-1143-control

city: Rio de Janeiro

first: Paulo

last: Ferreira

address: Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária

country: Brazil

institute: Universidade Federal do Rio de Janeiro

data_processing:
Quality of the sequences was evaluated by measuring the quality of the reads according to the percentage of bases having a base quality greater or equal than 30 (Q30)
3’ Illumina adapters (CTGTAGGCACCATCAAT) and “N” bases were trimmed
Using the UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) and  three different databases -  all plant t/rRNAs from Rfam, all Arabidopsis tRNAs from The Genomic tRNA Database and all plant t/rRNA sequences from EMBL release - reads with low-complexity (less than 3 different bases) and both sense and antisense matches with t/rRNAs were removed
Detection of conserved miRNAs with UEA sRNA toolkit-Plant version miRProf pipeline was done allowing three mismatches with mature miRNAs from miRBase (v17.0). Only reads with match to Sorghum bicolor were included in the analysis.
The output of the miRProf contains information about unique sequences counts. Counts were normalized in reads per 1 million (RPM) and total reads counts after the final trimming and filtering steps were used for normalization
Genome_build: Sorghum bicolor v1.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Saccharum hybrid cultivar SP70-1143

source_name: whole plant

growth_protocol: Acidovorax avenae subsp. avenae obtained from the Culture Collection of the Instituto Biológico (IBSBF) was grown in NA medium (beef extract 3 g/L; Peptone 5 g/L; NaCl 5 g/L) at 28ºC. In vitro-grown sugarcane plantlets were maintained at 28°C with an irradiance of 60 µmol photons m-2 s-1 and 12 h photoperiod

extract_protocol:
Total RNA was isolated from whole plants using Trizol (Invitrogen, CA, USA) as described by the manufacturer.
TruSeq Small RNA Sample Prep Kit

treatment_protocol: After the development of a root system, vigorous and pathogen-free plants were divided in two halves with a scalpel. One half was inoculated by immersing the root system for 5 minute in a suspension of A. avenae in distilled water (106 CFU mL-1), and then washed twice with distilled water in order to eliminate superficial bacteria. The other half was used as control, immersing the root system in distilled water by 5 minute and then washed twice with distilled water. Inoculated and control plants were transferred to MS medium and kept there for seven days. After this period, whole plants were harvested and examined for bacterial colonization by plate counting.

tag: genotype

tag: infection

value: control

tag: tissue

value: whole plant


title: SP70-1143-inoculated

value: inoculated with Acidovorax avenae subsp avenae


title: 3516_DLPFC_Control

status: Public on Nov 29 2012

city: Huntsville

first: Kevin

last: Bowling

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

data_processing:
Data processing for RRBS libraries was conducted as described by Gertz et al. 2011 (PLoS Genetics)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genomic position, read coverage, and percentage of methylation for each assayed CG for each brain tissue sample

source_name: Brain (dorsolateral prefrontal cortex)

extract_protocol:
DLPFC was dissected from whole human brain. Tissues were flash frozen in liquid nitrogen and homogenized in Qiagen buffer RLT using the MPBiomedical FastPrep. Genomic DNA was isolated using the Qiagen DNeasy blood and tissue kit. 1 ug of genomic DNA was used for sequencing library construction.
RRBS sequencing libraries were constructed as has been previously described from 1 ug of genomic DNA (Gertz et al. 2011, PLoS Genetics).

value: Heterogeneous brain tissue


title: 3196_DLPFC_Control


title: 2292_DLPFC_Control


title: 4063_DLPFC_Control


title: 3186_DLPFC_Control


title: 3519_DLPFC_Control


title: 3588_DLPFC_Control


title: 3433_DLPFC_Control


title: 3774_DLPFC_Control


title: 3275_DLPFC_Control


title: 2316_DLPFC_Control


title: 3965_DLPFC_Control


title: 3686_DLPFC_Control


title: 3523_DLPFC_Control


title: 2805_DLPFC_Control


title: 2248_DLPFC_Control


title: 1834_DLPFC_Control


title: Shep (alternate antibody)

description: ChIP-seq of Shep, second antibody

value: Shep, rabbit


title: 2664_DLPFC_Control


title: WT_dUTX663_3

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: Chromatin Immunoprecipitation of dUTX in WT_3

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned to the fly genome (UCSC dm3), or mouse genome (UCSC mm9), using Bowtie v0.12.7, allowing unique reads only and up to three mismatches of the 50bp read length.
Enrichment for some ChIP-seq samples was determined by MACS v1.4.1 using default settings, the dm genome, and the associated input sample.  The publication utilized a subset of peaks meeting the criteria (p < 1e-5 and fold change > 5, or FDR < 5%) but all peaks with p < 1e-5 are included in this submission.
Genome_build: UCSC dm3; UCSC mm9
Supplementary_files_format_and_content: txt.bam.bed file represents UCSC BED format for alignments.
Supplementary_files_format_and_content: peaks.tab file represents MACS v1.4.1 tab-delimited format for all enriched regions at p < 1e-5.

source_name: Schneider's Drosophila Line 2; S2 cells

growth_protocol: S2 cells were grown in SFX medium (Thermo/HyClone #SH30278.02) with 1% Penicillin/Streptomycin (Invitrogen #15140) at room temperature.  Mouse embryonic fibroblasts were grown in DMEM with 10% FBS supplemented with glutamine.

extract_protocol:
S2 cells (one T75 flask per histone antibody and two T75 flasks for other antibodies) were cross-linked in 1% formaldehyde (by adding 37% formaldehyde to medium) on a nutator for 15 min at room temperature (RT). Samples were quenched by adding 2.5 M glycine to a final glycine concentration of 225 mM and incubated on a nutator for 5 min at RT. Following centrifugation for 5 min at 2000 g at 4°C the supernatant was aspirated. The cell pellet was resuspended in 5 ml Orlando/Paro buffer (10 mM Tris HCl pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, 0.5 mM DTT, protease inhibitors [Roche, complete, EDTA-free, Cat No. 05056489]) and centrifuged for 5 min at 2000 g at 4°C. The supernatant was aspirated and the wash step with Orlando/Paro buffer repeated for another two times. The cell pellet (~100 µl for one T75 flask) was resuspended in 1.5 ml RIPA buffer (25 mM Tris pH 7.5, 140 mM NaCl, 1% Triton X-100, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.5% of N-lauroylsarcosine, 0.5 mM DTT, protease inhibitors [Roche, complete, EDTA-free, Cat No. 05056489]) per 100 µl of cell pellet and 1.5 ml samples sonicated for 15 min (50% on/off cycle, high) (Bioruptor, Diagenode) in 15 ml hard plastic tubes (Corning, 430055). Sonicated chromatin was centrifuged for 20 min at 14,000 rpm at 4° and the supernatant kept. 10 μl of the sonicated chromatin was kept for gel analysis (to check sizing pattern) and 50 μl was used as an Input control. Sizing samples were reverse cross-linked over night at 65ºC by adding 90 μl RIPA and 3 μl proteinase K (30 mg/μl) and input samples by adding 50 μl RIPA and 5 μl proteinase K and processed/purified in the same way as the ChIP samples (see below). The remaining chromatin was diluted two-fold with RIPA buffer (without N-lauroylsarcosine) and incubated over night with the respective antibody on a nutator at 4ºC. 60 μl of protein A agarose (Invitrogen, 15918-014) was washed in 5 ml RIPA buffer, centrifuged for 2 min at 1,000 rpm at 4ºC. The supernatant was aspirated, the chromatin sample added and incubated for 2 h on a nutator at 4ºC. After centrifugation for 2 min at 1,000 rpm at 4ºC the protein A agarose was transferred into a 1.5 ml tube, washed with 1 ml RIPA buffer, incubated for 5 min on a nutator at room temperature and centrifuged for 2 min at 2,500 rpm at 4ºC. The supernatant was aspirated and the previous washing steps repeated another five times. Elution was performed on a nutator at room temperature for 20 min with 300 μl elution buffer (0.1 M NaHCO3, 1% SDS) containing proteinase K (1 ml elution buffer and 5 μl proteinase K [30 mg/μl]) and the sample centrifuged for 2 min at 2,500 rpm at room temperature. The supernatant was kept and the elution step repeated. Elution fractions were pooled and reverse cross-linked over night at 65ºC. 1 µl of RNase A (R4642, Sigma) was added to reverse cross-linked samples followed by incubation for 1 h at 37°C. DNA was isolated with the Qiagen PCR purification kit (#28106) and eluted in 50 μl H2O and DNA concentration determined by Pico Green Assay (Invitrogen #P7581).  Mouse embryonic fibroblasts (MEFs) ChIP was performed according to a previously described protocol (Wang et al. 2009). Briefly, approximately 10^7 MEFs for each assay were cross-linked with 1% formaldehyde and sonicated. 10 µg of antibody and 50 µl protein A agarose were used in the ChIP assays.
Libraries were prepared with the Illumina TruSeq RNA Sample Preparation Kit (#RS-122-2001,RS-122-2002) according to Illumina's instructions, adapted for multiplexing ChIP-seq samples by starting at the end repair step using 1/3 of the adapters.  Libraries were sequenced on the Illumina Hi-Seq 2000 following the manufacturer's protocols.

treatment_protocol: We used 10 µg of dsRNA per 1.5 x 106 cells per 60 mm well (6 well plate) or 80 µg of dsRNA per 12 x 106 cells per T75 flask with 2.5 ml SFX medium(Thermo/HyClone #SH30278.02) and 1% Penicillin/Streptomycin (Invitrogen #15140) per 60 mm well and 20 ml SFX medium (1% Penicillin/Streptomycin) per T75 flask. dsRNA was mixed with the corresponding volume of S2 cells (0.6 x 106 S2 cells/ml) and distributed in either 60 mm wells or T75 flasks. RNAi-mediated knockdown was performed for 5 days.  MEFs are homozygous wild-type or homozygous knock-outs of MLL1 or MLL3 as described in (Wang et al. Mol Cell Biol. 2009 November; 29(22): 6074–6085)

tag: cell type

value: WT

value: (rb) α-dUTX (#663, Ali Shilatifard)


title: 3281_DLPFC_Control


title: 3228_DLPFC_Control


title: 3706_DLPFC_Control


title: 3572_DLPFC_Control


title: 2619_DLPFC_Control


title: 3018_DLPFC_Control


title: Escherichia coli control

city: Warsaw

first: Matthias

last: Bochtler

address: Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology

data_processing:
Removal of genome amplification primers or primer concatamers (identification with TagCleaner, removal with Cutadapt)
Removal of additional five flanking bases on either side of reads
Mapping of sequences to M. penetrans and E. coli genomes using Bismark (which uses bowtie for actual alignments)
Extraction of sequence contexts (in house software)
Collection of all reads for each site
Determination of fractional methylation for each site (based on genome accession codes NC_004432 for M. penetrans and NC_010473 for E. coli)
Genome_build: NC_004432 for M. penetrans and NC_010473 for E. coli
Supplementary_files_format_and_content: output file: collection of all reads for each site
Supplementary_files_format_and_content: methylation_sites file: determination of fractional methylation for each site
Supplementary_files_format_and_content: recognition_sequences file: determination of fraction of methylated cytosines for possible methyltransferase target sequences

organism: Escherichia coli

source_name: genomic DNA

extract_protocol:
M. penetrans DNA obtained from Prof. Y. Sasaki, E. coli (ER2566, NEB) DNA was isolated using Genomic Mini Kit from A&A Biotechnology, according to manufacturer's protocol.
library was constructed commercially by Genomed (http://www.genomed.pl/), library preparation kit: TruSeq DNA Seq Sample Prep Kit v2 (nr kat FC-121-2001), sequencing kit: MiSeq Reagent Kit (300-cycles PE) (nr kat MS-102-1001)

treatment_protocol: genomic DNA was bisulfite converted

tag: protocol

value: bisulfite converted


title: Mycoplasma penetrans

organism: Malacoplasma penetrans


title: Leaves phosphorous sufficient rep1 PsL1

city: St Paul

first: Sam

last: Yang

state: MN

address: 411 Upper Buford Circle

department: ARS

institute: USDA

data_processing: The initial base calling and quality filtering of the Illumina GA-IIx image data was performed using the default parameters of the Illumina GA Pipeline GERALD stage (www.illumina.com). Further filtering based on the read size (size>75bp) and homopolymers was performed using custom written code. The Oases program (Sammeth, Foissac, & Guigo 2008) together with the velvet algorithm (Zerbino and Birney, 2008) with k-mer 29  was used for de novo assembly of the Solexa GA-IIx EST reads. Next, 8,441 Sanger ESTs downloaded from the public database (http://www.ncbi.nlm.nih.gov) were combined with de novo assembled Illumina sequences using CAP3 program using the default parameter (Huang X. & Madan A. 1999). Finally, the redundant sequences were collapsed into one using CD-HIT-EST algorithm (Li W. & Godzik A 2006) producing a total of 125,821 Lupin Gene Index (LAGI 1.0) sequences with average length of 1,155 bp. For digital gene expression analysis, the raw digital gene expression counts were measured by quantifying the number of Illumina GA-IIx reads that were mapped to the reference sequences (LAGI1.0) using bowtie program (Langmead et al., 2009) using the default parameter. The raw digital gene expression counts were normalized using the RPKM (reads/Kb/Million) method previously described (Mortazavi et al., 2008; Nagalakshmi et al., 2008). To identify differentially expressed genes, an expression profile matrix was built representing the digital gene expression count for each gene in each library, then imported into the Genedata Expressionist Analyst module (http://www.genedata.com/). A t-test was performed to identify differentially expressed genes in 4 pair-wise comparison (PdR vs. PsR, PdL vs. PsL, PdR vs. PdL, PsR vs. PsL) (p<0.01, â¥2-fold difference).

organism: Lupinus albus

source_name: Leaves +P rep1

growth_protocol: White lupin (Lupinus albus L. var. Ultra) plants were grown in a growth chamber at 20/15 Â°C under a 16 h photoperiod (300 Âµmol photons m-2 s-1) as described by Gilbert et al. (2000). The Pi-sufficient [1 mM Ca(H2PO4)2] and Pi-deficient [1 mM CaSO4] solutions were provided to white lupin plants with three biological replications per condition. Roots and leaves were harvested at 14 days after emergence (DAE).

extract_protocol: Total RNA was purified from 12 samples [(+P & -P) x (roots & leaves) x (three biological replicates)] using RNeasy KIT (Qiagen, Valencia, CA, USA). Contaminating genomic DNA was removed from each RNA sample using DNase I. RNA samples were quantified using Quant-iTâ¢ RiboGreenÂ® RNA Reagent (www.invitrogen.com) and the RNA integrity was checked with RNA6000 Nano Assay using the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA). cDNA library preparation and sequencing reactions were conducted in the Biomedical Genomics Center, University of Minnesota. Illumina library prep, clustering and sequencing reagents were used throughout the process following the manufacturerâs recommendations (www.illumina.com). Briefly, mRNAs were purified using poly-T oligo-attached magnetic beads and then fragmented. The first and the second strand cDNAs were synthesized and end repaired. Adaptors were ligated after adenylation at the 3â-ends.  After gel purification, cDNA templates were enriched by PCR. cDNA libraries were validated using a High Sensitivity Chip on the Agilent2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA). The cDNA library was quantified using PicoGreen Assay and by qPCR. The samples were clustered on a flow cell using the cBOT. After clustering, the samples were loaded on the Illumina GA-II machine.  The rep1 cDNA libraries were run on one lane per library. For the rep2 and rep3 libraries, barcode was given to each library during the cDNA library construction then two libraries were run together per lane. The samples were sequenced using a single read with 76 cycles. Initial base calling and quality filtering of the Illumina GA-IIx image data were performed using the default parameters of the Illumina GA Pipeline GERALD stage (www.illumina.com). Additional filtering for homopolymers and read size (<76bp) was performed using custom written code.

tag: tissue type

value: Leaves

tag: treatment

value: phosphorous sufficient soil


title: Leaves phosphorous sufficient rep3 PsL3

source_name: Leaves +P rep3

treatment_protocol: White lupin (Lupinus albus L. var. Ultra) plants were grown in a growth chamber at 20/15 Â°C under a 16 h photoperiod (300 Âµmol photons m-2 s-1) as described by Gilbert et al. (2000). The Pi-sufficient [1 mM Ca(H2PO4)2] and Pi-deficient [1 mM CaSO4] solutions were provided to white lupin plants with three biological replications per condition. Roots and leaves were harvested at 14 days after emergence (DAE).


title: Leaves phosphorous sufficient rep2 PsL2

source_name: Leaves +P rep2


title: Leaves phosphorous deficient rep1 PdL1

source_name: Leaves -P rep1

value: phosphorous deficient soil


title: Leaves phosphorous deficient rep2 PdL2

source_name: Leaves -P rep2


title: Roots phosphorous sufficient rep2 PsR2

source_name: Roots +P rep2

value: Roots


title: Leaves phosphorous deficient rep3 PdL3

source_name: Leaves -P rep3


title: Roots phosphorous sufficient rep3 PsR3

source_name: Roots +P rep3


title: Roots phosphorous deficient rep2 PdR2

source_name: Roots -P rep2

value: Proteoid roots


title: Roots phosphorous sufficient rep1 PsR1

source_name: Roots +P rep1


title: Roots phosphorous deficient rep1 PdR1

source_name: Roots -P rep1


title: Escherichia coli M.MpeI methylated in vitro methylated genomic DNA


title: Prx1CreER-EA1N2

status: Public on Nov 28 2012

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

data_processing:
Base called using Illumina CASAVA version 1.8.2
Aligned with novoalign version 2.07.03, parameters -r Random -k -o SAM
RPKM for each gene calculated using DefinedRegionScanSeq application in Useq package
Genome_build: mm9 plus known splice junctions

source_name: Clear Cell from Prx1CreERT2

extract_protocol:
Qiagen RNEasy kit plus DNAse
Illumina TruSeq RNA Sample Prep Kit

value: Clear Cell from Prx1CreERT2


title: Bmi1CreER-EA1N1

source_name: Clear Cell from Bmi1IRESCreERT2

value: Clear Cell from Bmi1IRESCreERT2


title: Prx1CreER-EA1N4


title: Bmi1CreER-EA1N2


title: Chest1

source_name: Control

value: Control


title: Chest5


title: Total small RNAs from uap56 mutant, ovary, oxidized

city: Worcester

first: Jie

last: Wang

address: 364 Plantation St.

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description: oxidized

data_processing:
For each sequence read, the first occurrence of the 6-mer perfectly matching the 5′ end of the 3′ linker was identified. Sequences without a match were discarded.
Genome Build:
uap56.ox.pooled.inserts.txt: dm3

source_name: uap56 mutant overy ox

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated from manually dissected ovaries from 2–4 day flies using mirVana (Ambion, Austin, TX, USA). The RNA was quantified by absorbance at 260 nm. To deplete 2S rRNA, 100 μg total RNA was annealed with 200 pmole of a complementary DNA oligonucleotide (5'-AGT CTT ACA ACC CTC AAC CAT ATG TAG TCC AAG CAG CAC T-3') in 20 μl at 95°C for 2 min, then the temperature was gradually decreased over 1 h to room temperature. 2S rRNA was digested with 2 units of RNase H (Invitrogen) in a 30 μl reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, and 10 mM DTT. After 2S rRNA depletion, 18–29 nt small RNA was purified from a 15% denaturing urea-polyacrylamide gel (National Diagnostics, Atlanta, GA, USA). Half of the purified RNA was oxidized with 25 mM NaIO4 in 60 mM borax, 60 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 100 pmole of 3! pre-adenylated adapter (5'-rAppTCG TAT GCC GTC TTC TGC TTG T/ddC/-3') was ligated to oxidized or un-oxidized small RNAs using mutant Rnl2 (amino acids 1-249, K227Q) (17-23B) (Addgene, Cambridge, MA, USA) at 4°C for 12 h in 20 μl in 50 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 10 mM DTT, 60 μg/ml BSA, 10% (v/v) DMSO, and 40 U RNasin (Promega, Madison, WI, USA). 3´ ligated product was purified from a 15% denaturing urea-polyacrylamide gel (National Diagnostics), and then ligated to 100 pmole of 5! RNA adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3´) using T4 RNA ligase (Ambion, Austin, TX, USA) at room temperature for 6 h in 20 μl of 50 mM Tris-HCl, pH 7.8, 10 mM MgCl2, 10 mM DTT, 1 mM ATP, and 10% DMSO. The ligated product was purified from a 10% denaturing urea-polyacrylamide gel (National Diagnostics). Half the ligated product was used to synthesize cDNA using Superscript III (Invitrogen) and the reverse transcription primer (5´-CAA GCA GAA GAC GGC ATA CGA-3´), and half was used as a minus
RT control. The small RNA library was amplified using forward (5´-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GA-3´) and reverse (5´-CAA GCA GAA GAC GGC ATA CGA-3´) primers, and then purified from a NuSieve GTG agarose gel (Lonza, Basel, Switzerland).

treatment_protocol: 0-2 days flies fed with yeast for 2 days

value: uap56 mutant

value: ovary


title: Chest3


title: Total small RNAs from w1118, ovary, un-oxidized

description: un-oxidized

data_processing:
For each sequence read, the first occurrence of the 6-mer perfectly matching the 5′ end of the 3′ linker was identified. Sequences without a match were discarded.
Genome Build:
w1118.unox.inserts.txt: dm3

source_name: w1118 ovary unox


title: Total small RNAs from uap56 mutant, ovary, un-oxidized

description: un-oxidized

data_processing:
For each sequence read, the first occurrence of the 6-mer perfectly matching the 5′ end of the 3′ linker was identified. Sequences without a match were discarded.
Genome Build:
uap56.unox.pooled.inserts.txt: dm3

source_name: uap56 mutant ovary unox


title: Chest4


title: TATCreEA1N179-Larm

source_name: Clear Cell from TATCre

value: Clear Cell from TATCre


title: Bone3


title: TATCreEA1N178-Lleg


title: TATCreEA1N123-Rleg


title: Roots phosphorous deficient rep3 PdR3

source_name: Roots -P rep3


title: Myf5-SSM2/PLUCN44

source_name: synovial sarcoma

value: synovial sarcoma


title: Myf5-SSM2/PLUCN39-9


title: TATCreEA1N123-RLN


title: Myf5-SSM2/PLUCN39-5


title: Chest2


title: yal008w heterozygous diploid, Replicate 1

city: La Jolla

first: Menzies

last: Chen

state: CA

address: 9500 Gilman Drive MC 0688

department: Bioengineering

institute: UCSD

data_processing:
Base-calling provided by Illumina stock software. Details on what is used by the UCSD core can be found at microarrays.ucsd.edu
Reads were aligned via Bowtie 0.12.5 with the following arguments (-m 1 -B 1)
Data were filtered to only accept non-clonal reads
Counts for each ORF were tallied as the median number of non-clonal reads overallping positions in the last 200 bases of each yeast ORF (Nagalakshmi, 2011)
Genome_build: scerevisiae genome downloaded from SGD in 06/2012
Supplementary_files_format_and_content: tab-delimited file contains a matrix with each row representing each yeast ORF and each column representing RNA-Seq measurements in each experiment. Each cell reports the number of counts observed in the corresponding experiment for the corresponding ORF.

source_name: yeast mRNA extract

growth_protocol: YPD; log-growth from OD 0.2 to 1.0 at 30*C.

extract_protocol:
Hybrid Trizol Reagent RNA extraction and RNEAsy column purification
mRNA were purified via Oligo-DT dynabeads twice; purified mRNA were fragmented to yield fragments averaging 200-300-bp.Illumina adapters were then ligated and amplified, followed by size-selection and qPCR quantitation.

treatment_protocol: No treatment (conditions lack G418)

tag: strain background

value: yal008w heterozygous


title: yal008w heterozygous diploid, Replicate 3


title: yal022c heterozygous diploid, Replicate 3

value: yal022c heterozygous


title: Myf5-SSM2/PLUCN37-7


title: yal022c heterozygous diploid, Replicate 2


title: Col1CreRb1p53N31

source_name: osteosarcoma

value: osteosarcoma


title: yal031c heterozygous diploid, Replicate 3

value: yal031c heterozygous


title: Col1CreRb1p53N27


title: yal022c heterozygous diploid, Replicate 1


title: yal031c heterozygous diploid, Replicate 2


title: yal067c heterozygous diploid, Replicate 3

value: yal067c heterozygous


title: yal008w heterozygous diploid, Replicate 2


title: Col1CreRb1p53N26Right


title: yal031c heterozygous diploid, Replicate 1


title: Col1CreRb1p53N22


title: Myf5-SSM2/PLUCN37-4


title: R26CreEA1N4

source_name: Clear Cell from Rosa26CreER

value: Clear Cell from Rosa26CreER


title: yal067c heterozygous diploid, Replicate 2


title: R26CreEA1N5


title: Wild-type, Replicate 6

value: Wild-type


title: R26CreEA1N3


title: Myf5-SSM2/PLUCN37-8


title: Wild-type, Replicate 5


title: RIPseq_w1_IP

description: RNA immunoprecipitation (RIP)

data_processing:
Library strategy: RIP-Seq
Base calling and demultiplexing was performed using CASAVA 1.8
Alignments were performed using TopHat version 2.0.4
bedGraph files were generated from bam files from Tophat, and were normalized by the sequencing depth and the number of times the reads are mapped to the genome.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated from bam files from Tophat, and were normalized by the sequencing depth and the number of times the reads are mapped to the genome.

extract_protocol: UAP56-Venus and sz-Venus were immunoprecipated by ANTI-FLAG® M2 Affinity Gel (Sigma A2220) and eluted with 200μg/ml FLAG® Peptide (Sigma F3290).  Three biological replicates were performed for each IP.   Total RNA was extracted from the input lysate and the beads using RNeasy Micro Kit (Qiagen) using the manufacturer’s protocol.  Strand-specific RNA sequencing was performed after depletion of ribosomal RNAs using Ribo-Zero (Epicenter Inc) by a modification of the procedure of Parkhomchuk et al. (Parkhomchuk et al., 2009), described in detail elsewhere (Z. Zhang and P. D. Zamore, manuscript in preparation).

tag: rip antibody

value: UAP-Venus


title: RIPseq_sz-Venus_Input

description: RNA immunoprecipitation (RIP)

source_name: sz-Venus expressed

tag: strain


title: Wild-type, Replicate 4


title: R26CreEA1N1


title: RIPseq_sz-Venus_IP

description: RNA immunoprecipitation (RIP)


title: Wild-type, Replicate 2


title: yal067c heterozygous diploid, Replicate 1


title: RIPseq_w1_Input

description: RNA immunoprecipitation (RIP)


title: Prx1CreRb1p53N38


title: Wild-type, Replicate 3


title: RIPseq_UAP-Venus_IP

description: RNA immunoprecipitation (RIP)

source_name: UAP-Venus expressed


title: MLLN_ChIPSeq

status: Public on Nov 27 2012

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.7 with default parameters. All 36-bp-long reads were mapped to the reference human genome sequence, hg18, using Illumina’s ELAND aligner with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277 (PMID 21736739)) and annotated to genes and/or promoters based on hg18 RefSeq genes downloaded from the UCSC Genome Browser.
Genome_build: hg18
Supplementary_files_format_and_content: BIGWIG: Counts.
Supplementary_files_format_and_content: BED: Peaks.

source_name: Acute lymphoblastic leukemia cells with MLL/AF4 translocation, MLLN ChIP

growth_protocol: The human RS4;11 ALL cells were maintained in Roswell Park Memorial Institute medium (RPMI-1640, Invitrogen, CA) with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
ChIP: For histone ChIP, RS4;11 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. For MLL and AF4 ChIP, RS4;11 cells were double-fixed with 2mM Disuccinimidyl Glutarate and then 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight, and after increasing stringency washes, immunocomplexes were recovered and DNA was isolated. The ChIP protocol in RS4;11 cells was followed as outlined in Milne et al. (PMID 19277579), using a formaldehyde fixation protocol for H3K79me2 and H3K4Me3, and a 45 minute, 2mMDSG and a 30 minute 1% double-fixation protocol for MLLN and AF4C.

Library construction: Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library Preparation Kit following the manufacturer's instructions (Illumina, CA). Briefly, 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

value: RS4;11 ALL cells

tag: chip antibody

value: MLLN

tag: chip antibody host

value: rabbit

tag: antibody vendor

value: Bethyl Laboratories

tag: antibody catalog #


title: H3K4me3_ChIPSeq

source_name: Acute lymphoblastic leukemia cells with MLL/AF4 translocation, H3K4me3 ChIP

value: Active Motif


title: input_H3K79me2_ChIPSeq

description: Paired with the H3K79me2 and H3K4me3 ChIP-seq.

source_name: Acute lymphoblastic leukemia cells with MLL/AF4 translocation, input


title: RIPseq_UAP-Venus_Input

description: RNA immunoprecipitation (RIP)


title: input_MLLN_ChIPSeq

description: Paired with the MLLN ChIP-seq.


title: input_AF4_HiSeq_ChIPSeq

description: Paired with the AF4 ChIP-seq.


title: H3K79me2_ChIPSeq

source_name: Acute lymphoblastic leukemia cells with MLL/AF4 translocation, H3K79me2 ChIP

value: Millipore


title: Wild-type, Replicate 1

tag: genotype/variation


title: Day154_rep4

status: Public on Nov 26 2012

city: Mississippi State

first: Juliet

middle: D

last: Tang

state: MS

department: Forest Products

institute: Mississippi State University

data_processing:
Raw sequence data was processed using Firecrest (image analysis) and Bustard (basecalling) as part of the Illumina GA Pipeline v1.4.0.  The raw sequence data is provided for each sample as a SCARF file.  Reads were trimmed and filtered to remove poor quality sequence according to the following criteria:  bases with "B" quality scores were trimmed, reads that had < 38 bases left after trimming were discarded, and any read that began with an "N" was discarded.  An ultrafast alignment tool, called Bowtie v0.12.7 was used to map the filtered FASTA dataset against the predicted CDS obtained from the v1.0 assembly of the Fibroporia radiculosa TFFH 294 genome (ProjectID: 72357).  Bowtie options were set to limit the output to unique alignments and a maximum of 2 mismatches were allowed in the first 28 bases of the read.  The number of unique alignments to each CDS (identified by the locus tag number) is provided in each sample count file.  The raw count data was then analyzed by edgeR in Bioconductor to identify differentially expressed genes.  A supplemental file is included that links the locus tag with the annotation, the CDS sequence, and localization motif for complete genes (start and stop codon).  The assembly was created using Velvet 0.7.55.  Genes were predicted with GeneMark-ES v2.  Annotations were based on conceptual translations and were obtained in July 2011 using the Blast2GO suite (v 2.4.9).
Genome Build:
Day154_rep4_count.txt: EMBL (project ID 72357)

organism: Fibroporia radiculosa TFFH 294

source_name: hyphae

growth_protocol: The fungus was grown in solid state cultures modified from the AWPA E22 accelerated soil block test to accommodate larger wood wafers and longer times of exposure to reach the desired wood decay state.

extract_protocol: Libraries were constructed according to standard protocols outlined in the Illumina mRNA-Seq Sample Prep Kit.  5 ug of total RNA was used to construct one library from each sample.  Library concentrations ranged from 11 to 102 nM and each library contained a peak fragment size between 363 to 398 bp.  All libraries were diluted to 10 nM prior to sequencing.  Short read sequencing of the libraries were done in 7 lanes on one single-end flow cell run of an Illumina GAIIx instrument (76 nt read length; day 31, n = 3; day 154, n = 4) with one lane reserved for the instrument control sample.

treatment_protocol: The preservative (0.8% solution of CuCO3:dimethyldidecylammonium carbonate, 2:1) was applied to the wood using full-cell pressure treatment and treated to a typical ground contact retention (5.47 kg/m3).

tag: developmental stage

tag: compression strength

value: Wood exhibits 52% loss in compression strength


title: Day154_rep2

data_processing:
Raw sequence data was processed using Firecrest (image analysis) and Bustard (basecalling) as part of the Illumina GA Pipeline v1.4.0.  The raw sequence data is provided for each sample as a SCARF file.  Reads were trimmed and filtered to remove poor quality sequence according to the following criteria:  bases with "B" quality scores were trimmed, reads that had < 38 bases left after trimming were discarded, and any read that began with an "N" was discarded.  An ultrafast alignment tool, called Bowtie v0.12.7 was used to map the filtered FASTA dataset against the predicted CDS obtained from the v1.0 assembly of the Fibroporia radiculosa TFFH 294 genome (ProjectID: 72357).  Bowtie options were set to limit the output to unique alignments and a maximum of 2 mismatches were allowed in the first 28 bases of the read.  The number of unique alignments to each CDS (identified by the locus tag number) is provided in each sample count file.  The raw count data was then analyzed by edgeR in Bioconductor to identify differentially expressed genes.  A supplemental file is included that links the locus tag with the annotation, the CDS sequence, and localization motif for complete genes (start and stop codon).  The assembly was created using Velvet 0.7.55.  Genes were predicted with GeneMark-ES v2.  Annotations were based on conceptual translations and were obtained in July 2011 using the Blast2GO suite (v 2.4.9).
Genome Build:
Day154_rep2_count.txt: EMBL (project ID 72357)


title: AF4_HiSeq_ChIPSeq

source_name: Acute lymphoblastic leukemia cells with MLL/AF4 translocation, AF4 ChIP

value: Abcam

tag: antibody lot#


title: Prx1CreRb1p53N28thigh


title: Day154_rep1

data_processing:
Raw sequence data was processed using Firecrest (image analysis) and Bustard (basecalling) as part of the Illumina GA Pipeline v1.4.0.  The raw sequence data is provided for each sample as a SCARF file.  Reads were trimmed and filtered to remove poor quality sequence according to the following criteria:  bases with "B" quality scores were trimmed, reads that had < 38 bases left after trimming were discarded, and any read that began with an "N" was discarded.  An ultrafast alignment tool, called Bowtie v0.12.7 was used to map the filtered FASTA dataset against the predicted CDS obtained from the v1.0 assembly of the Fibroporia radiculosa TFFH 294 genome (ProjectID: 72357).  Bowtie options were set to limit the output to unique alignments and a maximum of 2 mismatches were allowed in the first 28 bases of the read.  The number of unique alignments to each CDS (identified by the locus tag number) is provided in each sample count file.  The raw count data was then analyzed by edgeR in Bioconductor to identify differentially expressed genes.  A supplemental file is included that links the locus tag with the annotation, the CDS sequence, and localization motif for complete genes (start and stop codon).  The assembly was created using Velvet 0.7.55.  Genes were predicted with GeneMark-ES v2.  Annotations were based on conceptual translations and were obtained in July 2011 using the Blast2GO suite (v 2.4.9).
Genome Build:
Day154_rep1_count.txt: EMBL (project ID 72357)


title: R26CreEA1N2


title: small RNAs (18-29nt) from wild-type ovarian somatic cells

city: Vienna

first: Grzegorz

last: Sienski

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

data_processing:
small RNA-seq libraries: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings; after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9.
small RNA-seq libraries: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

GRO-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq file was adapter' ATCGTATGCCGTCTTCTGCTTGT' clipped using cutadapt, version 1.0, default settings; after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9.
GRO-seq: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

RNA-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); fastq files containing 2nd mate were reverse complemented and used together with fastq files containing 1st mate as single-end library; N-containing reads were discarded; reads were trimmed to high-quality bases 6-56 using HomerTools, version 3.9 and mapped to genome and transcriptome using in-house developed pipeline.

ChIP-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); reads were trimmed to bases 2-50 using HomerTools, version 3.9;  N-containing reads were discarded; smaller than 50nt-long reads were discarded.
ChIP-seq: reads were mapped with bowtie v0.12.7 to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1

DNA-seq: basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0); N-containing reads were discarded; smaller than 100nt-long reads were discarded; TEs insertions were called using in-house developed pipeline.
Supplementary_files_format_and_content: DNA-seq: file contains coordinates of TEs insertions called in OSC
Supplementary_files_format_and_content: RNA-seq, GRO-seq, ChIP-seq: file contains density coverage of uniquely mapped reads to dm3
Genome_build: dmel_release 5

source_name: small RNAs (18-29nt)_wild-type OSCs

growth_protocol: flies were grown at 25 degrees; OSC were grown at 27 degrees on M3 medium

extract_protocol:
GRO-seq was done according to Core et al. 2008; ChIP-seq as described in Lee et al. 2006; RNA-seq as in Zhong et al. 2011
small-RNAs were cloned as described in Brennecke et al. 2007

treatment_protocol: OSC were transfected twice with siRNAs and analyzed after 4 days

value: wild-type

tag: tissue/cell type

value: Ovarian Somatic Cells (OSC)

tag: molecule subtype

value: total RNA


title: Prx1CreRb1p53N42

tag: tissue

value: osteosarcoma


title: Day31_rep2

data_processing:
Raw sequence data was processed using Firecrest (image analysis) and Bustard (basecalling) as part of the Illumina GA Pipeline v1.4.0.  The raw sequence data is provided for each sample as a SCARF file.  Reads were trimmed and filtered to remove poor quality sequence according to the following criteria:  bases with "B" quality scores were trimmed, reads that had < 38 bases left after trimming were discarded, and any read that began with an "N" was discarded.  An ultrafast alignment tool, called Bowtie v0.12.7 was used to map the filtered FASTA dataset against the predicted CDS obtained from the v1.0 assembly of the Fibroporia radiculosa TFFH 294 genome (ProjectID: 72357).  Bowtie options were set to limit the output to unique alignments and a maximum of 2 mismatches were allowed in the first 28 bases of the read.  The number of unique alignments to each CDS (identified by the locus tag number) is provided in each sample count file.  The raw count data was then analyzed by edgeR in Bioconductor to identify differentially expressed genes.  A supplemental file is included that links the locus tag with the annotation, the CDS sequence, and localization motif for complete genes (start and stop codon).  The assembly was created using Velvet 0.7.55.  Genes were predicted with GeneMark-ES v2.  Annotations were based on conceptual translations and were obtained in July 2011 using the Blast2GO suite (v 2.4.9).
Genome Build:
Day31_rep2_count.txt: EMBL (project ID 72357)

value: Wood exhibits less than 5% loss in compression strength


title: Day31_rep3

data_processing:
Raw sequence data was processed using Firecrest (image analysis) and Bustard (basecalling) as part of the Illumina GA Pipeline v1.4.0.  The raw sequence data is provided for each sample as a SCARF file.  Reads were trimmed and filtered to remove poor quality sequence according to the following criteria:  bases with "B" quality scores were trimmed, reads that had < 38 bases left after trimming were discarded, and any read that began with an "N" was discarded.  An ultrafast alignment tool, called Bowtie v0.12.7 was used to map the filtered FASTA dataset against the predicted CDS obtained from the v1.0 assembly of the Fibroporia radiculosa TFFH 294 genome (ProjectID: 72357).  Bowtie options were set to limit the output to unique alignments and a maximum of 2 mismatches were allowed in the first 28 bases of the read.  The number of unique alignments to each CDS (identified by the locus tag number) is provided in each sample count file.  The raw count data was then analyzed by edgeR in Bioconductor to identify differentially expressed genes.  A supplemental file is included that links the locus tag with the annotation, the CDS sequence, and localization motif for complete genes (start and stop codon).  The assembly was created using Velvet 0.7.55.  Genes were predicted with GeneMark-ES v2.  Annotations were based on conceptual translations and were obtained in July 2011 using the Blast2GO suite (v 2.4.9).
Genome Build:
Day31_rep3_count.txt: EMBL (project ID 72357)


title: Day31_rep1

data_processing:
Raw sequence data was processed using Firecrest (image analysis) and Bustard (basecalling) as part of the Illumina GA Pipeline v1.4.0.  The raw sequence data is provided for each sample as a SCARF file.  Reads were trimmed and filtered to remove poor quality sequence according to the following criteria:  bases with "B" quality scores were trimmed, reads that had < 38 bases left after trimming were discarded, and any read that began with an "N" was discarded.  An ultrafast alignment tool, called Bowtie v0.12.7 was used to map the filtered FASTA dataset against the predicted CDS obtained from the v1.0 assembly of the Fibroporia radiculosa TFFH 294 genome (ProjectID: 72357).  Bowtie options were set to limit the output to unique alignments and a maximum of 2 mismatches were allowed in the first 28 bases of the read.  The number of unique alignments to each CDS (identified by the locus tag number) is provided in each sample count file.  The raw count data was then analyzed by edgeR in Bioconductor to identify differentially expressed genes.  A supplemental file is included that links the locus tag with the annotation, the CDS sequence, and localization motif for complete genes (start and stop codon).  The assembly was created using Velvet 0.7.55.  Genes were predicted with GeneMark-ES v2.  Annotations were based on conceptual translations and were obtained in July 2011 using the Blast2GO suite (v 2.4.9).
Genome Build:
Day31_rep1_count.txt: EMBL (project ID 72357)


title: Rrp6D Clr4D

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
base calls were performed using CASAVA, or ELAND, or BUSTARD for files sequenced on MiSeq, Ilumina Genome Analyser IIx, and HiSeq2000 respectively
The sequence reads were trimmed for adapters and aligned to the S. pombe genome version released on April 2007 using novoalign program.
The parameters for novoalign were as follows: "-m" to treat the data as small RNA and "-a" to automatically trim the adapters
We used custom Python scripts to count number of times each location in the genome was seen in the data on the + and the - strand.
The processed data is uploaded as SGR file.  This file is similar to a wig file, first column denotes 'chromosome", second column denotes "position" on the chromosome, and the last column denotes number of times the position was seen in the data.
A negative value on 3rd column denotes the number of times the position was seen when reads mapped to the "-" (minus) strand, and a positive value denotes the number of times the given position was seen when the reads mapped to the "+" (plus) strand.
The counts were nomalized to million mapped reads.
Genome_build: Spombe Genome Released in April 2007
Supplementary_files_format_and_content: The data is uploaded as SGR file where first column denotes the chromosome, second column denotes the position on the chromosome counted from the 5' end on the + strand, and the 3rd column denotes the count (normalized to million mapped reads).

organism: Schizosaccharomyces pombe

source_name: Rrp6 and Clr4 double deletion

extract_protocol:
Yeast total RNAs are extracted by using MasterPure Yeast RNA purification kit (epicentre). Fly total RNAs are extracted by using specific buffer(0.5M NaCl, 0.2M Tris-HCl(pH 7.5), 0.01M EDTA, 1% SDS), glass beads, and phenol chloroform.
The protocol is described in [RNA. 2010 Dec;16(12):2537-52].

tag: genotype

value: Rrp6D Clr4D


title: Rrp6D Rdp1D

source_name: Rrp6 and Rdp1 double deletion

value: Rrp6D Rdp1D


title: Rrp6D Ago1D

source_name: Rrp6 and Ago1 double deletion

value: Rrp6D Ago1D


title: Rrp6D

source_name: Rrp6 Deletion


title: Day154_rep3

data_processing:
Raw sequence data was processed using Firecrest (image analysis) and Bustard (basecalling) as part of the Illumina GA Pipeline v1.4.0.  The raw sequence data is provided for each sample as a SCARF file.  Reads were trimmed and filtered to remove poor quality sequence according to the following criteria:  bases with "B" quality scores were trimmed, reads that had < 38 bases left after trimming were discarded, and any read that began with an "N" was discarded.  An ultrafast alignment tool, called Bowtie v0.12.7 was used to map the filtered FASTA dataset against the predicted CDS obtained from the v1.0 assembly of the Fibroporia radiculosa TFFH 294 genome (ProjectID: 72357).  Bowtie options were set to limit the output to unique alignments and a maximum of 2 mismatches were allowed in the first 28 bases of the read.  The number of unique alignments to each CDS (identified by the locus tag number) is provided in each sample count file.  The raw count data was then analyzed by edgeR in Bioconductor to identify differentially expressed genes.  A supplemental file is included that links the locus tag with the annotation, the CDS sequence, and localization motif for complete genes (start and stop codon).  The assembly was created using Velvet 0.7.55.  Genes were predicted with GeneMark-ES v2.  Annotations were based on conceptual translations and were obtained in July 2011 using the Blast2GO suite (v 2.4.9).
Genome Build:
Day154_rep3_count.txt: EMBL (project ID 72357)


title: WT

source_name: Wild type

value: WT


title: non-lactation-miRNA

city: Hangzhou

first: Zhen

last: Li

address: 866 Yuhang Tang Road

country: China

institute: College of Animal Science, Zhejiang University

data_processing:
Small RNA reads were processed using Illumina’s Genome Analyzer and ACGT101-miR program was then used to clean the sequencing data.
the sequencing data were filtered out the sequencing data to mRNA, RFam, Repbase, and then mapped to miRbase. The mapped data were then aligned to genome and EST, databases revealing genome locations or annotations.
The rests of unmapped data were mapped to genome and EST, and secondary structure were predicted using UNAFold software
IDEG 6 was used to identify significant differentially expressed miRNAs
Genome_build: BTA 4.0

organism: Bos taurus

source_name: bovine

extract_protocol: Bovine mammary gland were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: mammary gland

tag: mammary gland stage

value: non-lactation


title: input DNA

city: Singapore

first: Gaye

last: Saginc

address: 60 Biopolis Street

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

data_processing:
35 bp long reads  were uniquely mapped to the Human Genome 19 (UCSC), using SOLID Bioscope 1.3.1 ChIP-Seq Module. For alignments, seed and extension approach was used. 30 bp seeds which aligned to the reference genome with at most 3 color mismatches were kept and extended up to 35 bp. Only reads with unique full length alignment (35 bp) allowing for 2 mismatches were used in the analysis.
Redundant reads (multiple reads aligning exactly to the same location) which are generally PCR-artefacts were filtered. Control-based ChIP-seq Analysis Tool version 3 (CCAT3) was performed for peak calling under default settings using reads which were mapped to unique regions in the genome.
Peaks with FDR superior than 0.2 are excluded from the analysis. For the downstream analysis, normalized fold enrichments reported by CCAT3 were used.
Genome_build: hg19 with random chr

source_name: HeLa cells

growth_protocol: HeLa cells were grown to 70-80% confluence in Dulbecco’s modified eagle medium (DMEM) which was supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 2 mM sodium pyruvate and 1 × PSF (penicillin, streptomycin and fungizone) at 37 °C with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10min at room temperature, followed by 125mM glycine treatment to inactivate the crosslinking. Chromatin extracts were sonicated to 200- 500bp fragments, followed by overnight immunoprecipitation at 4˚C.Then, protein-DNA complexes were de-crosslinked with overnight incubation at 65°C and DNA extraction was performed using Qiagen PCR purification kit.
After the quality of the ChIP DNA was controlled by checking the concentration and the enrichment of known targets in ChIP DNA over input with Quant-iT PicoGreen assay (Invitrogen) and real time PCR respectively, libraries were constructed using SOLID ChIP-Seq Kit (Applied Biosystems) following manufacturer's protocol. For each sample, 10 ng of ChIP DNA was purified using AMPure XP Kit (Agencourt), end-repaired and ligated to SOLID adaptors. After ligation, samples were nick-translated and amplified using primers specific to adaptors for 15 cycles. Samples were purified multiple times between each steps. Following the final purification step, size distribution and quantity of libraries were checked by performing DNA 1000 assay (Agilent). Samples with expected size distribution (165-365 bp) and quantity (min 2ng/ul in 10 ul) were sequenced using SOLID4 sequencer following manufacturer's instructions for fragment sequencing. Each sample was loaded to a quarter SOLID slide.

treatment_protocol: HeLa cells were separated into 3 groups: "control", "TNFα-treated" and "TNFα & MST-312-treated" group. Cells in the "TNFα & MST-312" group were treated with 1 uM of MST-312 (Sigma) for 48 hours prior to the ChIP procedure. Then cells except the control group were treated with TNFα (Calbiochem)to a final concentration of 10 ng/ul for 45mins before the ChIP procedure.  The control cells were treated with an equal volume of DMSO (vehicle), for 45mins. For a ChIP experiment, approximately 2 x 10^8 cells from 5 of 150 mm diameter cell culture plates were used.

tag: treatment

value: TNF-treated cells (45 min)

tag: cell type

value: Cervical cancer cell line

value: none, input DNA


title: lactation-miRNA

value: lactation


title: TNF-MSTtreated_p65_ChIP-seq

description: p65 ChIP-seq, with MST-312 treatment

value: TNF-MSTtreated

value: p65 (Santa Cruz, C-20, Cat no. SC372)


title: TNFtreated_p65_ChIPSeq

description: p65 ChIP-seq, with TNFα

value: TNFtreated


title: Cflo.Male.PolII

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

address: 1041 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania

description: DNA fragments sequenced following chromatin immunoprecipitation

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_PolII.Q.matrix.txt: C. floridanus v3.0

organism: Camponotus floridanus

source_name: Head and thorax from adult ants

growth_protocol: Ants were grown and maintained as a single colony in the laboratory of Juergen Liebig (ASU) at constant temperature and fed regularly using meal worms

extract_protocol: Total RNA was isolated from ants using QIAzol lysis reagent (Qiagen). PolyA mRNA was purified from total RNA samples using PolyT beads (Invitrogen mRNA Direct Kit). Sequencing libraries were constructed using the NEBNext mRNA Library Prep Kit (New England Biolabs) according to manufacturer’s instruction.     For ChIP-seq, head and thorax sections, or dissected whole-brains, of C. floridanus major, minor, and male ants were collected and homogenized first on dry ice, then on ice in crosslinking buffer (60mM KCl, 15mM NaCl, 4mM MgCl2, 0.1% Triton X-100, 50mM HEPES, pH 7.5 with protease inhibitor) with 1.8% formaldehyde for 10 min. For CBP ChIP, additional long chain crosslinking was carried out first with 500mM EGS (Ethylene Glycol-bis Succinimidylsuccinate, fresh made in DMSO) for 10 min, followed by 1.8% formaldehyde crosslinking for 10 min87. Crosslinking was terminated by adding 2.5M glycine to a final concentration of 125mM for 5 min. Cuticles were discarded and homogenate was transferred to a new tube and centrifuged for 3 min, 4000g at 4°C. Pellet was washed once with lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine with protease inhibitors) and centrifuged again. The resulting pellet was resuspended in lysis buffer and sonicated using a Bioruptor (Diagenode) for 10 min with 30 sec on and 30sec off cycles. Samples were centrifuged for 10min, 20,000g at 4oC and supernatant collected as starting material for ChIP.    A 30ul protein A and protein G bead mixture (Invitrogen) was used to ChIP each sample. Beads were washed 3 times with blocking buffer (0.25% BSA in PBS), then incubated with 5µg antibodies in 500ul blocking buffer for 4h to allow antibody binding. Following binding, beads were washed 3 times with blocking buffer. 500µg chromatin was added to beads for each ChIP and incubated overnight at 4°C. Beads were washed sequentially with following buffers: twice with lysis buffer, once with FA-500mM buffer (50mM HEPES-KOH, pH7.5, 500mM NaCl, 1mM EDTA, 0.1% TritonX-100), twice with LiCl buffer (10mM Tris-HCl pH8.0, 0.25M LiCl, 1mM EDTA, 0.5% NP40), and once with TE pH 8.0. Beads were then eluted three times with 100µl TES buffer each (50mM Tris-HCl, pH8.0, 10mM EDTA, 1% SDS) at 65°C for 15 min. 12µl 5M NaCl was added to the pooled elute, which was then incubate at 65°C overnight to reverse the crosslinking. Samples were then treated with 5µl 20mg/ml protease K at 37°C for 1h and purified for DNA. ChIP samples (purified DNA) were used for qPCR application or high throughput sequencing. Sequencing libraries were constructed according to manufacturer’s instruction (Illumina).

treatment_protocol: Contrast of naturally occurring major, minor, and male ant castes (adults)

tag: colony

value: Colony C4 from Florida Keys, FL, USA

tag: dev. stage

value: Adult

tag: caste

value: Male

tag: modification

value: RNA Pol II

value: Custom recombinant


title: Cflo.Minor.PolII

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_minor_PolII.Q.matrix.txt: C. floridanus v3.0

value: Minor

tag: antibody vendor


title: Cflo.Minor.Brain.RNA.R2

description: DNA fragments sequenced following RNA isolation and polyA+ purification

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
CX.Minor.brain.RNA.rep2.cufflinks.transcripts.gtf: C. floridanus v3.0

source_name: Whole-brain dissection from adult ants

value: Colony from Florida Keys, FL, USA

value: RNA (polyA+)

tag: antibody catalog #


title: Cflo.Male.H3K9ac

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_male_H3K9ac.Q.matrix.txt: C. floridanus v3.0

value: Abcam


title: Cflo.Major.PolII

data_processing:
Reads were mapping to the cflo v3.0 genome using Bowtie v0.12.7 allowing 1 mismatch over the entire read length and 50 alignments per read (-n 1 -k 50 --best). For ChIPseq, spuriously amplified reads were removed from read maps before data analysis (see Supplementary Methods); only the top 5 aligned reads were used for data analysis. Sample and caste specific, per-nucleotide ChIP enrichment scores were estimated using a Bayesian probabilistic model that integrates input, total histone, and PTM read maps. Resulting posterior probability values, P, are transformed using a phred-like function and further log transformed as follows: s = log2[ -10 log10(1-P)]. These scores, s, were further subject to between-sample normalization using a Z-transformation, that is subtracting genome-wide mean and scaling by standard deviation.
Genome Build:
C4_major_PolII.Q.matrix.txt: C. floridanus v3.0

value: Major


title: small RNAs (18-29nt) from restrictive

source_name: small RNAs_restrictive

tag: genotype/variation

value: flamRev(R)

tag: Stage

value: from 5-6 days old flies

value: ovaries

value: total RNA