title: input DNA for H3K4me3 ChIP

description: input for H3K4me3 (WGA with sigma kit)

data_processing:
Input-FB-CMM012__unique_hits.tags.txt; genome build: mm8
The tags were extended by 200 bp to make wiggle track for sequenced libraries binning whole genome in 200bp bins. For finding peaks in H3K4me3 ChIPseq Dfilter was used. The peaks are provided in supplementary material. The ChIPseq data was also used by EFilter to predict expression of gene in mouse forebrain. For Efilter GC correction was done for both ChIP libraries using corresponding input libararies.

source_name: input DNA for H3K4me3 ChIP


title: H3K4me3 ChIP-seq

status: Public on Jun 10 2013

type: SRA

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: WGA with sigma kit

library_source: genomic

data_processing:
forebrain-track-CMM008-H3K4me3.vstep.wig; genome build: mm8
H3K4me3-FB-CMM008_138_unique_hits.tags.txt; genome build: mm8
The tags were extended by 200 bp to make wiggle track for sequenced libraries binning whole genome in 200bp bins. For finding peaks in H3K4me3 ChIPseq Dfilter was used. The peaks are provided in supplementary material. The ChIPseq data was also used by EFilter to predict expression of gene in mouse forebrain. For Efilter GC correction was done for both ChIP libraries using corresponding input libararies.

molecule: genomic DNA

organism: Mus musculus

source_name: H3K4me3 ChIP

extract_protocol: Mouse embryonic forebrain tissues were micro-dissected and pooled from 11.5 dpc embryos. Dissected tissues were mechanically dissociated by passing cell strainer and fixed in 1% formaldehyde (diluted from 37% stock solution, Sigma, F8775) simultaneously following pre-treatment with 0.125% tripsin/versene solution. 36 forebrain pieces were used for each ChIP-seq library preparation. Cells were resuspended in SDS buffer and sonicated 12 times for 30 seconds with 30 seconds interval with Bioruptor water bath sonicator (Diagenode). Following sonication, samples were diluted with IP dilution buffer and incubated with 50 micro-litter affinity resin coupled with 10 micro-litter anti-H3K4me3 antibodies (Upstate, Cat# 07-473, Lot# 32497). Following washing steps, chromatin was reverse-crosslinked for purification of DNA. H3K4me3 ChIPed DNA and 0.5 % input DNA samples were amplified for 8 cycles with GenomePlex Single Cell Whole Genome Amplification Kit (WGA4, Sigma) using universal primer linked to BpmI restriction site. Amplified DNA samples were digested with BpmI to remove universal primer. After quantification of DNA with Quant-iT PicoGreen sdDNA Assay Kit (Invitrogen, P7589), 12 ng of the DNA sample was directly used for Illumina sequencing adaptor preparation. Illumina sequencing was performed using GAII platform in GIS. H3K36me3 data was obtained similarly using 15 micro-litter of anti-H3K36me3 antibody (Abcam, Cat# Ab9050, Lot# 707981). As DNA yield of H3K36me3 antibody ChIP was much higher, WGA amplification step was not performed and ChIP DNA was directly used for Illumina sample preparation.

tag: strain

tag: develepmental stage

tag: tissue

value: forebrain

tag: chip antibody

tag: chip antibody vendor

value: Upstate

tag: chip antibody catalog#

tag: chip antibody lot#


title: mRNA.6008.2h.TEM

city: Heidelberg

first: Ben

last: Howden

state: VIC

address: Austin Health

department: Infectious Diseases Department

country: Australia

institute: Austin Health

library_source: transcriptomic

data_processing:
Read clipping using nesoni clip tool. Nesoni url: http://vicbioinformatics.com/software.nesoni.shtml
Read alignment using SHRiMP 2.2.2. SHRiMP url: http://compbio.cs.toronto.edu/shrimp/
Alignment selection using nesoni filter tool. Only top scoring alignments were kept. Where there were multiple equal best alignments, one was chosen at random.
Counting of alignments to annotated CDS sequences and sRNA sequences, using nesoni count tool. Alignments were required to be on the correct strand.
Normalization factors to render expression levels comparable between samples were calculated using BioConductor package edgeR's implementation of the TMM normalization method.
Genome_build: CP002120.1
Supplementary_files_format_and_content: The *-count.csv files contain counts of the numbers of reads aligning to each feature. The accompanying *-counts-norm.txt files give normalization factors for each sample.

molecule: total RNA

organism: Staphylococcus aureus

growth_protocol: S. aureus were grown in Mueller Hinton broth for 2 or 6 hours.

extract_protocol: Total RNA was extracted using the Rneasy Kit (Qiagen). RNAs were then treated with the MICROBExpress kit (AMBION) to limit the contamination by rRNAs, following manufacturer’s recommendations. At each step, RNA quality was controlled by Bioanalyzer (Agilent) using the RNA Nano Chips, and quantity was assessed using the ND-8000 (NanoDrop Technologies. Extracted RNA was prepared to enrich for mRNA or sRNA as follows. For mRNA preparations, initial fragmentation using Zinc was followed by treatment with first Antartic Phosphatase and then with PNK enzyme. Single-stranded ligation of the 3’ Illumina v1.5 adapter was followed by single-stranded ligation of 5’ bar-coded adapter. Reverse transcription and PCR amplification was performed to generate a cDNA colonies template library, and gel purification with selection of fragments of 20-300 nts was performed. Quality control of the DNA colony template library was performed by cloning an aliquot into a TOPO plasmid and sequencing 8 clones. The same process was used for sRNA preparation, without the Zinc fragmentation, and using a size selection of 20-200 nt.

treatment_protocol: Antibiotics exposure was for 10 minutes at 0.5 x MIC.

tag: antibiotic

tag: growth time

value: 2 hours

tag: rna preparation

value: mRNA


title: Sendai Virus Infected

city: Evanston

first: William

last: Buggele

state: IL

address: 2200 Campus Dr.

country: USA

institute: Northwestern University

data_processing:
Sequence tags were processed and analyzed using BioScope software package (Applied Biosystems)
MicroRNA sequence tags were normalized by thousand mappable tags
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file of microRNA sequence tags per thousand mappable tags

organism: Homo sapiens

source_name: Alveolar epithelial cell line

growth_protocol: A549 cells were cultured in F12K media (Gibco) supplemented with 10% cosmic calf serum (Hyclone) and pennecilin and streptomycin

extract_protocol:
RNA was purified and size fractionated using miRNEASY RNA isolation kit and Rneasy MinElute Clean up kit (Qiagen)
Libraries were constructed using 1 microgram of small RNA and the Small RNA Expression Kit (Applied Biosystems)

treatment_protocol: Cells were either mock infected or infected with Sendai virus (5 pfu/cell) for 10 hours

tag: cell type

value: A549 cells

tag: infection status

value: Sendai Virus Infected

tag: rna type

value: low molecular weight RNA


title: mRNA.6008.6h.TEM

value: 6 hours


title: Neuron_Input

status: Public on Jun 09 2013

city: London

first: Matt

last: Burney

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

description: Sample 6

data_processing:
Reads were QC checked using FastQC
Reads were aligned using Bowtie, using 'best' alignment, with a seed sequence length of 15bp and Solexa quality v1.3 quality scores.
Duplicates were removed and reads were sorted and indexed using SamTools
Peaks were called using SICER, with a window size of 200bp and a gap size of 1 for H3K4me3 and 3 for H3K27me3, a threshold of 1 and a genome fraction of 0.75
Peaks were annotated to the nearest gene using the Iranges library and BiomaRt in R
Genome_build: mm9
Supplementary_files_format_and_content: Files contain raw output from SICER peak calling, with genomic coordinates (*bed files). Second processed file contains peak annotation to nearest Ensembl gene (*csv files)

source_name: Differentiated and FACS from NSCs

growth_protocol: NSCs were routinely cultured in Euromed-N (Euroclone) supplemented with 1x N2, 10ng/ml FGF2 and 10ng/ml EGF (Peprotech)

extract_protocol:
Cells were fixed in 1% HCHO and lysed in 1% SDS lysis buffer. Chromatin was sheared to 300bp and immunoprecipitated with antibodyies against H3K4me3, H3K27me3, total histone H3 and IgG. Total H3 was from Abcam (ab1791) and rabbit IgG from Santa Cruz (SC-2027) were used to precipitate all samples, in addition to the IPs done with H3K4me3 and H3K27me3. Only the K4/K27 were sequenced.
Libraries were prepared according to standard Illumina Solexa protocols

treatment_protocol: NSCs were differentiated into neurons in Euromed-N supplemented with 1/2x N2, 5ng/ml FGF2 and 1/2x B27. After four days, immature neurons were replated into N2B27 and matured for seven days, before FACS purification based on RedStar fluorescence.

value: differentiated neuronal progeny

tag: differentiation day

tag: redstar+

value: Positive

tag: passages


title: Neuron_H3K4me3

description: Sample 4

value: Active Motif

tag: chip antibody cat. #


title: NSC_H3K4me3

description: Sample 1

source_name: Derived from mESCs

tag: strain

value: neural stem cellsderived from mouse embryonic stem cells

value: Negative


title: NSC_H3K27me3

description: Sample 2


title: Neuron_H3K27me3

description: Sample 5


title: beta3

status: Public on Jun 07 2013

city: Oxford

first: Martijn

last: van de Bunt

address: OCDEM, Churchill Hospital, Headington

institute: Oxford Centre for Diabetes, Metabolism & Endocrinology

data_processing:
Pre-processing: removed residual adaptor sequences using  FASTX-toolkit. Sequences < 16 bases after adaptor stripping, and reads containing primarily N bases, were removed.
Alignment: novoalign v. 2.07.11, parameters -h 60 60 -t30 -s -m -l 16 -R 0 -r A 30
Post-processing: Reads mapping to contaminating sequences were excluded. The remaining reads were prioritised in order miRNA > ncRNA > genome, and alignments with the smallest edit distance were selected.
Quantification: Read counts. Where a read mapped between k alternative sequences in one reference, 1/k was added to the count of each. RNA sequences observed < 100 times across all samples were excluded.
Normalisation: according to Anders and Huber, Genome Biol, 2010
Genome_build: 1. Contaminating sequences of adaptors, linkers, adaptor-linker, and adaptor-tag combinations. 2. miRBase v17 hairpin sequences, combined with other known and predicted human small RNA sequences present in Ensembl v63. 3. Human reference genome (NCBI build 37).
Supplementary_files_format_and_content: tab-delimited text-file containing  transformed miRNA count data for all samples

source_name: Pancreatic beta-cell

extract_protocol:
total RNA extracted using Trizol solution
Illumina v1.5 or TruSeq v1 small RNA library protocol

value: FACS-enriched pancreatic beta-cells

tag: age

tag: Sex

value: Female

tag: bmi

tag: purity


title: H3K4me1

status: Public on Jun 08 2013

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

country: Spain

institute: CRG

data_processing:
Basecalls performed using Illumina pipeline version 1.4.0
ChIP-Seq reads were aligned to the reference genome (hg19) using GEM (http://www.ncbi.nlm.nih.gov/pubmed/22276185) keeping only uniquely mapped reads with up to 2 mismatches
We used Pyicos (http://regulatorygenomics.upf.edu/pyicos/) to call significant peaks with the following parameters: maximum of 4 duplicates, read extension of 130bp, control T0 subtraction, removed artificats, splitted the peaks where the read coverage goes below 5% of the peak summit and a Poisson analysis using peak-height with a p-value cutoff of <=0.001.
Genome_build: hg19
Supplementary_files_format_and_content: Tabulated txt files containing peaks found with H3K4 me3, H3K4 me1 and RNA Polimerase II.

source_name: T47D-MTVL breast cancer cell line

growth_protocol: Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
After hormone treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min at 37ºC for cross-linking. The reaction was stop by adding 125 mM glycine and incubated 5 min at room temperature. Cells were washed twice with cold PBS, and collected. Preparation of chromatin and ChIP experiments were performed as previously described (Strutt et al, Methods Mol Biol. 1999; 119:455-567). Immunoprecipitated DNA was purified by phenol:chloroform followed by ethanol precipitation
It was performed using the NEBNext DNA sample prep Reagents set 1

treatment_protocol: For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were incubated with R5020 (10 nM) for different times between 0 and 360 minutes

tag: treatment

value: unstimulated cells

tag: chip antibody

value: T47D-MTVL breast cancer cell line


title: beta2


title: beta1

value: Male


title: Isl3

source_name: Pancreatic islet

tag: tissue

value: Purified pancreatic islets


title: H3K36me3 ChIP-seq

description: noWGA

data_processing:
forebrain-track-CMM026-H3K36me3.vstep.wig; genome build: mm8
H3K36me3-FB-CMM026_184_unique_hits.tags.txt; genome build: mm8
The tags were extended by 200 bp to make wiggle track for sequenced libraries binning whole genome in 200bp bins. For finding peaks in H3K4me3 ChIPseq Dfilter was used. The peaks are provided in supplementary material. The ChIPseq data was also used by EFilter to predict expression of gene in mouse forebrain. For Efilter GC correction was done for both ChIP libraries using corresponding input libararies.

source_name: H3K36me3 ChIP

tag: develepmental stage

value: forebrain

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#

tag: chip antibody lot#


title: Isl2


title: H3K4me3

tag: cell type


title: wildtype rep2

city: Princeton

first: Trudi

last: Schupbach

state: NJ

address: Washington Rd

department: Molecular Biology

institute: HHMI/Princeton University

description: smallRNA profiling

data_processing:
The Drosophila melanogaster genome assembly dm3 from UCSC genome browser, excluding ChrYhet and ChrUExtra,was used as the reference genome. Sequence reads were trimmed of their adaptor sequences with FASTX toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/) with parameters -l 18 -Q33 -c -M 6 -a TCGTATGCCGTCTTCTGCTTGT. Bowtie 0.12.7 (http://bowtie-bio.sourceforge.net/index.shtml) was used to find exact matches in the genome for RNA reads with parameters -a -n 0 -e 1.
For the final processed WIG file, only uniquely mapped reads on genome were considered. For each biological replicate, the sequence read counts between wildtype and cuff mutant libraries were normalized by assuming the overall gene expression profiles were not affected between two conditions.
The WIG format files represented the sequence read counts in 100nts windows across each chromosome. Within each 100nts window, the first 50nts part represents the reads mapped on the plus strand and the last 50nts part represents the reads mapped on the minus strand. So, finally in the WIG file, window steps were set as 50nts with alternating counts on plus and minus strands.
Genome_build: dm3
Supplementary_files_format_and_content: UCSC WIG format

organism: Drosophila melanogaster

source_name: cn bw ovary

extract_protocol: Small RNA libraries from the cn bw control line, and from cuffwm25 homozygous ovaries were produced with the Small RNA Library Prep Kit (Illumina). Briefly, 20 μg total RNA extracted from the different genotypes was separated on a 15% denaturing polyacrylamide/urea gel electrophoresis (Invitrogen) for 1 h at 200 V. A gel slice corresponding to 18–30-nt-long RNAs was isolated and small RNAs were eluted and processed with the Small RNA Library Prep Kit as per the manufacturer's instructions. Small RNA libraries were subsequently sequenced on the Solexa Genome Analyzer II platform.

tag: genotype/variation

value: wildtype

value: ovary


title: cuff mutant rep1

description: smallRNA profiling

source_name: cuffwm25 ovary

value: cuff mutant


title: Isl1


title: cuff mutant rep2

description: smallRNA profiling


title: wildtype rep1

description: smallRNA profiling


title: Mock Infected

value: A549 cells

tag: infection status

value: Mock Infected

tag: rna type

value: low molecular weight RNA


title: MethylCap-Seq: GC B, Aicda+/+ rep1L

city: Amsterdam

first: Marc

middle: Arnaud

last: Hogenbirk

address: Plesmanlaan 121

department: biological stress response

country: Netherlands

institute: the Netherlands Cancer Institute

description: MethylCap-Seq

data_processing:
Bases were called using the standard Illumina pipeline
Reads we aligned to mm9 using BWA with default settings
Reads with mapping quality less than 37 were removed
Reads overlapping promotor regions were counted using bedTools
Genome_build: mm9
Supplementary_files_format_and_content: txt, readcounts in promotor regions

source_name: Aicda+/+ (low eluate)

growth_protocol: To isolate GC B cells, 2-mo-old Aicda-/- and Aicda+/+ mice were immunized by a single intraperitoneal injection of 10e8 sheep red blood cells in 200 μl HBSS. Ten days later, GC B cells (CD19+, PNAhigh, CD95+, DAPI-) were sorted from splenic single-cell suspensions

extract_protocol:
According manufacters protocol (Diagenode)
Illumina library construction

value: GC B cell


title: MethylCap-Seq: GC B, Aicda+/+ rep2M

description: MethylCap-Seq

source_name: Aicda+/+ (medium eluate)


title: MethylCap-Seq: GC B, Aicda+/+ rep1H

description: MethylCap-Seq

source_name: Aicda+/+ (high eluate)


title: MethylCap-Seq: GC B, Aicda+/+ rep1M

description: MethylCap-Seq


title: NSC_input

description: Sample 3

value: neural stem cellsderived from mouse embryonic stem cells

tag: differentiation day

tag: redstar+

tag: passages


title: MethylCap-Seq: GC B, Aicda-/- rep2L

description: MethylCap-Seq

source_name: Aicda-/- (low eluate)

tag: strain


title: RNA Polimerase II

value: Anti-RNAPII (ChIPAb+ Millipore)


title: MethylCap-Seq: GC B, Aicda-/- rep2M

description: MethylCap-Seq

source_name: Aicda-/- (medium eluate)


title: MethylCap-Seq: GC B, Aicda-/- rep1L

description: MethylCap-Seq


title: RNA-Seq: GC B, Aicda+/+  rep2

data_processing:
Reads we mapped to the reference genome using TopHat version 1.40
Aligned reads were counted using htseq-count by using the Ensembl mouse gtf release 66
Genome_build: mm9
Supplementary_files_format_and_content: txt, genecounts

source_name: GC B, Aicda+/+

growth_protocol: CD43 expressing cells were depleted from splenic single-cell suspensions of 2-mo-old Aicda-/- and Aicda+/+ mice using paramagnetic streptavidin-beads and biotinylated anti-CD43. From the remaining cells a fraction was used to sort naïve B cells (CD19+, IgM+, CD43-, DAPI-). From the other fraction in vitro activated B cells were derived by stimulation with LPS [20μg/ml] and IL-4 (10% of supernatant of IL-4 producing cells). In vitro activated B cells (CD19+, DAPI-) were sorted four days after culturing. To isolate GC B cells, 2-mo-old Aicda-/- and Aicda+/+ mice were immunized by a single intraperitoneal injection of 108 sheep red blood cells in 200 μl HBSS. Ten days later, GC B cells (CD19+, PNAhigh, CD95+, DAPI-) were sorted from splenic single-cell suspensions

extract_protocol: GC B cell were sorted, snap frozen, and RNA was harvested using Trizol reagent.

value: Aicda+/+


title: MethylCap-Seq: GC B, Aicda-/- rep1M

description: MethylCap-Seq


title: MethylCap-Seq: GC B, Aicda-/- rep2H

description: MethylCap-Seq

source_name: Aicda-/- (high eluate)


title: MethylCap-Seq: GC B, Aicda-/- rep1H

description: MethylCap-Seq


title: RNA-Seq: GC B, Aicda-/-  rep1

source_name: GC B, Aicda-/-

value: Aicda-/-


title: RNA-Seq: GC B, Aicda-/-  rep2


title: RNA-Seq: GC B, Aicda+/+  rep1


title: RNA-Seq: Activated B, Aicda+/+  rep4

source_name: Activated B, Aicda+/+

value: Activated B cell


title: MethylCap-Seq: GC B, Aicda+/+ rep2L

description: MethylCap-Seq


title: MethylCap-Seq: GC B, Aicda+/+ rep2H

description: MethylCap-Seq


title: RNA-Seq: Activated B, Aicda-/-  rep3

source_name: Activated B, Aicda-/-


title: RNA-Seq: Activated B, Aicda-/- rep2


title: RNA-Seq: Naive B, Aicda-/-  rep3

source_name: Naïve B, Aicda-/-

value: Naive B cell


title: RNA-Seq: Naive B, Aicda+/+  rep3

source_name: Naïve B, Aicda+/+


title: RNA-Seq: Naive B, Aicda+/+  rep4


title: RNA-Seq: Naive B, Aicda+/+  rep2


title: RNA-Seq: Activated B, Aicda-/-  rep4


title: RNA-Seq: Naive B, Aicda-/- rep2


title: RNA-Seq: Activated B, Aicda+/+  rep2


title: RNA-Seq: Naive B, Aicda-/-  rep4


title: RNA-Seq: Activated B, Aicda-/-  rep1


title: RNA-Seq: Naive B, Aicda+/+  rep1


title: InputAT

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

description: input DNA

data_processing:
Analysis was performed through HTSstation (http://htsstation.epfl.ch) using bowtie (version 0.12.7) to map data. PCR duplicate were removed from the mapping analysis. Data were normalized toward input and densities were generated according to (Noordermeer et al., 2011; Leleu et al., 2010). The telomeric 10X enriched H3K27Ac clusters were delineated by fusing 10X enriched peaks (15, 44) separated by less than 300 bp.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph of data normalised versus Input.

source_name: input DNA

extract_protocol:
Immuno-precipitated and whole cell extract DNA (input) were de-crosslinked at 65°C overnight, treated with RNAseA, proteinase K and purified by phenol/chloroform extraction.
ChIP products were sequenced with Illumina Genome Analyzer IIx. Data was mapped to the mouse genome using HTSstation (http://htsstation.vital-it.ch/).

treatment_protocol: Early forelimb buds, presumptive digits and proximal segments of E12.5 forelimbs were micro-dissected from mouse embryos, fixed in 1% formaldehyde for 15 minutes at room temperature, washed three times with 4°C PBS and stored at -80°C. Pools of 40 early forelimbs (E9.5), 10 limb buds (10.5), 10 autopods or 10 Proximal forelimbs were used for each experiment. ChIP was performed according to (Lee et al., 2006), using 2 μg of anti-H3K27Ac (ab4729, Abcam), and EZview Red protein G/A Affinity Gel (Sigma). Immuno-precipitated and whole cell extract DNA (input) were de-crosslinked at 65°C overnight, treated with RNAseA, proteinase K and purified by phenol/chloroform extraction.  using 2 μg of anti-H3K27Ac (ab4729, Abcam). 20ng of output were multiplexed using "Multiplexing Sample Preparation Oligonucleotide Kit" from Illumina. Material was sequenced with 100bp-paired ends sequencing protocol in Illumina HI-seq according to the manufacturer’s specifications.


title: DFL_E12_WT_d13

data_processing:
Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7). In the the smoothed and normalized data the a normalization of local intensity over chr2:71000000-78000000(mm9) was performed.
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (http://htsstation.epfl.ch) according to previously described procedure (Noordermeer et al., 2011).
Figures were made using a running mean algorithm using a window size of eleven fragments. 4C tracks were normalized to the same total intensity, over the chr2:71000000-78000000 coordinates, such as to see only changes in contacts distribution and to minimize PCR complexity bias in each samples. .
Both the mapping and the 4C-seq analysis were done through HTSstation (http://htsstation.epfl.ch/).
Genome_build: mm9
Supplementary_files_format_and_content: density files (bedGraph) and smoothed/normalized data (bedGraph), one per viewpoint, per tissue

source_name: Digits Forelimbs E12.5

extract_protocol:
Tissue was dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed in formaldehyde 2% for 10 min at room temperature and reaction was quenched on ice with glycine. Cells were further lysated with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, PIC 1x to isolate nuclei. Nuclei from pools were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation
4C PCR was sequenced with Illumina Genome Analyzer IIx. Data was mapped to the mouse genome using HTSstation (http://htsstation.vital-it.ch/).

treatment_protocol: Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al., 2011). Early limb buds were dissected from 40 E9.5 embryos, Digits and Proximal forelimbs from 10X E12.5 embryos. Tissue was dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed in formaldehyde 2% for 10 min at room temperature and reaction was quenched on ice with glycine. Cells were further lysated with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, PIC 1x to isolate nuclei. Nuclei from pools were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions and amplified using AmpliTaq DNA polymerase (Applied Biosystems) and inversed PCR primers flanked with adaptors allowing multiplexing. Hoxd13, Hoxd11, Hoxd9 and Hoxd1 PCR primers were described before (Noordermeer et al., 2011). For regions CNS(39) and CNS(65), the following primer sets were used: CNS(39)_inverse_forward: 5’AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTATCCAAGGAGAAAGGTGTTGGTC3', CNS(39)_inverse_reverse:5’CAAGCAGAAGACGGCATACGACAGGGCGTTGGGTCACTCT3', CNS(65)_inverse_forward:5’AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTATCTAGTGAGCCCCTACCAGGA3', CNS(65)_inverse_reverse:5’CAAGCAGAAGACGGCATACGAGGAGCCTTTGGGGTACACG-3’.

value: Digits Forelimbs

tag: age

tag: genotype

value: wild type


title: PFL_E12_K27Ac

description: Chromatin immuno-precipitated with antibody against H3K27Ac

source_name: Proximal Forelimbs E12.5

tag: chip antibody manufacturer

tag: chip antibody catalog #

value: Proximal Forelimbs


title: FL_E9_K27Ac

source_name: Early forelimb buds E9.5

tag: chip antibody

value: Abcam

tag: tissue

value: Forelimb buds


title: DFL_E12_WT_d11


title: FL_E10_K27Ac

source_name: Early forelimb buds E10.5


title: DFL_E12_WT_d1


title: DFL_E12_WT_d9


title: RNA-Seq: Naive B, Aicda-/-  rep1


title: PFL_E12_Inv(Nsi-Itga6)_d1

value: Inv(Nsi-Itga6) homozygote


title: RNA-Seq: Activated B, Aicda+/+  rep3


title: PFL_E12_WT_d11


title: T47D-overexpressing ELF5-input DNA-48hour

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

institute: Garvan Institute of Medical Research

description: T47D cell lines, overexpressing ELF5 with V5 tag, input DNA, replicate 2

data_processing:
Sequences were aligned against NCBI Build 36.3 of the human genome using MAQ (http://maq.sourceforge.net/) with default parameters.
The aligned reads were converted to BED format using a custom script.
Reads were filtered for uniquely mapped tags
Wiggle coverage files generated, normalised per million reads.
Genome_build: ncbi36.3
Supplementary_files_format_and_content: *.filter.bed.gz files contain the aligned reads, filtered for unique mappers only. These are standard BED6 formatted files (chr,start,stop,name=read_id,score=mapping_quality,strand)
Supplementary_files_format_and_content: *wig.gz files are standard wiggle files, at 20bp resolution, indicating read depth across the genome, normalised per 1e06 reads.

source_name: T47D cell line

growth_protocol: Human breast carcinoma T47D-EcoR (Musgrove et al., 2001) cell lines were grown in RPMI 1640 medium (Invitrogen) supplemented with 10 % Tet System Approved fetal bovine serum (FBS) (Clontech). Cells infected with pHUSH-ProEX-based produced by the Platinum E cell line (Morita et al., 2000). Transient transfection with plasmid constructs used FuGENE reagent (Roche) or Lipofectamine LTX (Invitrogen) according to manufacturer’s instructions.  Cells were maintained in the presence of puromycin (Sigma) at a concentration of 2μg/mL.

extract_protocol:
Cells were washed 2 times with cold PBS and scraped into 600 μl PBS with protease inhibitors (P8340, Sigma). Fixed cells were spun for 2 minutes at 6,000xg, washed as before and snap frozen in liquid nitrogen.
ChIP-Seq as previously described (doi:10.1016/j.ymeth.2009.03.001) using a 50%–50% mixture of V5-specific antibody and the Santa Cruz N20 anti ELF5 antibody, or no antibody for the input files. DNA was processed for Illumina sequencing using 36-bp reads on a GAIIx.

treatment_protocol: Drug treatments were performed with Dox (Clontech) at 0.1 μg/ml, R5020 (Du Pont) at 10 nM or 17β-estradiol (Sigma) at 10 mM. Dox-containing medium was changed every 24 hours to ensure optimum Dox activity. Adherent cells on tissue culture plates were incubated in fresh, warm, serum-free medium supplemented with 1% formaldehyde, at 37°C for 10 minutes.

tag: cell line

tag: treatment

value: doxycycline

tag: timepoint

tag: enrichment

value: input DNA


title: PFL_E12_WT_d13


title: PFL_E12_WT_d9


title: PFL_E12_WT_d1


title: FL_E9_WT_d13


title: FL_E9_WT_d9


title: FL_E9_WT_d11


title: FL_E9_WT_CNS(65)


title: COUP-TFII ChIP-seq

city: Houston

first: San-pin

last: Wu

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Sequence Analysis: The 50-nt sequence reads identified by the Sequencing Service (using Illumina’s Hi-Seq) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Determination of Fragment Density: Since the 5 ́-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3 ́- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 150 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a Wig file.
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: atria

extract_protocol:
Flash frozen tissues were sent to Active Motif for chromatin extraction
Libraries were prepared by Active Motif

value: Active Motif

value: atria


title: E4.5.NULL2

status: Public on Jun 06 2013

city: Farmington

first: Paul

last: Robson

state: CT

address: 10 Discovery Way

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
SOLiD BioScope Software for mapping and counting
Reference transcriptome was Ensembl
Expression values are in Reads Per Million (RPM) and not RPKM as the library construction stratgey aimed to generate transcriptome-wide cDNA amplification of similar length adjacent to ploy(A) tail rather than capturing the entire transcript length.
Transcripts were collapsed for gene-level analysis by selecting the most abundant transcript (combined expression for all samples) by developmental stage
Transcripts were filtered out unless they showed expression levels above 10 RPM for at least three of six individuals for each gene by developmental stage
Count data was re-standardized (RPM) by adjusting for library size with edgeR (Robinson et al., Bioinformatics, 2009) by developmental stage
Genome_build: Mouse July 2007 (NCBI37/mm9) Assembly
Supplementary_files_format_and_content: TAB-delimited text files text files include gene and transcript IDs, and RPM values for each sample by developmental stage

source_name: embryo

growth_protocol: embryos were flushed from oviducts or uteri at indicated developmental stages with M2 medium

extract_protocol:
Picopure (Arcturus Biosciences)
Oligo(dT)-primed RT followed by amplification of region adjacent to polyA tail as described in Tang et al (2010) Nature Protocols 5:516–535. Note this strategy leads to a strong 3'bias with read representation largely within the ~1kb 3'end of polyadenylated transcripts.

tag: developmental stage


title: FL_E9_WT_d1


title: RNA-Seq: Activated B, Aicda+/+  rep1

tag: genotype/variation

tag: cell type


title: E4.5.WT1


title: E4.5.WT2


title: E4.5.NULL1


title: FL_E9_WT_CNS(39)


title: E3.75.NULL2


title: E4.5.WT3


title: E3.75.WT2


title: E3.75.WT1


title: E2.5.NULL2


title: Input/IgG control


title: T47D-overexpressing ELF5-input DNA-24hour

description: T47D cell lines, overexpressing ELF5 with V5 tag, input DNA, replicate 1


title: E4.5.NULL3


title: E2.5.NULL3


title: E2.5.NULL1


title: E2.5.WT2


title: E3.75.WT3


title: E2.5.WT3


title: E2.5.WT1


title: E3.75.NULL1


title: Replicate 4, Day 14

city: Copenhagen

first: Mads

last: Bak

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

data_processing:
Tags were filtered and alignment against the mouse genome performed using SOAP (Li R, Li Y, Kristiansen K, Wang J., 2009, SOAP: short oligonucleotide alignment program, Bioinformatics. 2008, 24(5):713-4), and filtered tags were normalized to 1 million tags
Functional annotation was performed with DAVID Tools (http://david.abcc.ncifcrf.gov/summary.jsp).
Gene set enrichment analysis was performed using the Broad Institute software (http://www.broadinstitute.org/gsea/index.jsp).
Genome_build: mm9
Supplementary_files_format_and_content: Excel spread sheet. Log2 difference i expression values. Unfiltered data not available.
Supplementary_files_format_and_content: Log2 difference expression values is filtered by FDR and thus incomplete.

source_name: P19CL6 cell line

extract_protocol:
Illumina’s DGE Tag Profiling Kit
A total of 1 µg RNA per sample  was analyzed using Illumina’s DGE Tag Profiling Kit according to the manufacturer’s  protocol (version 2.1B)

tag: time

value: Day 14


title: Replicate 4, Day 10

value: Day 10


title: Replicate 4, Day 4

value: Day 4


title: Replicate 4, Day 7

value: Day 7


title: Replicate 4, Day 1

value: Day 1


title: E3.75.NULL3


title: Replicate 3, Day 10


title: Replicate 3, Day 4


title: Replicate 3, Day 7


title: Replicate 2, Day 14


title: Replicate 3, Day 14


title: Taf4 -/- Tg: hTAF4 wt, Clone 1

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: mRNA isolated from mouse taf4-/-; Tg:hTAF4 wt MEF cells

data_processing:
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long reads were mapped to the reference mouse genome sequence, mm9, using Tophat aligner (Trapnell et al, Bioinformatics 2009, 25 (9): 1105-1111) with the default parameters. The mRNA expression level for each gene was represented as FPKM (fragments per kilobase of transcript per million fragments mapped), called by Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515), and differential expression between control vs. knockout, wild type vs. knockout, and deletion vs. knockout were called by Cuffdiff in Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515).
Genome_build: mm9
Supplementary_files_format_and_content: wiggle track raw reads

source_name: Taf4 knockout with stable human TAF4 wildtype expressing cells

growth_protocol: The MEF cells were maintained in DMEM (Invitrogen, CA) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Libraries were prepared according to a version of Illumina's mRNA-Seq protocol (Illumina, CA)
Libraries were prepared using the Illumina RNA-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

value: MEF cells


title: Replicate 3, Day 1


title: Taf4 -/- Tg: hTAF4 Δ (TAFH-deleted), Clone 1

description: mRNA isolated from mouse taf4-/-; Tg:hTAF4Δ  MEF cells

source_name: Taf4 knockout with stable human TAF4 mt (TAFH-deleted) expressing cells


title: Taf4 -/- Tg: hTAF4 Δ (TAFH-deleted), Clone 2

value: Taf4 knockout with stable human TAF4 mt (TAFH-deleted)


title: Taf4 -/- (ko), replicate 2

description: mRNA isolated from mouse taf4-/- MEF cells

source_name: Taf4 knockout cells

value: Taf4 knockout


title: Replicate 2, Day 10


title: Taf4 -/- Tg: hTAF4 wt, Clone 2

value: Taf4 knockout with stable human TAF4 wildtype


title: Taf4 loxp/- (ctrl), replicate 2

description: mRNA isolated from mouse taf4loxp/- MEF cells

source_name: Taf4 wild type cells

value: Taf4 wild type


title: Taf4 loxp/- (ctrl), replicate 1


title: Replicate 2, Day 4


title: Replicate 1, Day 14


title: Replicate 1, Day 7


title: Replicate 2, Day 7


title: ESC-FC1801 In Vitro-Treated (MG2)

city: Los Angeles

first: Ascia

last: Eskin

state: California

address: 695 Charles Young Drive South  Gonda 5554

department: Human Genetics

institute: UCLA

description:
Sample 4
processed data file: gene_exp_diff_MG1_MG2_fromtophat120_cufflinks102_c0_081612.txt

data_processing:
Bases were called by Casava for GAIIx and by RTA for HiSeq.
Reads were aligned to mm9 genome using TopHat v1.2.0 with parameters  -G (using Ensembl NCBI37.58 GTF) and --no-novel-juncs. For the paired end reads, -r 275 was used for control and -r 248 was used for treated.
Transcripts were assembled using Cufflinks v1.0.2. Cuffdiff was used to compare each treated sample to the control sample, using Ensembl NCBI37.58 GTF, and --min-aligment option of 0.
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdif result files include FPKM values for each Sample, as well as q-value and fold change.

source_name: ESC-FC1801_in vitro_NXD30001

growth_protocol: ESC-FC1801 cells were rutinely cultured in serum-free N2 medium (DMEM/F12 with N2 supplement, 10ng/mL Neuregulin-β1, 2uM forskolin , 50ug/mL gentamycin, 1% fungizone).

extract_protocol: Cultured cells and tumor samples were homogenized in Trizol reagent and RNA was isolated using RiboPure total RNA isolation Kit (Ambion).  Libraries were prepared using protocol recommended from Illumina.

treatment_protocol: ESC-FC1801 cells in culture were treated with DMSO or 1 uM NXD30001 for 24 hours. Mice bearing an ESC-FC1801 tumor were administered with vehicle or NXD30001 at 100mg/kg, three tims a week, for four weeks.

tag: strain background

value: FVB/N

value: Nf2Flox/Flox, NF2-/- in vitro induced with Ad-Cre

tag: source cell type

value: mouse embryonic Schwann cells

tag: sample type

value: ESC-FC1801 cultured cells

tag: treated with

value: 1 uM NXD30001 for 24 hrs


title: ESC-FC1801 In Vitro-Control (MG1)

description:
Sample 3
processed data file: gene_exp_diff_MG1_MG2_fromtophat120_cufflinks102_c0_081612.txt

source_name: ESC-FC1801_in vitro_control

value: DMSO for 24 hours


title: ESC-FC1801 In Vivo-Treated

description:
Sample 2
processed data file: gene_exp_diff_Control_NXD30001_fromtophat120_cufflinks102_c0_081612.txt

source_name: ESC-FC1801_in vivo_NXD30001

value: NXD30001 at 100mg/kg, three times a week, for 4 wks


title: ESC-FC1801 In Vivo-Control

description:
Sample 1
processed data file: gene_exp_diff_Control_NXD30001_fromtophat120_cufflinks102_c0_081612.txt

source_name: ESC-FC1801_in vivo_control

value: vehicle, three times a week, for 4 wks


title: Erythroblast JH1HBA

first: Richard

middle: J

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

description: Circular Chromatin Conformation Capture Amplified DNA

data_processing:
Paired-end sequences, were mapped as single-end reads to overcome the built in assumptions of the relative positioning of paired-end sequences in the sequence aligning programs.  The sequences were mapped to an in silico Dpn II digested and repeat-masked version of HG18 (UCSC Genome browser NCBI build 36.1).  This digested version of HG18 was generated by mapping the position of all Dpn II sites in the unmasked HG18 sequence. This in silico digestion had to be performed on an unmasked version of the HG18 as repeat masking would also have masked some Dpn II restriction sites. These positions were then used to digest a repeat-masked version of the HG18 genome to generate a Multiple Fasta file of all repeat masked Dpn II fragments in HG18. Repeat-masking was performed using the latest “all mapped repeat” data for HG18 (UCSC tablebrowser HG18_Human_allrmsk.txt). The sequence data were mapped to the digested genome using three different aligners, MAQ (version 0.7.1)(31), Exonerate (version 2.2.1(32)) and Novoalign (2.05.13 www.novocraft.com) to exclude any aligner-specific effects, using the default stringencies for each program.  The alignments were post processed, using in-house Perl scripts, for uniqueness of alignment, with reads mapping to the a-globin genes being allowed to map to three locations of chromosome 16 due to the duplicated nature of the genes; all other reads had to align uniquely to the genome.
Solexa/Illunima paired-end reads.   The paired-end reads represent a 50bp sequence from each end of a sonicated DNA fragment of the inverse PCR products.  As sonication is mostly a random process then the paired-end reads randomly sample the sequence, at either end of approximately 500bp intervals, across the inverse PCR products.  This random sampling can be used to detect the ligation events, which underlie the 4C signal, where one end of the fragment maps to one Dpn II fragment and the other end of the fragment maps to another. Although, as described above, the paired-end reads were initially mapped as single reads the physical relationship between the paired-end reads was maintained in the naming structure of each read.  Using in-house Perl scripts this relationship could be used to call an interaction between these two fragments and ultimately count the total number of mapped interactions between all Dpn II fragments in the HG18 genome.  This dataset ignored all pairs which map to the same fragment (does not span a junction) and was further refined to remove interactions between fragments adjacent in the genome due to local interactions or non-digestion.  This dataset was further constrained so that each junction had to have a read in the capture fragment and hence represent a valid ligation event rather than non-specific amplification.
Both biological 4C paired-end sequenced replicates (named JH1 and JH2) were analysed as described above.  To identify the consistent signal between the two biological datasets an intersection of the two results was performed such that interaction fragments which existed in both datasets were kept and the number of interactions of that fragment with the a-globin promoter were averaged.  This analysis was made less stringent by the inclusion of fragments, which although they did not have exactly the same genomic coordinates, their coordinates fell within a 1kb window of genomic distance of a peak in the other replicate.  In this case the signal for each peak was not averaged with the other, rather each was included in the final dataset with their respective coordinates and number of interactions with the a-globin promoter.
This intersection dataset was then binned into a set of genomic regions representing, each human chromosome, the chromosome 16p terminal 1 Mb (chr16:1-1000000), the encode region Enm008 (chr16:1-500000), the region from the 16p telomere to the end of the globin q gene (chr16:1-170000), the area covering MCS-R1 to MCR-R3 (chr16:93900-111261) and region 1kb either side of the MCS-R2 element (chr16:102493-104848).
Genome_build: HG18
Supplementary_files_format_and_content: UCSC WIG/Peak format file containing read counts per interacting DpnII fragments, a third WIG/Peak file contains the overlap between the JH1 and JH2 datasets.

source_name: Erythroblast

growth_protocol: Basic Protocol 1: Preparation of Peripheral Blood Mononuclear Cells for Erythroid Cultures Cultures can be initiated with cells derived from a whole unit of blood obtained from normal donors (or polycythemic patients undergoing phlebotomy). The starting material, i.e., the “buffy-coat” fraction, is readily available, since it is routinely separated and discarded by the blood bank during preparation of packed red blood cells (RBC) and platelet-rich plasma. Anemic patients commonly show high frequencies of erythroid progenitors; cultures from anemic patients (e.g., thalassemia, sickle cell anemia) are usually initiated with cells derived from ~20 ml peripheral blood. Materials * Peripheral blood or buffy coat fraction * Phosphate-buffered saline (PBS), pH 7.4 (appendix 2A) * Ficoll-Hypaque (density = 1.077 g/ml) * 15- or 50-ml centrifuge tubes * Centrifuge 1. Dilute peripheral blood or the buffy coat fraction 1:1 (v/v) with PBS. Gently layer on top of a layer of Ficoll-Hypaque such that the Ficoll-Hypaque layer constitutes one-third of the total volume. Depending on the blood volume, use either 15- or 50-ml tubes. For convenience, tubes (available from Sigma) containing a special grid that separates the blood from the Ficoll can be used. 2. Centrifuge 20 min at 400 × g, at room temperature. Do not apply the brake. 3. Aspirate off the top layer (consisting of plasma and platelets), collect the interphase layer of mononuclear cells with a pipet, and transfer to a 50-ml tube. 4. Add 40 ml PBS, mix, then centrifuge 5 min at 160 × g, room temperature. Aspirate the supernatant, then resuspend the pellet in the residual buffer by tapping. 5. Add 40 ml PBS, mix, then centrifuge 5 min at 100 × g, room temperature, and aspirate the supernatant. Repeat this procedure for an additional wash. Use low-speed centrifugation in order to remove residual platelets. All procedures should be performed at room temperature. If the blood cannot be processed on the same day, leave overnight at room temperature. In experiments where Hb content is measured, special care has to be taken to avoid contamination by mature RBC that originated from the processed blood. This does not usually present a problem when normal blood is processed, but may occur with blood derived from patients, e.g., with thalassemia. The contaminating RBCs can be of patient origin and/or derived from transfused blood. In both cases, they may interfere with measurement of the Hb produced in vitro. When the interphase layer is heavily contaminated with RBC, the latter cells should be removed by osmotic hemolysis (see Support Protocol 6) prior to culturing. When only slightly contaminated, the mononuclear cells may be cultured without hemolysis; RBC tend to lyse and disappear during culture. Alternatively, they may be removed by Percoll separation at the second phase of the culture (see Support Protocol 7). [Top of Page] Basic Protocol 2: Erythroid Cell Culture Procedure The culture procedure is divided into two phases. The first is an EPO-independent phase in which peripheral blood mononuclear cells are isolated (described in Basic Protocol 1) and cultured in the presence of a combination of growth factors, but in the absence of EPO. During this phase, early erythroid-committed progenitors, called burst-forming units erythroid (BFUe), proliferate and differentiate into colony-forming unit erythroid (CFUe)–like progenitors. In the second phase, these cells, cultured in an EPO-supplemented medium, continue to proliferate and mature into orthochromatic normoblasts and enucleated erythrocytes. Materials * Complete MEM medium (see recipe) * Preselected FBS (see recipe); do not heat-inactivate * 50 mg/ml cyclosporin A (Sandoz) * Conditioned medium from 5637 human bladder carcinoma cell line (see recipe) * Mononuclear cells, washed (see Basic Protocol 1) * 10% (w/v) deionized BSA (see recipe) * 2-mercaptoethanol (Sigma) * 4 mg/ml dexamethasone sodium phosphate (Elkin-Sinn Pharmaceuticals, Cherry Hill N.J.) * Human holo-transferrin (Sigma) * Human recombinant stem cell factor (CytoLab Ltd.; http://www.cytolab.com/) * Human recombinant erythropoietin (EPO; Ortho Pharmaceutical) * 25- or 75-cm2 tissue culture flasks 1. Prepare Phase I medium by adding the following ingredients to complete MEM medium: * 10% (v/v) preselected FBS (not heat-inactivated) * 1 µg/ml cyclosporin A (add from 50 mg/ml stock) * 10% (v/v) conditioned medium from 5637 human bladder carcinoma cell line. 2a. For cells obtained from peripheral blood (10 to 20 ml): Plate the washed mononuclear cells in Phase I medium in 25-cm2 flasks at a culture volume equivalent to the original volume of blood. 2b. In the case of cells obtained from a whole blood unit (400 to 500 ml): Plate the washed mononuclear cells in Phase I medium in two 75-cm2 flasks at a culture volume of 80 to 100 ml. 3. Incubate the cultures at 37°C in a humidified, 5% CO2 incubator for 5 to 7 days. Full humidification is achieved by leaving a tray with water standing at the bottom of the incubator. 4. After the 5- to 7-day incubation in phase I, shake the cultures and harvest the nonadherent cells (do not trypsinize). 5. Centrifuge the cells 5 min at 160 × g, room temperature, and aspirate the supernatant. Fill the tube with complete MEM, centrifuge 5 min at 160 × g, room temperature, and aspirate the supernatant. Repeat for a second wash. 6. Prepare Phase II medium by adding the following ingredients to complete MEM medium: * 30% (v/v) preselected FBS (not heat-inactivated) * 1% (w/v) deionized BSA (add from 10% w/v stock) * 10–5 M 2-mercaptoethanol * 10–6 dexamethasone (add from 4 mg/ml stock) * 0.3 mg/ml human holo-transferrin * 10 ng/ml human recombinant stem cell factor * 1 U/ml human erythropoietin (EPO). 7. Plate cells in the original volume of phase II medium (as in step 2a or 2b according to the original blood volume) and incubate up to 14 days at 37°C in a humidified, 5% CO2, incubator.

extract_protocol:
After collecting the washed cells by centrifugation the pellet was resuspended in lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40, 1x Complete proteinase inhibitor (Roche)) and lysed for 15 minutes on ice.  After collection of the cells by centrifugation, the pellet was washed with 1ml of 1 x Dpn II digestion buffer (NEB) and the pellet was re-suspended for digestion by the addition of 60 μl of x10 Dpn II buffer and 440 μl of sterile H2O.  To this was added 7.5 μl 20% SDS to a final concentration of 0.3% and the resulting mixture was incubated at 37OC for 1 hour with shaking.  The SDS was then sequestered by the addition of Triton X-100 to a final concentration of ~2% (50 μl 20% Triton X-100) and incubated at 37OC for 1 hour with shaking. 500U Dpn II (NEB 5x concentration R0543M) was added and incubated overnight at 37OC with shaking. The enzyme was inactivated at 65OC for 25 min with SDS added to a final concentration of 1.5% (40 μl of 20 % SDS), this was re-suspended in a final volume of 7ml 1x ligation buffer (40mM Tris pH8.0, 10mM MgCl2 and 0.5 mM rATP) with 1% Triton X-100.  Following incubation at 37OC for 1 hour to sequester the SDS, the samples were cooled on ice for 2 minutes and 240U high concentration T4 DNA ligase (Fermentas) was added.  Following incubation overnight at 16OC with shaking, 300 mg of proteinase K was added and crosslinks reversed by incubation at 65OC overnight with rotation.  The samples were treated with 15mg RNase (Roche) at 37OC for 30 minutes.  Following phenol/chloroform extraction and ethanol precipitation, DNA was re-suspended in 500 μl 1x ligation buffer and 60U high concentration T4 DNA ligase (Fermentas) and incubated for 2 hours at 16OC at 1200rpm (Eppendorf Thermomixer comfort). Following phenol/chloroform extraction and ethanol precipitation, DNA was re-suspended in 100 μl water, of which 10 μl was used as template in Advantage-GC PCR (Clontech) as per manufacturer’s instructions using 34 cycles of amplification (cycling conditions were 94OC for 2 minutes; 34 cycles of 94OC for 30 seconds, annealing temperature for 30 seconds, 68OC for 5 minutes followed by a single extension cycle at 68OC for 8 minutes).  Primer sequences and annealing temperatures are presented in Table 1.  The resulting amplified DNA was ethanol precipitated and resuspended in 20 ml water,
DNA obtained from the 4C amplification was reduced to an average size of 500bp by sonication, either by shearing for 10 minutes using a Sonic Dismembrator 550 (cup horn, Fisher Scientific, Canada) or using a Covaris S2 sonicator (KBiosciences, Europe) using a duration of 90 seconds, intensity of 3 and a duty cycle of 5.  A 300bp to 600bp fraction was gel extracted from an 8% PAGE gel and prepared for paired-end sequencing using the manufacturer’s recommended protocol as briefly set out here. Sonicated DNA from a 4C amplification was prepared for sequencing by end repair, A-tailing and ligation of adapters (Illumina) as outlined in the manufacturer's recommendations. Following adapter ligation some minor modifications were made to the protocol: DNA was amplified with 18 cycles of PCR before size selection of 200-350bp fragments from a gel. The excised library was purified using the Qiaquick gel extraction kit (Qiagen) before quality checking on an Agilent bioanalyzer. DNA was quantified using the Quant-iTT dsDNA HS Assay Kit (Invitrogen) before dilution to 10nM. Paired-end reads of 51bp were generated on the Illumina GAII platform.

treatment_protocol: 1x107 cells were fixed with 2% formaldehyde in 10 ml of their growth medium for 10 minutes at room temperature with agitation.  Following quenching with 1.5 ml of 1M glycine cells were collected at 1200 rpm (Heraeus Multifuge 3 SR) at 4 OC for 5 minutes, resuspended and washed in 10 ml of 1x sterile Phosphate buffered Saline (PBS Gibco pH7.4).

tag: culture

value: Fibach Culture

value: Erythroblast

value: 4C amplification from the promoters of the human HBA gene


title: expanded FOXP3-losing

city: Xi'an

first: Haiqi

last: He

state: Shaanxi

address: West Yanta Road

country: China

institute: Xi'an Jiaotong University

data_processing:
Base-calling was performed using RTA version 1.12.4.2. and the data was transformed with BclConverter version 1.9.0.
Raw sequences were transformed into clean tags after removal of adaptor sequence, low-quality tags, tags with a copy number of 1 and tags that are too long or too short. The low-quality tags was defined as tags containing unkown base N.
The clean tags were mapped to hg19 using bowtie  with parameters -f -l 21 -n 1 -k 2 -m 2 --un unmapped_tag . Clean tags mapped to reference sequences from multiple genes were filtered. Only tags with perfect matching or 1 bp mismatch were considered for further analysis.
The number of unambiguous clean tags for each gene was calculated and normalized to TPM (number of transcripts per million clean tags) using a protocol from Morrissy et al., Genome Res, 2009. The number of normalized sequence tags of a gene locus=( the number of mapped tags in the gene locus/ the total number of sequence tags of the whole genome)×1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene symbols, TPM values, ontology information of gene-corresponding GO terms and so on.

source_name: CD4+CD25highCD127low/- Treg cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation from leukapheresis products of healthy volunteers. CD4+ T cells were enriched with the human CD4+ T Cell Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). CD4+CD25highCD127low/- Treg cells were isolated by FACS (BD Biosciences, USA) from enriched CD4+ T cells and cultured in X-Vivo 15 medium (Lonza, USA) supplemented with 5% human AB serum (Sigma-Aldrich, USA). Cells were stimulated with anti-CD3/CD28 Abs-coated beads (Invitrogen-Dynal, USA) in the presence of 500 U/ml recombinant human IL-2 (PeproTech, USA) for 8 days and then rested in the presence of 100 U/ml IL-2 for 14 days. After two cycles of stimulation, cells were rested for 4-5 days.

extract_protocol:
Total RNA was extacted using TriPure Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Expanded cells were sorted into FOXP3+ and FOXP3-losing cells by FACS (BD Biosciences, USA). For intracellular staining, washing and following cell sorting steps, the PBS with 0.1% diethyl pyrocarbonate (DEPC; Sigma-Aldrich, USA) was used. The buffer was autoclaved and supplemented with recombinant RNasin® Ribonuclease Inhibitor (Promega, USA) just before use.

value: CD4+CD25highCD127low/- Treg cells

tag: cell sorted

value: In vitro expanded FOXP3-losing Treg cells

tag: time in culture

value: 35 days


title: Erythroblast JH2HBA


title: expanded FOXP3+

value: In vitro expanded FOXP3+ Treg cells


title: Taf4 -/- (ko), replicate 1

tag: strain

value: MEF cells

value: Taf4 knockout


title: Replicate 1, Day 10

value: Day 10


title: T10608_S

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: In the processed data file the values for each chromosome were generated by dividing by 0.77.

data_processing:
Sequence reads were mapped to the S. cerevisiae reference genome using BioScope (version 1.3.1).
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the S phase (replicating) sample by counts from the G2 phase (non-replicating) sample for each strain.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor. This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).
Genome_build: sacCer1
Supplementary_files_format_and_content: Wig file containing normalised replication profile.

organism: Saccharomyces cerevisiae

source_name: Genomic DNA from S phase cells

growth_protocol: Cells were harvested from mid-log phase cultures grown in rich medium

extract_protocol:
Cells obtained from FACS were resuspended in 500 µL of 1.2 M sorbitol, 200 mM Tris-HCl (pH7.5), 20 mM EDTA, 0.1% b-mercaptoethanol. Cells were spheroplasted with Zymolyase and then treated with SDS, Proteinase K and RNase A. DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to SOLiD instructions.

treatment_protocol: Cells were sorted by DNA content, selecting S phase and G2 phase cells

tag: relevant genotype

value: MATa / MATalpha, ars919 / ars919, ars920 / ars920, RAD5 / RAD5, BUD4 / BUD4 leu2 / leu2, ura3 / ura3, trp1 / trp1 ade2 / ade2, his3 / his3

tag: growth phase

value: S


title: T10608_G2

source_name: Genomic DNA from G2 phase cells


title: Replicate 1, Day 4

tag: cell line

value: Day 4


title: K562_S_H3K4me3

city: Bethesda

first: Mirit

middle: I

last: Aladjem

state: MD

address: 37 Convent Dr. Building 37, Room 5068D

department: DNA Replication Group

institute: National Cancer Institute

description:
Chromatin IP against H3K4me3
Instrument model: Solexa 1G Genome Analyzer

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2657_hg18_S-K562_H3K4me3.bed: hg18
GA2657_hg18_S-K562_H3K4me3_pk.txt: hg18

source_name: Chronic myeloid leukaemia

growth_protocol: DMAEM 10% FCS

extract_protocol: Human K562 cells were grown at 37°C in a 5% CO2 atmosphere in Dulbecco’s modified Eagle medium (Invitrogen, Cat. no. 10564-011), supplemented with 10% heat-inactivated fetal calf serum.  Cell cycle specific fractions from exponentially growing populations were collected using centrifugal elutriation. ChIP analyses was performed with 1% formaldehyde-fixed cells using the Millipore ChIP assay kit (Cat. no. 17-295) following the manufacturer’s protocol. Chromatin from 2 × 107 cells was used for each ChIP experiment. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3′ A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer following manufacturer protocols.

treatment_protocol: centrifugal elutriation and chromatin isolation

value: Human erythromyeloblastoid leukemia cell line K562

value: Cultured cancer cell line

tag: cell cycle stage

tag: chip antibody

value: H3K4me3 (Millipore, Lot# RF0807002, cat# CS20580)


title: K562_S_H3K79me2

description:
Chromatin IP against H3K79me2
Instrument model: Solexa 1G Genome Analyzer

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2351_hg18_K562-S-K79me2.bed: hg18
K562_H3K79me2_hg18_S_pk.txt: hg18


title: K562_G2_H3K4me3

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2658_hg18_G2-K562_H3K4me3.bed: hg18
GA2658_hg18_G2-K562_H3K4me3_pk.txt: hg18


title: K562_G2_H3K79me2

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2352_hg18_K562-G2-K79me2.bed: hg18
K562_H3K79me2_hg18_G2_pk.txt: hg18


title: K562_G1_H3K79me2

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2350_hg18_K562-G1-K79me2.bed: hg18
K562_H3K79me2_hg18_G1_pk.txt: hg18


title: T9476_G2

description: In the processed data file the values for each chromosome were generated by dividing by 0.95.

value: MatA/MATalpha, DBF4-9myc::hphNT1/DBF4-9myc::hphNT1, RAD5/RAD5, BUD4/BUD4, leu2/leu2, ura3/ura3, trp1/trp1, ade2/ade2, his3/his3


title: T9476_S


title: Replicate 1, Day 1

value: Day 1


title: K562_S_input

description:
input control
Instrument model: Solexa 1G Genome Analyzer

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2354_hg18_K562-S-input.bed: hg18

value: none (input control)


title: T9394_G2

description: In the processed data file the values for each chromosome were generated by dividing by 0.8.

value: MATa, DBF4-9myc::hphNT1, RAD5, BUD4, leu2, ura3, trp1, ade2, his3


title: T10117_S

description: In the processed data file the values for each chromosome were generated by dividing by 0.48.

value: MATa / MATalpha, ctf19Δ::kanMX / ctf19Δ::kanMX, RAD5 / RAD5, BUD4 / BUD4 leu2 / leu2, ura3 / ura3, trp1 / trp1 ade2 / ade2, his3 / his3


title: K562_G2_input

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2355_hg18_K562-G2-input.bed: hg18


title: K562_G1_H3Kme3

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2656_hg18_G1-K562_H3K4me3.bed: hg18
GA2656_hg18_G1-K562_H3K4me3_pk.txt: hg18


title: BTEV-Ctrl, PU.1 ChIPseq

status: Public on Jun 05 2013

city: La Jolla

first: Michael

middle: T

last: Lam

address: 9500 Gilman Drive, MC 0651

department: School of Medicine

institute: University of California, San Diego

data_processing:
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.  Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BEDGRAPH (principle component values along the genome for Hi-C), text files (for all common, H3K4me1hi H3K4me3lo, and H3K4me1hi H3K4me3lo intergenic RevErb sites), and summary file (Signal for ChIPseq, GROseq, and 5'GROseq at RevErb bound peaks).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

source_name: RAW macrophages

growth_protocol: mouse bone marrow were differentiate to macrophages in RPMI medium containing 30% L-cell condition medium and 20% FBS.  After differentiation, bone marrow derived macrophages were grown in 10% RPMI supplement with 10ng/mL M-CSF.  RAW macrophages were cultured in RPMI with 10% FBS.

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody or with streptavidin-magnetic beads for biotinylated protein. Libraries were prepared according to Illumina's instructions. 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 (minus exo) 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, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a Genome Analyzer II (Illumina) or HiSeq 2000 (Illumina) following the manufacturer's protocols.
GRO-seq: GRO-Seq was performed as described (Core, L.J., Waterfall, J.J., and Lis, J.T., Science 322, 1845-1848 (2008)) with minor modifications.  Approximately 10 million nuclei per sample were extracted and used for run-on and BrU incorporation. BrU labeled nascent transcripts were immunoprecipiated with anti-BrU agarose beads (Santa Cruz Biotech), washed, eluted and precipitated in ethanol.  BrU precipitated RNA were subjected for first strand complementary DNA synthesis. First, polyA tailed was added using Poly(A)-polymerase (NEB). Reverse transcription was then performed using Scriptscript III Reverse Transcriptase (Invitrogen) with 5' phosphorylated primer containing  an abasic dSpacer furan with binucleotide barcode.  Excess primers were removed by Exonuclease I (Fermentas). First-strand cDNA products were fragment with basic hydrolysis and size-selected (105-400 nt) in a 10% polyacrylamide TBE-urea gel (Invitrogen). cDNA was subsequently circularlized using CircLigase (Epicentre), and relinearized at the abasic dSpacer furan with ApeI (NEB). The ssDNA template was amplified to generate DNA for sequencing by Phusion Hig-Fidelity DNA Polymerase (Thermo Science). PCR product was purified and size selected (140-225 bp) by gel electrophoresis on a non-denaturing 8% polyacrylamide TBE gel (Invitrogen). Purified DNA was then sequence on Illumina Genome Analyzer II according to the manuactuere’s instructions.
5'GRO-seq: For each RAW264.7 cell line, 20x106 nuclei were prepared from approximately 30x106 cells. Nuclear run-ons were performed in parallel on 100 μl aliquots containing 5x106 nuclei as for conventional GRO-Seq. Reactions were stopped and RNA was extracted with 450 μl TRIzol LS reagent (Invitrogen) each according to the manufacturer’s instructions. Following DNase treatment, the RNA was hydrolyzed in 20 μl total volume with 2 μl RNA fragmentation buffer (Ambion) for 10 minutes, and divalent cations were removed by gel filtration. Fragmented RNA was then 3’-dephosphorylated with polynucleotide kinase (Enzymatics), for 2 h at 37°C. The reaction was stopped with EDTA and PNK was inactivated and RNA denatured by heating the reaction to 75°C for 5 minutes, then cooled on ice for 2 minutes. BrdU-containing RNA fragments were precipitated using anti-BrdU agarose beads. The resulting RNA was dephosphorylated with calf intestinal phosphatase (NEB) and 5’-de-capped with tobacco acid pyrophosphatase (Epicentre). The reaction was stopped and RNA was extracted with Trizol LS, and libraries were prepared by ligating Illumina TruSeq-compatible adapters to the RNA 3’ and 5’ ends with truncated mutant RNA ligase 2 (K227Q) and RNA ligase 1 (NEB), respectively, followed by reverse transcription, cDNA isolation, and PCR amplification for 12 cycles. Final libraries were size-selected on PAGE/TBE gels to 60-110 bp insert size. A detailed protocol is available on request.

value: control RAW macrophages

tag: antibody

value: anti-PU.1 (Santa Cruz, SC-352)

tag: genetic background


title: K562_IgG

description:
Chromatin IP against IgG
Instrument model: Solexa 1G Genome Analyzer

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA1574_hg18_K562_IgG.bed: hg18

tag: cell type

value: All

value: IgG (Santa  Cruz, Lot# C2210, cat# SC-2027)


title: K562_H3K79me2

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA1573_hg18_K562_H3K79me2.bed: hg18


title: BLRP-RevErba, PU.1 ChIPseq

value: biotinylated RevErba expressing RAW macrophages


title: BLRP-RevErba, H3K4me1 ChIPseq

value: anti-H3K4me1 (Abcam, 8895)


title: K562_G1_input

data_processing:
Alignments: Sequence tags were obtained and mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The output of the Solexa Analysis Pipeline was converted to browser extensible data (BED) files for viewing the data in the UCSC genome browser. Data for each of the histone modifications is presented in BED files detailing the genomic coordinates of each tag as well as in BED files detailing summary windows displaying the number of tags in 200 bp windows.
Peaks: Peak selection was performed using the SISRS application to identify  H3K79me2 and H3K4me3 peaks for each cell cycle (G1, S, and G2).  The genomic input files for each cell cycle were used for controls for peak selection.  For example, the following generated the peak file for G1 H3K4me3 features: perl ./sissrs.pl -i GA2656_hg18_G1-K562_H3K4me3.bed -o GA2656_hg18_G1-K562_H3K4me3_pk.txt -s 3080000000  -p .005 -a -b ../cellcycleH3K79me/GA2353_hg18_K562-G1-input.bed -r
Genome Build:
GA2353_hg18_K562-G1-input.bed: hg18


title: BLRP-RevErba, H3K9ac ChIPseq

value: anti-H3K9ac (Millipore, 07-352)


title: RevErb DKO BMDM, H3K9ac ChIPseq

source_name: bone marrow dervied macrophages

value: bone marrow derived macrophages (Tie2-Cre; RevErbalpha flox/flox; RevErbbeta flox/flox)

value: C57Bl6 (Tie2-Cre; RevErbalpha flox/flox; RevErbbeta flox/flox)


title: BTEV-Ctrl, H3K9ac ChIPseq


title: T9394_S

value: S


title: RevErb WT BMDM, H3K9ac ChIPseq

value: bone marrow derived macrophages (RevErbalpha flox/flox; RevErbbeta flox/flox)

value: C57Bl6 (RevErbalpha flox/flox; RevErbbeta flox/flox)


title: BLRP-RevErba, 5'GRO-seq


title: T10117_G2


title: BTEV-Ctrl, 5'GRO-seq


title: RevErb WT BMDM, GRO-seq

source_name: bone marrow derived macrophages


title: 6128-ORSI-06May2011

city: Corvallis

last: Cronn

state: OR

address: 3200 SW Jefferson Way

department: PNW Research Station

institute: USDA Forest Service

data_processing:
Basecalls performed using CASAVA version 1.8.  Sequences were filtered for quality and adaptor contamination using default CASAVA settings.
Reads from the 3/25/2011, 4/7/2011, and 5/25/2011 samples were de novo assembled using the software Trinity version r2011-11-26.  The final transcriptome reference was created by clustering of the Trinity assembly with two other data sources.
Reads from the 3/10/2011, 4/22/2011, 5/6/2011, and 6/17/2011 collection dates were mapped to the transcriptome reference using bowtie2.0.0-beta7 (Langmead and Salzberg, 2012) using the following calls: bowtie2 --end-to-end -D 15 -R 2 -L 22 -i S,1,1.15 \ -x <index_basename> -U <fastq_input_files> -S <outfile.sam>.
processed data files format and content: Text file in csv format.  Expression counts for each gene across 47 samples (4 dates).  Samples are identified by sample_id, as listed in characteristics.

organism: Pseudotsuga menziesii

source_name: needle tissue from prior year growth

growth_protocol: Seeds from the various seed sources were planted in a common garden in the J. Herbert Stone Nursery in southern Oregon, USA (42.3° N, -122.9° W)

extract_protocol:
Needle tissue was collected from one year old needles (previous season’s growth).  Needles were flash frozen in liquid nitrogen on site and subsequently stored at -80°C until RNA extraction.  Frozen needles (~ 8 – 12) were mechanically homogenized on dry ice in a FastPrep-24 bead mill (MP, Solon, OH) with two ceramic beads and crushed garnet. To the ground tissue, we added 1.5 ml of ice-cold extraction buffer (3M LiCl/8M urea; 1% PVP K-60; 0.1M dithiothreitol(Tai et al., Plant Molecular Biology Reporter 22(1): 93, 2004), homogenized the tissue again to suspend the ground tissue in buffer, and then pelleted cellular debris at 200×g for 10 minutes at 4°C. The supernatant was transferred to an RNase-free tube and incubated overnight at 4°C. RNA was pelleted by centrifugation (20,000×g for 30 minutes, 4°C), rinsed with 70% EtOH (200 µl), and repelleted at 20,000×g for 5 minutes at 4°C. After removal of the supernatant, RNA pellets were air dried for 5 minutes and given a final clean-up using the ZR Plant RNA MiniPrep kit (Zymo Research, Irvine, CA).
Illumina RNA-Seq library preparation used 2 µg total RNA and followed the standard TruSeq protocol (Part #15026498 Rev. A), modified for strand-specific sequencing by the dUTP method (Parkhomchuk et al., Nucleic Acids Res 37(18):e123, 2009). The product of first-strand cDNA synthesis is desalted to remove unincorporated dNTPs using Sephadex G-50, and the second strand synthesis used a dUTP/dNTP mixture (Fermentas #R0251) in place of the standard dNTPs to incorporate dUTP into the second strand. All subsequent steps follow the Illumina protocol, except that the PCR cocktail is prepared with an additional uracil-specific excision reagent (New England Biolabs #M5505S), and the PCR cocktail was heated to 37°C for 15 minutes prior to PCR to degrade the uracil-containing strand.

tag: collection date

tag: dormancy state

value: post-budbreak

tag: source longitude_latitude_elev(m)

tag: flowcell

tag: index

value: CAGATC

tag: purpose

value: Expression


title: input DNA-ESC

city: Madison

first: Rupa

last: Sridharan

address: 2118 Wisconsin Institute for Discovery

institute: UW-Madison

data_processing:
Reads were mapped to mm9 genome using the Bowtie software and only those reads that aligned to a unique position with no more than two sequence mismatches were retained for further analysis
Significant binding events were called as peaks using MACS2.0  using an FDR of 0.05 and the –broadpeaks setting
Location analysis of called peaks was performed using the Sole-search tool
Genome_build: mm9
Supplementary_files_format_and_content: Variable step wig file that contains tag counts per 100bp windows. Only windows with counts are included

source_name: mouse ESC input

growth_protocol: ESCs and pre-iPSCs were grown in standard mouse ESC media

extract_protocol:
Cells were crosslinked with formaldehyde,lysates obtained from sonicated nuclei and Cbx3-DNA complexes were isolated with antibody.
Illumina/Solexa sequence preparation, sequencing, and quality control were performed according to Illumina protocols, with the minor modification of limiting the PCR amplification step to 10 cycles

value: mouse embryonic stem cells

value: none (input)


title: 1395-ORSI-07Apr2011

value: CTTGTA


title: Cbx3_ChIPSeq_pre-iPSC

source_name: mouse pre-iPSC / Cbx3 IP

value: fibroblast derived partially reprogrammed cells

value: Cbx3- Millipore-  05-690; clone 42s2


title: 395-WACA-07Apr2011

value: pre-budbreak

value: CGATGT


title: 3653-WACS-07Apr2011

value: ACAGTG


title: RevErb DKO BMDM, GRO-seq


title: 395-WACA-06May2011


title: 522-WACA-07Apr2011

value: TGACCA


title: 1395-ORSI-06May2011


title: input DNA-pre-iPSC

source_name: mouse pre-iPSC input


title: 8362-WACS-07Apr2011

value: GCCAAT


title: 3713-WACS-10Mar2011


title: 3650-WACS-10Mar2011


title: 388-WACA-10Mar2011


title: 6138-ORSI-10Mar2011


title: 1383-ORSI-10Mar2011


title: BTEV-Ctrl, H3K4me1 ChIPseq

value: control RAW macrophages

value: anti-H3K4me1 (Abcam, 8895)


title: 2x-Aa rep2

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

department: Genome Center

institute: UC Davis

description: Control: A. arenosa X A. arenosa

data_processing:
All sequence processing was done with custom python scripts available at the Comai lab wiki (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). We chose to process forward reads only so as not to inflate count scores. Sequences were trimmed using 4 separate scripts to remove adaptors, remove barcodes, convert Illumina 1.5+ fastq to sanger, and remove ambiguous bases. Reads that were shorter than 34-35 bp were discarded along with base quality score lower than Phred 20.
To assess gene expression, each biological replicate was aligned separately to both TAIR10 cDNA (available for download at ftp://ftp.arabidopsis.org//home/tair/Sequences//blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214) using Burrows-Wheeler Aligner (BWA) version 0.5.8c (Li and Durbin, 2009). Unmapped read were then aligned to a set of ~31K transposons annoted in the TAIR10 genomic gff file (available at http://www.arabidopsis.org)
After alignment, read counts were generated using a custom python script. Sequences that mapped to more than one gene model of the same gene were saved and counted as one read count while sequences that mapped to more than one gene were excluded.
TAIR10 cDNA (all gene models); TAIR10 transposable elements
TAIR10

organism: Arabidopsis arenosa

source_name: Arabidopsis arenosa var. Strecno seed

growth_protocol: All plants were grown under long day conditions (16 hrs light at 21°C and 8 hrs dark at 18°C) in a controlled environment facility at the University of California Davis, CA. For time course and expression analysis, the female Col-0 (seed stock ID CS6673) and C24 (seed stock ID CS22620) diploid ecotypes of A. thaliana were hemizygous for a male sterility construct (Paul et al., 1992) and were gifts from Dr. Rod Scott (University of Bath, United Kingdom). Diploid Arabidopsis arenosa var. Strecno was originally collected by Dr. Marcus Koch near Strecno Castle in Slovakia and was provided to us by Dr. M. Lysak. The male-sterile A. thaliana lines were used as seed parent and A. arenosa was used as the pollen donor for all interspecific crosses as the reciprocal cross is prevented by unilateral pollen incompatibility (Lewis and Crowe, 1958). A single pair of A. arenosa plants were used for all crosses in these experiments to reduce genetic variation due to heterozygosity in A. arenosa lines. Crosses were performed at 10 am to reduce circadian biases by pollinating fully developed stigmas by hand; no emasculation was necessary because of the male sterility construct.

extract_protocol: Approximately 10μg of total RNA was processed in preparation for Illumina Sequencing using a homemade kit. All enzymatic reactions followed manufacture’s protocol unless otherwise noted. Messenger RNA was purified from total RNA using Dynabeads (Invitrogen, Carlsbad, California), which purify poly-A containing transcripts. Then, cDNA was synthesized with random priming using SuperscriptIII (Invitrogen) followed by heat inactivation for 5 minutes at 85°C. Second strand cDNA was then synthesized as follows: We combined 5x second strand buffer [200 mM Tris-HCl, pH 7; 22 mM MgCl2; 425 mM KCl], water, and 10mM dNTPs with the first strand mix. The reaction was incubated on ice for 5 minutes and then DNA polymerase I (NEB, Ipswich, Massachusetts) and RNAseH (NEB, Ipswich, Massachusetts) were added and the reaction was incubated at 16°C for 2.5 hours. The double stranded cDNA was cleaned using Agencourt AMPure XP (Beckman Coulter Genomics, Danvers, Massachusetts) with a 1.8:1 (v/v), AMPure to library ratio. After cDNA synthesis, each library was chemically fragmented using 1 μl of NEB’s dsDNA Fragmentase for 30 minutes at 37°C and cleaned with AMPure. Fragmentation was followed by end repair with NEB’s End Repair Module Enzyme Mix and A-base overhangs, which are needed for adaptor ligation, were added with Klenow (NEB). End repair and A-base addition were both followed by AMPure cleanup. Barcoded Illumina adaptors for controls and regular Illumina adaptors for controls were ligated at room temperature using NEB Quick Ligase. To remove adapter contamination in library sequencing, we size selected our libraries using AMPure. Changing the amount of AMPure buffer changes bead size selection. We used 0.1:1 (v/v), AMPure: library to obtain fragments (library + adaptor) greater than 300 bp and eluted in 20 μl Qiagen Elution Buffer . 10 μl of each library was enriched using 15 μl Phusion 2x HF master mix (NEB), 3 μl water, and 2 μl 5 μM premixed PE primers with the following reaction conditions: 30 sec at 98°C; 14 cycles of 10 sec at 98°C, 30 sec at 65°C, and 30 sec at 72°C; final extension with 5 min at 72°C. Enriched libraries were purified with AMPure (0.8:1 v/v; AMPure: library) and quality and quantity was assessed using Agilent BioAnalyzer. Libraries were sequenced according to manufacture’s instructions. The hybrids were sequenced using Illumina’s HiSeq 2000 (100-bp paired-end reads) and the controls were sequenced using Illumina’s HiSeq 2000 (Illumina, San Diego) (100-bp paired-end reads) or Illumina’s Genome Analyzer IIx (40-bp single-end reads).

treatment_protocol: Seeds or siliques were harvested fresh from crosses and frozen on dry ice. Total RNA was obtained using Plant RNA Reagent (Invitrogen, Carlsbad, California). Frozen tissue was placed in a 1mL Dounce Tissue Grinder (Omni International, Kennesaw, GA) with 200 μL Plant RNA Reagent. The tissue was ground for approximately 30 seconds and then the extract was transferred to a clean tube. The grinder was washed with 300 μL of Plant RNA Reagent, which was combined with the tissue extract. RNA extraction proceeded with the manufacturer’s protocol and followed by a DNAse I (Invitrogen) digest at room temperature for 60 minutes according to manufacturer’s recommendation to remove any DNA contamination. RNA was eluted in 20 μL DNAse-free water and concentration was determined using a NanoDrop 1000 Spectophotometer. RNA was stored at -80°C for downstream applications.

tag: ecotype

value: A. arenosa X A. arenosa

tag: tissue

value: whole seeds

tag: time

value: 3 days after pollination


title: 3713-WACS-07Apr2011


title: 388-WACA-07Apr2011


title: Cbx3_ChIPSeq_ESC

source_name: mouse ESC / Cbx3 IP


title: 5497-WACA-07Apr2011


title: 3650-WACS-07Apr2011


title: 2x-Aa rep1

description: Control: A. arenosa X A. arenosa


title: 6138-ORSI-07Apr2011


title: 6128-ORSI-07Apr2011

value: post-budbreak

value: CAGATC


title: scnRNAs co-immunoprecipitated with HA-Twi1p-hAGO2Lmut

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Sequence reads were filtered as described (Schoeberl et al. 2012).
To study the base composition and thermodynamic stability of small RNAs, reads containing any bases other than A, C, G or T were excluded and the remaining reads were collapsed to non-redundant datasets. To study thermodynamic stability, 29 nt RNA sequences were mapped to the LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html) without allowing any mismatches. Then, the passenger strand scnRNA sequences were estimated. The local thermodynamic stabilities (kcal/mol) of 4 base pairs at the ends of the guide and passenger duplexes were calculated using the free energy parameters at 37ºC in 1 M NaCl (Freier et al. 1986) without including the initiation value. To study potential trimming and tailing reactions on small RNAs, 24-32 nt RNA sequences were mapped to the LMR genomic region by allowing two mismatches, and the mismatched positions in the scnRNAs were analyzed.
Genome_build: LMR genomic region (corresponding to bases 64,932-165,807 of the supercontig 231 in the 2nd assembly of the Tetrahymena thermophila micronuclear genome, obtained from Broad Institute Web site: http://www.broadinstitute.org/annotation/genome/Tetrahymena.1/MultiHome.html)
Supplementary_files_format_and_content: The .txt files represent abundance counts of the scnRNAs.

organism: Tetrahymena thermophila

extract_protocol:
Wild-type Tetrahymena thermophila strains B2086 and CU428 and the complete TWI1 KO strains (Mochizuki and Gorovsky 2004) were used for total RNA preparation. Twi1p was immunoprecipitated (Noto et al. 2010) from either wild-type cells using an anti-Twi1p antibody (Noto et al. 2010) or from the strains expressing HA-Twi1p and HA-Twi1p-hAGO2Lmut (Mochizuki and Kurth in press) using an anti-HA antibody (16B12, Covance). The cDNA libraries were constructed as described (Schoeberl et al. 2012). For multiplex sequencing, oligonucleotides listed below were used. Single-read 36- or 50-base sequences were generated using the Illumina GAII or HiSeq2000, respectively. Sequence reads were filtered as described (Schoeberl et al. 2012).
The 3' adapter for multiplex sequencing: 5’-App-NNN NAG ATC GGA AGA GCA CAC GTC T-3ddC; The 5' adapter for multiplex sequencing: 5'-ACA CUC UUU CCC UAC ACG ACG CUC UUC CGA UCU NNN-3'; The reverse-transcription primer for multiplex sequencing: 5’-CAA GCA GAA GAC GGC ATA CGA GAT BBB BBB GTG ACT GGA GTT CAGACG TGT GCT CTT CCG ATC T-3’ (“BBB BBB" = 6 base barcodes for maltiplex sequencing: 5'-CGT GAT-3', 5'-ACT TCG-3', 5'-GCC TAA-3', 5'- TGG TCA-3', 5'- CAC TGT-3', 5'-ATT GGC-3', 5'- GAT CTG-3', 5'- TCA AGT-3', 5'-CTG ATC -3', or 5'-AAG CTA-3'); The PCR amplification primer for multiplex sequencing: 5’-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAT CT-3’
The RNA was gel-fractionated, and a small RNA population, including scnRNAs (26–32 nt), was used to construct the cDNA library for deep sequencing.

tag: strain

tag: genotype

tag: ip antibody

value: anti-HA antibody (16B12, Covance)


title: 8362-WACS-10Mar2011

value: Expression


title: 3653-WACS-10Mar2011


title: 1383-ORSI-07Apr2011


title: 6128-ORSI-10Mar2011


title: 388-WACA-25May2011

value: Reference


title: 395-WACA-10Mar2011


title: 5497-WACA-25May2011


title: 3650-WACS-25May2011


title: C24 hybrid rep2 sil

description: Hybrid: A. thaliana eco. C24A9 X A. arenosa siliques

organism: Arabidopsis thaliana x Arabidopsis arenosa

source_name: Arabidopsis thaliana siliques

value: A. thaliana eco. C24 X A. arenosa

value: whole siliques


title: 3713-WACS-25May2011


title: C24 hybrid rep1 sil


title: Col-0 hybrid rep2 sil

description: Hybrid: A. thaliana eco. ColA9 X A. arenosa siliques

value: A. thaliana eco. Col-0 X A. arenosa


title: 1383-ORSI-25May2011


title: 3653-WACS-25May2011


title: Col-0 hybrid rep1 sil


title: 6138-ORSI-25May2011

value: CTTGTA


title: 522-WACA-10Mar2011

value: pre-budbreak


title: 395-WACA-25May2011

value: CGATGT


title: 1395-ORSI-25May2011


title: 522-WACA-25May2011

value: TGACCA


title: 5497-WACA-22Apr2011


title: 6128-ORSI-25May2011


title: 388-WACA-22Apr2011


title: eif3ha morphant, total mRNA

city: New York

first: Todd

last: Evans

state: New York

address: 1300 York Avenue  Box 282

institute: Weill Medical College of Cornell University

data_processing:
all data processing steps were performed in GobyWeb (Dorff, K. C. et al 2013 GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. Quantitative Methods (q-bio.QM); Genomics (q-bio.GN). (in press) arXiv:1211.6666).
Genome_build: Zv9.61
Supplementary_files_format_and_content: tab-separated files include RPKM values for each Sample

organism: Danio rerio

source_name: eif3ha morphant, total mRNA

extract_protocol:
RNA samples were extracted from either polysomal fractions or whole embryos using Trizol (Invitrogen), and polyA mRNA was prepared for sequencing using the Illumina mRNA-seq Sample Preparation Kit.
RNA and cDNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: ~24 hours post fertilization (hpf)

value: whole embryo


title: 3650-WACS-22Apr2011

value: GCCAAT


title: 3713-WACS-22Apr2011

value: ACAGTG


title: 1395-ORSI-10Mar2011


title: 8362-WACS-25May2011


title: scnRNAs co-immunoprecipitated with HA-Twi1p

value: HA-Twi1p-5 x HA-Twi1p-65


title: 6138-ORSI-22Apr2011

value: post-budbreak


title: wild-type, total mRNA

source_name: wild-type, total mRNA


title: wild-type, polysomal mRNA

source_name: wild-type, polysomal mRNA


title: 8362-WACS-22Apr2011


title: 1383-ORSI-22Apr2011

value: CAGATC


title: eif3ha morphant, polysomal mRNA

source_name: eif3ha morphant, polysomal mRNA