title: SAM19655384 M 85 AD III


title: SAM19655417 M 79 AD IV

status: Public on Dec 20 2017

type: SRA

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

library_source: transcriptomic

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

organism: Homo sapiens

source_name: RNA from fusiform gyrus

extract_protocol: RNA was extracted from frozen tissue sections. RIN scores ranged from 5 to 8.5.

tag: tissue

value: fusiform gyrus

tag: Sex

value: M

tag: age at death

tag: diagnosis

value: Alzheimer's disease

tag: braak score

value: IV

tag: caseid


title: SAM19655473 M 81 AD VI

value: VI


title: SAM19655481 F 79 CON III

value: F

value: control

value: III


title: SAM19655399 M 93 AD IV


title: SAM19655412 F 81 AD IV


title: SAM19655492 M 93 CON IV


title: SAM19655394 F 89 AD IV


title: SAM19655379 F 91 AD IV


title: SAM19655407 F 91 AD IV


title: SAM19655480 M 80 CON IV


title: SAM19655466 F 92 AD VI


title: SAM19655494 M 87 CON III


title: SAM19655506 F 78 CON IV


title: SAM19655387 F 91 AD IV


title: SAM19655477 M 64 AD VI


title: SAM19655467 M 80 AD V

value: V


title: SAM19655386 F 86 AD III


title: SAM19655391 F 86 AD IV


title: SAM19655464 M 76 AD V


title: SAM19655403 F 96 AD IV


title: SAM19655446 F 86 AD V


title: SAM19655438 M 81 AD V


title: SAM19655460 M 85 AD VI


title: SAM19655489 F 87 CON IV


title: SAM19655485 M 86 CON IV


title: SAM19655487 M 81 CON III


title: SAM19655503 F 80 CON III


title: SAM19655501 M 89 CON II

value: II


title: SAM19655395 F 92 AD IV


title: SAM19655409 F 88 AD IV


title: SAM19655493 F 80 CON III


title: SAM19655405 F 85 AD IV


title: SAM19655436 M 89 AD V


title: SAM19655468 F 60 AD VI


title: SAM19655396 F 85 AD IV


title: SAM19655392 F 98 AD IV


title: SAM19655440 F 91 AD V


title: SAM19655504 M 82 CON III


title: SAM19655512 F 91 CON IV


title: SAM19655393 F 88 AD IV


title: SAM19655437 F 86 AD V


title: SAM19655431 M 79 AD V


title: SAM19655505 M 92 CON III


title: SAM19655474 M 92 AD V


title: SAM19655510 F 83 CON II


title: SAM19655397 F 103 AD IV


title: SAM19655511 M 80 CON I

value: I


title: SAM19655447 M 84 AD V


title: SAM19655421 M 77 AD IV


title: SAM19655600 F 90 AD VI


title: SAM19655453 M 81 AD V


title: SAM19655470 F 74 AD VI


title: SAM19655500 M 92 CON III


title: SAM19655490 F 99 CON III


title: SAM19655428 M 85 AD IV


title: SAM19655465 M 78 AD VI


title: SAM19655455 F 70 AD VI


title: SAM19655441 M 80 AD VI


title: SAM19655488 M 82 CON IV


title: SAM19655442 M 89 AD VI


title: SAM19655410 M 86 AD IV


title: SAM19655507 M 86 CON III


title: SAM19655400 F 91 AD IV


title: SAM19655382 F 88 AD IV


title: SAM19655434 M 94 AD V


title: SAM19655509 M 73 CON III


title: SAM19655389 F 93 AD IV


title: SAM19655427 M 78 AD IV


title: SAM19655435 M 80 AD V


title: SAM19655402 F 97 AD IV


title: SAM19655497 M 82 CON III


title: SAM19655463 F 87 AD V


title: SAM19655462 F 97 AD V


title: ChIP-Seq_OpaA_NA1000+Rif

status: Public on Nov 01 2017

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

library_source: genomic

data_processing:
Base calling: HiSeq Control Software 1.5.15.1, RTA 1.13.48.0, CASAVA-1.8.2
Alignment: Bowtie-0.12.9, samtools-0.1.18
Peak calling and refinement : MACS2 Software (Galaxy Version 2.1.0.20151222.0)
Peak annotation: SeqMonk Software v0.34.1 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xls file reporting OpaA ChIP-Seq peaks (described in the paper) was generated by MACS2 and SeqMonk softwares. The sheet is organized in columns as follows: column 1: Peak # (order on chromosome); column 2: Peak start coordinates (bp); column 3: Peak end coordinates (bp); column 4: Peak length coordinates (bp); column 5: Peak summit coordinates (bp); column 6: Peak pileup; column 7: -LOG10(pvalue); column 8: Fold enrichment; column 9: -LOG10(qvalue); column 10: Closest CDS; column 11: GC% (+/-50pb window surrounding the peak summit) and column 12: DNA sequences (+/-75pb window surrounding the peak summit).

molecule: genomic DNA

organism: Caulobacter vibrioides

source_name: cultures

growth_protocol: Overnight saturated cultures of each Caulobacter crescentus strains were freshly diluted in PYE rich media (O.D.660nm~0.025) and cultures were grown at 30°C with aeration to mid-log phase (O.D.660nm~0.5).

extract_protocol:
Overnight saturated cultures of each C. crescentus strains were freshly diluted in PYE rich media (O.D.660nm~0.025) and cultures were grown at 30°C with aeration to mid-log phase (O.D.660nm~0.5). Then, after 10 min of antibiotic treatments (Rifampicin 30µg/ml; Novobiocin 100µg/ml; Chloramphenicol 1µg/ml) or without, cells were cross-linked in presence of 1% of formaldehyde and 10 μM of sodium phosphate (pH 7.6) during 10 minutes at room temperature and thereafter on ice for 30 min, then washed three times in phosphate buffered saline (PBS), re-suspended in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT and incubated during 10 minutes at 37°C after the addition of Ready-Lyse lysozyme solution (Epicentre, Madison, WI), according to the manufacturer's instructions. Lysates were then sonicated (Bioruptor® Pico, www.diagenode.com) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. Lysates were then diluted to 1 mL using ChIP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl plus protease inhibitors (Roche, www.roche.com) and pre-cleared with 80 μL of protein-A agarose (Roche, www.roche.com) and 100 µg BSA. 2% of each pre-cleared lysate was reserved as input sample. Then, the pre-cleared supernatants were incubated overnight at 4°C with OpaA Polyclonal antibodies (1:1,000 dilution). The immuno-complexes were captured after incubation with Protein-A agarose pre-saturated with BSA during 2 hours at 4°C and washed once with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), then once with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), once with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The complexes were eluted twice with 250 μL of elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and incubated overnight at 65°C with 300 mM NaCl to reverse the crosslinks. The samples were then treated with 2 µg of Proteinase K for 2 hours at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 100 μl of water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions.

tag: strain

tag: genotype

value: Wild type

tag: antibody

value: antibody was raised in rabbits against purified OpaA protein


title: ChIP-Seq_OpaA(rep1)_NA1000


title: ChIP-Seq_OpaA_NA1000+Chl


title: ChIP-Seq_OpaA(rep2)_NA1000


title: CD103+CD49a-CD8 TRM, biological replicate 6

status: Public on Feb 14 2017

city: Stockholm

first: Liv

last: Eidsmo

address: L8:02 Karolinska Univeristy Hospital

country: Sweden

institute: Karolinska Insitutet

data_processing:
Basecalling softwares: HCS1.5.15.1+ RTA1.13.48 +OLB 1.9.4; parameters are $OLB-1.9.4/bin/setupBclToQseq.py –b $BaseCalls -o $Bustard
Alignment: Bowtie alignment of gene reference, bowtie2-2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 16 -k 200; BWA alignment of genome reference, bwa-0.7.10, -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
Filtering: Remove reads with adapters; Remove reads with unknown bases more than 10%; Remove low-quality reads (which are defined as reads having more than 50% bases with quality value <= 10).
Additional: TopHat alignment of genome reference (for AS, NovelTU, ExtendGene), TopHat v2.0.10, -p 16 --solexa1.3-quals --segment-length 30 --segment-mismatches 2 -r 20 --mate-std-dev 20 --library-type fr-unstranded
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include expected.count values for each sample (*replicate#.txt) and all samples (all.gene.expected_count_ALL.txt). Gene ids in the processed data files (column 1) are the Gene IDs from the NCBI's Entrez Gene database (http://www.ncbi.nlm.nih.gov/gene/), and the "expected.count" values were obtained by the RSEM method.

molecule: total RNA

source_name: CD103+CD49a- CD8 TRM

extract_protocol:
Cells were sorted directly into Qiazol and stored at -80 degree before extraction using miRNeasy Mini Kit (Qiagen) according to manufacturer's protocol.
Library was constructed using SMART-Seq v4 Ultra Low Input RNA Kit (ClonTech) according to manufacturer's protocol.

treatment_protocol:
Epidermis were separate from dermal tissue after dispase treatment overnight. The epidermal tissue were further digested by collagenase. The resulting cell suspension were stained and sorted by FACS based on surface markers.
Epidermal T cells were sorted from epidermal cell suspension according to their cellular markers (live CD45+CD3+CD4-CD103+ CD49+/-) by a MoFlo XDP sorter.

tag: tissue origin

value: healthy skin

tag: cell type

value: epidermal CD8+CD103+CD49a- tissue resident memory T cells

tag: cell subset

tag: donor

value: Subject 6


title: ChIP-Seq_OpaA_GM3875

value: delta_opaA(ccna_03428) viable suppressor strain


title: CD103+CD49a-CD8 TRM, biological replicate 5

value: Subject 5


title: CD103+CD49a+CD8 TRM, biological replicate 6

source_name: CD103+CD49a+ CD8 TRM

value: epidermal CD8+CD103+CD49a+ tissue resident memory T cells


title: CD103+CD49a-CD8 TRM, biological replicate 7

value: Subject 7


title: CD103+CD49a+CD8 TRM, biological replicate 7


title: CD103+CD49a-CD8 TRM, biological replicate 4

value: Subject 4


title: HiC-TCC_WT_Rep1

status: Public on Jun 10 2017

city: Cambridge

first: Nezar

last: Abdennur

state: MA

address: 77 Massachusetts Ave

institute: MIT

description:
Tethered Chromosome Capture (TCC) variant of Hi-C
UNTR.1kb.cool.HDF5
UNTR.2kb.cool.HDF5
UNTR.5kb.cool.HDF5
UNTR.10kb.cool.HDF5
UNTR.20kb.cool.HDF5
UNTR.40kb.cool.HDF5
UNTR.50kb.cool.HDF5
UNTR.100kb.cool.HDF5
UNTR.200kb.cool.HDF5
UNTR.500kb.cool.HDF5
UNTR.1000kb.cool.HDF5
eigs.20kb.tsv
eigs.100kb.tsv
tads.lavaburst.corner.UNTR.20kb.txt
tads.lavaburst.modularity.UNTR.20kb.txt
tads.lavaburst.modularity.boundaryProbability.20kb.txt

data_processing:
Hi-C. Alignment: Hi-C reads were mapped using bowtie 2.2.8 and the iterative mapping strategy (Imakaev et al, 2011) implemented in the hiclib package. Filtering: PCR duplicates and reads mapped to multiple or zero locations were removed. After binning, low-coverage bins were removed using a maximum allowed median absolute deviation (MAD) filter on log genomic coverage, set to five MADs. To remove the short-range Hi-C artifacts we also filter contacts mapping to the same or adjacent genomic bins (i.e., first two diagonals). Binning: the filtered reads pairs were binned into 20kb and 100kb contact matrices using the cooler library and stored as binary cool HDF5 files. Normalization: the filtered 20kb and 100kb contacts matrices were then normalized using the iterative correction procedure (IC), such that the genome-wide sum of contact probability for each row/column equals 1.0.
ChIP-seq. We processed ChIP-seq data following the steps of the ENCODE pipeline [https://github.com/ENCODE-DCC/chip-seq-pipeline]. Alignment: we used bwa 0.7.12 (program bwa aln with parameters: -q 5 -l 32 -k 2). Filtering: PCR duplicates were marked using picardtools 2.7.1. Unmapped reads, non-primary alignments, and low quality alignments (mapQ < 30) were removed using samtools 1.3. Cross-correlation analysis was performed using phantompeakqualtools. Peaks and signal tracks were generated using MACS2. For Rad21, Smc3 and CTCF ChIP-seq, we followed the same steps with the following variations: reads from pooled mouse hepatocyte chromatin and HEK human chromatin (internal control and calibration) were mapped to the combined mm9 and hg19 assemblies using the bwa mem program. After filtering, reads were divided into those that mapped uniquely to either mm9 or hg19. A database of CTCF motif instances was produced by performing a PWM scan of the canonical mouse CTCF motif against the mm9 genome using the fimo tool from the MEME suite with default parameters. Peak files with motif annotations were generated by intersecting the peak files against the motif database using bedtools 2.26.0.
RNA-seq. We mapped the RNA-seq data to mm9 reference mouse genome assembly and GENCODE vM1 transcriptome using STAR v.2.5.0a and adapted scripts from the ENCODE RNA-Seq pipeline [https://www.encodeproject.org/pipelines/ENCPL002LSE/]. To obtain the tracks of local transcription, we aggregated the uniquely mapped reads into RPKM-normalized bigWig files using the built-in STAR functionality. To find differentially expressed genes, we aggregated the read counts at the gene level using HTSeq with the "union" option and called DE genes with DESeq2. Alignment with STAR v2.5.0.a was done using parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1. Signal tracks were generated using STAR with parameters: --runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded  --outWigReferencesPrefix chr.
Compartment eigenvectors. The compartment structure of Hi-C maps was detected using a modified procedure from (Imakaev et al, 2012). In short, compartments were quantified as the dominant eigenvector of the observed/expected 20kb and 100kb cis contacts maps upon subtraction of 1.0, as implemented in hiclib.
Domain detection. To identify contact domains, we used a segmentation that divides the genome into domains in such a way as to maximize a global domain scoring function. We used two different scoring functions: one was the corner score function from (Rao et al, 2014) and the other was based on network modularity, which is a metric widely used to detect communities in networks. The implementation of these and related algorithms is provided in the lavaburst package. To robustly call insulating boundaries across different conditions, we exploit the multi-resolution nature of the modularity score and compute the average marginal boundary scores on 20kb WT and ΔNipbl contact matrices sweeping over a range of gamma values to obtain a 1D boundary (i.e., insulation) track. Short intervals representing insulating loci were called by thresholding on the boundary score, and the common and unique loci to each condition were determined by interval intersection.
Genome_build: mm9
Supplementary_files_format_and_content: Cooler HDF5 files (extension .cool.HDF5) contain contact matrices and were generated using the cooler Python package; ChIP-seq signal track bigWigs were generated using MACS2, in units of SPMR; RNA-seq bigWig files were generated using STAR in units of RPM; Eigenvector text files are fixed step bedGraph-like files covering the whole genome with a column for the eigenvector in each condition (U=WT, T=TAM, N=NIPBL); TAD call text files are BED-like files where each row corresponds to a detected domain; the TAD boundary probabilities file is a bedGraph-like file covering the whole genome at 20kb with columns for the insulation tracks in conditions U=WT and N=NIPBL; The deseq2 CSV file contains estimated transcript abundances and differential expression statistics across the three conditions

organism: Mus musculus

extract_protocol:
Liver was dissected and the left lateral lobe was prepped for a two-step perfusion adapted from (Li et al 2010 & Goncalves et al 2007): First, the liver was perfused with an EDTA-containing buffer to remove Ca2+ from the tissue in order to weaken the integrity of the desmosomes, which were subsequently digested using a Ca2+ rich buffer containing collagenase. The freed hepatocytes were rinsed through a cell strainer and washed four times with ice-cold Ca2+ rich buffer without collagenase. For each wash, the cells were spun at low centrifugal force (60g for 1min) to enrich intact hepatocytes and reduce non-mesenchymal debris. Part of each sample was fixed with 1% PFA for 10 minutes at room temperature. Fixed and unfixed hepatocytes were aliquoted and frozen in liN2 for later use.
Hi-C: Roughly 100 million fixed hepatocytes per sample were processed according to (Kalhor et al, 2012) using HindIII. TCC libraries were PCR-amplified (12 cycles) and size selected. Equimolar pools of libraries were sequenced; ChIP-seq: Fixed aliquots of hepatocytes were hypotonically lysed and sonicated in 1% SDS/TE. An aliquot of each sample was reverse cross-linked in order to determine chromatin concentration and sonication efficiency. 20μg chromatin per sample was diluted in RIPA and incubated with 1.5μg of either αH3k4me3 antibody (C15410003-50, Diagenode) or αH3K27Ac antibody (ab4729, Abcam) at 4°C, overnight. The antibodies were retrieved with Dynabeads (IgA, Invitrogen) and bound chromatin was washed and eluted. After reverse cross-linking, the amount of ChIPped and input DNA was determined with Qubit (Thermo Fisher).  The libraries were prepared with NEBNext® ChIP-Seq Library Prep Kit for Illumina®. After amplification and size selection with E-Gel® SizeSelect™ (Thermo Fisher) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end). RNA-seq: RNA integrity was tested with Bioanalyzer (Agilent RNA Nano Kit) and ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Illumina) prior to library preparation.  Strand-specific libraries were prepared with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. After amplification and size selection with Agencourt AMPure XP beads (Beckmann Coulter) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end).

treatment_protocol: Treated 12 week old mice were injected with 1mg Tamoxifen (100μl of 10mg/ml Tamoxifen in corn oil) on 5 consecutive days. After keeping these mice for another 5 days without injection, they were sacrificed and the hepatocytes were harvested.

tag: treatment

tag: age

value: 12 weeks

value: liver


title: HiC-TCC_TAM_Rep2

description:
Tethered Chromosome Capture (TCC) variant of Hi-C
TAM.1kb.cool.HDF5
TAM.2kb.cool.HDF5
TAM.5kb.cool.HDF5
TAM.10kb.cool.HDF5
TAM.20kb.cool.HDF5
TAM.40kb.cool.HDF5
TAM.50kb.cool.HDF5
TAM.100kb.cool.HDF5
TAM.200kb.cool.HDF5
TAM.500kb.cool.HDF5
TAM.1000kb.cool.HDF5
eigs.20kb.tsv
eigs.100kb.tsv

value: tamoxifen


title: CD103+CD49a+CD8 TRM, biological replicate 4


title: HiC-TCC_TAM_Rep1


title: HiC-TCC_WT_Rep2


title: SAM19655429 F 101 AD VI

value: fusiform gyrus

value: F

value: Alzheimer's disease

value: VI


title: HiC-TCC_NIPBL_Rep1

description:
Tethered Chromosome Capture (TCC) variant of Hi-C
NIPBL.1kb.cool.HDF5
NIPBL.2kb.cool.HDF5
NIPBL.5kb.cool.HDF5
NIPBL.10kb.cool.HDF5
NIPBL.20kb.cool.HDF5
NIPBL.40kb.cool.HDF5
NIPBL.50kb.cool.HDF5
NIPBL.100kb.cool.HDF5
NIPBL.200kb.cool.HDF5
NIPBL.500kb.cool.HDF5
NIPBL.1000kb.cool.HDF5
eigs.20kb.tsv
eigs.100kb.tsv
tads.lavaburst.corner.NIPBL.20kb.txt
tads.lavaburst.modularity.NIPBL.20kb.txt
tads.lavaburst.modularity.boundaryProbability.20kb.txt


title: CD103+CD49a+CD8 TRM, biological replicate 2

value: Subject 2


title: Resuscitation rep1

status: Public on Aug 25 2016

first: Dunaduan

last: Ma

state: Ma

department: Koch Institute

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Sequence reads were mapped to NC_008796.fasta whole genome using BWA-MEM algorithm
Gene expression was calculated as gene-wised coverage of the sequencing reads
Genome_build: NC_008796.fasta;gi|121635883|ref|NC_008769.1|
Supplementary_files_format_and_content: abundance measurements

organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

source_name: Resuscitation_bacteria culture

growth_protocol: M. bovis BCG str. Pasteur 1173P2 were grown in roller bottles with 7H9 broth at 5 rpm and 37C.

extract_protocol:
Cell pellets were lysed by bead-beating in Trizol reagent (Invitrogen) and RNA purified with on-column DNaseI digest and PureLink miRNA spin columns (Ambion). The second PureLink miRNA spin column depletes tRNA. rRNA is depleted using the Ribo-ZeroTM Magnetic Kit for Bacteria (Epicentre, Illumina) as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq® RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: At mid-log growths, M. bovis BCG str. Pasteur 1173P2 cultures were pelleted, washed twice in Phosphate Buffered Saline (PBS) supplemented with 0.05% (v/v) tyloxapol and resuspended in the same solution. Cultures continued  in roller bottles at 5 rpm and 37C.

value: Pasteur 1173P2

tag: genotype/variation

value: wild type

value: Resuscitation after 20 days of starvation


title: Resuscitation rep2


title: Resuscitation rep3


title: Starvation day20 rep3

source_name: Starvation day20_bacteria culture

value: Starvation 20 days


title: CD103+CD49a-CD8 TRM, biological replicate 2

value: healthy skin

value: epidermal CD8+CD103+CD49a- tissue resident memory T cells


title: CD103+CD49a+CD8 TRM, biological replicate 5

value: epidermal CD8+CD103+CD49a+ tissue resident memory T cells

value: Subject 5


title: Starvation day20 rep2


title: ChIP-Seq_OpaA_NA1000+Novo

value: Wild type

value: antibody was raised in rabbits against purified OpaA protein


title: CD103+CD49a-CD8 TRM, biological replicate 1

value: Subject 1


title: CD103+CD49a+CD8 TRM, biological replicate 1


title: HiC-TCC_NIPBL_Rep2

value: tamoxifen

value: 12 weeks

value: liver


title: Starvation day20 rep1


title: Starvation day4 rep2

source_name: Starvation day4_bacteria culture

value: Starvation 4 days


title: Starvation day10 rep2

source_name: Starvation day10_bacteria culture

value: Starvation 10 days


title: Starvation day4 rep1


title: Starvation day4 rep3


title: Starvation day10 rep3


title: Log phase control rep3

source_name: Log phase control_bacteria culture

value: Log phase


title: Log phase control rep1

value: Pasteur 1173P2


title: Starvation day10 rep1

value: wild type


title: Log phase control rep2


title: aba2-1 stress

status: Public on Aug 05 2016

city: Taipei City

first: Paul

last: Verslues

address: No.128, Sec.2, Academia Rd., Nangang Dist.

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: seedlings grown for seven days under unstressed control conditions, transferred to low water potential (-1.2 Mpa) for 96 h before sample collection

data_processing:
basecalling and demultiplexing performed using CASAVA version 1.6
RNAseq reads were mapped to the TAIR10 genome using BLAT with default parameters
RPKM values were computed using Rackj 0.61 (http://rackj.sourceforge.net/)
Genome_build: TAIR10 (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Arabidopsis thaliana

source_name: aba2-1 stress

growth_protocol: Seeds plated on agar plates containing half strength Murashige-Skoog media with 2 mM MES buffer (pH 5.7) and stratified for 4 days at 4 C.  Plates were then position vertically in a rack and and kept under continuous light (80-100 micromol photons m-2sec-1 ) at 23 C in a controlled environment chamber.  Note that no sugar was added to any of the growth media used.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plant Mini Kit according to the manufacturer’s protocol.  RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Using the Illumina mRNA-seq kit, 10-15 ug of total RNA was for isolation of poly-A RNA by oligo-dT beads and subjected to cation-catalyzed fragmentation for four minutes at 94˚C. The mRNA fragments were then converted into ds cDNA by random priming, and the ends were repaired and A-tailed.
Multiplexing barcodes were added to the DNA fragment ends with modifications from the paired-end gDNA library prep kit. The ligation products were size-selected on agarose gel (200-400 bp), subjected to 18 cycles of PCR and cleaned up by Ampure beads (Beckman Agencourt). The absolute concentrations of the libraries were determined fluorometrically by Qubit (Invitrogen) and BioAnalyzer High Sensitivity DNA chip (Agilent).
Mixing of the differentially barcoded samples for each lane was based on qPCR-derived relative concentration for amplifiable fraction of each library. Briefly, the relative amplifiable concentration of each library was estimated by real-time PCR analyses (Roche Light Cycler 480) using the KAPA NGS Library qPCR kit (KAPA) by regression to the curve generated using the included standard of known concentration. Correlations between output clusters and qPCR concentrations were derived by plotting the relative concentrations of previously sequenced PhiX control and libraries against the output cluster numbers. The relative concentrations of the MID libraries were then estimated by regression.  The amount (fmoles) of each library to be mixed in a pool for each lane was determined based on the proportion each would account for in the projected output clusters (i.e. estimating the fmoles required per library for generating 300,000/8 = 37,500 raw clusters per tile if the lane to be used for sequencing a pool of 8 barcodes).  The sequencing was performed on an Illumina Genome Analyzer IIx

treatment_protocol: After seven days of growth, seedlings were transferred either to fresh plates of control media (-0.25 MPa) or to agar plates infused with polyethylene glycol 8000 (PEG) to impose low water potential (-1.2 MPa) stress.  Samples were collected 96 h after transfer (control and stress treatments).  Other seedlings which had been stress treated for 96 h were transferred to fresh plates of control media for 10 h before samples were collected (stress-release treatment).  The experiments were repeated three times proline accumulation was assayed in each experiment to check the reproducibility of the stress treatment.

value: stress

value: whole seedling


title: aba2-1 stress release

description: seedlings grown for seven days under unstressed control conditions, transferred to low water potential (-1.2 Mpa) for 96 h, then transferred back to control media for 10 h before sample collection

source_name: aba2-1 stress release

value: stress release


title: aba2-1 control

description: seedlings grown for seven days under unstressed control conditions, transferred to fresh control plates for 96 h before sample collection

source_name: aba2-1 control

value: unstressed control


title: WT stress release

source_name: WT stress release

value: wild type (Col-0)


title: WT control

source_name: WT control


title: p5cs1-4 control

source_name: p5cs1-4 control


title: p5cs1-4 stress

source_name: p5cs1-4 stress


title: p5cs1 stress release

source_name: p5cs1 stress release


title: WT stress

source_name: WT stress


title: Input DNA_shNS_C2C12, T24

status: Public on Dec 31 2015

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

data_processing:
Sequencing reads were aligned to the mm9 mouse genome assembly using Bowtie in –v mode, allowing up to  3 mismatches in the 50 nucleotides read, and keeping reads that align at one place in the genome.
Picard was used to filter out replicated reads
The files were converted to bed format, reads were stretched to 200 bp using bedTools’ slopBed, and base-wise read density was calculated across the genome using genomeCoverageBed from bedTools, using the -d and -bg option
peaks in the anti-Six4_shNS-C2C12 experiment were called using MACS version 2.0 using default parameters
All samples were processes as expalined above except for sample4 where reads from two sequencing runs of the same library were individually aligned to the genome using Bowtie. Aligned reads were combined together using Picard and duplicate reads were removed.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files represent the base-wise read density in the ChIP-seq experiments, across the genome. Bed file represents the peaks identified in the anti-Six4_shNS-C2C12 cells using MACS.

source_name: C2C12 cells

growth_protocol: Cells were grown in growth medium (GM) DMEM High Glucose (Hyclone) supplemented with 10% Characterized Fetal Bovine Serum (Hyclone); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone)

extract_protocol:
chromatin was prepared from formaldedyde cross-linked cells; shearing was done using a probe sonicator.
Libraries were prepared by McGill University and Génome Québec Innovation Centre

treatment_protocol: Cell lines were seeded and induced to differentiate for 24 hours once they got confluent using differentiation medium containing DMEM High Glucose (Hyclone); 2% Horse Serum (Invitrogen); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone).

tag: cell line

value: shNS C2C12


title: anti-Six4_shSix4_C2C12 , T24

value: shSix4 C2C12


title: Input DNA_C2C12, T24

value: parental C2C12


title: anti-Six4_shNS_C2C12, T24


title: anti-Flag_parental_C2C12, T24

value: anti-Flag


title: IgG_parental_C2C12, T24

value: normal rabbit IgG


title: KO-treated_rep1

status: Public on Aug 11 2016

type: RNA

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100 ul of the mixture was hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, No XDR, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain median signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were filtered out. Raw data were further filtered to retain only present probes (probes for which both replicates of at least one experimental condition are present). Probes with null expression values are those excluded because of these two filtering steps. Data were further processed in Expander 7, where median signals were quantile-normalized and log2-transformed.

source_name: KO macrophages_treated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300ng RNA using the Quick Amp Labeling Kit, one-color kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bone marrow cells from wild-type and FoxO3a-/- mice were differentiated into bone marrow derived macrophages using M-CSF. Mice were on a C57BL/6 background and age and gender matched mice were used at 9 weeks of age. Cells were grown in RPMI-1640 supplemented with 8% fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA from the cells was extracted at 6 hours post infection using RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Bone marrow derived macrophages were seeded on 6 well plates. Cells were left untreated or infected with Salmonella typhimurium (10 MOI).

tag: strain background

value: 9 wks

value: bone marrow derived macrophage

tag: infected with

value: Salmonella typhimurium


title: KO-treated_rep2


title: anti-Flag_Flag-Six4_C2C12, T24

value: Flag-Six4 C2C12


title: WT_rep1

source_name: WT macrophages_untreated

value: Wild-type


title: shSix4_C3H10T1/2+pBABE_T24_rep1

description: Gene Expression profiling of C2C12 24h after start of differentiation

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100 ul of the mixture was hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, 0.10 XDR, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw data were filtered for present probes, processed by Expander using processed signal where probes were normalized using quantile normalization and log2-transformed.

source_name: C3H10T1/2, shSix4, pBABE,  rep1

growth_protocol: Cells were grown in growth medium (GM) DMEM High Glucose (Hyclone); 10% Characterized Fetal Bovine Serum (Hyclone); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone)

extract_protocol: Total RNA was isolated with the Absolutely RNA Mini-Prep Kit (Stratagene) following the manufacturer's protocol. RNA quantity and quality was assessed with the NanoDrop ND-1000. Integrity of the RNA was determined by agarose gel

treatment_protocol: Cell lines were infected with retroviruses expressing MyoD or empty plasmid and induced to differentiate 24 hours later for an additional 24 hours using differentiation medium containing DMEM High Glucose (Hyclone); 2% Horse Serum (Invitrogen); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone).

value: shSix4 C3H/10T1/2

tag: virus

value: pBABE


title: KO_rep1

source_name: KO macrophages_untreated


title: shLuc_C3H10T1/2+pBABE_T24_rep3

description: Gene Expression profiling of C2C12 at the myoblast stage before differentiation

source_name: C3H10T1/2, shLuc, pBABE,  rep3

value: shLuc C3H/10T1/2


title: WT_rep2


title: shLuc_C3H10T1/2+pBABE-MyoD_T24_rep2

description: Gene Expression profiling of C2C12 at the start of differentiation (T0)

source_name: C3H10T1/2, shLuc, pBABE-MyoD,  rep2

value: pBABE-MyoD


title: shSix4_C3H10T1/2+pBABE-MyoD_T24_rep1

description: Gene Expression profiling of C2C12 at the myotube stage (96h after start of differentiation)

source_name: C3H10T1/2, shSix4, pBABE-MyoD,  rep1


title: WT-treated_rep2

source_name: WT macrophages_treated


title: WT-treated_rep1


title: shLuc_C3H10T1/2+pBABE_T24_rep1

source_name: C3H10T1/2, shLuc, pBABE,  rep1


title: shSix4_C3H10T1/2+pBABE-MyoD_T24_rep3

source_name: C3H10T1/2, shSix4, pBABE-MyoD,  rep3


title: shLuc_C3H10T1/2+pBABE-MyoD_T24_rep1

source_name: C3H10T1/2, shLuc, pBABE-MyoD,  rep1


title: shLuc_C3H10T1/2+pBABE_T24_rep2

source_name: C3H10T1/2, shLuc, pBABE,  rep2


title: shSix4_C3H10T1/2+pBABE-MyoD_T24_rep2

source_name: C3H10T1/2, shSix4, pBABE-MyoD,  rep2


title: shSix4_C3H10T1/2+pBABE_T24_rep2

source_name: C3H10T1/2, shSix4, pBABE,  rep2


title: KO_rep2


title: shSix4_C3H10T1/2+pBABE_T24_rep3

source_name: C3H10T1/2, shSix4, pBABE,  rep3


title: shLuc_C3H10T1/2+pBABE-MyoD_T24_rep3

source_name: C3H10T1/2, shLuc, pBABE-MyoD,  rep3


title: HUVEC_HT-FAIRE_REP1

status: Public on Sep 24 2015

city: Chapel Hill

first: Ian

middle: Jonathan

last: Davis

state: NC

address: 450 West Drive

department: Genetics, Pediatrics

institute: University of North Carolina

description: FAIRE DNA (open chromatin)

data_processing:
Reads were filtered for significant adapter contribution using TagDust
Reads were aligned to reference human genome (hg19) using Bowtie, allowing up to four potential alignments for a given read (-m) but picking the best overall alignment (--best). Two mismatches were allowed during alignment.
Reads from each replicate were concatenated prior to peak-calling
Peaks were called using MACS2, manually setting the shift size such that fragment lengths were assumed to be 200bp.
Genome_build: hg19
Supplementary_files_format_and_content: BED format of peak calls from MACS2 contains chromosome, start, stop, name, and significance of each peak.

source_name: Human Umbilical Vein Endothelial Cells

extract_protocol:
2 x 10^7 cells were formaldehyde crosslinked for 7 minutes, quenched with glycine, lysed, and sonicated as previously described (Simon et al. 2012).  Five percent of the sonicated material was separated and processed as input control by crosslink reversal, purification by phenol-chloroform extraction, and ethanol precipitation, as previously described (Simon et al. 2012).  The remainder of the sonicated lysate was diluted 1:5 with DNA Binding Buffer and processed through a ChIP DNA clean and concentrate column (Zymo Research #11-379) as per manufacturer’s instructions. Quantitative PCR was used to confirm FAIRE DNA enrichment at control genomic loci as described below. For high-throughput sequencing, FAIRE DNA from both replicates was prepared as per manufacturer’s recommendations using the TruSeq DNA Sample Prep Kit (Illumina) and 50-bp reads were sequenced
Illumina TruSeq as per manufacturer's recommendations

value: HUVEC


title: HUVEC_HT-FAIRE_REP2

description: FAIRE DNA (open chromatin)


title: siWIZ_input

status: Public on Sep 03 2015

description: input control

data_processing:
Reads were filtered to remove those with significant adapter contribution using TagDust
Reads were aligned to the reference human genome (hg19) using Bowtie v 0.12.7, allowing for up to 2 mismatches
Regions of significant ChIP enrichment relative to input control (“peaks”) were identified using MACS2 assuming fragments were 250bp in length
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: HEK293T cells

extract_protocol:
Chromatin immunoprecipitation was performed using the ChIP-IT High Sensitivity kit (Active Motif #53040) according to manufacturer’s instructions except that Input samples were purified by phenol:chloroform extraction.  The following antibodies were used: anti-H3K9me2 (Abcam #ab1220), anti-G9a (Abcam #ab40542), and Rabbit IgG (Jackson Immunoresearch #011-000-003).  ChIP samples were quantitated using the Qubit 2.0 Fluorometer (Invitrogen).  A portion of each sample was confirmed by qPCR. The remainder of the sample was submitted for high throughput sequencing.
Libraries were prepared for high-throughput using the Illumina TruSeq kit as per manufacturer’s recommendations.

value: siWIZ

tag: chip antibody


title: UNC0638_96hrs_input

description: input control


title: UNC0638_48hrs_input

description: input control


title: siWIZ_H3K9me2_ChIP_Rep1

description: ChIP-seq


title: NS_input

description: input control

value: NS


title: DMSO_48hrs_input

description: input control

value: DMSO


title: siWIZ_G9a_ChIP_Rep2

description: ChIP-seq


title: siWIZ_G9a_ChIP_Rep1

description: ChIP-seq


title: NS_G9a_ChIP_Rep2

description: ChIP-seq


title: siWIZ_H3K9me2_ChIP_Rep2

description: ChIP-seq


title: NS_H3K9me2_ChIP_Rep2

description: ChIP-seq


title: NS_G9a_ChIP_Rep1

description: ChIP-seq


title: NS_H3K9me2_ChIP_Rep1

description: ChIP-seq


title: UNC0638_H3K9me2_48hrs_ChIP_Rep2

description: ChIP-seq


title: UNC0638_H3K9me2_96hrs_ChIP_Rep2

description: ChIP-seq


title: DMSO_96hrs_input

description: input control


title: UNC0638_G9a_96hrs_ChIP_Rep2

description: ChIP-seq


title: UNC0638_G9a_48hrs_ChIP_Rep1

description: ChIP-seq


title: UNC0638_G9a_96hrs_ChIP_Rep1

description: ChIP-seq


title: DMSO_H3K9me2_48hrs_ChIP_Rep1

description: ChIP-seq


title: UNC0638_H3K9me2_48hrs_ChIP_Rep1

description: ChIP-seq


title: DMSO_H3K9me2_96hrs_ChIP_Rep1

description: ChIP-seq


title: UNC0638_H3K9me2_96hrs_ChIP_Rep1

description: ChIP-seq


title: UNC0638_G9a_48hrs_ChIP_Rep2

description: ChIP-seq


title: DMSO_H3K9me2_48hrs_ChIP_Rep2

description: ChIP-seq


title: DMSO_H3K9me2_96hrs_ChIP_Rep2

description: ChIP-seq


title: DMSO_G9a_96hrs_ChIP_Rep2

description: ChIP-seq


title: DMSO_G9a_96hrs_ChIP_Rep1

description: ChIP-seq


title: DMSO_G9a_48hrs_ChIP_Rep1

description: ChIP-seq


title: DMSO_G9a_48hrs_ChIP_Rep2

description: ChIP-seq


title: 14H038

status: Public on Jul 09 2015

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description: Sample 263

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for sequencing adapters and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: acute myeloid leukemia

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Stranded Sample Preparation (Illumina)

tag: tissue

value: Bone marrow

value: acute myeloid leukemia (AML) cells


title: 14H017

description: Sample 257

value: Heparinised blood


title: 13H158

description: Sample 247


title: 13H169

description: Sample 249


title: 13H179

description: Sample 250

value: EDTA Blood


title: 13H186

description: Sample 252


title: 13H159

description: Sample 248


title: 14H027

description: Sample 261


title: 14H019

description: Sample 258


title: 14H031

description: Sample 262


title: 14H012

description: Sample 255


title: 14H007

description: Sample 254


title: 14H015

description: Sample 256


title: 14H001

description: Sample 253


title: 13H185

description: Sample 251


title: 13H104

description: Sample 239


title: 13H150

description: Sample 246


title: 13H120

description: Sample 243


title: 13H110

description: Sample 241


title: 13H107

description: Sample 240


title: 13H139

description: Sample 244


title: 13H080

description: Sample 235


title: 13H114

description: Sample 242


title: 13H078

description: Sample 234


title: 13H101

description: Sample 238


title: 13H100

description: Sample 237


title: 13H073

description: Sample 233


title: 13H141

description: Sample 245


title: 13H083

description: Sample 236


title: 12H172

description: Sample 218


title: 13H065

description: Sample 232


title: 13H053

description: Sample 230


title: 13H019

description: Sample 226


title: 13H018

description: Sample 225


title: 12H176

description: Sample 221


title: 13H056

description: Sample 231


title: 12H151

description: Sample 215


title: 12H171

description: Sample 217


title: 12H116

description: Sample 209


title: 13H048

description: Sample 229


title: 13H006

description: Sample 223


title: 13H039

description: Sample 227


title: 12H195

description: Sample 222


title: 13H046

description: Sample 228


title: 13H009

description: Sample 224


title: 12H170

description: Sample 216


title: 12H138

description: Sample 212


title: 12H139

description: Sample 213


title: 12H175

description: Sample 220

value: Leukapheresis


title: 12H117

description: Sample 210


title: 12H106

description: Sample 208


title: 12H079

description: Sample 205


title: 12H067

description: Sample 204


title: 12H058

description: Sample 203


title: 12H149

description: Sample 214


title: 12H173

description: Sample 219


title: 12H055

description: Sample 201


title: 12H056

description: Sample 202


title: 12H124

description: Sample 211


title: 11H240

description: Sample 194


title: 12H007

description: Sample 195


title: 12H096

description: Sample 207


title: 11H231

description: Sample 191


title: 12H012

description: Sample 197


title: 11H186

description: Sample 187


title: 11H192

description: Sample 189


title: 11H177

description: Sample 185


title: 11H232

description: Sample 192


title: 12H091

description: Sample 206


title: 12H021

description: Sample 198


title: 12H033

description: Sample 199


title: 11H145

description: Sample 182


title: 11H157

description: Sample 183


title: 11H234

description: Sample 193


title: 11H138

description: Sample 180


title: 11H135

description: Sample 179


title: 12H010

description: Sample 196


title: 11H127

description: Sample 177


title: 11H140

description: Sample 181


title: 11H217

description: Sample 190


title: 11H187

description: Sample 188


title: 11H132

description: Sample 178


title: 12H039

description: Sample 200


title: 11H103

description: Sample 176


title: 11H183

description: Sample 186


title: 11H097

description: Sample 175


title: 11H017

description: Sample 171


title: 11H175

description: Sample 184


title: 11H010

description: Sample 169


title: 11H002

description: Sample 168


title: 10H149

description: Sample 165


title: 10H087

description: Sample 161


title: 10H078

description: Sample 160


title: 10H130

description: Sample 163


title: 10H136

description: Sample 164


title: 10H106

description: Sample 162


title: 11H035

description: Sample 173


title: 10H174

description: Sample 167


title: 10H051

description: Sample 156


title: 11H027

description: Sample 172


title: 10H066

description: Sample 158


title: 10H053

description: Sample 157


title: 10H034

description: Sample 153


title: 10H048

description: Sample 155


title: 11H014

description: Sample 170


title: 10H029

description: Sample 152


title: 10H040

description: Sample 154


title: 11H044

description: Sample 174


title: 10H007

description: Sample 148


title: 10H015

description: Sample 150


title: 10H005

description: Sample 147


title: 10H070

description: Sample 159


title: 10H173

description: Sample 166


title: 10H014

description: Sample 149


title: 10H001

description: Sample 146


title: 10H026

description: Sample 151


title: 09H090

description: Sample 140


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description: Sample 143


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description: Sample 139


title: 09H062

description: Sample 132


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description: Sample 137


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description: Sample 131


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description: Sample 130


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description: Sample 144


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description: Sample 145


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description: Sample 135


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description: Sample 138


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description: Sample 136


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description: Sample 142


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description: Sample 133


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description: Sample 127


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description: Sample 129


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description: Sample 128


title: 09H002

description: Sample 118


title: 08H137

description: Sample 116


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description: Sample 112


title: 08H082

description: Sample 109


title: 08H087

description: Sample 110


title: 09H042

description: Sample 126


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description: Sample 125


title: 09H024

description: Sample 124


title: 08H062

description: Sample 106


title: 09H013

description: Sample 121


title: 09H092

description: Sample 141


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description: Sample 122


title: 09H008

description: Sample 120


title: 08H113

description: Sample 115


title: 09H078

description: Sample 134


title: 09H005

description: Sample 119


title: 08H033

description: Sample 99


title: 08H104

description: Sample 113


title: 08H022

description: Sample 98


title: 08H088

description: Sample 111


title: 08H138

description: Sample 117


title: 08H018

description: Sample 97


title: 08H108

description: Sample 114


title: 08H004

description: Sample 95


title: 08H065

description: Sample 108


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description: Sample 96


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description: Sample 93


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description: Sample 103


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description: Sample 104


title: 07H155

description: Sample 92


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description: Sample 102


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description: Sample 101


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description: Sample 100


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description: Sample 90


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description: Sample 88


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description: Sample 91


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description: Sample 89


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description: Sample 86


title: 07H117

description: Sample 83


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description: Sample 94


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description: Sample 85


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description: Sample 84


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description: Sample 78


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description: Sample 79


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description: Sample 82


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description: Sample 81


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description: Sample 77


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description: Sample 67


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description: Sample 70


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description: Sample 65


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description: Sample 72


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description: Sample 69


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description: Sample 66


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description: Sample 71


title: 07H106

description: Sample 80


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description: Sample 61


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description: Sample 60


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description: Sample 59


title: 07H055

description: Sample 73


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description: Sample 62


title: 07H019

description: Sample 68


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description: Sample 75


title: 06H038

description: Sample 57


title: 06H026

description: Sample 55


title: 06H048

description: Sample 58


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description: Sample 63


title: 06H099

description: Sample 64


title: 06H029

description: Sample 56


title: 04H138

description: Sample 38


title: 05H099

description: Sample 47


title: 05H031

description: Sample 40


title: 05H180

description: Sample 48


title: 05H072

description: Sample 44


title: 05H090

description: Sample 45


title: 06H014

description: Sample 51


title: 05H193

description: Sample 49


title: 06H016

description: Sample 52


title: 05H097

description: Sample 46


title: 06H019

description: Sample 53


title: 04H123

description: Sample 34


title: 05H054

description: Sample 42


title: 04H120

description: Sample 33


title: 05H013

description: Sample 39


title: 04H132

description: Sample 36


title: 05H034

description: Sample 41


title: 06H021

description: Sample 54


title: 04H135

description: Sample 37


title: 04H118

description: Sample 32


title: 05H065

description: Sample 43


title: 04H117

description: Sample 31


title: 06H004

description: Sample 50


title: 04H111

description: Sample 29


title: 04H115

description: Sample 30


title: 04H103

description: Sample 28


title: 04H101

description: Sample 27


title: 04H096

description: Sample 26


title: 04H127

description: Sample 35


title: 03H024

description: Sample 9


title: 03H090

description: Sample 16


title: 04H054

description: Sample 23


title: 04H001

description: Sample 18


title: 02H033

description: Sample 5


title: 04H048

description: Sample 22


title: 03H022

description: Sample 8


title: 04H017

description: Sample 20


title: 02H046

description: Sample 7


title: 04H006

description: Sample 19


title: 03H081

description: Sample 15


title: 04H068

description: Sample 25


title: 03H028

description: Sample 10


title: 04H055

description: Sample 24


title: 03H070

description: Sample 14


title: 03H030

description: Sample 11


title: 04H039

description: Sample 21


title: 02H003

description: Sample 2


title: 02H026

description: Sample 4


title: 01H002

description: Sample 1


title: 03H060

description: Sample 13


title: 02H025

description: Sample 3


title: 09H022

description: Sample 123


title: 03H094

description: Sample 17


title: 07H009

description: Sample 22

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Sample Preparation (Illumina)


title: 07H005

description: Sample 21


title: 06H133

description: Sample 19


title: 06H146

description: Sample 20


title: 03H036

description: Sample 12


title: 02H043

description: Sample 6


title: 06H010

description: Sample 17


title: 06H011

description: Sample 18


title: 05H022

description: Sample 10


title: 05H008

description: Sample 9


title: 03H052

description: Sample 4


title: 03H016

description: Sample 2


title: 03H033

description: Sample 3


title: 04H140

description: Sample 8


title: 05H195

description: Sample 16


title: 05H078

description: Sample 12


title: 04H108

description: Sample 7


title: 05H030

description: Sample 11


title: 05H143

description: Sample 14


title: 04H078

description: Sample 6


title: 04H025

description: Sample 5


title: 02H009

description: Sample 1


title: 05H111

description: Sample 13


title: 05H186

description: Sample 15


title: 10H119

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2 on RefSeq annotation, dated 2014-04-16.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

value: acute myeloid leukemia


title: 07H137


title: 09H040


title: 12H183


title: 12H180


title: 12H166


title: 08H034


title: 08H042


title: 08H072


title: 11H107


title: 12H045


title: 12H098


title: 06H035


title: 13H058


title: 13H140


title: 05H118


title: 05H184


title: 03H065


title: 03H083


title: 11H179


title: 05H042


title: 13H066


title: 06H020


title: 10H008


title: 10H030


title: 08H099


title: 05H113


title: 05H136


title: 06H115


title: 11H205


title: 12H148


title: 03H095


title: 05H179


title: 04H030


title: 10H063


title: 07H038


title: 12H165


title: 10H046


title: 11H022


title: 04H063


title: 09H016


title: 04H050


title: 10H107


title: 11H104


title: 09H066


title: 04H061


title: 04H091


title: 06H151


title: 03H109


title: 07H144


title: 08H081


title: 03H112


title: 10H055


title: 12H044


title: 10H127


title: 04H080


title: 10H058


title: 12H042


title: 09H032


title: 09H098


title: 07H003


title: 07H041


title: 07H045


title: 06H117


title: 06H066


title: 08H139


title: 08H021


title: 05H066


title: 05H128


title: 04H041


title: 10H022


title: 03H067


title: 04H121


title: 08H129


title: 02H032


title: 01H001


title: 05H025


title: 12H057


title: 08H085


title: 06H152


title: 09H010


title: E2f3_3bmut_replicate3

status: Public on Jun 01 2015

type: genomic

description: ChIP-on-Chip

hyb_protocol: 12.5 ug of Cy5-labeled IP DNA (specific activity >20 pmol Cy5/ug DNA) and 12.5 ug of Cy3-labeled Input DNA (specific activity >25 pmol Cy3/ug DNA) were hybridized at 65°C for 40 hours with Agilent Oligo aCGH Hybridization Kit following the manufacturer's instructions. After hybridization, microarrays were washed: 1) 5 minutes at room temperature with OLIGO CGH WASH BUFFER1 (Agilent), 2) 5 minutes at 31°C with OLIGO CGH WASH BUFFER2 (Agilent), 3) 10 seconds at room temperature with Acetonitrile, and 4) 30 seconds at room temperature with Stabilization and Drying Solution. Microarrays were air-dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 1M array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Red. Green and Red PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters (protocol ChIP_105_Jan09). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
gMedian and rMedian values were combined together and imported into the CisGenome program for further processing. Numerical values were normalized using the quantiles method (quantile normalized intensities are included in the linked *Processed.txt files). Bound regions were called using the TileMap function in CisGenome.

source_name: E2F3b Mutant, neural precursor cells, E2F3 IP, Replicate3

label_protocol: Cyanine-5 (Cy5) labeled IP DNA and Cyanine-3 (Cy3) labeled Input DNA were prepared from 2ug of DNA using the Genomic DNA Enzymatic Labeling Kit according to the manufacturer's instructions, followed by cleaning up with Microcon YM-30 Centrifugal Filter Unit  (CHEMICON). Dye incorporation and labeled DNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in neural stem cell growth medium (SCM): DMEM-F12 with 0.6% D-Glucose, 2mM L-Glutamine, 0.5% Penicillin / Streptomycin, 25ug/mL Insulin, 0.1mg/mL Apotransferrin, 20uM Progesterone, 10ug/mL Putrescine, 30nM Selenium, 12.5ng/mL Fungizone, 20ng/mL bFGF

extract_protocol: Agilent Mammalian ChIP-on-Chip protocol was followed. Anti-E2f3 and E2f4 antibodies were purified by affinity chromatography from rabbit sera (Santa Cruz) immunized with a peptide mapping to the C-terminus of either E2f3 or E2f4. After cross-linking with Formaldyhyde (Fisher), cells were harvested and sonicated to obtain chormatin fragments around 250bp. DNA quantity and quality were examined by the NanoDrop ND-1000. Taking 250ug of chromatin and 10ug of antibody, DNA bound by E2f3 or E2f4 were immunoprecipitated. The total genomic DNA (Input) and immunoprecipitated DNA (IP) were extracted by phenol/chloroform/isoamyl alcohol. Input and IP DNA were amplied by LM-PCR.

treatment_protocol: no treatment protocol was used

value: E2f3b deficient

tag: assayed molecule

value: DNA bound by E2F3

source_name: E2F3b Mutant, neural precursor cells, E2F3 Input, Replicate3

value: Total DNA


title: E2f3_3amut_replicate3

description: ChIP-on-Chip

source_name: E2F3a Mutant, neural precursor cells, E2F3 IP, Replicate3

value: E2f3a deficient

source_name: E2F3a Mutant, neural precursor cells, E2F3 Input, Replicate3


title: E2f3_3bmut_replicate2

description: ChIP-on-Chip

source_name: E2F3b Mutant, neural precursor cells, E2F3 IP, Replicate2

source_name: E2F3b Mutant, neural precursor cells, E2F3 Input, Replicate2


title: E2f3_3bmut_replicate1

description: ChIP-on-Chip

source_name: E2F3b Mutant, neural precursor cells, E2F3 IP, Replicate1

source_name: E2F3b Mutant, neural precursor cells, E2F3 Input, Replicate1


title: E2f3_3amut_replicate2

description: ChIP-on-Chip

source_name: E2F3a Mutant, neural precursor cells, E2F3 IP, Replicate2

source_name: E2F3a Mutant, neural precursor cells, E2F3 Input, Replicate2


title: 02H017


title: E2f3_3amut_replicate1

description: ChIP-on-Chip

source_name: E2F3a Mutant, neural precursor cells, E2F3 IP, Replicate1

source_name: E2F3a Mutant, neural precursor cells, E2F3 Input, Replicate1


title: E2f3_wt_replicate2

description: ChIP-on-Chip

source_name: WT, neural precursor cells, E2F3 IP, Replicate2

value: wild-type

source_name: WT, neural precursor cells, E2F3 Input, Replicate2


title: E2f4_wt_replicate2

description: ChIP-on-Chip

source_name: WT, neural precursor cells, E2F4 IP, Replicate2

value: DNA bound by E2F4

source_name: WT, neural precursor cells, E2F4 Input, Replicate2


title: E2f4_wt_replicate3

description: ChIP-on-Chip

source_name: WT, neural precursor cells, E2F4 IP, Replicate3

source_name: WT, neural precursor cells, E2F4 Input, Replicate3


title: E2f3_wt_replicate1

description: ChIP-on-Chip

source_name: WT, neural precursor cells, E2F3 IP, Replicate1

source_name: WT, neural precursor cells, E2F3 Input, Replicate1


title: E2f3_wt_replicate3

description: ChIP-on-Chip

source_name: WT, neural precursor cells, E2F3 IP, Replicate3

source_name: WT, neural precursor cells, E2F3 Input, Replicate3


title: E2f4_wt_replicate1

description: ChIP-on-Chip

source_name: WT, neural precursor cells, E2F4 IP, Replicate1

source_name: WT, neural precursor cells, E2F4 Input, Replicate1


title: 11H129

status: Public on Feb 05 2014

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: acute myeloid leukemia


title: 11H019


title: 11H170


title: 10H161


title: 12H030


title: 11H151


title: 10H113


title: 10H109


title: 09H046


title: 10H031


title: 09H054


title: 09H031


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Colorie Restricted-Rep4

status: Public on Aug 01 2014

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100 ul of the mixture was hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: tibialis anterior

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the Quick Amp Labeling Kit, one-color kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were assayed with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated with the Trizol Reagent (Invitrogen) and DNAseI treated with the Absolutely RNA Mini-Prep Kit (Stratagene) following the manufacturer's protocol. RNA quantity and quality was assessed with the NanoDrop ND-1000. Integrity of the RNA was determined by agarose gel electrophoresis.

value: Control

value: Colorie Restricted


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Ad Lib-Rep4

value: Undernourished

value: Ad Lib


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Ad Lib-Rep1


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Colorie Restricted-Rep1


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Ad Lib-Rep4


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Colorie Restricted-Rep2


title: 11H008


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Ad Lib-Rep3


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Colorie Restricted-Rep4


title: 09H018


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Colorie Restricted-Rep3


title: 08H012


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Colorie Restricted-Rep2


title: 08H112


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Ad Lib-Rep2


title: 08H118


title: tibialis anterior-MotherDiet_Undernourished-OffspringDiet_Colorie Restricted-Rep1


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Ad Lib-Rep3


title: 07H069


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Ad Lib-Rep1


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Colorie Restricted-Rep3


title: 05H094


title: 06H045


title: 06H135


title: 02H060


title: 11H160

status: Public on Nov 06 2013

data_processing:
Basecalls performed using CASAVA 1.8
Sequenced reads were mapped to the reference genome using CASAVA 1.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

value: blood


title: 11H126

value: bone marrow


title: 11H095


title: 11H083


title: 08H048


title: 11H058


title: 11H072


title: 11H046


title: 07H042


title: 11H021


title: 10H095


title: 11H009


title: 10H101


title: 11H006


title: 10H166


title: 10H072


title: 10H092


title: 10H068


title: 11H142


title: 10H056


title: 10H052


title: tibialis anterior-MotherDiet_Control-OffspringDiet_Ad Lib-Rep2


title: 09H111


title: 06H028


title: 07H135


title: 07H062


title: 09H083


title: 05H181


title: 07H160


title: 10H115


title: 10H089


title: 05H149


title: 03H116


title: 04H112


title: 03H041


title: 05H050


title: 04H133


title: 05H163


title: 04H024


title: 03H119


title: 07H099


title: BCBL1

status: Public on Sep 05 2013

description: BCBL1 PEL Cell Line

data_processing:
Library strategy: FAIRE-seq
CASAVA v1.8.2 for BC1, KSHV-BJAB, KSHV-HUVEC, L1-TIVE.  CASAVA v1.7 for BCBL1 samples
Reads were filtered using TagDust
Reads were aligned to NC_009333 using Bowtie.  Reads were permitted to align to up to four locations in the genome, but the single best possible alignment was chosen.
Regions with significantly enriched FAIRE signal were differentiated from background using MACS2 assuming the average fragment length was 250bp.
Genome_build: NC_009333.1
Supplementary_files_format_and_content: BED formatted file containing peak locations on NC_009333.1 and the -log10 q-value.

organism: Human gammaherpesvirus 8

source_name: BCBL1 PEL Cell Line

growth_protocol: Latent KSHV-infected lymphoma cell lines (BC1, BCBL1, and KSHV-BJAB) were cultured in RPMI 1640 supplemented with 100 ug/mL streptomycin sulfate, 100 U/mL penicillin G (Life Technologies), 2mM L-glutamine, 0.05mM 2-mercaptoethanol, 0.075% sodium bicarbonate, 1 U/mL IL-6 (PeproTech Inc), and 10% FBS and were maintained at 37°C in 5% CO2. KSHV-BJAB cells were also maintained under 0.2-mg/mL hygromycin selection. Latent KSHV-infected endothelial L1-TIVE cells were grown in Dulbecco modified Eagle medium (DMEM) supplemented with 100 ug/mL streptomycin sulfate and 100 U/mL penicillin G and 5% FBS. Latently infected KSHV-human umbilical vein endothelial cells (HUVEC) were cultured in endothelial growth medium (EGM-2; Clonetics) supplemented with 0.5 ug/mL puromycin.

extract_protocol:
Cells were lysed, and then sonicated to shear DNA to an average fragment length of 200 to 400 bp. Sheared DNA was then collected by phenol-chloroform extraction.
FAIRE-enriched DNA was then prepared for sequencing using the Illumina Truseq DNA Sample Preparation Kit V2 (Illumina) per the manufacturer’s instructions or was prepared by the UNC High-Throughput Sequencing Facility (BCBL1 and non-cross-linked BCBL1 control)

treatment_protocol: ~1.0e7 cells were cross-linked with formaldehyde (final concentration 1%) for 5 minutes and quenched for 5 minutes with 125mM Glycine

tag: host

value: Human B-Cells

tag: sequenced molecule

value: Viral and Human Genomic DNA


title: L1-TIVE

description: Long-term KSHV-infected Telomerase-Immortalized Endothelial Cell Line

value: Human Endothelial Cells


title: 02H053


title: KSHV-HUVEC

description: KSHV-Infected HUVEC Cell Line

source_name: KSHV-Infected HUVEC Cell Line

value: KSHV-HUVEC


title: 02H066


title: 09H043


title: 06H144


title: BC1

description: BC1 PEL Cell Line

source_name: BC1 PEL Cell Line


title: KSHV-BJAB

description: KSHV-Infected BJAB Cell Line

source_name: KSHV-Infected BJAB Cell Line

value: KSHV-BJAB


title: EWS502_H3K4me3_ChIP

status: Public on Nov 09 2011

description: Chromatin IP against H3K4me3

data_processing: Reads from chromatin immunoprecipitations were aligned to the reference human genome (hg18) with Bowtie using default parameters, and unambiguously placed reads were retained. Biological replicates were then merged and reads were extended in silico to a final length of 200 bp.  Any extended reads that overlapped large-scale repetitive elements were then removed. Reads from FAIRE were allowed to potentially map to up to four genomic locations, but the best scoring alignment was chosen. Biological replicates were then merged and reads were extended in silico to a final length of 134 bp.  Any extended reads that overlapped large-scale repetitive elements were then removed.

source_name: Ewing Sarcoma cells

growth_protocol: EWS502 were cultured in RPMI 1640 supplemented with 15% FBS, HUVEC cells were cultured in Vasculife Basal Media (Lifeline Technologies) supplemented with 10% FBS.  Both cell lines were maintained at standard growth conditions of 37o and 5% CO2

extract_protocol: For chromatin immunoprecipitation, chromatin was isolated and immunoprecipitation was performed as described (Davis et al. 2006) using 2 ug of anti-HA antibody (Abcam ab9110), anti-H3K4me1 (Abcam ab8895), anti-H3K4me2 (Abcam ab32356), anti-H3K4me3 (Abcam ab12209), or anti-H3K27me3 (Millipore 07-449). FAIRE was performed on three independent cell harvests as previously described (Giresi et al. 2007). All libraries were prepared as per Illumina's recommendations, including two rounds of purification with Agencourt AMPure XP beads.

treatment_protocol: A short hairpin region complementary to the 3' untranslated region of FLI1 together with PCR-generated HA-EWS-FLI and HA-FLI1 were cloned into pLL5.5 (Rubinson et al. 2003). Lentivirus was produced in HEK293T cells as described (Rubinson et al. 2003). EWS502 or HUVEC cells were infected with lentivirus in the presence of polybrene (6 µg/mL) for 3 h after which media was changed. Chromatin or RNA was isolated at 72 h.


title: HUVEC_FLI1_input

description: input DNA

source_name: Primary endothelial cells

value: HUVEC


title: EWS502_H3K4me1_ChIP

description: Chromatin IP against H3K4me1


title: HUVEC_FLI1_ChIP

description: Chromatin IP against HA-FLI1

value: HA


title: EWS502_H3K4me2_ChIP

description: Chromatin IP against H3K4me2


title: EWS502_H3K27me3_input

description: input DNA


title: EWS502_H3K27me3_ChIP

description: Chromatin IP against H3K27me3


title: EWS502_FAIRE

description: Formaldehyde-Assisted Isolation of Regulatory Elements


title: EWS502_knockdown_Rep3

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA-normalized, log-transformed exon-level estimates of expression were calculated using Partek. Expression values were then determined at the gene level. Differentially expressed genes were determined by an ANOVA (Partek Genomics Suite, p < 0.05) comparing gene expression under conditions of EWS-FLI or FLI1 knockdown only to knockdown with ectopic transcription factor expression
probe group file: HuEx_1_0-st-v2.r2.pgf
meta-probeset file: HuEx_1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

source_name: Ewing Sarcoma cells, EWS-FLI knockdown only

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: EWS502 were cultured in RPMI 1640 supplemented with 15% FBS, HUVEC cells were cultured in Vasculife Basal Media (Lifeline Technologies) supplemented with 10% FBS.  Both cell lines were maintained at standard growth conditions of 37C and 5% CO2

extract_protocol: RNeasy (QIAGEN)

treatment_protocol: A short hairpin region complementary to the 3’ untranslated region of FLI1 together with PCR-generated HA-EWS-FLI and HA-FLI1 were cloned into pLL5.5 (Rubinson et al. 2003). Lentivirus was produced in HEK293T cells as described (Rubinson et al. 2003). EWS502 or HUVEC cells were infected with lentivirus in the presence of polybrene (6 µg/mL) for 3 h after which media was changed. Chromatin or RNA was isolated at 72 h (see below).


title: EWS502_FLI1_Rep2

source_name: Ewing Sarcoma cells, EWS-FLI knockdown + HA-FLI1 expression


title: EWS502_knockdown_Rep2


title: HUVEC_EWS-FLI_Rep2

source_name: Primary Endothelial cells, FLI1 knockdown + HA-EWS-FLI expression


title: HUVEC_FLI1_Rep3

source_name: Primary Endothelial cells, FLI1 knockdown + HA-FLI1 expression


title: EWS502_FLI1_Rep1


title: HUVEC_EWS-FLI_Rep3


title: HUVEC_FLI1_Rep1


title: HUVEC_knockdown_Rep2

source_name: Primary Endothelial cells, FLI1 knockdown only


title: HUVEC_EWS-FLI_Rep1


title: EWS502_EWS-FLI_Rep1

source_name: Ewing Sarcoma cells, EWS-FLI knockdown + HA-EWS-FLI expression


title: HUVEC_FLI1_Rep2


title: HUVEC_knockdown_Rep1


title: EWS502_EWS-FLI_Rep2


title: HUVEC_EWS-FLI_input

description: input DNA


title: EWS502_EWS-FLI_Rep3


title: EWS502_FLI1_ChIP

description: Chromatin IP against HA-FLI1


title: EWS502_FLI1_Rep3


title: EWS502_FLI1_input

description: input DNA


title: HUVEC_EWS-FLI_ChIP

description: Chromatin IP against HA-EWS-FLI


title: EWS502_EWS-FLI_ChIP

description: Chromatin IP against HA-EWS-FLI


title: 06H088

value: Bone marrow

value: acute myeloid leukemia


title: EWS502_knockdown_Rep1


title: 10H038

value: Heparinised blood


title: HUVEC_knockdown_Rep3


title: EWS502_EWS-FLI_input

description: input DNA


title: 09H115


title: 09H113


title: C2C12_Time_course_Myotube_Rep3

status: Public on Jul 05 2010

description: Gene Expression profiling of C2C12 at the myotube stage (96h after start of differentiation).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

Raw data were processed using GeneSpring GX (Agilent). Using the gMedian signal transformed to log base 2, the probes were normalized within the sample to the 75th percentile and the samples were then normalized by baseline transformation through the median of each sample.

source_name: C2C12, Myotube

growth_protocol: Cells were grown in growth medium (GM) DMEM High Glucose (Hyclone); 10% Characterized Fetal Bovine Serum (Hyclone); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone).

extract_protocol: Total RNA was isolated with the Absolutely RNA Mini-Prep Kit (Stratagene) following the manufacturer's protocol. RNA quantity and quality was assessed with the NanoDrop ND-1000. Integrity of the RNA was determined by agarose gel.

treatment_protocol: To induce differentiation, cells were grown in differentiation medium (DM) DMEM High Glucose (Hyclone); 2% Horse Serum (Invitrogen); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone).

tag: differentiation timepoint

value: Myotube


title: C2C12_Time_course_Myotube_Rep2


title: C2C12_Time_course_Myotube_Rep1


title: Six1_ChIP-on-Chip_T24_Rep3  (Agilent 022329)

description: ChIP-on-Chip

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters (protocol ChIP_105_Jan09). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data were acquired from three microarrays (Arrays A, B and C) composing the set. gMedian and rMedian values of each microarray were combined together and imported into the CisGenome program for further processing. Numerical values were log-transformed (base 2) and were normalized using the quantiles method. Bound regions were called using the TileMap function in CisGenome.

source_name: C2C12, T24, IP, Replicate3

extract_protocol: Agilent Mammalian ChIP-on-Chip protocol was followed. Anti-Six1 antibody was purified by affinity chromatography from rabbit sera (Open Biosystems) immunized with full-length Six1 recombinant protein. Normal rabbit IgG (Pierce Chemicals) was used as a negative control antibody. After cross-linking with Formaldyhyde (Fisher), cells were harvested and sonicated to get chormatin fragments around 500bp. DNA quantity and quality were examined by the NanoDrop ND-1000. Taking 250ug of chromatin and10ug of antibody, DNA and Six1 were immunoprecipitated. The total genomic DNA (Input) and immunoprecipitated DNA (IP) were extracted by phenol/chloroform/isoamyl alcohol. Input and IP DNA was amplied by LM-PCR.

treatment_protocol: To induce differentiation, cells were grown in differentiation medium (DM) DMEM High Glucose (Hyclone); 2% Horse Serum (Invitrogen); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone)

tag: time point

source_name: C2C12, T24, Input, Replicate3


title: C2C12_Time_course_T24_Rep2

description: Gene Expression profiling of C2C12 24h after start of differentiation.


title: Six1_ChIP-on-Chip_Myoblast_Rep2 (Agilent 022332)

description: ChIP-on-Chip

source_name: C2C12, Myoblast, IP, Replicate2

value: Myoblast

source_name: C2C12, Myoblast, Input, Replicate2


title: Six1_ChIP-on-Chip_T24_Rep1 (Agilent 022332)

description: ChIP-on-Chip

source_name: C2C12, T24, IP, Replicate1

source_name: C2C12, T24, Input, Replicate1


title: C2C12_Time_course_T24_Rep1


title: Six1_ChIP-on-Chip_T24_Rep3 (Agilent 022332)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_Myotube_R1 (Agilent 022332)

description: ChIP-on-Chip

source_name: C2C12, Myotube, IP, Replicate1

source_name: C2C12, Myotube, Input, Replicate1


title: Six1_ChIP-on-Chip_Myotube_Rep2  (Agilent 022329)

description: ChIP-on-Chip

source_name: C2C12, Myotube, IP, Replicate2

source_name: C2C12, Myotube, Input, Replicate2


title: Six1_ChIP-on-Chip_Myoblast_Rep1 (Agilent 022332)

description: ChIP-on-Chip

source_name: C2C12, Myoblast, IP, Replicate1

source_name: C2C12, Myoblast, Input, Replicate1


title: Six1_ChIP-on-Chip_Myotube_Rep3  (Agilent 022329)

description: ChIP-on-Chip

source_name: C2C12, Myotube, IP, Replicate3

source_name: C2C12, Myotube, Input, Replicate3


title: Six1_ChIP-on-Chip_Myoblast_Rep3  (Agilent 022329)

description: ChIP-on-Chip

source_name: C2C12, Myoblast, IP, Replicate3

source_name: C2C12, Myoblast, Input, Replicate3


title: Six1_ChIP-on-Chip_Myotube_R3 (Agilent 022328)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_T24_Rep2 (Agilent 022332)

description: ChIP-on-Chip

source_name: C2C12, T24, IP, Replicate2

source_name: C2C12, T24, Input, Replicate2


title: Six1_ChIP-on-Chip_Myoblast_Rep1 (Agilent 022328)

description: ChIP-on-Chip


title: C2C12_Time_course_T24_Rep3


title: C2C12_Time_course_T0_Rep3

description: Gene Expression profiling of C2C12 at the start of differentiation (T0).


title: C2C12_Time_course_T0_Rep1


title: Six1_ChIP-on-Chip_Myoblast_Rep3 (Agilent 022332)

description: ChIP-on-Chip


title: C2C12_Time_course_T0_Rep2


title: Six1_ChIP-on-Chip_Myotube_R2 (Agilent 022328)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_Myoblast_Rep2 (Agilent 022328)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_Myotube_R3 (Agilent 022332)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_Myoblast_Rep2  (Agilent 022329)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_Myotube_R2 (Agilent 022332)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_T24_Rep1 (Agilent 022328)

description: ChIP-on-Chip


title: C2C12_Time_course_Myoblast_Rep3

description: Gene Expression profiling of C2C12 at the myoblast stage before differentiation.

source_name: C2C12, Myoblast


title: Six1_ChIP-on-Chip_T24_Rep2 (Agilent 022328)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_T24_Rep3 (Agilent 022328)

description: ChIP-on-Chip

source_name: C2C12, T24, IP, Replicate3

source_name: C2C12, T24, Input, Replicate3


title: Six1_ChIP-on-Chip_T24_Rep1  (Agilent 022329)

description: ChIP-on-Chip

source_name: C2C12, T24, IP, Replicate1


title: Six1_ChIP-on-Chip_Myoblast_Rep3 (Agilent 022328)

description: ChIP-on-Chip


title: Six1_ChIP-on-Chip_T24_Rep2  (Agilent 022329)

description: ChIP-on-Chip


title: C2C12_siRNA_Myogenin_R4

description: Gene Expression profiling of C2C12 24h after start of differentiation when cells were transfected with an siRNA sequence against Myogenin.

source_name: C2C12, siRNA Myogenin

growth_protocol: Cells were grown in growth medium (GM) DMEM High Glucose (Hyclone); 10% Characterized Fetal Bovine Serum (Hyclone); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone). At the start of differentiation, the cells were grown in differentiation medium (DM) DMEM High Glucose (Hyclone); 2% Horse Serum (Invitrogen); 1% L-Glutamine (Hyclone); 1% Penicillin / Streptomycin (Hyclone).

treatment_protocol: The cells were transfected, 24h before the start of differentiation, with 100 pmol of siRNA (Dharmacon) using the Lipofectamine2000 (Invitrogen) using the manufacturer's protocol.

tag: cell type

value: myoblasts

tag: sirna treatment

value: siMyogenin


title: C2C12_Time_course_Myoblast_Rep2


title: C2C12_Time_course_Myoblast_Rep1


title: C2C12_siRNA_Myogenin_R3


title: C2C12_siRNA_Myogenin_R2


title: Six1_ChIP-on-Chip_Myotube_Rep1  (Agilent 022329)

description: ChIP-on-Chip

source_name: C2C12, Myotube, IP, Replicate1


title: Six1_ChIP-on-Chip_Myotube_R1 (Agilent 022328)

description: ChIP-on-Chip

source_name: C2C12, Myotube, Input, Replicate1


title: C2C12_siRNA_Six1&4_R4

description: Gene Expression profiling of C2C12 24h after start of differentiation when cells were transfected with an siRNA sequence individually targeting Six1 and Six4.

source_name: C2C12, siRNA Six1&4


title: Six1_ChIP-on-Chip_Myoblast_Rep1 (Agilent 022329)

description: ChIP-on-Chip


title: C2C12_siRNA_Six1&4_R3


title: C2C12_siRNA_Six1&4_R1


title: C2C12_siRNA_Six4_R4

description: Gene Expression profiling of C2C12 24h after start of differentiation when cells were transfected with an siRNA sequence against Six4.

source_name: C2C12, siRNA Six4


title: C2C12_siRNA_Myogenin_R1


title: C2C12_siRNA_Six1&4_R2


title: C2C12_siRNA_Six4_R2


title: C2C12_siRNA_Six4_R3


title: C2C12_siRNA_Six1_R3

description: Gene Expression profiling of C2C12 24h after start of differentiation when cells were transfected with an siRNA sequence against Six1.

source_name: C2C12, siRNA Six1


title: C2C12_siRNA_Six1_R4


title: C2C12_siRNA_Six4_R1


title: C2C12_siRNA_Control_R3

description: Gene Expression profiling of C2C12 24h after start of differentiation when cells were transfected with a control siRNA sequence.

source_name: C2C12, siRNA Control

value: Control


title: C2C12_siRNA_Control_R1


title: C2C12_siRNA_Six1_R2


title: C2C12_siRNA_Control_R4


title: C2C12_siRNA_Control_R2


title: C2C12_siRNA_Six1_R1