title: H3K4me3 control Mouse Macrophages ChIPseq

status: Public on Dec 21 2012

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: Chromatin IP against H3K4me3

data_processing:
ChIPseq: Reads (32 bp) were aligned to the Human (Homo Sapiens) reference genome (hg18, NCBI Build 36) and Mouse (mm9). Bed and wiggle files were generated using the standard ELAND pipeline.
RNAseq: RNA-seq: Total RNA was extracted from Monocytes with the RNeasy kit. DNase treatment was done for 15 min and the concentration was measured with a Qubit fluorometer (Invitrogen). 250 ng of total RNA was treated by Ribo-Zero rRNA Removal Kit (epicentre) to remove  ribosomal RNAs  according to manufacturer instructions. 16 µl of purified RNA was fragmented by addition of 4 µl 5x fragmentation buffer (200 mM Tris acetate pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and incubated at 94°C for exactly 90 seconds. After ethanol precipitation first strand cDNA was synthesized from the fragmented RNA with SuperscriptIII (Invitrogen) using random hexamers. First strand cDNA was purified by Qiagen mini elute columns and second strand cDNA was prepared in the presence of dUTP instead of dTTP.  Double stranded cDNA was purified by Qiagen mini elute columns and used for Illumina sample prepping and sequencing according to the manufacturars instructions. RNA-seq reads were mapped to HG18 and used for bioinformatical analysis. RPKM (reads per kilobase of gene length per million reads) (Mortazavi  et al. 2008) values for RefSeq genes were computed using tag counting scripts and used to analyze gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: bed and wig files

source_name: Macrophages

extract_protocol: Collected tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA  was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.Approximately one microgram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Two libraries were constructed from genomic DNA isolated from seed coat. One library was spiked in ~ three nanogram of unmethylated lambda DNA as all other libraries; the other library was spiked in ~ three nanogram of methylated lambda DNA to serve as a control for over conversion (i.e. conversion of methylated cytosine to uracil) during the bisulfite conversion step. The methylated lambda DNA was generated by treating unmethylated lambda DNA with CpG Methyltransferase (New England BioLabs). Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: saline(control)

tag: cell type

value: macrophage

tag: antibody

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog #

tag: antibody lot #

tag: genetic background


title: rat_c_spleen

type: SRA

city: Cambridge

first: Jason

last: Merkin

email: jmerkin@mit.edu, jjmerkin@gmail.com

state: MA

address: 31 Ames St

department: Biology

country: USA

institute: MIT

description: Sample 53

library_source: transcriptomic

data_processing:
Base-calling: Illumina Real Time Analysis, scoring metric v1.5
Long-read (76-108bp libraries) were mapped with TopHat v1.1.4 with the following additional parameters: --no-novel-indels, -r [inner length], --segment-length 20, --solexa-1.3-quals, --coverage-search -g [species.gtf]
junctions from all long read (76-108bp libraries) were combined and all libraries were mapped by TopHat v1.1.4 with the following parameters: --no-novel-indels, -r [inner length], --segment-length 20, --solexa-1.3-quals, --coverage-search, -j [species_junction_file.bed] -g [species.gtf]
Cufflinks v1.0.2 was run on the long read libraries with the following parameters: --min-isoform-fraction 0.00, --pre-mrna-fraction 0.00, -g [species.gtf], --max-intron-length 100000, -u, -b [genome.fa], --library-type ff-firststrand
Transcripts from libraries within a species were combined with CuffCompare v1.0.2 with the following parameters: -r [species.gtf]
Cufflinks v1.0.2 was run on all libraries with the following parameters: --min-isoform-fraction 0.05, --pre-mrna-fraction 0.10, -G [combined_species.gtf from above], --max-intron-length 100000, -u, -b [genome.fa], --library-type ff-firststrand
Transcripts from libraries from each individual were combined with CuffCompare v1.0.2 with the following parameters: -r [combined_species.gtf]
Genome_build: mouse: mm9, rat: rn4, cow: bt4, chicken: gg3, rhesus: rhemac2, human: hg19
Supplementary_files_format_and_content: mapped reads

molecule: total RNA

organism: Rattus norvegicus

growth_protocol: standard lab/farm conditions

extract_protocol:
Animals were sacrificed with no input from the authors (i.e. each group/facility utilized their standard method). Tissues samples were isolated from each organ, placed into an appropriate volume of RNALater, and incubated at 4C overnight. Each sample was then homogenized in a bead-mill in a phenol/chlorofom solution and RNA was isolated by and treated with DNAse on a Qiagen miRNEasy column.
Strand-specific libraries were generated using the standard RNA-Seq protocol / dUTP method, with the “second-day” done on the Beckman-Coulter SPRIworks machine. Briefly, before second-strand synthesis, samples are precipitated first and the second strand is made using a dNTP solution that replaces dTTP with dUTP. Before the final PCR step, libraries are treated with an enzyme that removes dUTP from dsDNA.

treatment_protocol: RNALater

tag: strain

value: Sprague-Dawley

tag: tissue

value: spleen


title: rat_c_skm

description: Sample 52

value: skeletal muscle


title: rat_c_testes

description: Sample 54

value: testes


title: rat_c_liver

description: Sample 50

value: liver


title: rat_c_lung

description: Sample 51

value: lung


title: rat_c_heart

description: Sample 48

value: heart


title: rat_c_colon

description: Sample 47

value: colon


title: Mouse brain rep2

status: Public on Dec 22 2012

city: Toronto

first: Nuno

middle: L

last: Barbosa-Morais

state: ON

address: 160 College Street, Room 908

department: The Donnelly Centre

country: Canada

institute: University of Toronto

description:
Sample 2
The 'Mouse_brain.bw' file merges data from both Mouse brain rep1 and Mouse brain rep2 samples and is available on the 'Mouse brain rep1' sample records (as supplementary file).

data_processing:
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences for all species were downloaded from Ensembl. For each gene, a canonical transcript was selected for gene expression analysis based on the hierarchy derived from the BioMart associated transcript names. For the cases in which such information was not available, the longest protein-coding transcript was selected as the gene representative.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: mm9, galGal3, anoCar2, xenTro2, tetNig2
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the mappability and the total read count for each canonical transcript, for each Sample. To generate bigWig files we aligned the mRNA-Seq data against the respective genomes using TopHat; genomeCoverageBed (part of the BEDTools suite) was run on the resulting BAM files for the quantification of genomic coverage, outputting bedGraph files; bedGraphToBigWig (dowloaded from UCSC) was then used to generate bigWig files from the bedGraph files.

organism: Mus musculus

extract_protocol:
About 20 μg of each tissue was homogenized in 700 μl QIAzol Lysis Reagent (Qiagen) using ceramic beads (Precellys). RNA was extracted according to manufacturer’s recommendations. Briefly, 140 μl of chloroform was added to the homogenate. After phase separation, 450 μl of isopropanol was added to the upper, aqueous phase. The yield and quality of the total RNA were monitored by spectrophotometry at 260, 280, and 230 nm using a Bioanalyzer Eukaryote Total RNA Nano Series II chip (Agilent).
10 μg extracted total RNA was DNase-treated (Turbo DNase, Ambion) and polyadenylated RNA was enriched twice from total RNA using polyATtract mRNA isolation system IV (Promega). RNA was reversed transcribed and converted into double-stranded cDNA (SuperScript cDNA synthesis kit, Invitrogen), sheared by sonication followed by end-repairment, A-tailing, paired end adapter (Illumina) ligation and, prior to PCR amplification, cDNA was UNG-treated to maintain strand-specificity. cDNA was amplified by 15 cycles of PCR and size selected (200-300 bp).

tag: gender

value: mixed

tag: age

value: adult

value: brain

tag: molecule subtype

value: poly-A enriched RNA


title: rat_b_spleen

description: Sample 44

value: BN/SsNHsd


title: rat_b_testes

description: Sample 45


title: PRG1 IP input, insert size 18-40 nt adult

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: Caenorhabditis elegans PRG1 Input

data_processing:
remove 5' barcode and its variants containing a single mutation, and then remove the 3' linker or the partial linker of at least 2nt at the very 3' end. And then for CapSeq, additional 8 nt was removed from the 3' end because of random priming.
Bowtie 0.12.7, blastn 2.2.25 and custom PERL (5.10.1) scripts were used to map and analyze the sequence. In general, all post-mapping analyses were performed using custom PERL scripts. Please contact Weifeng Gu at weifeng.gu@umassmed.edu for detailed PERL scripts or the related database.
Small RNA was normalized to 5 million of matched non-structural reads and mRNA was normalized to 10 million of sense protein coding reads
Gbrowse 1.70 is used to visualize the alignments.
Genome_build: WormBase release WS215, Repbase 15.10, and miRBase release 16 for C. elegans, and NCBIM37.67, miRBase 18 and non-coding RNA database fRNAdb 3.4 for mouse.
Supplementary_files_format_and_content: Fasta format for sequence with id containing the RNA read number (_xNo.)

organism: Caenorhabditis elegans

source_name: wild type, N2, adult

growth_protocol: Normal condition on OP50 plate at 20 oC

extract_protocol: A. CapSeq protocol:  To destroy 5.8S, 18S, and 26S rRNA, 0.5-2 µg of total RNA was treated with 0.1 U/µl Terminator exonuclease (Epicentre, TER51020) in 20 µl volume containing 1U/µl of SUPERase·InTM (Ambion, AM2696) and 1 X buffer A at 30 oC for 1-2 hr. The efficiency of the above reaction could be monitored by resolving the sample on a 5% denaturing PAGE gel visualized by Ethidium Bromide.  To de-phosphorylate tRNA and 5S rRNA, the above reaction was diluted into 100 µl with 10 µl of 10X DNase I buffer, 20 U more of SUPERase·InTM, 30 U of CIP (NEB, M0290S), 5 U of DNase I (Ambion, AM2222), and H2O, and incubated at 37 oC for 30 minutes. The RNA was extracted using phenol/chloroform with phase-lock column (5PRIM, 2302830), and precipitated with 0.3M NaAc (pH 5.2) and at least 1 volume of isopropanol plus 30 µg of glycoblue (Ambion, AM9515), a procedure called as RNA cleanup. To expose the 5' phosphate in the cap structure, the RNA was treated with 0.25 U/µl TAP (tobacco acid pyrophosphatase, Epicentre, T19050) in 10 µl reaction containing 1U/µl SUPERase·InTM and  1 X TAP buffer at 37 oC for 1 hour, and then cleaned up, but without additional glycoblue because glycoblue was already added in the previous step.  The RNA was ligated with 5 µM of barcoded 5’ linkers in 10 µl reaction containing 1 X buffer, 1 U/µl of SUPERase·InTM, 2 U/µl of T4 RNA ligase (Takara, 2050A), 10% DMSO, and 0.1 µg/µl BSA at 15 oC for 8 hours, and cleaned up without additional glycoblue.   To make cDNA, the precipitated RNA was annealed with 50 pmole of RT oligo plus 10 nmole of dNTP (each nucleotide) in a 13 µl reaction at 65 oC for 5 min, and then chilled on ice for at least 2 minutes. The sample was incubated with 5 U/µl Superscript III (Invitrogen, 18080), 10 mM DTT, 1 U/µl SUPERase·InTM, and 1 X buffer, all of which brought in 7 µl volume to the previous annealing reaction. The RT was incubated at 15, 25, and 37 oC each for 15 min, and then at 50 oC for 30 min to finish the RT reaction. The RT was heat-inactivated at 85 oC for 5 min. To destroy RNA, 1 µl each of RNase A (Ambion, AM2270) and RNase H (Ambion, AM2292) is added to the RT reaction at 37 oC for 20 min. To increase the cDNA quantity, the RT reaction was diluted into 100 µl PCR reaction containing 1 X PCR buffer, 0.01 U/µl ExTaq (Takara, RR001B), 0.05 µM of oligo CMO13729, 0.2 mM dNTP, and H2O, and a linear PCR was performed for 12 cycles with condition 94 oC 20 s, 52  oC 20 s, and 72 oC 30 s. The cDNA of desired size (here ~ 130 to 170 nt  for most samples or ~ 50-130 nt for ya0217), visualized using SYBRGold (Invitrogen, S-11494) with 5S and 5.8S RNA from the total RNA as size marker, was purified from a 15% denaturing PAGE gel. The cDNA was eluted using TE buffer (10 mM Tris pH 7.5, 1mM EDTA) containing 0.3 M NaCl for 6 hours to overnight with constant vortexing, filtered through 0.45 µm Spin-x column (Costar, 19442-758), and precipitated with isopropanol and glycoblue, as above. The whole procedure after PCR above was defined as PAGE gel purification.  To obtain the optimal PCR cycle number to produce the cDNA, a testing PCR was performed in 50 µl reaction containing 1 X buffer, 0.2 µM each of oligo CMO13279 and solexa3sh, 20% of the eluted linear PCR product, 0.25 mM dNTP and 0.025 U/µl ExTaq, for 15 cycles with condition 94 oC 20 s, 52 oC 20 s, and 72 oC 30 s. And then 5 µl each of oligo solexa3 and CMO13278, each at 10 µM stock concentration, was added. 3 µl of PCR product was sampled at 3, 6, 9 and 12 more cycles, and then resolved on a 8% native PAGE gel visualized using Ethidium Bromide with 10 bp DNA marker (Invitrogen 10821-015).  The optimal PCR cycle number was defined as the one at which the PCR reaction produces the cDNA of the desired size (here insert size 100 to 130 nt for most samples or 20-100 for ya0217) without obvious bulged products (diffusive band running much more slowly). This was the condition to make the final cDNA amplicons.  To check the quality of the library, TA cloning followed by colony PCR was performed to obtain individual cDNA species sequenced using the traditional method. Finally, single end 76 or 100 nt sequence was obtained using Illumina Genome Analyzer or Hi-Seq.    Oligo used in Capseq:  RT oligo: CAGAAGACGGCATACGANNNNNNNN (N, random nucleotide)  PCR oligo:  solexa3: CAAGCAGAAGACGGCATACGA  solexa3sh: GCAGAAGACGGCATACGA  CM13279: GTTCTACAGTCCGACGATC   CM13278: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC  5' linker: DNA/RNA hybrid oligo (RNA preceded with ‘r’, otherwise DNA)  TCTAC-rArGrUrCrCrGrArCrGrArUrC-barcode  Barcodes: A-rTrGrArC, B-rCrArGrT, C-rGrCrTrG, D-rArTrCrA    B. Small RNA cloning:  We used ligation dependent method, as described (Gu et al., Molecular cell 36, 231-244, 2009) to make small RNA libraries. PRG-1 IP was performed using the same antibody and method, as described (Batista et al., Mol Cell 31, 67-78, 2008; Gu et al., Molecular cell 36, 231-244,2009). Unlike CIP-PNK cloning or ligation independent cloning, TAP cloning, which clones much less degradation products, was used to clone RNA from PRG-1 IP, the oxidized sample for enriching for the 3’ modified RNA (Gu et al., 2009), and the corresponding control samples. To clone capped small RNA, 18-40 nt RNA was first purified from 40 µg of total RNA using a 15% denaturing PAGE gel, and then treated with 0.5 U/µl CIP in 100 µl reaction containing 0.5 U/µl SUPERase·InTM and 1X CIP buffer at 37 oC for 1 hour. The dephosporylated RNA was cleaned up, ligated with a 3' linker, gel-purified, and split into two parts: one quarter treated with PNK and the rest treated with TAP. The treatment and the following cloning protocol were described previously (Gu et al.,Molecular cell 36, 231-244, 2009). Except the previously published oxidized sample (the first step of beta-elimination) and its control, other samples were cloned using 5' 4nt-barcoded linker. Single-end 36nt sequence was obtained using illumina genome analyzer.

tag: 5' barcode

value: ATCA

tag: 3' linker

value: CTGTAG

tag: genotype/variation

value: wild type


title: rat_b_liver

description: Sample 41


title: rat_b_kidney

description: Sample 40

value: kidney


title: H3K4me3 Candida Mouse Macrophages ChIPseq

description: Chromatin IP against H3K4me3

library_source: genomic

molecule: genomic DNA

tag: treatment

value: low dose C.albicans

value: macrophage

value: Diagenode


title: Lizard brain

description: Sample 12

organism: Anolis carolinensis


title: rat_b_lung

description: Sample 42


title: rat_b_brain

description: Sample 37


title: rat_b_colon

description: Sample 38


title: rat_a_testes

description: Sample 36

value: testes


title: rat_a_liver

description: Sample 32

value: liver


title: rat_b_heart

description: Sample 39


title: CapSeq, insert size 100-130 nt L1

description: Caenorhabditis elegans long capped RNA

source_name: wild type, N2, L1 stage

value: CAGT

value: TCGTATGCC

value: L1 stage


title: rat_c_brain

description: Sample 46

value: Sprague-Dawley


title: rat_a_kidney

description: Sample 31


title: rat_a_lung

description: Sample 33

value: lung


title: rat_a_skm

description: Sample 34

value: skeletal muscle


title: rat_a_colon

description: Sample 29

value: colon


title: rat_a_brain

description: Sample 28

value: brain


title: rat_a_spleen

description: Sample 35

value: spleen


title: rat_c_kidney

description: Sample 49


title: flagCbx8_flagChIPseq

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

description: Sample 3

data_processing:
Base calling were done using Illumina’s analysis Pipeline  in two stages with: RTA Version: 1.09 Illumina machine, and configureBclToQseq.py version 1.9.0, on the unix server.
The default Illumina pipeline quality filter is used, which uses a threshold of CHASTITY >= 0.6. Chastity for a given base call is defined as "the ratio of the highest of the four (base type) intensities to the sum of highest two."
Duplicate sequence reads were removed to avoid PCR bias
Base calling: Bowtie alignment algorithm for Illumina sequence format (version 1.1.2)
Reads were mapped to the mouse genome (NCBI37/mm9)
Peak detection was  performed using MACS1.0.1 (Genome size 1.87e+9, tag size 36bp, cutoff peak detection 1e-5).
Empty vector was used for negative control ChIP-signal, in addition a cross background analysis was performed in which Cbx7 ChiP signal served as control for Cbx8 peakcalling and the other way around.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using Bowtie

source_name: Bone marrow cells_flagCbx8_flagChIP

growth_protocol: Bone marrow cells isolated from C57BL/6 mice, injected with 5FU five days prior to sacrifice, were retrovially transduced with empty vector, flag-Cbx7 and flag-Cbx8. Transduced GFP+ cells were sorted by FACS  and cultured in StemSpan (StemCell Technologies) supplemented with 10% fetal bovine serum, 300 ng/mL polyethylene glycol–complexed recombinant rat stem cell factor (Amgen), 20 ng/mL recombinant murine interleukin-11 (R&D Systems), 1 ng/mL Flt3 ligand (Amgen), and penicillin and streptomycin for 7 days.

extract_protocol: Chromatin immunoprecipitation assays (ChIP) of transduced bone marrow cells were in essence performed and analyzed as described previously (Frank S.R. etal., Genes Dev. 15, 2069-82 , 2001) with some minor adjustments. Flag-ChiP using M2 Flag-agarose beads was performed in IP150 buffer and complexes were washed 4x in 500mM wash buffer (1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA pH 8.0 ,20mM Tris-HCl pH 8.0) and the final wash step was performed in TE buffer. DNA samples obtained from the ChIP assays were adaptor-ligated and amplified (New England Biolabs kit E6040).

value: hematopoietic stem/progenitor cells

tag: transduced with

tag: culture age

value: 7 days

tag: chip antibody

value: M2 Flag-agarose beads

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #

tag: chip antibody lot #


title: empty-vector_flagChIPseq

description: Sample 1

source_name: Bone marrow cells_empty vector_flagChIP

tag: cell type

value: empty vector


title: H3K4me3 day1 RPMI ChIPseq

description: Chromatin IP against H3K4me3

data_processing:
ChIPseq: Reads (32 bp) were aligned to the Human (Homo Sapiens) reference genome (hg18, NCBI Build 36) and Mouse (mm9). Bed and wiggle files were generated using the standard ELAND pipeline.
RNAseq: RNA-seq: Total RNA was extracted from Monocytes with the RNeasy kit. DNase treatment was done for 15 min and the concentration was measured with a Qubit fluorometer (Invitrogen). 250 ng of total RNA was treated by Ribo-Zero rRNA Removal Kit (epicentre) to remove  ribosomal RNAs  according to manufacturer instructions. 16 µl of purified RNA was fragmented by addition of 4 µl 5x fragmentation buffer (200 mM Tris acetate pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and incubated at 94°C for exactly 90 seconds. After ethanol precipitation first strand cDNA was synthesized from the fragmented RNA with SuperscriptIII (Invitrogen) using random hexamers. First strand cDNA was purified by Qiagen mini elute columns and second strand cDNA was prepared in the presence of dUTP instead of dTTP.  Double stranded cDNA was purified by Qiagen mini elute columns and used for Illumina sample prepping and sequencing according to the manufacturars instructions. RNA-seq reads were mapped to HG18 and used for bioinformatical analysis. RPKM (reads per kilobase of gene length per million reads) (Mortazavi  et al. 2008) values for RefSeq genes were computed using tag counting scripts and used to analyze gene expression levels.
Genome_build: hg18
Supplementary_files_format_and_content: bed and wig files

organism: Homo sapiens

source_name: Monocytes

value: Untreated cultured in RPMI (day1)

value: primary monocyte

tag: antibody

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog #

tag: antibody lot #


title: rat_a_heart

description: Sample 30

tag: strain

tag: tissue

value: heart


title: flagCbx7_flagChIPseq

description: Sample 2

source_name: Bone marrow cells_flagCbx7_flagChIP


title: H3K4me3 day0 ChIPseq

description: Chromatin IP against H3K4me3

value: untreated (day0)


title: rat_b_skm

description: Sample 43

value: BN/SsNHsd


title: Strand specific BG duplo RNAseq

description: Strand specific RNAseq in Monocytes

data_processing:
ChIPseq: Reads (32 bp) were aligned to the Human (Homo Sapiens) reference genome (hg18, NCBI Build 36). Bed and wiggle files were generated using the standard ELAND pipeline.
RNAseq: RNA-seq: Total RNA was extracted from Monocytes with the RNeasy kit. DNase treatment was done for 15 min and the concentration was measured with a Qubit fluorometer (Invitrogen). 250 ng of total RNA was treated by Ribo-Zero rRNA Removal Kit (epicentre) to remove  ribosomal RNAs  according to manufacturer instructions. 16 µl of purified RNA was fragmented by addition of 4 µl 5x fragmentation buffer (200 mM Tris acetate pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and incubated at 94°C for exactly 90 seconds. After ethanol precipitation first strand cDNA was synthesized from the fragmented RNA with SuperscriptIII (Invitrogen) using random hexamers. First strand cDNA was purified by Qiagen mini elute columns and second strand cDNA was prepared in the presence of dUTP instead of dTTP.  Double stranded cDNA was purified by Qiagen mini elute columns and used for Illumina sample prepping and sequencing according to the manufacturars instructions. RNA-seq reads were mapped to HG18 and used for bioinformatical analysis. RPKM (reads per kilobase of gene length per million reads) (Mortazavi  et al. 2008) values for RefSeq genes were computed using tag counting scripts and used to analyze gene expression levels.

growth_protocol: The PBMC fraction was obtained by density centrifugation of blood from healthy volunteer diluted 1:1 in pyrogen-free saline over Ficoll–Paque (Pharmacia Biotech). Cells were washed twice in saline and suspended in RPMI culture medium. Cells were counted in a Coulter counter (Beckman Coulter). Adherent monocytes from were obtained in 150 mm dishes by incubating 150 x10e6 PBMCs for 1 hour in a total volume of 20 mL. Cell culture was maintained in RPMI supplemented with 10% human pool serum.

extract_protocol: Chromatin was fixed in 1% formaldehyde for 15 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antibodies, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

treatment_protocol: For priming, monocytes were pre-incubated with either cell culture medium (RPMI) or beta-glucan (10µg/ml) for 24 hours. After a wash-out period of 7 days, adherent monocytes were collected and counted before further treatment.

tag: growth protocol

value: 24hrs Beta glucan treated and than cultured in RPMI till day7

tag: sample type

value: Total RNA isolated from 24 hrs beta glucan treated Monocytes at day7


title: Strand specific RPMI RNAseq

description: Strand specific RNAseq in Monocytes

value: Untreated cultured in RPMI till day 7

value: Total RNA isolated from untreated Monocytes at day7


title: Strand specific BG RNAseq

description: Strand specific RNAseq in Monocytes


title: H3K27me3 BG ChIPseq

description: Chromatin IP against H3K27me3

value: Antibody H3K27me3(Millipore, Cat No. 07-449, Lot DAM:1588246)

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: H3K27me3 RPMI ChIPseq

description: Chromatin IP against H3K27me3


title: Strand specific RPMI duplo RNAseq

description: Strand specific RNAseq in Monocytes

value: Untreated cultured in RPMI till day7


title: H3K4me3 RPMI duplo ChIPseq

description: Chromatin IP against H3K4me3

value: Antibody H3K4me3(Diagenode, Cat No. pAb-003-050, Lot No. A.3152-001P)


title: H3K4me3 BG duplo ChIPseq

description: Chromatin IP against H3K4me3


title: H3K4me3 BG first ChIPseq

description: Chromatin IP against H3K4me3


title: H3K4me3 RPMI first ChIPseq

description: Chromatin IP against H3K4me3


title: mouse_c_spleen

description: Sample 26

value: spleen


title: mouse_c_testes

description: Sample 27

value: testes


title: mouse_c_liver

description: Sample 23

value: liver


title: mouse_c_lung

description: Sample 24

value: lung


title: mouse_c_heart

description: Sample 21


title: mouse_c_colon

description: Sample 20

value: colon


title: mouse_c_brain

description: Sample 19

value: brain


title: mouse_b_skm

description: Sample 16

value: skeletal muscle


title: mouse_b_spleen

description: Sample 17


title: mouse_b_kidney

description: Sample 13

value: kidney


title: mouse_b_brain

description: Sample 10


title: mouse_a_spleen

description: Sample 8


title: mouse_a_skm

description: Sample 7


title: mouse_b_colon

description: Sample 11


title: H3K4me3 day1 BG ChIPseq

description: Chromatin IP against H3K4me3

tag: treatment

value: 24hrs Beta glucan treated (day1)

value: primary monocyte

value: Diagenode


title: mouse_a_liver

description: Sample 5


title: mouse_a_colon

description: Sample 2


title: mouse_a_kidney

description: Sample 4


title: mouse_a_brain

description: Sample 1


title: chicken_c_skm

description: Sample 133

organism: Gallus gallus


title: chicken_c_testes

description: Sample 135


title: chicken_c_spleen

description: Sample 134


title: chicken_c_liver

description: Sample 131


title: chicken_c_lung

description: Sample 132


title: mouse_b_testes

description: Sample 18


title: chicken_c_heart

description: Sample 129

value: heart


title: chicken_c_brain

description: Sample 127


title: chicken_c_colon

description: Sample 128


title: chicken_c_kidney

description: Sample 130


title: chicken_b_testes

description: Sample 126


title: chicken_b_spleen

description: Sample 125


title: chicken_b_skm

description: Sample 124


title: chicken_b_lung

description: Sample 123


title: chicken_b_liver

description: Sample 122


title: chicken_b_heart

description: Sample 120


title: mouse_a_testes

description: Sample 9


title: mouse_b_liver

description: Sample 14


title: mouse_b_lung

description: Sample 15


title: chicken_b_colon

description: Sample 119


title: chicken_a_testes

description: Sample 117


title: chicken_b_brain

description: Sample 118


title: chicken_a_spleen

description: Sample 116


title: chicken_a_skm

description: Sample 115


title: chicken_a_lung

description: Sample 114


title: chicken_a_kidney

description: Sample 112


title: chicken_a_colon

description: Sample 110


title: chicken_a_liver

description: Sample 113


title: chicken_a_heart

description: Sample 111


title: chicken_a_brain

description: Sample 109


title: CENP-A ChIPSeq_JT53

city: Bangalore

first: Kaustuv

last: Sanyal

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

data_processing:
Basecalls performed using OLB version 1.9.3, Demultiplexing and FASTQ conversion performed using CASAVA 1.7.0.
Raw data QC and adapter filtering performed using SeqQC_V2.1 internal software.
Chip Seq reads were aligned to C.albicans Assembly version 21 using bowtie-0.12.8 with the following parameters (-v(mismatch) 3 –best(best alignment) -m(Number of alignment) 1 ).
Alignment file to binary sorted alignment file performed using samtools-0.1.7a.
Binary alignment file to bed file conversion using BEDTools-Version-2.12.0. Bed to Peak calling performed using Homer v3.8.1 with the default parameters().
Genome_build: C.albicans Assembly version 21
Supplementary_files_format_and_content: .bed peak file generated using Homer v3.8.1.

organism: Candida albicans

source_name: C.albicans strain J225, IP

growth_protocol: C. albicans cells were grown to log phase at 30oC

extract_protocol:
Lysates were clarified from sonicated nuclei and CENPA-DNA complexes were isolated with antibody.
Libraries for multiplex ChIP Sequencing were constructed using NEXTflex™ ChIP-Seq Sample Preparation Kitprotocol outlined in “Preparing Samples for ChIP Sequencing of DNA” (BIOO Scientific# IP-5143-01). Briefly, DNA was subjected to a series of enzymatic reactions that repair frayed ends and phosphorylate the fragments. The end repaired fragments were subjected to two rounds of SPRI clean up with Agencourt AMPURE XP beads (Beckman Coulter #A63881) for size selection of DNA inserts between 300 to 400bp. The size selected fragments were adenylated with a single nucleotide 3'dATP overhang (BIOO Scientific# IP-5143-01) and adaptors were ligated (NEXT Flex adapters). The fragments with ligated adapters were enriched with 18 cycles of PCR. The prepared libraries were quantified using Qubit and validated for quality by running an aliquot on a High Sensitivity Bioanalyzer Chip (Agilent). Libraries were sequenced on the Illumina Genome Analyzer IIx (GAIIx) following the manufacturer's protocols.

tag: growth conditions

value: Log phase grown C. albicans cells

tag: media

value: YPDU

tag: protein

value: Prot A CENP-A/Cse4

value: Anti-Prot A (Sigma, Cat# P2921)


title: Input_JT54

source_name: C.albicans strain J226, Input

tag: chip antibody

value: none (input)


title: Input_JT44

source_name: C.albicans RM1000AH, Input


title: CENP-A ChIPSeq_JT41

source_name: C.albicans  strain J178, IP

value: YPSU

value: Myc-CENP-C

value: Anti- Myc antibodies (Calbiochem, Cat # OP10L)


title: Input_JT52

source_name: C.albicans strain J225, Input


title: CENP-A ChIPSeq_JT55

source_name: C.albicans strain J226, IP


title: CENP-A ChIPSeq_JT20

source_name: C.albicans strain J227, IP

value: Polyclonal anti-Cse4 antibodies (Sanyal K & Carbon J PNAS 99, 12969 - 12974 (2002))


title: Input_JT19

source_name: C.albicans strain J227, Input


title: CENP-A ChIPSeq_JT15

source_name: C.albicans strain J191, IP


title: CENP-A ChIPSeq_JT45

source_name: C.albicans RM1000AH, IP


title: chicken_b_kidney

description: Sample 121


title: cow_c_testes

description: Sample 108

organism: Bos taurus

value: testes


title: Input_JT13

source_name: C.albicans strain J191, Input


title: Input_JT10

source_name: C.albicans strain J181, Input


title: CENP-A ChIPSeq_JT11+68

source_name: C.albicans strain J181, IP


title: cow_c_spleen

description: Sample 107

value: spleen


title: cow_c_skm

description: Sample 106

value: skeletal muscle


title: cow_c_lung

description: Sample 105

value: lung


title: cow_c_kidney

description: Sample 103

value: kidney


title: cow_c_liver

description: Sample 104

value: liver


title: cow_c_brain

description: Sample 100

value: brain


title: cow_b_skm

description: Sample 97


title: cow_b_testes

description: Sample 99


title: cow_b_spleen

description: Sample 98


title: cow_b_lung

description: Sample 96


title: Input_JT40

source_name: C.albicans  strain J178, Input


title: cow_b_kidney

description: Sample 94


title: cow_a_spleen

description: Sample 89


title: cow_a_skm

description: Sample 88


title: cow_b_colon

description: Sample 92

value: colon


title: cow_a_testes

description: Sample 90


title: cow_b_liver

description: Sample 95


title: cow_b_heart

description: Sample 93

value: heart


title: cow_a_heart

description: Sample 84


title: cow_a_liver

description: Sample 86


title: cow_a_lung

description: Sample 87


title: cow_a_colon

description: Sample 83


title: cow_b_brain

description: Sample 91


title: cow_a_brain

description: Sample 82


title: rhesus_c_spleen

description: Sample 80

organism: Macaca mulatta


title: rhesus_c_testes

description: Sample 81


title: cow_a_kidney

description: Sample 85


title: SJD male

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

description: Small RNA sequence data

data_processing:
Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads, except for libraries Tu_Male, Tu_P0, SJD_Male, SJD_P0, SJDxTuF1, TuxSJDF1, TuxSJDF2 and SJDxTuF2, which do not have a barcode. 3' adapter seqeunce starts with 'TCGTATG'.
Reads were mapped to D.rerio genome assembly using megablast software.
Genome_build: Zv9
Supplementary_files_format_and_content: Text file with read counts

organism: Danio rerio

source_name: Testes

growth_protocol: Animals were grown under standard conditioni

extract_protocol: Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. 5' and 3' adaptors were ligated. RNA was not treated with any enzymes before ligation steps.

tag: gender

value: male

value: SJD

tag: developmental stage

value: Adult

value: Testes


title: Tu Male

description: Small RNA sequence data

value: Tu


title: cow_c_heart

description: Sample 102


title: TuxSJDF2 Individual 2

description: Small RNA sequence data

source_name: Ovary

value: female

value: Hybrid SJD and Tu

value: Ovary


title: cow_c_colon

description: Sample 101


title: rhesus_c_skm

description: Sample 79


title: TuxSJDF2

description: Small RNA sequence data


title: rhesus_c_kidney

description: Sample 76


title: TuxSJDF1 Individual 2

description: Small RNA sequence data


title: TuxSJDF1 Individual 1

description: Small RNA sequence data


title: rhesus_c_heart

description: Sample 75


title: Tu P0 Individual 2

description: Small RNA sequence data


title: rhesus_c_colon

description: Sample 74


title: TuxSJDF1

description: Small RNA sequence data


title: rhesus_c_brain

description: Sample 73


title: rhesus_b_testes

description: Sample 72

value: testes


title: rhesus_b_lung

description: Sample 69


title: Tu P0 Individual 1

description: Small RNA sequence data


title: rhesus_b_kidney

description: Sample 67


title: rhesus_b_spleen

description: Sample 71

value: spleen


title: TuxSJDF2 Individual 1

description: Small RNA sequence data


title: rhesus_b_skm

description: Sample 70

value: skeletal muscle


title: rhesus_b_colon

description: Sample 65


title: SJDxTuF2

description: Small RNA sequence data


title: SJDxTuF1 Individual 2

description: Small RNA sequence data


title: Tu P0

description: Small RNA sequence data


title: rhesus_c_lung

description: Sample 78

value: lung


title: rhesus_b_brain

description: Sample 64


title: SJDxTuF2 Individual 1

description: Small RNA sequence data


title: SJDxTuF1 Individual 1

description: Small RNA sequence data


title: SJDxTuF2 Individual 2

description: Small RNA sequence data


title: SJDxTuF1

description: Small RNA sequence data


title: rhesus_c_liver

description: Sample 77


title: rhesus_b_heart

description: Sample 66


title: rhesus_a_testes

description: Sample 63


title: SJD P0 Individual 2

description: Small RNA sequence data


title: rhesus_a_spleen

description: Sample 62


title: SJD P0 Individual 1

description: Small RNA sequence data


title: SJD P0

description: Small RNA sequence data


title: rhesus_a_skm

description: Sample 61


title: rhesus_a_lung

description: Sample 60


title: rhesus_b_liver

description: Sample 68


title: rhesus_a_liver

description: Sample 59


title: mouse_a_lung

description: Sample 6


title: rhesus_a_kidney

description: Sample 58

value: kidney


title: rhesus_a_heart

description: Sample 57


title: EB_rep1_MspI

status: Public on Dec 20 2012

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

country: China

institute: Agricultural Genomes Institute at Shenzhen

description:
EB.sites.modification.txt.gz
HpaII library (indicating unmodified, methylated or hydroxymethylated cytosines) for replicate 1 of embryoid body cells derived from H9 hESCs

data_processing:
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean HMST-seq reads were mapped to hg19 virtual library with no more than one mismatch using open-source programming language Perl.
Average tags of each site for  HMST-seq library between replicates were used for further analysis, then a previously published method Global Rank-invariant Set Normalization (GRSN) from Pelz, C.R et al., BMC Bioinformatics, 2008; was adapted for our data normalization among libraries. A rank-invariant set of sites were selected in iterative manner as unmodified “C” tags and used to generate a robust average reference, and lowess algorithm was used to normalize tag counts among all libraries. The hydroxymethylation abundance of specific CCGG site can be determined as the ratio between tag counts of “C+mC+hmC” and “C+mC” libraries. In a similar way, ratio between tag counts of “C+mC” and “C” libraries can represent the methylation abundance. Furthermore, a statistics test based on Poisson distribution was performed between two libraries based on the normalized tag counts to identify significantly modified sites. The CCGG sites possessing significantly different tag counts between two libraries (sequencing depth > 10X, P-value<0.05), meanwhile ratio of tag counts larger than 1, were determined as significantly modified sites with 5-hmC or 5-mC.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include tags abundance, p-value of Poisson test and FDR for each sample.

source_name: embryoid body cells

growth_protocol: For maintenance of H9 hESCs, MEF feeder layer was obtained from CF-1 mouse embryos and cultured in MEF medium, which is composed of 90% DMEM (GIBCO 12430) supplemented with 10% FBS (Biochrom S0615). Before freezing cells, MEFs were cultured for 3h at 37℃ in mitomycin C (Sigma M0503) medium that is composed of MEF medium supplemented with 10 ug/ml mitomycin C. For culturing H9 ES cells, MEF-conditioned medium was produced by conditioning MEFs for at least 24 hours in the medium composed of DMEM/F12 (GIBCO 11330) supplemented with 20% knockout serum replacement (GIBCO 10828), 2 mM L-glutamine (GIBCO 25030), 2 mM nonessential amino acids (GIBCO 11140), 0.1 mM 2-mercaptoethanol (GIBCO 21985-023), and 4 ng/ml recombinant human fibroblast growth factor-basic (bFGF; GIBCO 13256-029).   Prior to differentiation, hESCs were cultured on MEFs that were prepared 24 hours in advance, transferred from MEFs onto Matrigel (Invitrogen,354234), and cultured in MEF-conditioned medium. Clumps of hESCs (~5 million cells per plate) were then plated in suspension onto ultra-low adhesion dishes (Corning) in DMEM (Gibco 12430) containing 20% FBS (Biochrom S0615), which promoted the formation of embryoid bodies (EBs).

extract_protocol:
Genomic DNA was extracted from H9 hESCs and EBs using QIAamp DNA Blood Mini Kit (QIAGEN)
HSMT-Seq library construction followed the same protocol from Li, J. et al. BMC Genomics, 2009., except that three independent libraries with initially different enzyme digestion were constructed for each sample, which were termed “C” library, “C+mC” library and “C+mC+hmC”, respectively. For “C+mC” library construction, an aliquot of genomic DNA from each sample was first glucosylated by incubating 1 µg of DNA substrates with 3 μ l (30 units) of T4 β-glucosyltransferase (β-GT) (NEB) for 16 hour at 37°C in a total 100 μ l reaction containing 1X NEBuffer 4 supplemented with 80µM UDP-Glc. After glucosylation, the aliquot of glucosylated DNA was then digested with 300 units of MspI (NEB). For the “C” or “C+mC+hmC” libraries, the aliquots of DNA without glucosylation were directly digested with 300 units of HpaII or MspI (NEB), respectively. The enzyme digestion reactions were carried out at 37°C for 16 hours in a 50 μl of either NEBuffer 1 (HpaII) or NEBuffer 4 (MspI). After digestion, the digested aliquots of DNA from all three libraries were ligated with biotinylated linker, fragmented by NlaIII, captured by streptavidin-conjugated beads, digested with MmeI to generate short sequence tags (16-17bp), and ligated with sequencing linkers and amplified by PCR. Then the purified tags were sequenced using Illumina HiSeq 2000 according to the manufacturer’s instructions.

tag: cell type

value: ES-derived embryoid body cells


title: mouse_a_heart

description: Sample 3


title: rhesus_a_brain

description: Sample 55

value: brain


title: H9_hmedip

data_processing:
Library strategy: hMeDIP-seq
Illumina BclConverter-1.9.0 software used for basecalling.
Low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21) 24. Mismatches of no more than two bases were allowed in the alignment.
Region between pair-end reads mapped to the genome was regarded as an enriched fragment. If only one of the pair-end reads mapped to the genome, the read was extended to 200bps and the extended read was regarded as an enriched fragment. Based on these enriched fragments, wig files were generated by calculating the average  fragment numbers in each 100bp window on the genome.
Genome_build: hg19
Supplementary_files_format_and_content: H9_hmedip.wig.gz        Average hMeDIP enriched fragments number in each 100bp window on the genome

source_name: embryonic stem cells

growth_protocol: For maintenance of H9 hESCs, MEF feeder layer was obtained from CF-1 mouse embryos and cultured in MEF medium, which is composed of 90% DMEM (GIBCO 12430) supplemented with 10% FBS (Biochrom S0615). Before freezing cells, MEFs were cultured for 3h at 37℃ in mitomycin C (Sigma M0503) medium that is composed of MEF medium supplemented with 10 ug/ml mitomycin C. For culturing H9 ES cells, MEF-conditioned medium was produced by conditioning MEFs for at least 24 hours in the medium composed of DMEM/F12 (GIBCO 11330) supplemented with 20% knockout serum replacement (GIBCO 10828), 2 mM L-glutamine (GIBCO 25030), 2 mM nonessential amino acids (GIBCO 11140), 0.1 mM 2-mercaptoethanol (GIBCO 21985-023), and 4 ng/ml recombinant human fibroblast growth factor-basic (bFGF; GIBCO 13256-029).

extract_protocol:
Genomic DNA was extracted from H9 hESCs using QIAamp DNA Blood Mini Kit (QIAGEN)
Prior to immunoprecipitation, 5 µg of genomic DNA was sonicated to a mean size of 200bp fragments, followed with end repair, <A> base addition and adapter ligation steps according to Illumina Paired-End protocol. MeDIP-seq and hMeDIP-seq libraries were constructed on 500 ng of adapter ligated DNA using the Magnetic Methylated DNA Immunoprecipitation kit (Diagenode) and hMeDIP 10rxns kit (Active Motif) following the manufacturer’s instructions, respectively. After immunoprecipitation, the captured products were then eluted and purified on a single ZYMO DNA Clean & Concentrator-5 column following the manufacturer’s instructions. Finally, PCR amplification was carried out using platinum pfx DNA polymerase (Invitrogen) with a thermal cycling program of 94°C 2 min, 12cycles of 94 °C 15s, 60°C 30s, 72°C 30 then prolonging with 5min at 72°C and products could be hold at 12°C. Amplification quality and quantity were evaluated by 2100 Analyzer and QPCR. The libraries were sequenced using Illumina HiSeq 2000 according to the manufacturer’s instructions.

value: embryonic stem cells

tag: passages

tag: cell line


title: rhesus_a_colon

description: Sample 56

value: colon


title: H9_medip

data_processing:
Illumina BclConverter-1.9.0 software used for basecalling.
Low-quality reads were omitted and the clean reads were aligned to the UCSC human reference genome (hg19) using SOAP2 (Version 2.21) 24. Mismatches of no more than two bases were allowed in the alignment.
Region between pair-end reads mapped to the genome was regarded as an enriched fragment. If only one of the pair-end reads mapped to the genome, the read was extended to 200bps and the extended read was regarded as an enriched fragment. Based on these enriched fragments, wig files were generated by calculating the average  fragment numbers in each 100bp window on the genome.
Genome_build: hg19
Supplementary_files_format_and_content: H9_medip.wig.gz         Average MeDIP enriched fragments number in each 100bp window on the genome


title: EB_rep1_HpaII

description:
EB.sites.modification.txt.gz
HpaII library (indicating unmodified cytosines) for replicate 1 of embryoid body cells derived from H9 hESCs


title: EB_rep2_BGT

description:
EB.sites.modification.txt.gz
BGT library (indicating unmodified or methylated cytosines) for replicate 2 of embryoid body cells derived from H9 hESCs


title: H9_rep1_MspI

description:
H9.sites.modification.txt.gz
HpaII library (indicating unmodified, methylated or hydroxymethylated cytosines) for replicate 1 of H9 human embryonic stem cells


title: H9_rep1_BGT

description:
H9.sites.modification.txt.gz
BGT library (indicating unmodified or methylated cytosines) for replicate 1 of H9 human embryonic stem cells


title: H9 XIST-

city: Paris

first: Céline

last: Vallot

address: 35 rue Hélène Brion

country: France

data_processing:
Basecalls were performed using CASAVA version 1.7
RNA-Seq reads were aligned to the current version of the human genome (hg19) using Bowtie-0.12.7 with the following parameters: -v 2 -k 10 -m 10 -y --best
Reads per millions of mapped reads (RPM) was used to estimate expression
SAM tools Mpileup was used to analyze allelic expression of X-linked transcripts using published H9 SNP data (GEO:GSM377524)
Genome_build: hg19

source_name: hESC

extract_protocol: RNA was harvested using Trizol reagent. 10µg of total RNA was depleted of rRNA using the Ribo-Zero rRNA removal kit (EpiCentre). Sequencing libraries with fragment size 200-400bp were prepared using a strand-specific ScriptSeq kit (EpiCentre) according to manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2000 using paired-end protocols (Illumina) with 100 bp read lengths for all samples.

tag: passage

tag: xist expression

value: XIST-


title: EB_rep2_HpaII

description:
EB.sites.modification.txt.gz
HpaII library (indicating unmodified cytosines) for replicate 2 of embryoid body cells derived from H9 hESCs


title: EB_rep2_MspI

description:
EB.sites.modification.txt.gz
HpaII library (indicating unmodified, methylated or hydroxymethylated cytosines) for replicate 2 of embryoid body cells derived from H9 hESCs


title: H9_rep2_MspI

description:
H9.sites.modification.txt.gz
HpaII library (indicating unmodified, methylated or hydroxymethylated cytosines) for replicate 2 of H9 human embryonic stem cells


title: H9_rep2_BGT

description:
H9.sites.modification.txt.gz
BGT library (indicating unmodified or methylated cytosines) for replicate 2 of H9 human embryonic stem cells


title: H9 XIST+

value: XIST+


title: H9_rep2_HpaII

description:
H9.sites.modification.txt.gz
HpaII library (indicating unmodified cytosines) for replicate 2 of H9 human embryonic stem cells


title: EB_rep1_BGT

description:
EB.sites.modification.txt.gz
BGT library (indicating unmodified or methylated cytosines) for replicate 1 of embryoid body cells derived from H9 hESCs


title: mouse_c_skm

description: Sample 25

tag: strain

tag: tissue


title: mES_H2AZ_shluc_ctrl_for_MLL4KD_rpt

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: Chromatin IP against H2A.Z.

data_processing:
Basecalls were performed using GAPipeline 1.3.2 or CASAVA 1.0.
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).
Genome_build: mm8
Supplementary_files_format_and_content: BED

source_name: mouse ES cells, shluc control, H2AZ ChIP

growth_protocol: CMTi-1 and R1 murine ES cell lines were routinely cultured on feeder-coated dishes in ES-qualified DMEM (Cat #SLM-220-B; Millipore) supplemented with 20% ES-qualified FES (Cat #SCRR-30-2020; ATCC), 2mM L-glutamine (Cat #TMS-002-C; Millipore), 100 units/ml penicillin/streptomycin (Cat #TMS-AB2-C; Millipore), 0.1mM non-essential amino acids ( Cat # TMS-001-C; Millipore), 0.1mM2-mercaptoethanol (Cat #ES-007-E; Millipore), 1mM sodium pyruvate (Cat #25-000-CI; Cellgro), and 1,000 units/ml LIF (Esgro, Cat #ESG1107; Millipore). The cells were trypsinized and replated or re-fed every second day. To generate EBs, ES cells were dissociated into a suspension of single cells using trypsin and then diluted to 10,000 cells/ml in 6-well petri dishs (Corning) in ES medium (see growth conditions for ES cells) lacking leukemia inhibitory factor (LIF). Cultures were maintained in a humidified chamber under 5% CO2 at 37C. EBs were allowed to grow for up to 14 days.

extract_protocol: Library constructions for BNase-Seq, ChIP-Seq, MNase-Seq and RNA-Seq follow the protocols as described previously in (Epigenetics Chromatin. 2012 5:10. PMID: 22734930), (Cell. 2007 May 18;129(4):823-37. PMID: 17512414), (Cell. 2008 Mar 7;132(5):887-98. PMID: 18329373) and (Nucleic Acids Res. 2009 Sep;37(16):e106. PMID: 19528076), respectively.

treatment_protocol: Lentiviral Infections: The RNA interference construct targeting mouse H2A.Z was generated by inserting the cDNA sequence of H2A.Z (or MLL4) into pGreenPuro Lentivector (containing a GFP marker) as described in the manual (System Biosciences). The lentiviral particles were packaged by transfecting 293T cells with the shRNA constructs or shLuciferase constructs for 2 days, and lentiviral supernatants were then harvested. Mouse ES cells were transduced with the lentiviral supernatants. After 4 days, 10-50 GFP+ cells were sorted and plated into a feeder coated 6-well plate. One week later, individual colonies were selected, expanded, and knockdown efficiency was analyzed by RT-PCR and Western blot.

tag: condition

value: shluc control for shMLL4 mES cells

tag: antibody (vendor

value: catalog#, or reference):anti-H2AZ antibody (Abcam:AB4147)


title: mES_H2AZ_MLL4KD_rpt

description: Chromatin IP against H2A.Z.

source_name: mouse ES cells, shMLL4, H2AZ ChIP

value: shMLL4 mES cells


title: mES_H3K4me3_MLL4KD_rpt

description: Chromatin IP against H3K4me3.

source_name: mouse ES cells, shMLL4, H3K4me3 ChIP

value: catalog#, or reference):anti-H3K4me3 antibody (Millipore:17-614)


title: mES_RARa_H2AZKD

description: Chromatin IP against RARAa.

source_name: mouse ES cells, shH2A.Z, RARa-ChIP

value: shH2A.Z mES cells

value: catalog#, or reference):anti-RARa-antibody (Santa Cruz:SC-551, lot#:B2212)


title: H9

data_processing:
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. Clean reads were aligned to the hg19 genome assembly using SOAPaligner version 2.21 with no more than one mismatch
Tags of gene per Megabase of library size (TPM) were calculated using a protocol from Hoen, Ariyurek, et al., Nucleic Acids Research, 2008; Morrissy, Morin, et al. Genome Research, 2009.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

extract_protocol: 4μg of the total RNA isolated from each sample was used for digital gene expression (DGE) library construction. Briefly, the total RNA was treated with Oligo(dT) magnetic bead to purify mRNA and then synthesized double-stranded cDNA using Oligo(dT) as primer. The cDNA was digested with NlaIII and ligated to a first adapter containing a restriction site recognized by MmeI. After dephosphorylation with alkaline phosphatase CIAP, the purified MmeI-digested products were linked to a second adapter. Then, the double adapter-flanked tags from the mRNAs were amplified by PCR using Phusion DNA polymerase and Gex PCR primers following the manufacturer’s protocol. PCR was carried out using the following program: 98℃ for 30s, followed by 15 cycles of 98℃ for 10 s, 60℃ for 30 s and 72℃ for 15 s, and then 72℃ for 10 min. The resulting～95-bp PCR products were purified by 6% TBE PAGE electrophoresis gels using Spin-X filter columns. Finally, mRNA libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer’s protocol.


title: EB


title: mouse_c_kidney

description: Sample 22


title: mES_H3K4me3_shluc_ctrl_for_MLL4KD_rpt

description: Chromatin IP against H3K4me3.

source_name: mouse ES cells, shluc control, H3K4me3 ChIP


title: mES_OCT4_H2AZKD_rpt

description: Chromatin IP against Oct4.

source_name: mouse ES cells, shH2A.Z, Oct4-ChIP

value: catalog#, or reference):anti-Oct4-antibody (Abcam:Ab19857)


title: mES_Suz12_H2AZKD_rpt

description: Chromatin IP against Suz12.

source_name: mouse ES cells, shH2A.Z, Suz12 ChIP

value: catalog#, or reference):anti-Suz12 antibody (Abcam:Ab12201)


title: mES_Oct4_H2AZKD

description: Chromatin IP against Oct4.


title: mES_OCT4_shluc_ctrl_for_H2AZKD_rpt

description: Chromatin IP against Oct4.

source_name: mouse ES cells, shluc control, Oct4-ChIP

value: shluc control for shH2A.Z mES cells


title: mES_H3K4me3_H2AZKD_rpt

description: Chromatin IP against H3K4me3.

source_name: mouse ES cells, shH2A.Z, H3K4me3 ChIP


title: mES_RbBP5_shluc_ctrl_for_H2AZKD_rpt

description: Chromatin IP against RbBP5.

source_name: mouse ES cells, shluc control, RbBP5 ChIP

value: catalog#, or reference):anti-RbBP5 antibody (Bethyl:A300-109A)


title: mES_H3K27me3_H2AZKD_rpt

description: Chromatin IP against H3K27me3.

source_name: mouse ES cells, shH2A.Z, H3K27me3 ChIP

value: catalog#, or reference):anti-H3K27me3 antibody (Millipore:07-449)


title: mES_RbBP5_H2AZKD_rpt

description: Chromatin IP against RbBP5.

source_name: mouse ES cells, shH2A.Z, RbBP5 ChIP


title: mES_Suz12_shluc_ctrl_for_H2AZKD_rpt

description: Chromatin IP against Suz12.

source_name: mouse ES cells, shluc control, Suz12 ChIP


title: jwyin_srf_sictrl_ChIPSeq

city: Shanghai

first: Jingwen

last: Yin

address: yueyang road

institute: SIBCB, CAS

data_processing: All single-read sequencing reads were aligned to the mm9 genome assembly by Bowtie program (http://bowtie-bio.sourceforge.net/index.shtml) and parameters are followings: -v1, --best, --strata, -k2, -m1

source_name: 10T1/2 cells knockdown control

growth_protocol: 10T1/2 cells were maintained in Dulbecco’s modified Eagle’s medium containing 10% FBS (Hyclone)

extract_protocol: Purified DNA of multiple samples was prepared for sequencing according to the ChIP procedure. About 10 ng ChIP’ ed DNA were used for DNA library construction using ChIP-seq Sample Prep Kit (Illumina) following the manufacture’s recommendation. Adapter-modified DNA between 200 and 350 bp were isolated by agarose gel electrophoresis and purified. Then, DNA was enriched by 18 cycles of linker-mediated-PCR using primers from Illumina. 7 pmol linker-ligated DNA were applied to the flow-cell using the cBOT (Illumina) device. Samples were the subjected to 76 bases of sequencing on Genome analyzer IIx (Illumina) according to Illumina’s standard protocols.

treatment_protocol: Med23-specific RNAi (si23) or Control (sictrl) oligos were introduced using retrovirus systerm (pSIREN; Clonetech) into C3H10T1/2 cells to knock down Med23 level or serve as control, and si23 and sictrl 10T1/2 stable cell lines were established after puromycin selection for 48 hours. ChIP-seq analysis using anti-SRF antibody were performed in sictrl and si23 C3H10T1/2 cell to compare the effect of Med23-deficiency on SRF binding on whole genome or our focus genes.

value: anti-SRF

tag: antibody vendor/catalog

value: Santa Cruz Biotechnology/sc-335

value: sictrl 10T1/2

tag: background mouse strain


title: jwyin_srf_si23_ChIPSeq

source_name: 10T1/2 cells knockdown Med23


title: mES_H3K27me3_shluc_ctrl_for_H2AZKD_rpt

description: Chromatin IP against H3K27me3.

source_name: mouse ES cells, shluc control, H3K27me3 ChIP

value: embryonic stem cells


title: mES_OCT4_shluc_ctrl_for_H2AZKD

description: Chromatin IP against Oct4.


title: iPS_KH2-SC_MEF_1-5 K4

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description:
Sample name: KH2-SC_MEFiPS_1-5.K4
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

data_processing:
alignment using bwa
coverage using genomeCoverageBed in bedtools
conversion of coverage to bigWig format using bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: content is coverage (i.e., number of reads aligning at each position in the genome) and format is bigWig (see genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: Sorted cells

growth_protocol: Mouse Embryonic fibroblast (MEFF) cultures were established from E13.5 embryos from a reprogrammable mice strain carrying one copy of the OKSM cassette and Rosa26-M2rtTA allele (het/het) or carrying two copies of the OKSM cassette and Rosa26-M2rtTA allele (ho/ho). Reprogramming was performed in ESC medium (KODMEM with 15% FBS, L-Glutamin, penicillin-streptomycin, non-essential amino acids, b-mercaptoethanol and 1000 U/ml LIF) in the presence of doxycycline.

extract_protocol:
iPSCs were harvested when they reached about 50% confluency and preplated on non-gelatinized T25 flasks for 45 minutes to remove feeder cells. Intermidiates cell types were harvest after FACS sorting.
ChIP complexes were eluted with 1% SDS in 100 mM NaHCO3 and crosslinks were reversed by incubating samples over night at 65C.
DNA fragments were purified using the QIAquick PCR Purification Kit Cat number: 28104.
Libraries for sequencing were prepared using ChIP-Seq Sample Prep Kit from Illumina, Cat IP-102-1001

treatment_protocol: Harvested cells were incubated with antibodies against Thy1.2 (PE conjugated, 53-2.1, eBiosciences) and SSEA-1 (mouse IgM, MC-480, Developmental Hybridoma Bank) for 20 minutes. Cells were washed in PBS and then incubated for 20 minutes with APC conjugated anti mouse IgM, (eBioscience) and Pacific Blue-conjugated streptavidin (Invitrogen). The cells were washed in PBS, resuspended in propidium iodide 5% FBS/PBS solution and passed through a 40mm cell strainer to achieve single cell suspension. Cells were sorted on a FACSAria (BD Biosciences ) and/or analysed in a LSRII (BD Bioscience).  For analysis and/or sorting of intermediates, cells were stained with Thy1.2 and SSEA1 antibodies and sorted or analyzed as indicated.

tag: mark

value: Anti-Trimethyl Histone H3 (Lys4) Antibody, (Millipore, clone:CMA304, catalog#:05-1339, lot#:2024897)

tag: time after induction[days]

tag: cell stage

value: iPS

value: NEG

value: POS

tag: gfp


title: mES_RNASeq_H2AZKD

description: RNA-Seq.

data_processing:
GA2563_mouse_R1_shH2A.Z_RNASeq.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

molecule: polyA RNA

source_name: mouse ES cells, H2A.Z KD

value: RNA-Seq H2A.Z knockdown

value: catalog#, or reference):none


title: iPS_KH2-SC_MEF_1-5 K27

description:
Sample name: KH2-SC_MEFiPS_1-5.K27
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

tag: chip antibody

value: Anti-trimethyl Histone H3 (Lys27) Antibody (Millipore, catalog#:ABE44, lot#:1966928)


title: EB_shluc_ctrl_for_H2AZKD_day7

description: RNA-Seq.

data_processing:
GA2757-mouse-CMTI-1-EB-shLuc-a-day7-RNA-seq.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse embryoid bodies, shluc control, day7

value: embryoid bodies

value: mouse EB shluc control day7


title: mES_RNASeq_shluc_ctrl_for_H2AZKD

description: RNA-Seq.

data_processing:
GA2566_mouse_R1_shLuc_RNASeq.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shluc control

value: RNA-Seq shluc control for H2A.Z knockdown or MLL4 knockdown


title: EB_H2AZKD_day7

description: RNA-Seq.

data_processing:
GA2758-mouse-CMTI-1-EB-shH2AZ-2d-day7-RNA-seq.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse embryoid bodies, shH2A.Z, day7

value: mouse EB shH2A.Z day7


title: EB_H2AZKD_day3

description: RNA-Seq.

data_processing:
GA2754-mouse-CMTI-1-EB-shH2AZ-2d-day3-RNA-seq.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse embryoid bodies, shH2A.Z, day3

value: mouse EB shH2A.Z day3


title: EB_shluc_ctrl_for_H2AZKD_day3

description: RNA-Seq.

data_processing:
GA2753-mouse-CMTI-1-EB-shLuc-a-day3-RNA-seq.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse embryoid bodies, shluc control, day3

value: mouse EB shluc control day3


title: mES_H3K4me3_shluc_ctrl_for_H2AZKD_rpt

description: Chromatin IP against H3K4me3.

source_name: mouse ES cells, shluc control, H3K4me3 ChIP

value: shluc control for shH2A.Z mES cells

value: catalog#, or reference):anti-H3K4me3 antibody (Millipore:17-614)


title: mES_H2AZ_MLL4KD

description: Chromatin IP against H2A.Z.

data_processing:
GA2970-mouse-R1-shMLL4-anti-H2A.Z-r490l6-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shMLL4, H2A.Z ChIP

value: shMLL4 mES cells

value: catalog#, or reference):anti-H2AZ antibody (Abcam:AB4147)


title: Day9_SSEA1+ M2 K4

description:
Sample name: KH193.K4
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

value: Anti-Trimethyl Histone H3 (Lys4) Antibody, (Millipore, clone:CMA304, catalog#:05-1339, lot#:2024897)

value: Intermediates


title: mES_H3K4me3_MLL4KD

description: Chromatin IP against H3K4me3.

data_processing:
GA2972-mouse-R1-shMLL4-H3K4me3-r491l8-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shMLL4, H3K4me3 ChIP

value: embryonic stem cells


title: Day9_SSEA1+ M2 K27

description:
Sample name: KH193.K27
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

value: NEG

value: POS


title: H9_rep1_HpaII

description:
H9.sites.modification.txt.gz
HpaII library (indicating unmodified cytosines) for replicate 1 of H9 human embryonic stem cells

source_name: embryonic stem cells


title: Day12_GFP+ M2 K4

description:
Sample name: KH197.K4
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).


title: mES_H2AZ_shluc_ctrl_for_MLL4KD

description: Chromatin IP against H2A.Z.

data_processing:
GA2969-mouse-R1-shLuc-anti-H2A.Z-r490l5-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shluc control, H2A.Z ChIP

value: shluc control for shMLL4 mES cells


title: mES_RARa_shluc_ctrl_for_H2AZKD

description: Chromatin IP against RARAa.

source_name: mouse ES cells, shluc control, RARa-ChIP

value: catalog#, or reference):anti-RARa-antibody (Santa Cruz:SC-551, lot#:B2212)


title: mES_H3K4me3_shluc_ctrl_for_MLL4KD

description: Chromatin IP against H3K4me3.

data_processing:
GA2971-mouse-R1-shHLuc-H3K4me3-r490l8-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).


title: mES_RbBP5_H2AZKD

description: Chromatin IP against RbBP5.

data_processing:
GA2936-mouse-CMT1-shH2A.Z-2d-RbBP5-r488l5-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shH2A.Z, RbBP5 ChIP

value: shH2A.Z mES cells

value: catalog#, or reference):anti-RbBP5 antibody (Bethyl:A300-109A)


title: mES_Suz12_H2AZKD

description: Chromatin IP against Suz12.

data_processing:
GA2938-mouse-CMTI-1-shH2A.Z-2d-Suz12-r489l6-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shH2A.Z, Suz12 ChIP

value: catalog#, or reference):anti-Suz12 antibody (Abcam:Ab12201)


title: Day3_SSEA1+ M2 K27

description:
Sample name: KH181.K27
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

value: Anti-trimethyl Histone H3 (Lys27) Antibody (Millipore, catalog#:ABE44, lot#:1966928)


title: mES_Mnase_H2AZKD

description: Direct sequencing following MNase digestion on x-linked chromatin.

data_processing:
GA2807_CMT1_shH2A.Z-2d_MNase_0.1U_r520l2.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shH2A.Z, MNase

value: catalog#, or reference):none


title: KH2-MEF_m2 K27

description:
Sample name: KH177.K27
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

value: MEF


title: mES_Bnase_H2AZKD

description:
Direct sequencing following Benzonase digestion on native chromatin.
Fragments were barcoded by "CCAACT".

data_processing:
Library strategy: Benzonase
GA3411-Index10-CCAACT-group-B_CMTI-I-shH2A.Z-2d-0.0006858U-ul-Benzonase-220bp-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shH2A.Z, Benzonase


title: mES_Mnase_shluc_ctrl_for_H2AZKD

data_processing:
GA2804-CMT1-shLuc-a-MNase-0.1U_r520l1.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shluc control, MNase

value: shluc control for shH2A.Z mES cells


title: Day12_GFP+ M2 K27

description:
Sample name: KH197.K27
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

source_name: Sorted cells


title: mES_Suz12_shluc_ctrl_for_H2AZKD

description: Chromatin IP against Suz12.

data_processing:
GA2937-mouse-CMT1-shLuc-a-SUZ12-r488l6-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shluc control, Suz12 ChIP


title: mES_Bnase_shluc_ctrl_for_H2AZKD

description:
Direct sequencing following Benzonase digestion on native chromatin.
Fragments were barcoded by "AATTAT".

data_processing:
Library strategy: Benzonase
GA3408-Index5-AATTAT-group-B_CMTI-I-shluc-a-0.0006858U-ul-Benzonase-220bp-m1_noDup.bed.gz; genome build: mm9
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shluc control, Benzonase


title: mES_H3K4me3_H2AZKD

description: Chromatin IP against H3K4me3.

data_processing:
GA2932-mouse-CMT1-shH2A.Z-2d-H3K4me3-r488l8-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shH2A.Z, H3K4me3 ChIP

value: catalog#, or reference):anti-H3K4me3 antibody (Millipore:17-614)


title: mES_H3K4me3_shluc_ctrl_for_H2AZKD

description: Chromatin IP against H3K4me3.

data_processing:
GA2931-mouse-CMT1-shLuc-a-H3K4me3-r488l7-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).


title: mES_H3K27me3_shluc_ctrl_for_H2AZKD

description: Chromatin IP against H3K27me3.

data_processing:
GA2967-mouse-CMT1-shHLuc-a-H3K27me3-r490l3-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shluc control, H3K27me3 ChIP

value: catalog#, or reference):anti-H3K27me3 antibody (Millipore:07-449)


title: mES_RbBP5_shluc_ctrl_for_H2AZKD

description: Chromatin IP against RbBP5.

data_processing:
GA2935-mouse-CMT1-shHLuc-a-RbBP5-r488l4-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shluc control, RbBP5 ChIP


title: Input DNA 14-17h mef2 replicate 3

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

data_processing:
mef2_14to17h_wce_3.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

organism: Drosophila melanogaster

source_name: muscle FAC sorted from dissociated embryos

growth_protocol: D. melanogaster embryos were  collected and aged on yeasted apple juice plates at 25 °C and 60 % humidity.

extract_protocol: ChIP-seq: DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step on a 2 % agarose gel (150-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

tag: genetic background

tag: time point

value: 14 to 17h AEL


title: Input DNA toll10b

data_processing:
toll10b_wce_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

source_name: Toll10b mutant

value: embryos were collected from Toll10b/+ females obtained from a balanced stock (Toll10b/TM3, Sb, Ser and Toll10b/OR60)

value: 02 to 04h AEL


title: Input DNA 2-4h oregon R

data_processing:
oregonr_02to04h_wce_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

source_name: Oregon R (wild-type)

value: Oregon R


title: mES_WT_acH2AZ

description: Chromatin IP against acetylated H2A.Z.

data_processing:
GA1142-mouse-ES-Ac-H2A.Z-r338l7r342l5-m1_noDup-pool.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, WT, acetylated H2A.Z ChIP

tag: cell type

value: embryonic stem cells

value: mES WT

value: catalog#, or reference):anti-acH2AZ antibody (Abcam:Ab18262)


title: KH2-MEF_m2 K4

description:
Sample name: KH177.K4
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

data_processing:
alignment using bwa
coverage using genomeCoverageBed in bedtools
conversion of coverage to bigWig format using bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: content is coverage (i.e., number of reads aligning at each position in the genome) and format is bigWig (see genome.ucsc.edu/goldenPath/help/bigWig.html)

value: Anti-Trimethyl Histone H3 (Lys4) Antibody, (Millipore, clone:CMA304, catalog#:05-1339, lot#:2024897)

value: POS

value: NEG


title: Input DNA 10-12h mef2 replicate 3

data_processing:
mef2_10to12h_wce_3.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: 10 to 12h AEL


title: muscle FAC sorted from dissociated embryos MNase-seq

data_processing:
Read pairs were aligned with bowtie v0.12.7 to the UCSC dm3 release genome. Unique reads with up to 2 mismatches and a mate-pair distance of 234bp or less were retained.
Genome Build:
mef2_14to17h_mnase_1.bed: dm3

extract_protocol: Cell lysates were digested with micrococcal nuclease and mononucleosomal DNA was purified. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step on a 2 % agarose gel (150-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

value: muscle

value: 14h to17h AEL

tag: genotype

value: w*


title: Input DNA 10-12h mef2 replicate 2

data_processing:
mef2_10to12h_wce_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 10-12h mef2 replicate 4

data_processing:
mef2_10to12h_wce_4.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 10-12h mef2 replicate 1

data_processing:
mef2_10to12h_wce_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 14-17h mef2 replicate 1

data_processing:
mef2_14to17h_wce_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 14-17h mef2 replicate 2

data_processing:
mef2_14to17h_wce_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: mES_H3K27me3_H2AZKD

description: Chromatin IP against H3K27me3.

data_processing:
GA2968-mouse-CMT1-shHH2A.Z-2d-H3K27me3-r490l4-m1_noDup.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, shH2A.Z, H3K27me3 ChIP

tag: cell line

value: shH2A.Z mES cells


title: Input DNA 8-10h mef2 replicate 4

data_processing:
mef2_08to10h_wce_4.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: 08 to 10h AEL


title: Day3_SSEA1+ M2 K4

description:
Sample name: KH181.K4
ChIPed DNA
*p.cov.bigWig: processed data file (plus strand).
*m.cov.bigWig: processed data file (minus strand).

value: Intermediates


title: Input DNA 8-10h mef2 replicate 3

data_processing:
mef2_08to10h_wce_3.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 6-8h mef2 replicate 3

data_processing:
mef2_06to08h_wce_3.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: 06 to 08h AEL


title: Input DNA 8-10h mef2 replicate 2

data_processing:
mef2_08to10h_wce_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: mES_WT_H2AZ

description: Chromatin IP against H2A.Z.

data_processing:
GA1141-mouse-ES-H2A.Z-Final-DNA-m1-r338l6r356l7_noDup-pool.bed.gz; genome build: mm8
Sequence reads were obtained and mapped to the mouse (mm8) genome with Bowtie. Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).

source_name: mouse ES cells, WT, H2A.Z ChIP

value: catalog#, or reference):anti-H2AZ antibody (Abcam:AB4147)


title: Input DNA 8-10h mef2 replicate 1

data_processing:
mef2_08to10h_wce_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 6-8h mef2 replicate 1

data_processing:
mef2_06to08h_wce_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 10-12h elav

data_processing:
elav_10to12h_wce_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

source_name: neurons FAC sorted from dissociated embryos


title: H3K27me3 ChIP-seq from Drosophila muscle cells toll10b

data_processing:
toll10b_h3k27me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: embryos were collected from Toll10b/+ females obtained from a balanced stock (Toll10b/TM3, Sb, Ser and Toll10b/OR60)

value: 02 to 04h AEL

value: H3K27me3 (ab6002, abcam)

tag: chip antibody manufacturer

value: abcam

tag: chip antibody catalog #


title: H3K27me3 ChIP-seq from Drosophila muscle cells 10-12h

data_processing:
mef2_10to12h_h3k27me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: H3K27me3 ChIP-seq from 2-4 h wild type embryos

data_processing:
oregonr_02to04h_h3k27me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

source_name: Oregon R (wild type)

value: Oregon R


title: H3K4me3 ChIP-seq from Drosophila muscle cells

data_processing:
mef2_06to08h_h3k4me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: 06 to 18h AEL

value: H3K4me3 (ab8580, abcam)


title: H3K27me3 ChIP-seq from Drosophila muscle cells 14-17h

data_processing:
mef2_14to17h_h3k27me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: 14 to 17h AEL


title: Pol II ChIP-seq from 2-4 h wild type embryos, 4H8 antibody, replicate 1

data_processing:
oregonr_02to04h_pol_4h8_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: Pol II (CTD48H, Millipore)

value: Millipore


title: H3K27me3 ChIP-seq from Drosophila muscle cells 8-10h

data_processing:
mef2_08to10h_h3k27me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: H3K27me3 ChIP-seq from Drosophila muscle cells 6-8h

data_processing:
mef2_06to08h_h3k27me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from Drosophila Toll10b mutant embryos, 8WG16 antibody, replicate 2

data_processing:
toll10b_pol_8wg16_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: Pol II (8WG16, Covance)

value: Covance


title: H3K27me3 ChIP-seq from Drosophila neuronal cells

data_processing:
elav_14to17h_h3k27me3_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 14-17 h Drosophila muscle cells, 8WG16 antibody, replicate 2

data_processing:
mef2_14to17h_pol_8wg16_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 14-17 h Drosophila muscle cells, 8WG16 antibody, replicate 1

data_processing:
mef2_14to17h_pol_8wg16_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 14-17 h Drosophila muscle cells, 4H8 antibody, replicate 2

data_processing:
mef2_14to17h_pol_4h8_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from Drosophila Toll10b mutant embryos, 8WG16 antibody, replicate 1

data_processing:
toll10b_pol_8wg16_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Input DNA 6-8h mef2 replicate 2

data_processing:
mef2_06to08h_wce_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 10-12 h Drosophila muscle cells, 8WG16 antibody, replicate 1

data_processing:
mef2_10to12h_pol_8wg16_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: 10 to 12h AEL


title: Pol II ChIP-seq from 10-12 h Drosophila muscle cells, 8WG16 antibody, replicate 2

data_processing:
mef2_10to12h_pol_8wg16_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 10-12 h Drosophila muscle cells, 4H8 antibody, replicate 1

data_processing:
mef2_10to12h_pol_4h8_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 8-10 h Drosophila muscle cells, 4H8 antibody, replicate 2

data_processing:
mef2_08to10h_pol_4h8_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

value: 08 to 10h AEL


title: Pol II ChIP-seq from 8-10 h Drosophila muscle cells, 8WG16 antibody, replicate 2

data_processing:
mef2_08to10h_pol_8wg16_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 8-10 h Drosophila muscle cells, 4H8 antibody, replicate 1

data_processing:
mef2_08to10h_pol_4h8_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 6-8 h Drosophila muscle cells, 8WG16 antibody, replicate 1

data_processing:
mef2_06to08h_pol_8wg16_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 8-10 h Drosophila muscle cells, 8WG16 antibody, replicate 1

data_processing:
mef2_08to10h_pol_8wg16_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 6-8 h Drosophila muscle cells, 4H8 antibody, replicate 1

data_processing:
mef2_06to08h_pol_4h8_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from 6-8 h Drosophila muscle cells, 4H8 antibody, replicate 2

data_processing:
mef2_06to08h_pol_4h8_2.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Pol II ChIP-seq from Drosophila neuronal cells, 8WG16 antibody, replicate 1

data_processing:
elav_10to12h_pol_8wg16_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.


title: Toll10b mutant MNase-seq

data_processing:
toll10b_mnase_1.bed; genome build: dm3
Read pairs were aligned with bowtie v0.12.7 to the UCSC dm3 release genome. Unique reads with up to 2 mismatches and a mate-pair distance of 213bp or less were retained.

value: Toll10b mutant


title: H3K27me3-Pol II reChIP from 2-4 h wild type embryos

data_processing:
oregonr_02to04h_h3k27me3-pol_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.

tag: chip antibody 1

value: H3K27me3 (ab6002, abcam), Pol II (CTD4H8, Millipore)

tag: chip antibody 1 manufacturer

tag: chip antibody 1 catalog #

tag: chip antibody 2

value: Pol II (CTD4H8, Millipore)

tag: chip antibody 2 manufacturer

tag: chip antibody 2 catalog #