title: Late male whole animal, replicate 2

city: Minneapolis

first: Mary

middle: B

last: Kroetz

state: MN

address: 515 Delaware St SE, 5-143 Moos Tower

department: Genetics, Cell Biology & Development

institute: University of Minnesota

data_processing:
Basecalls performed using CASAVA version 1.8
Sequence reads were trimmed on Galaxy Fastq Quality Trimmer, rRNA was removed by RiboPicker,(http://ribopicker.sourceforge.net/)
Duplicates removed by Picard 1.56, Reads mapped by TopHat version 1.4.1
Differential expression called by Cuffdiff v2.1.1
Genome_build: WS220, ce10
Supplementary_files_format_and_content: bigWig files and Cuffdiff output

source_name: dissociated L1 larval cells

growth_protocol: Starved, hatched L1s were fed for given time followed by dissociation, and gonadal cells were FACS sorted

extract_protocol:
RNA extraction with TRIzol, rRNA depletion with Ribo-Zero, TruSeq
Libraries were prepared for TruSeq at the University of Minnesota Genomics Center following Illumina protocol, but polyA selection step was omitted

tag: time point

value: 15 hours after feeding starved hatched L1s

tag: Sex

value: male

value: dissociated whole animals


title: Late hermaphrodite whole animal, replicate 2

status: Public on Nov 09 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Caenorhabditis elegans

value: hermaphrodite

tag: tissue


title: Early hermaphrodite whole animal, replicate 2

value: 9.5 hours after feeding starved hatched L1s


title: Late male Z1/Z4-daughters, replicate 2

value: gonadal precursors (Z1/Z4 daughters)


title: Late male whole animal, replicate 1


title: Early hermaphrodite whole animal, replicate 1


title: Early male whole animal, replicate 3


title: Early male whole animal, replicate 1


title: Late hermaphrodite Z1/Z4-daughters, replicate 1


title: Late hermaphrodite whole animal, replicate 1


title: Early hermaphrodite Z1/Z4, replicate 2

value: gonadal precursors (Z1/Z4)


title: Early hermaphrodite Z1/Z4, replicate 1


title: Early hermaphrodite whole animal, replicate 3


title: Late hermaphrodite Z1/Z4-daughters, replicate 2


title: Early male whole animal, replicate 2


title: Early male Z1/Z4, replicate 1


title: Early male Z1/Z4, replicate 3


title: Early male Z1/Z4, replicate 2


title: AMA1 SET4 MxEmb Rep2 ChIPSeq

city: New York

first: Sevinc

last: Ercan

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description:
processed data file: AMA1_SET4_embryos_peaks.bed
processed data file: AMA1_SET4_embryos_average.wig.gz

library_source: genomic

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.0.1 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.2 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks per subunits, reads from the replicates were combined using the samtools utility merge version 0.1.19, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
Genome_build: WS220
Supplementary_files_format_and_content: Wig files were generated using MACS version 1.4.2, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position. Bed files were generated by combining replicate reads and using MACS version 1.4.2 at two different p-values. Only peaks at the more stringent cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringent p-value.

molecule: genomic DNA

source_name: whole worms

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C temperature.

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 % sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

tag: strain

tag: developmental stage

value: embryo

tag: matching input

tag: antibody

value: AMA1 Q2357  Rabbit polyclonal is against the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: Input_SET4_MxEmb_Rep4

value: none (input)


title: EpiLC Input nChIPseq2

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
ChIP-seq reads were extended to 250nt for lcChIP and 150nt or 300nt for H3K27me3 and H3K9me2 nChIP respectively. Reads were aligned to the mouse reference genome (GRCm38/mm10) using bowtie with parameters –m 2 –v 0 (Langmead et al., 2009). Genome-wide ChIP vs. Input profiles were normalized by the total number of mapped reads per 200 nt (RPKM). In analogy, ChIP-seq vs. Input counts on promoters or gene bodies were normalized by the total number of mapped reads and by size (RPKM).
RNA-seq reads were all trimmed to 40nt and then adapter- and quality-trimmed, and aligned with Tophat2 (Kim et al., 2013) against the mouse reference (GRCm38/mm10) genome. Read counts per ENSEMBL were obtained by htseq-count (Anders et al., 2014).
Genome_build: GRCm38/mm10

organism: Mus musculus

source_name: EpiLC

growth_protocol: see extra colum

extract_protocol:
EpiLCs were induced for 48h from 2i/LIF ESCs as previously described (Hayashi et al., 2011).
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the mononucleosome fractions were isolated

treatment_protocol: no treatment

tag: background

value: mixed background

tag: age

value: 2 days post induction

tag: genotype

tag: tissue/cell type

value: epiblast-like cells


title: P7_Thy1_Rep1

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 whole genome using tophat version 2.0.9 with parameters : -p 8 --splice-mismatches 1  --segment-mismatches 2 --solexa1.3-quals
FPKM and differential expression were calculated using the Cufflinks suite version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Testis

extract_protocol:
Cells were isolated from C57Bl/6 mice at postnatal day 0,7,12,14 (labeled P0 to P14 respectively). These cells were further selected for specific markers (Oct4, Thy1, Id4 or Kit).
Cell populations labeled with GFP were selected for GFP via FACS. FACS analysis involved isolations from P0 Vasa-GFP+ (JAX Lab, 006954), P0 and P7 Oct4-GFP+ (JAX Lab, 008214); and P7Id4-GFP+ (J. Oatley). Cells were sorted using FACSCalibur (BD Biosciences, SanJose, CA). The percentage of live cells was >95%, by exclusion of propidium iodide.
Isolation of either the THY1+ or c-KIT+ stem cell subtypes from C57Bl/6 mice was carried out with a magnetic cell-sorting (MACS) separator (MiltenyiBiotec, Bergisch-Gladbach, Germany) using anti-CD117 (KIT) antibody or anti-CD90.2 (THY1) (MiltenyiBiotec).
Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit (Cat # 80004), ribosomal RNA was depleted using RiboZero kit.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

tag: cell markers

tag: cell type

value: Spermatogonia

value: postnatal day 7


title: AMA1 SET4 MxEmb Rep1 ChIPSeq


title: Late male Z1/Z4-daughters, replicate 1


title: AMA1 CB428 MxEmb Rep3 ChIPSeq

description:
processed data file: AMA1_CB428_embryos_peaks.bed
processed data file: AMA1_CB428_embryos_average.wig.gz


title: wdr82sh_sh1137_4sU_unstranded_LPS_4h

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: supplementary file: wdr82sh_4sU_unstranded_genes.fpkm_tracking.txt

data_processing:
Library strategy: 4sU-seq
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches. For stranded samples processing the --library-type was set to fr-secondstrand or to fr-firststrand according to library preparation
Transcripts abundance were quantified using Cufflinks 2.1.1 (PMID: 20436464)
Differentially expressed genes were called using Cuffdiff 2.1.1 (PMID: 23222703)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM) (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: At day zero bone marrow cells were isolated from FVB/hsd mice and 3 × 10^6 cells/well in a 6-well plate were seeded in BM medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cells were infected two times pr day for two days consecutive days after plating, using supernatants from transfected Phoenix-ECO packaging cells. After the last infection, cells where transferred to 10 cm culture plates, and puromycin selection (3.5 μg/ml) was started.

extract_protocol:
For sequencing of poly-A RNA, RNA was isolated with RNeasy (Qiagen) with DNAse I treatment. The Illumina kit TruSeq RNA preparation kit (RS-122-2001) with oligo-dT-based polyA-selection was used for cDNA-library synthesis. Briefly, after polyA-isolation, the RNA molecules are fragmented, followed by reverse transcription into cDNA with random primers. Then, second strand cDNA synthesis is performed with DNA Polymerase I in the presence of RNase H. The cDNA fragments are then end-repaired, a single A-base is added to the 5«ends and adapters are ligated. The cDNA is a amplified with PCR (15 cycles) to generate the final cDNA library. In order to obtain nascent 4-thio-Uridine (4sU) labelled RNA, 4sU was added to the cell culture medium at a final concentration of 300 mM for 45 min before harvesting the cells. The 4sU-labeled RNA was isolated as described (Rabani M. et al., 2011). Briefly, RNA was isolated with Trizol (Invitrogen), then 50 ug of total RNA was labeled with biotin (EZ-link HPDP-biotin, Thermo Scientific), and unbound biotin was removed with MaXtract high density tubes (Qiagen). Biotinylated RNA was isolated with MyOne Streptavidin T1 Dyneabeads (Invitrogen) for 15 min at room temperature, followed by washing of the beads according to manufacturers instructions. The 4sU-labelled RNA was finally eluted with 95% Formamide (Sigma) in 10 mM EDTA at 65¡C for 10 min, and purified on RNeasy MinElute spin columns (Qiagen), and eluted in 14 ul H2O. A total of 40-100 ng of 4sU-labelled RNA was used for cDNA-library synthesis using Illumina kits, skipping the step of either ribosomal depletion or polyA-selection, starting from the RNA fragmentation step.
TruSeq RNA Sample Preparation kit (RS-122-2001) or the kit processing the RNA to retain strand information (Truseq Stranded Total RNA Sample Preparation kit (RS-122-2201), or in the Epicentre ScriptSeq RNA-Seq Library Preparation Kit (SSV21124) was used (for second and first strand synthesis respectively). The Illumina stranded RNAseq kit are based on the dUTP method as described in Levin et. al, Nat. Methods, 2010.

treatment_protocol: BMDMs were either untreated or treated for 4 hrs with lipopolysaccharide (LPS, 10 ng/ml).

value: FVB/Hsd

value: BMDM cells (7th day of differentiation)

tag: library type

value: Unstranded

tag: treatment

value: LPS (10 ng/ml)


title: AMA1 N2 MxEmb Rep3 ChIPSeq

description:
processed data file: AMA1_N2_embryos_peaks.bed
processed data file: AMA1_N2_embryos_average.wig.gz


title: AMA1 CB428 MxEmb Rep1 ChIPSeq


title: SET1 L2 heterozyg Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt

data_processing:
Basecalls were performed using CASAVA version 1.8.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.2.0 using default parameters supplying gene annotations.
Raw counts for each gene were generated using htseq-count version 0.6.0 using default parameters.
Spike-in data was mapped to both the C. elegans genome and the C. briggsae genome build cb4. Reads mapping to both genomes were removed from further analysis.
genome build: WS220
processed data files format and content: FPKM text file contains the FPKM values for each gene for each replicate.  RNAseq counts text file contains the raw counts for each gene for each of the replicates in the spike-in experiments.

molecule: polyA RNA

growth_protocol: Larvae were collected after overnight embryo hatching and growth for 24 hours on NGM plates.

extract_protocol:
RNA was extracted by freeze cracking embryos by freezing in liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA was cleaned up through Qiagen RNeasy column.
mRNA was purified from .5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212

treatment_protocol: Packed larvae were resuspended in 10V of Trizol and frozen at -80C.


title: SET1 L2 homozyg Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: DPY27 RNAi L3 Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: Synchronized L1s were placed on dpy-27 RNAi seeded plates (NGM+amp+tet+IPTG) and collected at 24 hours.

value: N2, DPY-27 RNAi


title: Vector RNAi L3 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: Synchronized L1s were placed on empty vector seeded plates (NGM+amp+tet+IPTG) and collected at 24 hours.

value: N2, Vector RNAi


title: Vector RNAi mixed embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: Synchronized L1s were placed on empty vector seeded plates (NGM+amp+tet+IPTG) and grown to adults. Embryos were collected by bleaching).

treatment_protocol: Packed embryos were resuspended in 10V of Trizol and frozen at -80C.

value: mixed embryo


title: DPY27 RNAi L3 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Vector RNAi mixed embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Vector RNAi L3 Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: DPY27 RNAi mixed embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: Synchronized L1s were placed on dpy-27 RNAi seeded plates (NGM+amp+tet+IPTG) and grown to adults. Embryos were collected by bleaching).


title: Vector RNAi L3 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET1 L2 homozyg Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: DPY27 RNAi L3 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: DPY27 RNAi L3 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Vector RNAi mixed embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: DPY27 RNAi mixed embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Vector RNAi mixed embryo Rep5 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Vector RNAi mixed embryo Rep6 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET1 L2 homozyg Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Vector RNAi mixed embryo Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: DPY27 RNAi mixed embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: DPY27 RNAi mixed embryo Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Vector RNAi L3 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET4 L3 Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: AMA1 CB428 MxEmb Rep2 ChIPSeq


title: SET1 L2 heterozyg Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET1 L2 heterozyg Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET4 L3 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET4 L3 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Early hermaphrodite Z1/Z4, replicate 3

value: 9.5 hours after feeding starved hatched L1s

value: hermaphrodite


title: SET4 L3 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET4 mixed embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: For mixed embryo collections, asynchronus parents were bleached and embryos collected.


title: N2 L3 collection 2 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: Larvae were collected after overnight embryo hatching and growth for 24 hours on NGM plates


title: SET4 mixed embryo Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 L3 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET4 mixed embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L3 collection 2 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: wdr82sh_sh1137_4sU_stranded_LPS_45min_DRB_untreated

description: supplementary file: wdr82sh_4sU_stranded_DRB_genes.fpkm_tracking.txt

value: Stranded (first-strand synthesis)


title: BS553 L1 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: Larvae were collected after overnight embryo hatching and growth for 6 hours on NGM plates


title: CB428 L3 Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L3 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 mixed embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 mixed embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 mixed embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L3 collection 2 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L3 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 L3 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SET4 mixed embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: BS553 L1 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 mixed embryo Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: BS553 L1 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L3 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L1 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L1 Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L1 Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 L3 collection 2 Rep4 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 L3 Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: BS553 comma Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: For staged embryo collections, parents were synchronized by bleaching gravid worms, allowing embryos to hatch overnight and growing the synchronized L1s on NGM plates for ~60 hours or until the first embryos were seen in hermaphrodite gonads. After bleaching, comma embryos were aged for 4 hours in M9 buffer then collected.

value: comma embryo


title: siH19_methylation

city: Farmington

last: Zhang

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
BaseCalling performed using BCL2Fastq version 1.8.4
Using Bismarck v0.11.1 to align reads against mouse mm10 reference genome
Methylation calling performed by Zymo Research proprietary pipeline
Genome_build: mouse mm10
Supplementary_files_format_and_content: bed file

source_name: Mouse C3H myoblast (Sigma-Aldrich)

growth_protocol: Undifferentiated myoblasts were maintained in growth medium (GM) (DMEM, Gibco, 11965-092, supplemented with 10% fetal bovine serum, heat inactivated, 1% penicillin/streptomycin, 1% L-glutamine and 1-mM sodium pyruvate). To prepare for differentiation, cells were seeded at a density of 1.6 × 10^5 cells/well or 1.0 × 10^4 cells/well in GM in 6-well or 48-well plates, respectively. Differentiation was initiated 2 days later when cells became confluent by replacing GM with differentiation medium (DM) containing 2% horse serum in place of 10% FBS.

extract_protocol:
Genomic DNA was extracted by using Quick-gDNA MicroPrep kit from Zymo Research company according to the protocol
Libraries were prepared from 200-500 ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator™-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR, Cat#D4005) for sequencing on an Illumina HiSeq.

treatment_protocol: Mouse CH3 Myoblasts were induced to differentiate into myotubes, which were transfected with either control siRNA or siH19. 48h after transfection, cells were harvested and genomic DNA was extracted.

value: Myotube differentiated from Differenting Mouse C3H

tag: sirna


title: N2 comma Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: siCon_methylation

value: siControl


title: N2 comma Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: MK4 hetero early embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt

growth_protocol: For staged embryo collections, parents were synchronized by bleaching gravid worms, allowing embryos to hatch overnight and growing the synchronized L1s on NGM plates for ~60 hours or until the first embryos were seen in hermaphrodite gonads. Early embryos were collected by bleaching and immediate collection.

value: early embryo


title: N2 comma Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: ESC H3K27me3 nChIPseq1

source_name: ESC

extract_protocol:
Cells were cultured in N2B27 2i/LIF conditions on gelatin (Ying et al., 2008) supplemented with 1% KSR.
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the mononucleosome fractions were isolated

value: mixed background

value: 2i/LIF embryonic stem cells

value: H3K27me3 (Millipore, 07-449)


title: ESC H3K27me3 nChIPseq2


title: ESC H3K9me2 nChIPseq4

extract_protocol:
Cells were cultured in N2B27 2i/LIF conditions on gelatin (Ying et al., 2008) supplemented with 1% KSR.
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the dinucleosome fractions were isolated

value: H3K9me2 (Abcam, ab1220)


title: ESC Input nChIPseq4


title: MK4 hetero early embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: BS553 comma Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: SOX15 shRNA biological rep1 (RNA-Seq)

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description:
Sample name: SOX15-2
processed data file: Differential_gene_exp.diff

data_processing:
base-calling: bcl2fastq, version 02.14.01.07 for Illumina NextSeq 500 with default settings.
alignment: Starstatic, version 2.3.1 with default settings
normalized and differential expression: Cufflinks, version 2.0.2; settings: default; Cuffdiff was used with default settings.
Genome_build:hg19
Supplementary_files_format_and_content: [RNA-Seq] Individual samples have an FPKM gene tracking file from Cufflinks, estimating transcript abundance for that sample, along with confidence intervals. Data is also represented as differential expression table prepared using Cuffdiff with an FDR of 5%, which contains average normalized FPKM values for Control SC and Sox15 knockout samples, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.

organism: Homo sapiens

source_name: CPA cells

growth_protocol: Cells were harvested and frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.
The TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Cells were infected with non specific or SOX15 shRNA

tag: cell line

value: Barrett's esophagus cell line, CPA

tag: genotype/variation

value: SOX15 depletion


title: MK4 early embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: ESC Input nChIPseq1


title: Control biological rep1 (RNA-Seq)

description:
Sample name: SC1
processed data file: Differential_gene_exp.diff

value: control


title: siH19 rep2

data_processing:
RTA 2.1.3 software was used for basecalling.
Alignments were made using Tophat 2.0.7,  FPKM estimation of reference genes and transcripts were made using Cufflinks2 (TopHat Alignment 1.0.0 embedded in illumina BaseSpace platform).
Relative expression of genes and transcripts between siCon and siH19 samples was determined using Cuffdiff 2.1.1.
Genes and transcripts that have significant differentiatial expression between siCon and siH19 triplicates (q Value <0.05) were presented in the processed data file.
genome build: mm10
processed data files format and content: tab-delimited text files include averaged RPKM values for each condition.

source_name: differentiated myotubes_siH19 (H19 knockdown)

extract_protocol:
Total RNA was harvested using PureLink RNA Mini Kit.
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Human/Mouse/Rat, setA (Cat# rs-122-2201) according to the sample preparation protocol. Briefly, 1 ug total RNA was subjected to Ribo-Zero depletion to remove rRNAs. The remaining RNA was purified, fragmented, and primed with random hexamers for cDNA synthesis. After first and second cDNA synthesis, cDNA fr agments were adenylated and then ligated to indexing adapters. The cDNA fragments were enriched by PCR, purified, and then sequenced on an illumina NextSeq500 using paired-end chemistry and 76-bp cycles.

treatment_protocol: Mouse CH3 Myoblasts were induced to differentiate into myotubes. 40h after induction of differentiation, cells were transfected with either control siRNA or H19 siRNA. 48h later, cells were harvested for RNA extraction.

value: Mouse C3H myoblast (Sigma-Aldrich)

value: Day 4 - Differenting Mouse C3H myotube

tag: transfected with

tag: time point

value: 48h after transfection


title: Control biological rep2 (RNA-Seq)

description:
Sample name: SC2
processed data file: Differential_gene_exp.diff


title: MK4 early embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt

tag: strain


title: SOX15 shRNA biological rep2 (RNA-Seq)

description:
Sample name: SOX15-3
processed data file: Differential_gene_exp.diff


title: Input (ChIP-Seq)

description: Sample name: Input ChIP

data_processing:
base-calling: bcl2fastq, version 02.14.01.07 for Illumina NextSeq 500 with default settings.
alignment: Bowtie2, version 2.1.0 with default settings; removed multiply mapped reads and pcr duplicates
peak-calling: macs, version 1.4.1 using -S and -w
Genome_build:hg19
Supplementary_files_format_and_content: [ChIP-Seq] bed and wig files

extract_protocol:
Cells were harvested and stored at -80°C for subsequent sonication and ChIP. Cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG, Pierce 20593) in PBS for 45 min, followed by 10 min with 1% formaldehyde (Pierce 28906) in PBS, at room temperature. ChIP and ChIP-seq were performed as described previously (Kim et al., 2009), using 30 μL slurry of streptavidin-conjugated magnetic beads (Invitrogen 65601).
Rubicon Truplex-fd preo kit was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: pulldown

value: input control


title: MK4 early embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt

tag: developmental stage


title: SOX15 ChIP (ChIP-Seq)

description: Sample name: Bio SOX15 ChIP

value: Bio-SOX15 was pulled down using Dynabeads MyOne Streptavidin T1 for six hours at 4 degrees (Invitrogen, catalog number 65601)


title: siH19 rep1


title: siCon rep3

source_name: differentiated myotubes_control siRNA


title: ESC H3K9me2 nChIPseq3

tag: antibody


title: siH19 rep3


title: siCon rep2


title: BS553 comma Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: ESC Input nChIPseq2

tag: background


title: ESC Input nChIPseq3


title: BS553 early embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: BS553 early embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: nucleosome core particles (+SM) rep 2; BY4741

city: Bethesda

first: Alan

middle: G.

last: Hinnubusch

state: MD

address: 6 Center Dr. Bldg 6, Rm 230

institute: NICHD

description:
MNase limit digest
Biological replicate 2
AGH01_4

data_processing:
Paired-end sequences of immunoprecipited DNA or nucleosomal DNA were aligned to the yeast genome (SacCer2) using Bowtie2 with default settings.
Histone H3 and Rpb3 occupancies profiles were created using custom perl programs.
The processed data (bigWig files) were converted from the fastq files supplied here. Analysis of the aligned reads were size-selected as described in the article.
The .bw files for the Rpb3 samples include only unique read pairs.
length used in AGH0*.bw files: range: 120 - 160 bp
Genome_build: SacCer2
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 30 min to induce Gcn4, or without adding SM (no SM).

extract_protocol:
In ChIP-seq experiments, cells were cross-linked with formaldehyde before harvesting. In MNase-seq experiments, nuclei were prepared from unfixed yeast cells and then digested with MNase. Mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details. The antibodies used in this study are anti-H3 antibody from Abcam (Cat#ab1791) and anti-Rpb3 antibody from NeoClone (Cat# W0012)
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

value: MATa his3delta1 leu2delta met15delta ura3delta


title: nucleosome core particles (no SM) rep 2; BY4741

description:
MNase limit digest
Biological replicate 2
AGH01_2


title: BS553 early embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: CB428 early embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: nucleosome core particles (no SM) rep 1; BY4741

description:
MNase limit digest
Biological replicate 1
AGH01_1


title: Wild Type + T3 rep5

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads quality was evaluated from FastQC.
Reference Genome was indexed from Bowtie (Langmead B et al. 2009) and sequence reads were aligned using TopHat (Trapnell C et al. 2009). Mapping data quality was evaluated from Qualimap (Garcia-Alcalde F et al. 2012)
We quantified reads to specific genes and transcripts using the Python module HT-SEQ (Anders S et al. 2015).
RNA-Seq data were normalized using Trimmed Mean of M values (Robinson MD and A Oshlack 2010) from EdgeR.
Genome_build: Mouse sequenced genome GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include TMM values for each sample.

source_name: cerebrocortical cells

growth_protocol: Pregnant dams were euthanized with CO2 on gestational day 17.5, and the fetuses were extracted and euthanized by decapitation. The cerebral cortices were dissected in PBS containing 1% BSA and 0.1% Glucose. The tissue was disaggregated by enzymatic digestion with 0.4 mg/ml Papain (Roche) and passed through a 0.9 mm syringe in the presence of DNAse I (Roche). The homogenate was centrifuged and the cells were suspended in culture medium: Neurobasal Medium (Gibco® Life Technologies) containing 2% B27 supplement (Gibco® Life Technologies), 1x Glutamax (Gibco® Life Technologies), 10 U/ml Penicillin, and 10 U/ml Streptomycin. Eight hundred µl aliquots of the cell suspension containing 6 x 105 cells were added to 600 µl of culture medium containing horse serum (1:1), and laminin (1mg/ml) (Sigma)/well in poly-L-ornithine-coated 12-well plates (Sigma Chemical Co, St Louis, MO). The cells were incubated for 2 h at 37 ºC, and the medium was replaced for culture medium.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit (Quiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
500 ng of total RNA were used with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA) to construct index-tagged cDNA libraries. Libraries were quantified using a Quant-iT™ dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and sequence-by-synthesis single reads of 75 base length using the TruSeq SBS Kit v5 (Illumina) were generated on the Genome Analyzer IIx following the standard RNA sequencing protocol. Reads were further processed using the CASAVA package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

treatment_protocol: After 9 days incubation with periodic medium changes, the medium was replaced with culture medium without B27 and incubated for 24 hours before adding T3 (Sigma) at a final concentration of 10 nM. The cells were harvested 24 hours later. Cells without T3 were incubated in parallel.

tag: tissue

value: cerebral cortex

tag: mouse


title: CB428 early embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Wild Type + T3 rep6


title: Wild Type + T3 rep1


title: Wild Type + T3 rep3


title: Rpb3 ChIP-seq (+SM) Experiment 2; HQY1657/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH1119_12

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta Ptet-SNF2 gcn5delta::kanMX4 ydj1delta::hphMX4


title: Wild Type + T3 rep2


title: Rpb3 ChIP-seq (+SM) Experiment 3; HQY1657/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH27_10


title: Wild Type rep3

value: not T3


title: Wild Type rep4


title: CB428 early embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt

value: early embryo


title: Zebrafish embryo 24 hours post fertilization

city: Los Angeles

first: Andrew

last: Smith

state: CA

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

data_processing:
Reads were mapped using rmap-bs (http://smithlabresearch.org/software/rmap/).
Methylomes were constructed using MethPipe (http://smithlabresearch.org/software/methpipe/).
Genome_build: danRer7
Supplementary_files_format_and_content: The processed data are in tab-delimited text format which includes single CpG coverage and methylation level information.

organism: Danio rerio

source_name: Whole embryo

extract_protocol:
phenol/chloroform
Standard Paired-end library preperation strategy with 5mC adapters as discribed (Hodges et al 2011)

value: 24 HPF


title: Wild Type rep1


title: Wild Type rep6


title: siCon rep1

value: siControl


title: Wild Type rep2


title: N2 embryo Rep3 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: N2 embryo Rep2 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Wild Type + T3 rep4


title: nucleosome core particles (+SM) rep 1; BY4741

description:
MNase limit digest
Biological replicate 1
AGH01_3


title: Zebrafish embryo 8 hours post fertilization

value: 8 HPF


title: Rpb3 ChIP-seq (+SM) Experiment 1; HQY1657/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH1018_12


title: Wild Type rep5


title: Zebrafish embryo 4 hours post fertilization

value: 4 HPF


title: Zebrafish embryo 2 hours post fertilization

value: 2 HPF


title: N2 embryo Rep1 RNASeq

description: processed data file: RNAseq_FPKMs.txt


title: Input_SET4_L3_spikein_Rep2

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.0.1 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.2 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks per subunits, reads from the replicates were combined using the samtools utility merge version 0.1.19, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
genome build: WS220
processed data files format and content: Wig files were generated using MACS version 1.4.2, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position.  Bed files were generated by combining replicate reads and using MACS version 1.4.2 at two different p-values. Only peaks at the more stringent cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringent p-value.

growth_protocol: L3s were isolated by growing hatched L1 larvae on OP50 seeded NGM plates for 24 hours at 20C temperature.

extract_protocol:
Frozen, ground, and crosslinked larva samples were resuspended in FA buffer+sarkosyl+protease inhibitors (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl, 0.1% sarkosyl), and sonicated to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of extract was spiked in with 0.1-0.2 mg of C. Briggsae AF16 extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: L3 collections were made by freezing worms in liquid nitrogen, then were ground into a frozen powder, then treated with 1% formaldehyde for 10 minutes, washed with M9, and collected by centifugation for extract preparation.

value: none (input)


title: Input_SET4_L3_spikein_Rep1


title: Rpb3 ChIP-seq (+SM) Experiment 1; HQY1627

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH1018_4

value: MATa his3delta1 leu2delta met15delta ura3delta Ptet-SNF2


title: Rpb3 ChIP-seq (+SM) Experiment 2; HQY1623

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH1119_8

value: MATa his3delta1 leu2delta met15delta ura3delta Ptet-SNF2 gcn5delta::kanMX4


title: Rpb3 ChIP-seq (+SM) Experiment 1; HQY1623

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH1018_8


title: Rpb3 ChIP-seq (+SM) Experiment 3; HQY1627

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH28_8


title: Input_N2_L3_spikein_Rep1


title: Rpb3 ChIP-seq (+SM) Experiment 2; HQY1627

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH1119_4


title: Input_SET4_embryo_spikein_Rep1

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C temperature.

value: embryo


title: Input_N2_embryo_spikein_Rep1


title: Input_SET4_L3_Rep2


title: WGBSeq EpiLC 6

description:
genomic DNA bisulfite converted
EpiLC.CG.3X.bedgraph

data_processing:
WGBSeq reads were  were quality-trimmed and aligned to the bisulfite-converted genome with Bismark with parameters -n -l 40
Genome_build: GRCm38/mm10

extract_protocol:
EpiLCs were induced for 48h from 2i/LIF ESCs as previously described (Hayashi et al., 2011).
160 ng of sonicated DNA was used for library preparation using Ovation Ultralow Methyl-Seq Library System (Nugen). This entailed a 3.5 h bisulfite conversion of adapter-ligated DNA using EZ DNA Methylation-Direct (Zymo Research). The DNA was amplified using 7 cycles. Once libraries were prepared they were sequenced using HiSeq2000 with paired-end 100nt read length.

value: mixed background

tag: tissue/cell type

value: epiblast-like cells


title: WGBSeq EpiLC 5


title: WGBSeq EpiLC 4


title: WGBSeq EpiLC 1


title: WGBSeq EpiLC 2


title: WGBSeq EpiSC 6

description:
genomic DNA bisulfite converted
EpiSC.CG.3X.bedgraph

source_name: EpiSC

extract_protocol:
EpiSCs were grown in feeder-free conditions in fibronectin (Millipore) coated dishes. Culture media contained: N2B27 medium supplemented with bFGF (12 ng/ml) and ActivinA (20 ng/ml).
160 ng of sonicated DNA was used for library preparation using Ovation Ultralow Methyl-Seq Library System (Nugen). This entailed a 3.5 h bisulfite conversion of adapter-ligated DNA using EZ DNA Methylation-Direct (Zymo Research). The DNA was amplified using 7 cycles. Once libraries were prepared they were sequenced using HiSeq2000 with paired-end 100nt read length.

value: X-GFP

value: epiblast stem cells


title: Rpb3 ChIP-seq (+SM) Experiment 3; HQY1595

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH28_4

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4 ydj1delta::hphMX4


title: WGBSeq EpiLC 3


title: Rpb3 ChIP-seq (+SM) Experiment 1; HQY1595

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH1018_6


title: Input_CB428_L3_Rep2


title: Rpb3 ChIP-seq (+SM) Experiment 3; HQY1623

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH28_10


title: WGBSeq EpiSC 5


title: Rpb3 ChIP-seq (+SM) Experiment 3; HQY1598/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH13_6

value: MATa his3delta1 leu2delta met15delta ura3delta snf2delta::kanMX4 ydj1delta::hphMX4/lcGCN4


title: WGBSeq EpiSC 3


title: Input_CB428_MxEmb_Rep2

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 % sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

value: mixed embryo


title: WGBSeq EpiSC 2


title: WGBSeq EpiSC 1


title: Input_N2_L3_Rep4


title: Input_N2_L3_Rep3


title: Input_SET4_MxEmb_Rep3


title: SAM16462055 ΔCop1β ΔETV4/5β

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using gSNAP -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: islets

extract_protocol:
Islets were harvested from mice, cultured, then handpicked. Total RNA was extracted and purified using a Qiagen RNAeasy kit with DNAse digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed

tag: age

value: 3-4 months

value: Cop1fl/fl; Etv4ko/+; Etv5fl/fl; Pdx1.CreERT2


title: SAM16462053 ΔCop1β ΔETV4/5β


title: Rpb3 ChIP-seq (+SM) Experiment 2; HQY1598/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH13_5


title: Rpb3 ChIP-seq (+SM) Experiment 1; HQY1598/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH13_4


title: SAM16462052 ΔCop1β ΔETV4/5β


title: Rpb3 ChIP-seq (+SM) Experiment 3; 7285

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH28_3

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4


title: SAM16462049 ΔCop1β

value: Cop1 fl/fl; Pdx1.CreERT2


title: Rpb3 ChIP-seq (+SM) Experiment 2; 7285

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH1119_5


title: SAM16462051 ΔCop1β


title: Rpb3 ChIP-seq (+SM) Experiment 1; 7285

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH1018_5


title: Input_N2_MxEmb_Rep2


title: SAM16462050 ΔCop1β


title: Input_SET4_L3_Rep1


title: WGBSeq EpiSC 4


title: Input_N2_MxEmb_Rep1


title: SAM16462048 ΔCop1β


title: Input_CB428_L3_Rep1


title: Rpb3 ChIP-seq (+SM) Experiment 3; 1586

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH28_1

value: MATa his3delta1 leu2delta met15delta ura3delta snf2delta::kanMX4


title: SAM16462044 control

value: Cop1 fl/fl


title: GSM1111824_input_N2_embryo

extract_protocol: Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

value: none (input)


title: Rpb3 ChIP-seq (+SM) Experiment 2; 1586

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH12_8


title: SAM16462046 control


title: SAM16462054 ΔCop1β ΔETV4/5β


title: Input_N2_L3_Rep2


title: Rpb3 ChIP-seq (+SM) Experiment 3; 3012

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH28_2

value: MATa his3delta1 leu2delta met15delta ura3delta ydj1delta::kanMX4


title: SAM16462047 control


title: Input_SET4_MxEmb_Rep2


title: Input_N2_L3_Rep1


title: SAM16462045 control


title: Input_SET4_MxEmb_Rep1


title: SAM19862289 ΔCop1β ΔETV1/4/5β

value: Cop1fl/fl; Etv1fl/fl; Etv4ko/ko; Etv5fl/fl; Pdx1.CreERT2


title: SAM19862288 ΔCop1β ΔETV1/4/5β


title: Rpb3 ChIP-seq (+SM) Experiment 2; HQY1595

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH1119_6


title: SAM19862287 ΔCop1β ΔETV1/4/5β


title: Rpb3 ChIP-seq (+SM) Experiment 3; 249

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH23_11

value: MATa his3delta1 leu2delta met15delta ura3delta gcn4delta::kanMX4


title: H4K20me1 SET4 L3 Rep2 spike-in ChIPSeq

description:
processed data file: H4K20me1_SET4_L3_spikein_average.wig.gz
processed data file: H4K20me1_SET4_L3_spikein_peaks.bed

tag: matching input raw data file

value: H4K20me1 Abcam (ab9051)


title: SAM19862286 ΔCop1β ΔETV1/4/5β


title: Input_CB428_MxEmb_Rep3


title: Input_CB428_MxEmb_Rep1


title: Input_N2_YA_Rep1

growth_protocol: Young adult (YA) worms were isolated by growing hatched L1 larvae on OP50 seeded NGM plates for 44 hours at 25C temperature.

extract_protocol:
Frozen, ground, and crosslinked larva samples were resuspended in FA buffer+sarkosyl+protease inhibitors (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl, 0.1% sarkosyl), and sonicated to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: YA collections were made by freezing worms in liquid nitrogen, then were ground into a frozen powder, then treated with 1% formaldehyde for 10 minutes, washed with M9, and collected by centifugation for extract preparation.

value: YA


title: H4K20me1 SET4 L3 Rep1 spike-in ChIPSeq


title: SAM19862283 ΔCop1β


title: Rpb3 ChIP-seq (+SM) Experiment 1; 3012

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH12_9


title: Rpb3 ChIP-seq (+SM) Experiment 1; 1586

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH12_7


title: SAM19862282 ΔCop1β


title: SAM19862285 ΔCop1β


title: Rpb3 ChIP-seq (+SM) Experiment 1; 249

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH12_1


title: Rpb3 ChIP-seq (+SM) Experiment 3; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH03_6

value: MATa his3delta1 leu2delta met15delta ura3delta


title: Rpb3 ChIP-seq (+SM) Experiment 2; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH03_5


title: H4K20me1 N2 L3 Rep1 spike-in ChIPSeq

description:
processed data file: H4K20me1_N2_L3_spikein_Rep1.wig.gz
processed data file: H4K20me1_N2_L3_spikein_Rep1_peaks.bed


title: Rpb3 ChIP-seq (+SM) Experiment 2; 3012

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH12_10


title: Rpb3 ChIP-seq (+SM) Experiment 1; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH03_4


title: H4K20me1 SET4 MxEmb Rep1 spike-in ChIPSeq

description:
processed data file: H4K20me1_SET4_embryo_spikein_Rep1.wig.gz
processed data file: H4K20me1_SET4_embryo_spikein_Rep1_peaks.bed

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 % sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of extract was spiked in with 0.1-0.2 mg of C. Briggsae AF16 extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.


title: SAM19862279 ΔCop1β


title: Rpb3 ChIP-seq (no SM) Experiment 3; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH03_3


title: SAM19862279 control


title: Rpb3 ChIP-seq (no SM) Experiment 2; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH03_2


title: H4K20me1 N2 MxEmb Rep1 spike-in ChIPSeq

description:
processed data file: H4K20me1_N2_embryo_spikein_Rep1.wig.gz
processed data file: H4K20me1_N2_embryo_spikein_Rep1_peaks.bed


title: Rpb3 ChIP-seq (+SM) Experiment 2; 249

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH12_2


title: H4K20me1 SET4 L3 Rep2 ChIPSeq

description:
processed data file: H4K20me1_SET4_L3_average.wig.gz
processed data file: H4K20me1_SET4_L3_peaks.bed


title: SAM19862280 control


title: Rpb3 ChIP-seq (no SM) Experiment 1; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH03_1


title: H4K20me1 SET4 L3 Rep1 ChIPSeq


title: H4K20me1 CB428 L3 Rep2 ChIPSeq

description:
processed data file: H4K20me1_CB428_L3_average.wig.gz
processed data file: H4K20me1_CB428_L3_peaks.bed


title: SAM19862281 control


title: H3 ChIP-seq (+SM) Experiment 2; HQY1657/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH09_12

value: MATa his3delta1 leu2delta met15delta ura3delta Ptet-SNF2 gcn5delta::kanMX4 ydj1delta::hphMX4


title: SAM19862278 control


title: RNAseq G9aKO4

source_name: Epiblast E6.25

growth_protocol: see extra colum

extract_protocol:
Single E6.25 epiblast were dissected as previously described (Tesar et al., 2007).
750 pg of RNA from each sample was amplified using Ovation RNA-seq System V2 (Nugen). Quality of cDNA was confirmed by measuring the expression of G9a, Ezh2, Oct4 and Nanog by qPCR .  For every sample 1.5 μg of cDNA was sheared to ~230 bp using S220 Focused-ultrasonicator (Covaris). Fragmented cDNA was then concentrated using Qiagen Reaction Clean Up Kit (MinElute). 500 ng of each sample was used as input for library preparation using Encore Rapid DR Multiplex Library System (Nugen).

value: mixed background

value: E6.25 dpc

value: epiblast


title: H4K20me1 N2 L3 Rep2 ChIPSeq

description:
processed data file: H4K20me1_N2_L3_average.wig.gz
processed data file: H4K20me1_N2_L3_peaks.bed


title: RNAseq Ezh2KO3

value: Ezh-/-


title: H3 ChIP-seq (+SM) Experiment 1; HQY1657/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH08_12


title: H3 ChIP-seq (+SM) Experiment 3; HQY1623

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH25_10

value: MATa his3delta1 leu2delta met15delta ura3delta Ptet-SNF2 gcn5delta::kanMX4


title: H3 ChIP-seq (+SM) Experiment 2; HQY1623

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH09_8


title: RNAseq Ezh2KO2


title: H3 ChIP-seq (+SM) Experiment 1; HQY1623

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH08_8


title: H4K20me1 SET4 Rep3 ChIPSeq

description:
processed data file: H4K20me1_SET4_embryos_average.wig.gz
processed data file: H4K20me1_SET4_embryos_peaks.bed

value: embryo


title: H4K20me1 N2 L3 Rep1 ChIPSeq


title: RNAseq Ezh2Cntr3

value: Ezh+/+


title: RNAseq Ezh2Cntr2


title: H3 ChIP-seq (+SM) Experiment 3; HQY1627

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH25_8

value: MATa his3delta1 leu2delta met15delta ura3delta Ptet-SNF2


title: H3 ChIP-seq (+SM) Experiment 2; HQY1627

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH09_4


title: H4K20me1 SET4 Rep1 ChIPSeq


title: H4K20me1 CB428 Rep3 ChIPSeq

description:
processed data file: H4K20me1_CB428_embryos_average.wig.gz
processed data file: H4K20me1_CB428_embryos_peaks.bed


title: H4K20me1 SET4 Rep2 ChIPSeq


title: H3 ChIP-seq (+SM) Experiment 1; HQY1627

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH08_4


title: H4K20me1 CB428 Rep2 ChIPSeq


title: H4K20me1 CB428 L3 Rep1 ChIPSeq


title: H3 ChIP-seq (+SM) Experiment 3; HQY1657/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH27_5


title: RNAseq G9aCntr4


title: H4K20me1 CB428 Rep1 ChIPSeq


title: H4K20me1 N2 MxEmb Rep3 ChIPSeq

description:
processed data file: H4K20me1_N2_embryos_average.wig.gz
processed data file: H4K20me1_N2_embryos_peaks.bed


title: H3 ChIP-seq (+SM) Experiment 3; HQY1595

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH25_4

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4 ydj1delta::hphMX4


title: H3 ChIP-seq (+SM) Experiment 2; HQY1595

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH09_6


title: RNAseq G9aCntr3


title: CB-5083 treated

city: Burlingame

first: Stevan

middle: Nicholas

last: Djakovic

state: California

address: 866 Malcolm Rd #100

institute: Cleave Biosciences

data_processing:
The pipeline mRNAv8-RSEM (EA-Quintiles) was used to analyze RNA-seq data.
Reads were aligned to External RNA Controls Consortium (ERCC) sequences. A subset of the reads (~1 million reads) were aligned to spiked-in control sequences (PhiX and other Illumina controls used during library preparation), residual sequences (globin and ribosomal RNA), and poly-A/T sequences that persisted after clipping.  The reads were also aligned to a sampling of intergenic regions to assess DNA contamination level and set the RPK (reads per thousand bases) threshold to call a transcript as present.
RSEM v1.2.0  was used to quantify normalized gene counts using parameters optimized for Illumina 50x50 paired-end sequencing
The UCSC knownGene transcriptome was used
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RSEM gene counts, gene name, gene function and chromosone location

source_name: HCT116 cells_CB-5083

growth_protocol: HCT116 cells were cultered in McCoy's 5a Medium with 10% FBS

extract_protocol:
RNA was isolated with the PureLink® RNA Mini Kit (Ambion™)
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit

treatment_protocol: HCT116 cells were treated for 8 hours with DMSO or 1uM CB-5083

value: Colon

tag: cancer type

value: colorectal


title: H3 ChIP-seq (+SM) Experiment 1; HQY1595

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH08_6


title: H4K20me1 N2 MxEmb Rep2 ChIPSeq


title: RNAseq G9aKO3


title: RNAseq G9aKO2


title: RNAseq G9aCntr2


title: caki_Input_DNA_2

city: Milano

first: Davide

last: Cittaro

address: via Olgettina 58

department: Center for Traslational Genomics and Bioinformatics

country: Italy

institute: Ospedale San Raffaele

description: ChIP-seq analysis on untreated growing Caki-1 cells. Total chromatin (input). Replicate 2.

data_processing:
Read tags were aligned to reference genome using bwa mem 0.7.5
Properly paired tags with alignment quality higher than 15 were used to build bedgraph files with bedtools genomecov
Smoothed profiles were created using dspchip, using a hanning window of 65kbp. Input was subtracted from IP signals. Negative values were removed
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files. Score for raw signal is the base coverage. Score for smoothed signal is normalized coverage smoothed with dspchip.

source_name: caki-1 cell line

growth_protocol: Caki-1 cells were cultured in  RPMI supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
CHIP followed by phenol/chloroform extraction and EtOH precipitation.
TruSeq ChIP Sample Prep Kit, Illumina

value: kidney; Derived from metastatic site - skin

tag: chip antibody

tag: chip antibody provider

tag: chip antibody catalog


title: H4K20me1 N2 MxEmb Rep1 ChIPSeq

source_name: whole worms


title: caki_Input_DNA_1

description: ChIP-seq analysis on untreated growing Caki-1 cells. Total chromatin (input). Replicate 1.

tag: cell line


title: DMSO treated

source_name: HCT116 cells_DMSO


title: H3 ChIP-seq (+SM) Experiment 3; HQY1598/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH13_3

value: MATa his3delta1 leu2delta met15delta ura3delta snf2delta::kanMX4 ydj1delta::hphMX4/lcGCN4


title: caki_H3K4me1_abcam_2

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K4me1  antibody (Abcam). Replicate 2.

value: Abcam


title: RNAseq Ezh2Cntr1


title: H3 ChIP-seq (+SM) Experiment 2; HQY1598/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH13_2


title: RNAseq G9aKO1


title: caki_H3K4me1_abcam_1

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K4me1  antibody (Abcam). Replicate 1.


title: DPY27 N2 YA Rep2 ChIPSeq

description:
processed data file: DPY27_N2_YA_average.wig.gz
processed data file: DPY27_N2_YA_peaks.bed

value: YA

value: DPY-27 JL00001 Rabbit polyclonal to 1-409 aa. (Ercan et al. Nat Genet. 2007) is against the antigen 1-409 aa


title: DPY27 N2 YA Rep1 ChIPSeq


title: RNAseq G9aCntr1


title: H3 ChIP-seq (+SM) Experiment 3; 7285

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH25_3

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4


title: caki_H3K4me3_millipore_2

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K4me3  antibody  (Millipore). Replicate 2.

value: Millipore


title: DPY27 N2 L3 Rep2 ChIPSeq

description:
processed data file: DPY27_N2_L3_average.wig.gz
processed data file: DPY27_N2_L3_peaks.bed


title: EpiLC H3K9me2 nChIPseq4

source_name: EpiLC

extract_protocol:
EpiLCs were induced for 48h from 2i/LIF ESCs as previously described (Hayashi et al., 2011).
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the dinucleosome fractions were isolated

value: mixed background

value: 2 days post induction

value: epiblast-like cells

value: H3K9me2 (Abcam, ab1220)


title: H3 ChIP-seq (+SM) Experiment 2; 7285

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH09_5


title: Epiblast H3K27me3 lcChIPseq2

extract_protocol:
Epiblast cells were isolated from E6.25 pre-gastrulating embryos coming from outbred MF1 females crossed with ΔPE-Oct4-EGFP (GGOF) stud males. After recovering embryos from the decidua, Reichert’s membrane was dissected out and extraembryonic cone was also removed. Remaining tissue was used to prepare single cell suspension and sorting using MoFlo high-speed cell sorter (Beckman Coulter) based on EGFP expression.
lcChIP-seq was performed by using a modified published method (Ng et al., 2013). Isolated DNA was primed using WGA4 kit (Sigma). The next step involved library amplification using HiFi Library Amplification master mix (Kappa biosciences) and BpmI-primer (CCGGCCCTGGAGTGTTGGGTGTGTTTGG). These reactions were incubated in a thermocycler using following conditions: 98 °C for 3 min; 11-12 X (98 °C for 10 sec; 65 °C for 30 sec; 72 °C for 1 min); 72 °C for 7 min: or 4 °C as suggested. The number of cycles depended on the amount of DNA precipitated and so 11 cycles were used for H3K9me2 and 12 for H3K27me3. Amplified DNA was purified with Agencourt RNA clean XP beads. Adapter trimming was performed by BpmI digestion, secondary adaptor ligation and a second round of digestion (Ng et al., 2013). Digested DNA was purified with Agencourt RNA clean XP bead and used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen).

value: E6.25 dpc

value: epiblast

value: H3K27me3 (Millipore, 07-449)


title: H3 ChIP-seq (+SM) Experiment 1; 7285

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH08_5


title: caki_H3K4me3_millipore_1

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K4me3  antibody  (Millipore). Replicate 1.


title: H3 ChIP-seq (+SM) Experiment 1; HQY1598/p1217

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH13_1


title: DPY27 SET4 MxEmb Rep2 ChIPSeq

description:
processed data file: DPY27_SET4_embryos_average.wig.gz
processed data file: DPY27_SET4_embryos_peaks.bed

value: embryo


title: Epiblast Input lcChIPseq2


title: caki_H3K9me3_abcam_2

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K9me3  antibody ( Abcam). Replicate 2.


title: H3 ChIP-seq (+SM) Experiment 3; 1586

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH25_1

value: MATa his3delta1 leu2delta met15delta ura3delta snf2delta::kanMX4


title: Epiblast Input lcChIPseq4


title: H3 ChIP-seq (+SM) Experiment 2; 1586

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH0406_10-2


title: caki_H3K9me3_millipore_2

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K9me3  antibody (Millipore). Replicate 2.


title: Epiblast H3K9me2 lcChIPseq4


title: DPY27 SET4 MxEmb Rep1 ChIPSeq


title: DPY27 CB428 MxEmb Rep3 ChIPSeq

description:
processed data file: DPY27_CB428_embryos_average.wig.gz
processed data file: DPY27_CB428_embryos_peaks.bed


title: DPY27 CB428 MxEmb Rep2 ChIPSeq


title: H3 ChIP-seq (+SM) Experiment 1; 1586

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH0406_10-1


title: caki_H3K9me3_abcam_1

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K9me3  antibody ( Abcam). Replicate 1.


title: DPY27 CB428 MxEmb Rep1 ChIPSeq


title: caki_KDM5C_bethyl_1

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-KDM5C  antibody (Bethyl). Replicate 1.

value: Bethyl


title: caki_H3K9me3_millipore_1

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-H3K9me3  antibody (Millipore). Replicate 1.

value: kidney; Derived from metastatic site - skin


title: H3 ChIP-seq (+SM) Experiment 2; 3012

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH0406_11-2

value: MATa his3delta1 leu2delta met15delta ura3delta ydj1delta::kanMX4


title: H3 ChIP-seq (+SM) Experiment 3; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH0220_6

value: MATa his3delta1 leu2delta met15delta ura3delta


title: caki_KDM5C_abcam_1

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-KDM5C  antibody (Abcam). Replicate 1.

value: Abcam


title: H3 ChIP-seq (+SM) Experiment 3; 3012

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH25_2


title: EpiLC Input nChIPseq4


title: H3 ChIP-seq (+SM) Experiment 2; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH0220_5


title: CSB M CHIP

city: Philadelphia

first: Jieun

last: Jeong

address: 3400 Civic Center Blvd

institute: The University of Pennsylvania

description: Sample 1

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie 0.12.7 using option of -k 1 –m 1 --best --strata
Peaks were called using Homer with a default option (FDR = 0.001 and Poisson p-value cutoff = 0.0001) on ChIPed samples against matching input samples
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated after peak calling

extract_protocol:
CHIP protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature. Crossed-linked cells were sonicated at 40% amplitude (30 sec on, 90sec off, for 24 min total) using The Branson 101-135-126 Sonifier.  Chromatin IP (ChIP) was performed using monoclonal anti-CSB antibody against the N-terminal 507 amino acids (1B1) [Dr. Hua-Ying Fan, Univ. of Pennsylvania, PMID 23028371].
To generate the library from ChIP experiment, ChIP-Seq Library Protocol with multiplexing was used. This protocol was developed before Illumina released its multiplex truSeq ChIP-seq kit, and the details can be found on http://ngsc.med.upenn.edu/. According to the protocol, 10 ng of ChIP DNA product was used to start the library construction.

tag: cell type

value: fibroblast

tag: treated with

value: menadione

value: Mouse monoclonal anti-CSB N Terminus (1B1)


title: caki_KDM5C_bethyl_2

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-KDM5C  antibody (Bethyl). Replicate 2.


title: H3 ChIP-seq (no SM) Experiment 2; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 2
AGH0220_2

extract_protocol:
In ChIP-seq experiments, cells were cross-linked with formaldehyde before harvesting. In MNase-seq experiments, nuclei were prepared from unfixed yeast cells and then digested with MNase. Mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details. The antibodies used in this study are anti-H3 antibody from Abcam (Cat#ab1791) and anti-Rpb3 antibody from NeoClone (Cat# W0012)
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: strain


title: WHIM12 ZNF165 IP

city: Dallas

first: Angelique

last: Whitehurst

state: TX

address: 5323 Harry Hines Blvd.

department: Simmons Cancer Center

institute: UT Southwestern

description: Illumina® HiSeq 2500 using 50SR V3 reagents

data_processing:
Base calling was performed using CASAVA (v1.8.4)
Reads were aligned to hg19 assembly using Bowtie2. Aligned reads were sorted and filtered for high qaulity reads using samtools. Duplicate reads were removed using picard tools.
Peak calling  was performed using HOMER findPEAKS using FDR cut off of 0.001, a cumulative Poisson p-value of <0.0001 and a required 4-fold enrichment of normalized sequenced reads of ZNF165-V5 over input sample
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files

source_name: breast cancer tumor derived cell line stably expressing ZNF165-V5

growth_protocol: WHIM12 cells were grown in MEM (Gibco) and split 1:3 every two days.

extract_protocol:
Nuclei from WHIM12 cells stably expressing control or ZNF165-V5 were isolated, sonicated and immunopreciptated with V5 antibody.
5 ng of ChIP-ed DNA underwent library preparation using the KAPA HTP Library Preparation Kit.
ChIP-ed DNA was end repaired, 3’ end adenylated and barcoded with multiplex adaptors. Ampure XP beads were used to purify DNA. Library size was assessed using the Agilent 2100 Bioanalyzer. The Invitrogen Qubit® Fluorometer was then used to quantify samples prior to normalizing and pooling.

treatment_protocol: WHIM12 were lentivirally infected with pLX302 control or pLx302.V5-ZNF165  and selected with puromycin for 5 days before performing ChIP experiment.

tag: tumor type

value: TNBC

value: WHIM12 stably expressing ZNF165-V5

value: Polyclonal V5 Antibody (Abcam, catalog# 9116)


title: WHIM12 ZNF165 Input

value: none (input)


title: DPY27 N2 L3 Rep1 ChIPSeq

description:
processed data file: DPY27_N2_L3_average.wig.gz
processed data file: DPY27_N2_L3_peaks.bed

tag: developmental stage

tag: antibody

value: DPY-27 JL00001 Rabbit polyclonal to 1-409 aa. (Ercan et al. Nat Genet. 2007) is against the antigen 1-409 aa


title: CSB M input DNA

description: Sample 3


title: H3 ChIP-seq (no SM) Experiment 3; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 3
AGH0220_3


title: H3 ChIP-seq (+SM) Experiment 1; 3012

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH0406_11-1


title: H3 ChIP-seq (no SM) Experiment 1; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH0220_1


title: H3 ChIP-seq (+SM) Experiment 1; BY4741

description:
Formaldehyde-fixed and sonicated
Biological replicate 1
AGH0220_4


title: RNAseq Ezh2KO1

data_processing:
ChIP-seq reads were extended to 250nt for lcChIP and 150nt or 300nt for H3K27me3 and H3K9me2 nChIP respectively. Reads were aligned to the mouse reference genome (GRCm38/mm10) using bowtie with parameters –m 2 –v 0 (Langmead et al., 2009). Genome-wide ChIP vs. Input profiles were normalized by the total number of mapped reads per 200 nt (RPKM). In analogy, ChIP-seq vs. Input counts on promoters or gene bodies were normalized by the total number of mapped reads and by size (RPKM).
RNA-seq reads were all trimmed to 40nt and then adapter- and quality-trimmed, and aligned with Tophat2 (Kim et al., 2013) against the mouse reference (GRCm38/mm10) genome. Read counts per ENSEMBL were obtained by htseq-count (Anders et al., 2014).
Genome_build: GRCm38/mm10

tag: background

value: mixed background

value: E6.25 dpc

value: Ezh-/-

value: epiblast


title: APC-KRAS Bcl9/9l-WT tumor 13

status: Public on Nov 08 2015

city: Basel

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description:
Sample name: BAK_13
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.

data_processing:
Basecalls performed using Illumina HiSeq Control Software 2.0.12.0, default parameters.
Demultiplexing-software: configureBclToFastq.pl from Casava 1.82 allowing 1 mismatch on index sequence.
Demultiplexed read files were mapped to a mouse reference transcriptome (GRCm38/mm10, Ensembl) with CLC genomics workbench 7.0.3 (CLC bio).
Counts of unique genes as defined by default settings of CLC software were exported (see respective processed files).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text matrix, unique gene counts (gene symbols obtained from mm10 assembly) as defined by default alignment settings using CLC genomics workbench 7.0.3 (CLC bio).

source_name: colorectal tumor

extract_protocol:
Sample extraction: Macrodissected colon tumor sample, fresh frozen
Fresh frozen samples were homogenized manually with an RNAse free pestle. Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, 740955.250) according to the manufacturer’s instructions.All samples were ethanol precipitated. RNA integrity of each sample was assessed using a Fragment Analyzer (Advanced Analytical).
Sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina, RS-122-2101) according to the manufacturer’s instructions.

tag: tumor model

value: APC-KRAS

tag: genotype/variation

value: APC-1638N/wt, Vil-KrasG12V/+, Bcl9-loxP/loxP, Bcl9l-loxP/loxP


title: APC-KRAS Bcl9/9l-WT tumor 15

description:
Sample name: BAK_15
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.


title: APC-KRAS Bcl9/9l-WT tumor 17

description:
Sample name: BAK_17
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.


title: APC-KRAS Bcl9/9l-WT tumor 14

description:
Sample name: BAK_14
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.


title: APC-KRAS Bcl9/9l-WT tumor 16

description:
Sample name: BAK_16
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.


title: APC-KRAS Bcl9/9l-KO tumor 32_2a

description:
Sample name: BAK_32_2a
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.

value: APC-1638N/wt, Vil-KrasG12V/+, Bcl9-loxP/loxP, Bcl9l-loxP/loxP, Vil-Cre


title: APC-KRAS Bcl9/9l-KO tumor 5

description:
Sample name: BAK_5
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.


title: Bcl9/9l-WT healthy colon epithelium 2

description:
Sample name: Col_2
Loss of Bcl9/9l proteins was assessed in EDTA extracts of healthy murine colon epithelium.

source_name: EDTA-dissociated colon epithelial cells

extract_protocol:
Sample extraction: EDTA-dissociated colon epithelial cells, fresh frozen
Fresh frozen samples were homogenized manually with an RNAse free pestle. Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, 740955.250) according to the manufacturer’s instructions.All samples were ethanol precipitated. RNA integrity of each sample was assessed using a Fragment Analyzer (Advanced Analytical).
Sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina, RS-122-2101) according to the manufacturer’s instructions.

value: healthy epithelial cells

value: Bcl9-loxP/loxP, Bcl9l-loxP/loxP


title: APC-KRAS Bcl9/9l-KO tumor 32_1b

description:
Sample name: BAK_32_1b
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.


title: APC-KRAS Bcl9/9l-KO tumor 32_1a

description:
Sample name: BAK_32_1a
Loss of Bcl9/9l proteins was assessed in a genetic model (mutated APC and Kras) of murine colon cancer.


title: Bcl9/9l-WT healthy colon epithelium 3

description:
Sample name: Col_3
Loss of Bcl9/9l proteins was assessed in EDTA extracts of healthy murine colon epithelium.


title: Bcl9/9l-KO healthy colon epithelium 5

description:
Sample name: Col_5
Loss of Bcl9/9l proteins was assessed in EDTA extracts of healthy murine colon epithelium.


title: AOM-DSS Bcl9/9l-WT tumor 4

description:
Sample name: AOM_WT_4
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.

value: AOM-DSS


title: AOM-DSS Bcl9/9l-WT tumor 3

description:
Sample name: AOM_WT_3
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: Bcl9/9l-WT healthy colon epithelium 1

description:
Sample name: Col_1
Loss of Bcl9/9l proteins was assessed in EDTA extracts of healthy murine colon epithelium.


title: AOM-DSS Bcl9/9l-KO tumor 2

description:
Sample name: AOM_KO_2
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: AOM-DSS Bcl9/9l-KO tumor 4

description:
Sample name: AOM_KO_4
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: AOM-DSS Bcl9/9l-WT tumor 1

description:
Sample name: AOM_WT_1
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: AOM-DSS Bcl9/9l-KO tumor 3

description:
Sample name: AOM_KO_3
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: Bcl9/9l-KO healthy colon epithelium 7

description:
Sample name: Col_7
Loss of Bcl9/9l proteins was assessed in EDTA extracts of healthy murine colon epithelium.


title: AOM-DSS Bcl9/9l-KO tumor 1

description:
Sample name: AOM_KO_1
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: SOX_PARE_rep2

status: Public on Nov 07 2015

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

description: PARE-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of adapter using Cutadapt (Martin M, 2011)
Removal of reads in which the sequence after adapter trimming was > 22 nt or < 19 nt (because PARE protocol should generate tags of ~20 nt)
Alignment using Tophat2, restricted to annotated parts of human genome; only used reads that mapped uniquely for remainder of analyses (parameters: -N 0 --bowtie1 -T -x 1; other set as default)
Peaks were detected using custom pipeline (PyDegradome) that detects peaks by comparing a test and a control sample
Genome_build: ENSEMBL GRch37
Supplementary_files_format_and_content: tab-delimited files listing peaks detected when using SOX samples as the test samples and  the GFP samples as controls, or viceversa (the latter ouput was used to generate a set of control SOX-independent peaks for other analyses); each peak is represented by three lines, one giving the position and various parameters, the second listing read counts in control sample and the third listing the read counts in the test sample. Read counts are listed starting 10 nt before the 5' end of the detected peak and ending 10 nt after the3'  end of the peak; user-defined parameters for PyDegradome: ratio = 4, window =4, confidence interval = 99.99%

growth_protocol: HEK 293T were grown in high-glucose DMEM + 10% fetal bovine serum

extract_protocol:
Total RNA was harvested and extracted using Trizol reagent; as part of PARE protocol, poly(A)+ RNA was purified from total RNA
Library were constructed following method in Zhai et al., Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods 2014; 67(1):84–90.

treatment_protocol: cells were transduced with inducible shRNA against Xrn1 and treated with doxycycline (replicate 1) or transfected twice with siRNA against Xrn1 (replicate 2); 4 days after start of treatment, either GFP-SOX or GFP alone were transfected for ~24 hrs

tag: transfected construct

value: GFP-SOX

tag: knock-down

value: Xrn1 siRNA


title: H3K27me2_H3K27me3_dim-5_HT1

city: Eugene

first: Eric

last: Selker

state: OR

address: 1585 E 13th Ave

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
The raw data (fastq) files were mapped to the Ncrassa12 genome using Bowtie2, generating .sam files
Samtools was next used to convert sam files to bam files, remove duplicates, sort the bam files, and create index files for the bam files to view later.
The bam files, along with their indices, were then converted into tdf files using IGVtools.  The Ncrassa12 genome was used as a reference genome and window size was set to 200 bp.
Genome_build: Ncrassa version 12
Supplementary_files_format_and_content: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp.  The tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV.

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC

extract_protocol:
Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP or 30 min in 1% formaldehyde for GFP ChIP.  Tissue was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power.  DNA was purified using the QIAquick PCR purification kit  and eluted in 25 μl of water.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 18 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking

tag: tissue

value: mycelia

value: anti-H3K27me2/3 (Active Motif, 39535)

tag: genotype

value: dim5 nonsense mutation in SET domain


title: GFP_PARE_rep2

description: PARE-seq

value: GFP


title: SOX_PARE_rep1

description: PARE-seq

value: Xrn1 shRNA


title: caki_KDM5C_abcam_2

description: ChIP-seq analysis on untreated growing Caki-1 cells. Immunoprecipitation was performed using  anti-KDM5C  antibody (Abcam). Replicate 2

value: kidney; Derived from metastatic site - skin

tag: chip antibody

value: Abcam


title: H3K27me2_H3K27me3_dim-7_L488stop

value: dim7 nonsense mutation at L448


title: AOM-DSS Bcl9/9l-WT tumor 5

description:
Sample name: AOM_WT_5
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: GFP_PARE_rep1

description: PARE-seq


title: AOM-DSS Bcl9/9l-WT tumor 2

description:
Sample name: AOM_WT_2
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: AOM-DSS Bcl9/9l-KO tumor 5

description:
Sample name: AOM_KO_5
Loss of Bcl9/9l proteins was assessed in chemically induced AOM-DSS murine colon tumors.


title: Esrrb_Hh_2

status: Public on Nov 06 2015

city: San Marcos

first: Yuan

last: Lu

address: university drive

institute: Xiphophorus Genetic Stock Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adaptor sequence were trimmed off, then low quality basecall was trimmed off, at last, low quality sequence reads were filtered out.
Short sequencing reads were aligned to mus musculus genome mm9, gene expression value is quantified as FPKM.
Differentially gene expression was analyzed using Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: text files with FPKM data; output from cufflinks

growth_protocol: Paracrine Hh-responsive mouse embryonic fibroblast cells NIH3T3 were obtained from American Type Culture Collection (ATCC, Cat. No. CRL-1658). NIH3T3 cells are cultured in DMEM supplement with 10% Newborn Calf Serum (NBCS). The cells were transfected with pcDNA3.1 (Zeo+) empty vector (Promega, Madison, WI) as control, or pcDNA3.1 (Zeo+)-Esrrb expression vector using Fugene HD (Promega, Madison, WI), and were further selected by supplementing 150ug/ml Zeocine (Invitrogen, Grand Island, NY) to the culture medium for three weeks. Two independent transfections were performed and established cells from each transfection were pooled together.

extract_protocol:
Total RNA was extracted using Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured until confluent, and are treated with 1:100 diluted Hh-CM for 48 hours, in phenol-red free DMEM supplement with 5% NBCS.

tag: passages

value: five to six

value: embryonic fibroblast


title: pcDNA3.1_Hh_1


title: Esrrb_1


title: pcDNA3.1_Hh_2


title: Esrrb_2


title: H3K27me2_H3K27me3_TSH-1

value: TSH1 deletion


title: Bcl9/9l-KO healthy colon epithelium 6

description:
Sample name: Col_6
Loss of Bcl9/9l proteins was assessed in EDTA extracts of healthy murine colon epithelium.


title: pcDNA3.1_2


title: Esrrb_Hh_1


title: pcDNA3.1_1


title: Trim33.WT2.testis.RNAseq

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

data_processing:
For ChIP-seq, sequenced reads were provided by the sequencing service provider (Active Motif) in a .fastq.gz format. Reads were mapped to the mouse mm9 genome by the service provider, using the BWA program using default settings.
For ChIP-seq, peak calling was done by the service provider (Active Motif) using MACS (Version 1.4.2) by first filtering out duplicate reads and reads with a mapping quality of less than 25, then using default parameters and the following options -s 75--bw 200 -m 10 30 –p 0.0000001
For RNA-seq, sequenced reads were provided by the sequencing service provider (Australian Genome Research Facility) in a .fastq.gz format. Reads were mapped to the mouse mm9 genome using the program Tophat (version 2.0.11) with the following parameters: -I 100000 --library-type=fr-unstranded --read-edit-dist 3 --no-coverage-search --read-mismatches 3
For RNA-seq, read counts for gene exons were extracted using the program htseq-count (version 0.6.1) with the options -s no -m intersection-strict. Normalization and differnetial gene expression was assessed using the R-package DEseq, with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: For processed ChIP-seq data, Bigwig format files showing the fragment density for 32 nucleotide binds along the genome. For processed RNA-seq data, tab-delimited text files include raw read counts for each of the samples

extract_protocol:
Testis were removed from mice and flash frozen on dry ice, RNA was harvested using Trizol reagent. Libraries were constructed using the illumina TruSeq RNA Sample Preparation kit (cat Num RS-122-2201).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: Testis

tag: age

value: 84 days post partum


title: Trim33.Het3.testis.RNAseq


title: Trim33.Het1.testis.RNAseq


title: Trim33.WT1.testis.RNAseq


title: Trim33.Het4.testis.RNAseq


title: Trim33.WT3.testis.RNAseq


title: CBP-gp ChIP-seq

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

data_processing:
Uniquely mapping reads where mapped to the Drosophila melanogaster genome (release 5)
Log2 ratio between IP and input read density was calculated
Data was median smoothed using 100 bp windows
Smoothed ratio values every 35 bp was extracted
Genome_build: Drosophila melanogaster genome release 5
Supplementary_files_format_and_content: sgr files containing smoothed log2 ratio of IP over input (35 bp resolution)

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila S2 cells were grown to a density of 0.2 - 1 x 107 cells/ml and fixed in 1 % formaldehyde for 15 min at ambient temperature. The reaction was quenched by 0.16 M glycine pH 7.0 for 5 min and washed in PBS.

extract_protocol:
After fixation, the cells were washed and sonicated using a Bioruptor (Diagenode) to generate chromatin extract. Chromatin extract was cleared by centrifugation and used in ChIP with affinity-purified anti-Drosophila CBP antibodies, pre-bound to a mix of Protein A and G Dynabeads. CBP bound DNA was purified, and sent to Uppsala Genome Center for SOLiD (TM) ChIP-Seq Library preparation (Rev date 18 March 2010), size selection (100-150 bp + adapters 90bp ≈250 bp), and SOLiD sequencing.
Libraries were prepared for sequencing using standard SOLiD protocols

value: affinity-purified guinea-pig antibody raised against aa 1-178 in Drosophila CBP (nejire)

tag: cell line


title: CBP-rb ChIP-seq

value: affinity-purified rabbit antibody raised against aa 2540-3190 in Drosophila CBP (nejire)


title: input CBP-rb


title: input CBP-gp


title: Tip60_ChIPseq

city: Illkirch

first: Sarina

last: Ravens

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling was done with the Illumina pipeline (1.8.2) and FASTQ files have been generated using CASAVA v1.8.2.
The sequence alignment was done by the software Bowtie (0.12.7).
FASTQ files have been generated using CASAVA v1.8.2.
Bed files were generated by the Illumina pipeline (1.8.2) and sorted for unique reads.
Genome_build: mm9
Supplementary_files_format_and_content: bed files

source_name: mESCs

extract_protocol:
mESCs were cross-linked with 1% formaldehyde for 10 minutes at room temperature, lysded and shared mechanically using the Covaris E210 to obtain a chromatin fragment size of 200-500bp. For the IP histone-DNA complexes 6 ug of the anti-Tip60 antibody mixture (RLPV, CLGT and CLHF polyclonal sera) was used, which was a gift from B. Amati. DNA was purified with Qiaquick (Qiagen) columns.
Ten ng of precipitated DNA was used for Solexa sequencing. To create a genomic library we followed the instructions of the NEBNext protocol (Biolabs, E6240). Librarys were validated with the Agilent Bioanalyzer.


title: gDNA_CD4_H3K4me3_Control_rep15

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

department: Department of Biomedicine

country: Estonia

institute: University of Tartu

data_processing:
Read trimming and quality control. Raw reads were trimmed with Trim Galore! version 0.3.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the paired-end mode and the Phred score threshold set to 30. The quality control with FastQC version 0.10.0 was performed before and after trimming.
Alignment. The trimmed paired-end reads were aligned to the human reference genome (hg19) with bowtie2 version 2.0.2 allowing clipping of read ends with the option --local.
Filtering of aligned reads. The SAMtools software suite (http://www.htslib.org/) was used to retain only properly paired alignments with mapping quality ≥ 30 and the duplicated reads were removed with MarkDuplicates from the Picard tools (http://broadinstitute.github.io/picard/).
Peak calling. Peaks were called with MACS2 (https://github.com/taoliu/MACS/). Both cell types (CD4+ and CD8+ T cells) and ChIP experiments (H3K4me3 and H3K27ac) have two input sample BAM files that were merged into single BAM files, which were used as controls in peak calling. The mappable genome size (-g 2627947484) for 50 bp reads was taken from [1]. Only the peaks with q-value <0.01 were considered to be significant. Peaks were filtered against the blacklisted regions given in wgEncodeDacMapabilityConsensusExcludable.bed.gz (available on the series record).   1. Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R et al. Fast computation and applications of genome mappability. PLoS One, 2012;7:e30377.
Differential enrichment analysis. The analysis of differentially enriched peaks was performed with the R/Bioconductor package “DiffBind” [1]. Samples were read in in batch and then split by cell type and histone modification. The statistical methods for assessing the difference of the peak signals in GD and control samples were provided by the R/Bioconductor package “edgeR” [2]. Before the statistical test, the counts in the input sample were subtracted from counts in the ChIPed samples and the resulting library sizes were used for normalization. Peaks with a fold change difference of 1.5 and with the FDR adjusted p-value < 0.01 were considered for further analysis.    1. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature, 2012;481:389-93.  2. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010;26:139-40.
Genome_build: hg19
Supplementary_files_format_and_content: The peak lists are in ENCODE narrowPeak format that is described on the UCSC Genome Browser help pages: http://genome-euro.ucsc.edu/FAQ/FAQformat.html

source_name: Genomic DNA, CD4 cells, H3K4me3 ChIP, healthy control

extract_protocol:
Peripheral blood mononuclear cells were extracted using Ficoll-Paque (GE Healthcare) gradient centrifugation. CD8+ T-cells and CD4+ T cells were purified by consecutive positive separation using microbeads (CD4+ #130-045-101; CD8+ #130-045-201) and AutoMACS technology (Miltenyi Biotec) according to the manufacturer's protocol. The purified cells were fixed in 1% formaldehyde and stored as cell pellets in a -80°C freezer. ChIP assays were performed using Auto Histone ChIP-seq kit (Diagenode) with minor modifications. Briefly, IP-Buffer (2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, 1% Triton X-100) was used in exchange for kit Buffer H in IP reactions. DNA from 4-6 x 106 cells was fragmented with the Bioruptor sonicator (Diagenode) to fragments of 200-400 basepairs. Sheared chromatin from 1 million cells was immunoprecipitated with 2 μg of anti-H3K4me3 antibody (Millipore 07-473) or 2 μg of anti-H3K27Ac antibody (Abcam Ab4729) using the SX-8G IP-Star Automated System (Diagenode). ChIP-DNA was purified with MinElute PCR Purification Kit (Qiagen).
The purified ChIP and input DNAs were quantified by Qubit 2.0 Fluorometer (Life Technologies) prior to library preparation with the Ovation® Ultralow DR Multiplex System 1-96 kit (NuGeneration Limited) according to manufacturer’s instructions. The barcoded libraries were quantified by Qubit 2.0 Fluorometer and validated with Agilent 2200 TapeStation analysis (Agilent Technologies, Inc.). The ChIP-seq libraries were sequenced with HiSeq 2500 (Illumina) producing 50 bp paired-end reads. Phage PhiX sequencing library was included as 1% spike-in in the sequencing runs.

value: blood

tag: diagnosis

value: Healthy control

tag: cell type

value: CD4 T cells

tag: gender

value: Female


title: Trim33.Het2.testis.RNAseq

tag: strain


title: gDNA_CD8_H3K4me3_Control_rep17

source_name: Genomic DNA, CD8 cells, H3K4me3 ChIP, healthy control

value: CD8 T cells


title: gDNA_CD8_H3K4me3_input_rep1

description: Input DNA sample from CD8 cells for H3K4me3 ChIPs

source_name: Genomic DNA, CD8 cells, input, Graves' patient

value: Graves' patient

value: Input


title: gDNA_CD8_H3K4me3_input_rep2

source_name: Genomic DNA, CD8 cells, input, Healthy control

value: Male


title: gDNA_CD8_H3K4me3_Graves_rep13

source_name: Genomic DNA, CD8 cells, H3K4me3 ChIP, Graves' patient


title: gDNA_CD8_H3K4me3_Graves_rep14


title: gDNA_CD4_H3K4me3_input_rep2

description: Input DNA sample from CD4 cells for H3K4me3 ChIPs

source_name: Genomic DNA, CD4 cells, input, Healthy control


title: gDNA_CD4_H3K4me3_Control_rep14


title: gDNA_CD4_H3K4me3_Graves_rep14

source_name: Genomic DNA, CD4 cells, H3K4me3 ChIP, Graves' patient


title: gDNA_CD4_H3K4me3_Graves_rep13


title: gDNA_CD4_H3K4me3_Graves_rep11


title: gDNA_CD8_H3K4me3_Control_rep14


title: gDNA_CD4_H3K4me3_input_rep1


title: gDNA_CD4_H3K4me3_Control_rep13


title: gDNA_CD8_H3K4me3_Graves_rep12


title: gDNA_CD8_H3K4me3_Control_rep16


title: gDNA_CD4_H3K4me3_Graves_rep10


title: gDNA_CD8_H3K4me3_Graves_rep11


title: gDNA_CD4_H3K4me3_Graves_rep9


title: gDNA_CD8_H3K4me3_Graves_rep10


title: gDNA_CD8_H3K4me3_Control_rep12