title: L1.5_smRNA_seq

city: Wuhan

first: Zhonghui

last: Tang

address: Huazhong Agricultural University

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by BGI miRNA analysis pipeline
Genome_build: miRBase database (Version 15)
Supplementary_files_format_and_content: tab-delimited text files include small RNA length, small RNA frequency and small RNA sequence

organism: Triticum aestivum

source_name: spike tissue

extract_protocol: We analyzed spikes from anthers at three developmental stages (including the T0 stage): 1.5-mm anthers in which secondary sporogenous cells were formed; 2.2-mm anthers in which all cell layers were present and mitosis had ceased; and 3.0-mm anthers at the meiotic division stage (Tang et al., 2011). To maximize the morphological synchronicity of samples at each individual stage, approximately 20 spikes were collected from primary stems at each stage. The spikes at corresponding stages were also harvested from stems of plants kept in control conditions, using leaf age index and anther length as guide. Total RNAs were isolated from spike tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. After total RNA isolation, size-selected small RNAs (smRNAs) 16 to 30 nt in length were obtained from total RNA by size fractionation. SmRNA libraries were constructed following the instructions of the manufacturer.

tag: developmental stage

value: anther length ~ 1.5 mm

tag: treatment

value: Cold treatment


title: L3.0_smRNA_seq

status: Public on Mar 29 2012

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

value: anther length ~ 3.0 mm


title: T0_smRNA_seq

value: anther length ~ 1.0 mm

value: Control


title: L2.2_smRNA_seq

value: anther length ~ 2.2 mm


title: C2.2_smRNA_seq


title: C1.5_smRNA_seq


title: hnRNP L-like over expression

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

department: Biochemistry

country: Germany

institute: University of Giessen

data_processing: Alignments against the human genome (assembly hg19) and exon-junctions (based on human mRNA and EST data) were done using BWA (Burrows-Wheeler Aligner). The alternative splicing targets were predicted using both read-density and junction-read-counts information (Rösel et al., EMBO J. 2011).

organism: Homo sapiens

source_name: hnRNP L-like over expression

growth_protocol: Cells were grown in RPMI medium supplemented with 10% FBS, 2 mM L-glutamine, 1 mM sodium pyrivate, Pen-Strep, and 50 uM beta-mercaptoethanol.

extract_protocol: Libraries were constructed from total RNA and the mRNA-Seq libraries were prepared for Solexa high-throughput sequencing by Illumina standard protocols. Sequencing was done in a single-read, 76-base mode.

treatment_protocol: DG75 cells were transfected with 2 ug LL-V5-His plasmid, or as a control, 1 ug eGFP.

tag: cell line


title: C3.0_smRNA_seq


title: H3K9acS10ph_Kc_ChIPseq

city: Atlanta

first: Wendy

middle: A

last: Kellner

state: GA

address: 1510 Clifton Road

department: Biology

country: USA

institute: Emory University

description: Chromatin IP against H3K9acS10ph

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting.
Peaks: Wiggle files were generated and peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS1.4.0alpha2) algorithm using equal numbers of unique reads for input and ChIP samples.
Genome_build: DM3

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

tag: cell line source

value: Female late embryo derived cell line

tag: antibody


title: MCF10A

city: Detroit

first: RAYMOND

middle: R

last: MATTINGLY

state: MI

address: 540 East Canfield

department: Pharmacology

institute: Wayne State University

data_processing:
Sequence reads were obtained and mapped to the human (March, 2006) genomes using novoalign with default parameters. Only the reads that map to the unique genome positions were considered.
Genome Build:
MCF10A_2_novo.bed: hg18
MCF10A_3_novo.bed: hg18

source_name: normal mammary epithelial cells

growth_protocol: All the experiments in the present study were conducted using in vitro three dimensional (3D) organotypic culture models with reconstituted basement membrane (rBM).  In the 3D rBM overlay protocol, single cells were seeded onto culture dishes previously coated with polymerized rBM (Cultrex®) and were overlaid with media containing 2% rBM when the cells had attached.

extract_protocol: We used Trizol to extract the RNA from our samples. Libraries of template molecules for high throughput DNA sequencing were prepared using Illumina mRNA Sequencing Sample Preparation kit.  First, using Sera-Mag oligo (dT) beads, mRNA molecules were purified from the total RNA. Then the purified mRNA samples were fragmented under elevated temperature conditions.  Subsequently, first strand cDNA synthesis was done from the cleaved RNA fragments using reverse transcriptase and random primers.  This was followed by second strand synthesis using DNA polymerase I and RNaseH (using SuperScript II from Invitrogen).  These cDNA fragments were then subjected to repair end process with T4 DNA polymerase and Klenow.   The 3’ ends were then adenylated to prepare for adapter ligation.  After paired end ligation of adapters, the samples were purified on 1.2% agarose recovery FlashGelTM.  The library of products of desired size (150-200bp) was then selected for further enrichment with 15 cycles of polymerase chain reaction (PCR) amplification.

tag: disease status

value: normal

tag: Stage


title: JIL-1_Kc_ChIPseq

description: Chromatin IP against JIL-1


title: liver input

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the mouse genome (July 2007; mm9, NCBI Build 37) using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).

organism: Mus musculus

source_name: liver input

extract_protocol:
Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.
Standard Illumina DNA library construction

treatment_protocol: harvest time protocol : Mice were entrained for 3 days on a 12 hour light/dark cycle before livers were harvested at ZT8.

tag: strain

tag: gender

value: male

tag: age

value: 20 wk

tag: time point

tag: tissue

value: liver

tag: chip antibody


title: H3K4me3_Kc_ChIPseq

description: Chromatin IP against H3K4me3


title: H3K4me1_Kc_ChIPseq

description: Chromatin IP against H3K4me1


title: streptomycin treatment

status: Public on Mar 28 2012

city: Saint Paul

first: Timothy

middle: J.

last: Johnson

state: MN

address: 1971 Commonwealth Ave

department: Veterinary Biosciences

institute: University of Minnesota

data_processing:
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition.
Genome Build:
Streptomycin_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1
Strep_treatment_genomemappedreads_statistical_output.txt: NC_000913.2

organism: Escherichia coli

source_name: bacteria grown at 37° C with shaking until log phase with streptomycin treatment

growth_protocol: E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5.

extract_protocol: Cells were pelleted and RNA was purified using a commercially available RNA extraction kit (Qiagen).  RNA preparations were then subjected to a DNase treatment to eliminate DNA contamination from the sample (Qiagen).  A treatment was also included to deplete ribosomal RNA using a commercially available kit (MicrobExpress, Ambion).  The two biological replicates for each growth condition were pooled for sequencing.

value: streptomycin (50 µg/mL final concentration)


title: ampicilin treatment

data_processing:
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition.
Genome Build:
Ampicilin_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1
Amp_Treatment_genomemappedreads_statistical_output.txt: NC_000913.2

source_name: bacteria grown at 37° C with shaking until log phase with ampicilin treatment

value: ampicillin (50 µg/mL final concentration)


title: H3K27ac_Kc_ChIPseq

description: Chromatin IP against H3K27ac


title: no treatment

data_processing: cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition.

source_name: bacteria grown at 37° C with shaking until log phase


title: 3B13_d12_MethylC-seq

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

description: MethylC-seq

data_processing: 100 bp fastq reads were truncated to 76 bp and aligned to the genome (hg18) using BS-Seeker, allowing for up to two mismatches with the reference sequence.  Custom perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage.  Methylation data for both DNA strands were combined.  Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates.  Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%

source_name: H9 cells

growth_protocol: H9 hESCs were grown feeder-free on Matrigel and transduced with either the DNMT3B KD or MIS virus.  GFP-positive colonies were mechanically dissociated to isolate individual subclones.  The individual subclones were on Matrigel in hESC medium (modified Eagle's medium/F-12 containing 20% KnockOut serum replacer, 0.1 mM nonessential amino acids, 1 mM L-glutamine, 0.1 mM beta-mercaptoethanol) that had been conditioned on mouse embryonic fibroblasts (MEFs) and then supplemented with 4 ng/ml bFGF

extract_protocol: DNA from H9 human embryonic stem cells was fragmented to ~300bp using Diagenode's Bioruptor.  To create the sequencing libraries, 5 ug of DNA was end repaired using 1X T4 DNA ligase buffer, 400 uM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 minutes at 20 degrees Celsius.  After PCR purifying (Qiagen), adenine bases were appended to the ends using 1X NEB 2 buffer, 200 uM dATP, and 15 U Klenow Fragment (3' to 5' exo-, NEB) for 30 minutes at 37 degrees Celsius.  After another DNA purification using the PCR MinElute kit (Qiagen), 3 uL of Illumina's methylated sequencing adapters were ligated on using 1X ligase buffer and 5 uL Quick T4 DNA Ligase (NEB) for 30 minutes at room temperature.  After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions.  The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.

treatment_protocol: In order to differentiate hESCs into neuroepithelium (NE), colonies were detached from feeders (day 0) with dispase (1 mg/mL) until the edges of the colonies began to lift.  The clumps of cells were gently blown off and washed once with hESC medium without bFGF.  The aggregates were cultured in hESC medium (without bFGF) for 4 days in Ultra Low Attachment flasks.  Then, aggregates were grown in neural induction medium (DMEM/F12, N2 supplement, nonessential amino acids, 2 Î¼g/ml heparin, and 10 ng/ml bFGF) for up to 3 additional days. On day 7, the aggregates were plated onto laminin-coated tissue culture plates.

tag: days differentiated

value: 12 days

tag: sirna

value: DNMT3B knockdown #3B13


title: mis24_d12_MethylC-seq

description: MethylC-seq

value: mismatch control #24


title: 3B13_hESC_MethylC-seq

description: MethylC-seq

value: 0 days


title: REV-ERB beta

source_name: liver_REV-ERB beta_ChIP

value: REV-ERB beta


title: mis24_hESC_MethylC-seq

description: MethylC-seq


title: sperm X1-3

city: San Francisco

first: Michelle

middle: M

last: Chan

institute: UCSF

description:
Msp1 digested bisulfite converted genomic DNA
Reduced representation bisulfite sequencing libraries are designed to enrich for a consistent subset of CpGs in the genome using MspI digestion (C'CGG cutting), adapater ligation and bisulfite conversion to generate base resolution maps of cytosine methylation on a consistent genome scale

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
sperm-X1-3.cpgs.txt: mm9

source_name: sperm X1-3

growth_protocol: Isolated embryos were cultured in C02 buffered KSOM medium supplemented with amino acids (Millipore) until isolation at a perscribed stage.  Oocytes and embryos were isolated from gonadotropin primed females and sperm collected from the cauda epidinymis of recently mated male mice

extract_protocol: Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries

treatment_protocol: NoPB embryos were subjected to laser assisted polar body biopsy using an 8 mm piezo pipette in batches of 5 embryos in M2 medium microdrops (Millipore) under mineral oil and cultured to the described stage.  ICM was isolated using rabbit anti mouse serum (Sigma Aldrich) and Guinea pig complement serum to ablate the outer trophectoderm of E3.5 blastocysts.  E6.5 and E7.5 embryos were dissected from the implanted decidua in PBS.

value: sperm


title: sperm2 X1-3

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
sperm2-X1-3.cpgs.txt: mm9

source_name: sperm2 X1-3


title: florfenicol treatment

data_processing:
cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition.
Genome Build:
Florfenicol_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1
Flor_treatment_genomemappedreads_statistical_output.txt: NC_000913.2

source_name: bacteria grown at 37° C with shaking until log phase with florfenicol treatment

value: florfenicol (30 µg/mL final concentration)


title: H3K27acS28ph_Kc_ChIPseq

description: Chromatin IP against H3K27acS28ph


title: REV-ERB alpha

source_name: liver_REV-ERB alpha_ChIP

value: REV-ERB alpha


title: 4 cell No PB BDF1-X1-4

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
4cellNoPB-BDF1-X1-4.cpgs.txt: mm9

source_name: 4 cell No PB

value: 4 cell

value: polar body removed


title: 8 cell No PB BDF1-X1-3

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
8cellNoPB-BDF1-X1-3.cpgs.txt: mm9

source_name: 8 cell No PB

value: 8 cell


title: zygote NoPB2-BDF1-X1-5

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
zygoteNoPB2-BDF1-X1-5.cpgs.txt: mm9

source_name: zygote No PB

value: zygote


title: 4 cell No PB BDF1-X1-5

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
4cellNoPB-BDF1-X1-5.cpgs.txt: mm9


title: zygote NoPB2-BDF1-X1-4

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
zygoteNoPB2-BDF1-X1-4.cpgs.txt: mm9


title: zygote No PB BDF1-X1-5

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
zygoteNoPB-BDF1-X1-5.cpgs.txt: mm9


title: zygote No PB BDF1-X1-4

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
zygoteNoPB-BDF1-X1-4.cpgs.txt: mm9


title: 2 cell No PB BDF1-X1-5

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
2cellNoPB-BDF1-X1-5.cpgs.txt: mm9

source_name: 2 cell No PB

value: 2 cell


title: E75-BDF1-BDF1-2

description: Msp1 digested bisulfite converted genomic DNA

data_processing:
E75-BDF1-BDF1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

extract_protocol:
Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries
Reduced representation bisulfite sequencing libraries are designed to enrich for a consistent subset of CpGs in the genome using MspI digestion (C'CGG cutting), adapater ligation and bisulfite conversion to generate base resolution maps of cytosine methylation on a consistent genome scale

value: BDF1 x X1 cross


title: E65-BDF1-BDF1-4

data_processing:
E65-BDF1-BDF1-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: Liver-2

data_processing:
Liver-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

source_name: Liver

value: Liver


title: Heart-1

data_processing:
Heart-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

source_name: Heart

value: Heart


title: Brain-4

data_processing:
Brain-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

source_name: Brain

value: Brain


title: E65-BDF1-BDF1-3

data_processing:
E65-BDF1-BDF1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: Liver-1

data_processing:
Liver-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: E65-BDF1-X1-1

data_processing:
E65-BDF1-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: sperm X1-4

data_processing:
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.
Genome Build:
sperm-X1-4.cpgs.txt: mm9

source_name: sperm X1-4


title: ICM-BDF1-X1-4

data_processing:
ICM-BDF1-X1-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

source_name: ICM

value: ICM


title: ICM-BDF1-BDF1-5

data_processing:
ICM-BDF1-BDF1-5.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

value: BDF1 x BDF1 cross


title: ICM-BDF1-AJ-3a

data_processing:
ICM-BDF1-AJ-3a.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

value: BDF1 x AJ cross


title: ICM-BDF1-X1-4a

data_processing:
ICM-BDF1-X1-4a.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: ICM-BDF1-AJ-3

data_processing:
ICM-BDF1-AJ-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: ICM-AJ-C57B6-2a

data_processing:
ICM-AJ-C57B6-2a.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

value: AJ x C57B6 cross


title: E65-BDF1-BDF1-2

data_processing:
E65-BDF1-BDF1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell No PB 2-BDF1-X1-2

data_processing:
8cellNoPB2-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

value: subjected to laser assisted polar body biopsy


title: Brain-2

data_processing:
Brain-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: ICM-AJ-C57B6-2

data_processing:
ICM-AJ-C57B6-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell No PB 2-BDF1-X1-1

data_processing:
8cellNoPB2-BDF1-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: ICM-BDF1-X1-6

data_processing:
ICM-BDF1-X1-6.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell No PB 2-BDF1-X1-3

data_processing:
4cellNoPB2-BDF1-X1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell-BDF1-BDF1-1

data_processing:
8cell-BDF1-BDF1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell-BDF1-X1-8

data_processing:
8cell-BDF1-X1-8.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell-BDF1-BDF1-5

data_processing:
8cell-BDF1-BDF1-5.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell-BDF1-BDF1-4

data_processing:
8cell-BDF1-BDF1-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell-BDF1-BDF1-3

data_processing:
8cell-BDF1-BDF1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell No PB 2-BDF1-X1-1

data_processing:
4cellNoPB2-BDF1-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell-BDF1-X1-6

data_processing:
4cell-BDF1-X1-6.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell No PB -BDF1-X1-1

data_processing:
4cellNoPB-BDF1-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell No PB -BDF1-X1-3

data_processing:
4cellNoPB-BDF1-X1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell No PB 2-BDF1-X1-2

data_processing:
4cellNoPB2-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell-BDF1-X1-5

data_processing:
4cell-BDF1-X1-5.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell-BDF1-X1-2

data_processing:
8cell-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell No PB -BDF1-X1-1

data_processing:
8cellNoPB-BDF1-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell-BDF1-X1-2

data_processing:
4cell-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell-BDF1-BDF1-4

data_processing:
4cell-BDF1-BDF1-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 8cell No PB -BDF1-X1-2

data_processing:
8cellNoPB-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell No PB -BDF1-X1-3

data_processing:
2cellNoPB-BDF1-X1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell No PB -BDF1-X1-2

data_processing:
2cellNoPB-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell-BDF1-X1-4

data_processing:
2cell-BDF1-X1-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell No PB -BDF1-X1-1

data_processing:
2cellNoPB-BDF1-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell-BDF1-BDF1-3

data_processing:
2cell-BDF1-BDF1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell-BDF1-X1-2

data_processing:
2cell-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell-BDF1-BDF1-1

data_processing:
2cell-BDF1-BDF1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: zygote No PB -BDF1-X1-3

data_processing:
zygoteNoPB-BDF1-X1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

source_name: zygote


title: zygote No PB -BDF1-X1-2

data_processing:
zygoteNoPB-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: zygote-BDF1-BDF1-1

data_processing:
zygote-BDF1-BDF1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: oocytes-BDF1-2

data_processing:
oocytes-BDF1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

source_name: oocytes

value: oocytes


title: zygote-BDF1-X1-4

data_processing:
zygote-BDF1-X1-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: zygote-BDF1-X1-3

data_processing:
zygote-BDF1-X1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: sperm-C57B6-2

data_processing:
sperm-C57B6-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

source_name: sperm

value: sperm


title: oocytes-C57B6-4

data_processing:
oocytes-C57B6-4.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: oocytes-BDF1-1

data_processing:
oocytes-BDF1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 2cell No PB 2-BDF1-X1-2

data_processing:
2cellNoPB2-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: zygote-BDF1-BDF1-2

data_processing:
zygote-BDF1-BDF1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: 4cell-BDF1-BDF1-1

data_processing:
4cell-BDF1-BDF1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: sperm-X1-1

data_processing:
sperm-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: Period[0], CT68

status: Public on Mar 27 2012

city: Philadelphia

first: Michael

last: Hughes

state: PA

address: 421 Curie Bvd, Brb 835

institute: UPenn

description:
Per68
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT68.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT68.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT68

growth_protocol: 3- to 5-day-old adult female flies were maintained on standard food and housed at 25 degrees in complete darkness.

extract_protocol: Total RNA was purified using the PicoPure kit from MDS. RNA amplification and rRNA depletion were performed using the RiboAmp kit from MDS (polyA) and the Ovation RNAseq kit from NuGEN (non-polyA).  Fragmentation, cDNA synthesis, and adaptor ligation were performed using standard protocols.

treatment_protocol: Brains were manually dissected in PBS at CT24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, and 68.

tag: background strain

value: Canton S

tag: genotype

value: adult

value: female

value: brain


title: Period[0], CT64

description:
Per64
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT64.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT64.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT64

tag: developmental stage


title: Period[0], CT60

description:
Per60
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT60.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT60.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT60


title: Period[0], CT52

description:
Per52
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT52.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT52.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT52


title: Period[0], CT56

description:
Per56
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT56.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT56.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT56


title: Period[0], CT48

description:
Per48
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT48.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT48.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT48


title: Period[0], CT40

description:
Per40
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT40.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT40.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT40


title: Period[0], CT44

description:
Per44
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT44.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT44.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT44


title: Period[0], CT28

description:
Per28
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT28.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT28.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT28


title: zygote No PB -BDF1-X1-1

data_processing:
zygoteNoPB-BDF1-X1-1.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

tag: treatment

value: zygote


title: Period[0], CT32

description:
Per32
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT32.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT32.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT32


title: 4cell No PB -BDF1-X1-2

data_processing:
4cellNoPB-BDF1-X1-2.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.


title: Period[0], CT24

description:
Per24
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT24.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT24.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT24


title: oocytes-ICR-3

data_processing:
oocytes-ICR-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

value: ICR


title: Canton S, CT68

description:
CS68
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT68.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT68.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT68

value: wildtype


title: Foxtail millet stem

status: Public on Mar 31 2012

city: Shenzhen

first: Zhijun

last: Zheng

address: #11 Building 2/F│Beishan Industrial Zone│Yantian District

institute: BGI

description: Sequenced reads were generated from millet stem

data_processing:
Align reads against millet genome using Tophat v1.2.0 with parameters set to be "--max-intron-length 20000 -m 1 -r 20 --mate-std-dev 20  --coverage-search --microexon-search". This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AGTC00000000.
Genome_build: AGTC01000000

organism: Setaria italica

source_name: stem

growth_protocol: seeding on nutrient medium, grew in greenhouse for 40days

extract_protocol: total RNA extraction protocol and standard 200bp library protocol provided by Illumina

tag: landrace

value: Zhang-gu

value: stem


title: Canton S, CT64

description:
CS64
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT64.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT64.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT64


title: Canton S, CT60

description:
CS60
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT60.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT60.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT60


title: Canton S, CT40

description:
CS40
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT40.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT40.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT40


title: the immunoprecipitated AGO2 complex from Col-0 under 100Gy γ-irradiation/1.5h recovery, 13-day seedlings

city: Beijing

first: Yijun

last: Qi

address: #7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute of Biological Sciences

data_processing: All reads obtained from Illumina GA IIx were sorted into respective libraries by parsing their barcodes. Then the adaptor sequences were removed using ‘vectorstrip’ in the EMBOSS package. Small RNA reads with length of 18-28nt were retained.

organism: Arabidopsis thaliana

source_name: 13-day seedlings

growth_protocol: All plants were grown in Murashige and Skoog (MS) medium at 16-h-light/8-h-dark photoperiod. Human DR-GFP/U2OS cells [U2OS derivative cell line harboring an integrated HR reporter construct (DR-GFP)] were grown in Dulbecco's modified Eagle's medium with 10% fetal bovine serum.

extract_protocol: Small RNAs were extracted from whole plants or the purified AGO2 complex by Trizol reagent (Invitrogen), resolved on a 15% denaturing PAGE gel, and visualized by SYBR-Gold (Invitrogen) staining. Gel slices within the range of 18-28 nt were excised, and the RNAs were eluted and purified for small RNA library construction. Cloning of small RNAs from Arabidopsis and human cells was carried out essentially as described in Mi et al., Cell, 2008.  The Illumina GA IIx was used for sequencing.

treatment_protocol: Columbia-0 plants were treated with 100 Gy γ-irradiation and placed in a growth chamber at 22℃ for 1.5 h. Seedlings without γ-irradiation treatment were used as controls.

value: Columbia-0 wild type

tag: ip

value: seedlings

value: 13-day old

tag: rna

value: small RNA


title: the immunoprecipitated AGO2 complex from Col-0 under 0Gy γ-irradiation/1.5h recovery, 13-day seedlings


title: Canton S, CT52

description:
CS52
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT52.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT52.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT52


title: 2cell No PB 2-BDF1-X1-3

description: Msp1 digested bisulfite converted genomic DNA

data_processing:
2cellNoPB2-BDF1-X1-3.cpgs.txt; genome build: mm9
Sequence reads were aligned to the Mouse Genome Build 37 (mm9) using a computational pipeline taking into account bisulfite conversion and the strain background. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The cpg files were joined and the positions were tiled to non-overlapping 100bp windows to produce the mousePMD100bpMe.txt file.

value: BDF1 x X1 cross


title: Canton S, CT44

description:
CS44
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT44.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT44.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT44


title: Canton S, CT32

description:
CS32
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT32.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT32.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT32


title: T (DSB-triggering) line, Col-0 13-day seedlings

description: contains 3 techinical replicates

tag: line

value: T


title: DU.GUS line,Col-0 13-day seedlings

description: contains 3 techinical replicates


title: Canton S, CT24

description:
CS24
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT24.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT24.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT24


title: E14_medium.MethylCap

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

country: Netherlands

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

description: 1 to 30 ng was used for library preparation using the ChIP-seq DNA sample Prep Kit (Illumina, cat# IP-102–1001) using the recommended protocol. After ligation of adapters, a 300 bp band is excised using the E-Gel system (Invitrogen), which correspond to a 234 bp fragment of genomic DNA. PCR enrichment of adapter-ligated DNA was done using 14 cycles of PCR.

data_processing: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse (mm9) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Mus Musculus mm9 genome assembly.

source_name: Embryonic stem cells

growth_protocol:
HCT116 cells were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (all Gibco/Invitrogen) at 37 °C in 5% CO2 atmosphere.
ES cells were cultured in normal cell culture containing ES-grade serum supplemented with LIF. These cells were grown on gelatin-coated plates

extract_protocol: MethylCap (Capturing of methylated DNA) was done using in automated procedure using a SX-8G/IP-StarTM robot (Diagenode). 2 ug of His6-GST-MBD (Diagenode) was incubated with 1 ug of fragmented DNA in binding buffer (BB, 20 mM Tris-HCl pH 8.5, 0.1% Triton X-100) with 200 mM NaCl in a final volume of 200 ul. This solution is mixed at 4 C for 2 h. Magnetic GST-beads were prepared by washing 35 µl of a well-mixed beads suspension (Promega) with 200 µl of binding buffer + 200 mM NaCl at 4 C. The suspension was mixed and a magnet was used to collect the beads. After removal of the supernatant the procedure is repeated once. After the second wash the supernatant is removed, but the beads are not allowed to get dry. The GST-MBD solution is added to the washed beads and this suspension is mixed for another hour at 4C. After removal of the supernatant (the 'flow-through') the beads-GST-MBD-DNA complexes are washed/eluted. 200 µl of binding buffer with increasing concentrations of NaCl is added and the suspension is rotated for 10 min at 4 C. Beads are captured on the magnet, and the supernatant is collected. Three different eluates were collected (LOW, MEDIUM, HIGH), corresponding 500 mM, 600 mM and 800 mM NaCl. For MethylCap-BS-seq, only HIGH eluates were used.

tag: origin

value: Embryonic stem cells

tag: technique

value: MethylCap-sequencing

tag: binding protein

tag: binding protein vendor

value: Diagenode


title: E14_high.MethylCap


title: the immunoprecipitated AGO2 complex from RxT line, Col-0 13-day seedlings

description: contains two biogical replicates

tag: strain

value: RxT


title: Canton S, CT48

description:
CS48
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT48.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT48.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT48

value: Canton S

value: adult

tag: gender

value: female

tag: tissue

tag: time point


title: Canton S, CT28

description:
CS28
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT28.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT28.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT28

value: brain


title: Period[0], CT36

description:
Per36
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
Per_CT36.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT36.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, per0, CT36


title: RxT line in AGO4 corresponding wild-type background, 13-day seedlings

value: La-er AGO4 corresponding wild-type


title: Canton S, CT36

description:
CS36
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT36.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT36.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT36

value: wildtype


title: RxT line in ago2-1 mutant background, 13-day seedlings

value: Columbia-0 ago2-1 mutant


title: RxT line in AGO2 corresponding wild-type background, 13-day seedlings

value: Columbia-0 AGO2 corresponding wild-type


title: RxT line in NRPE1 corresponding wild-type background, 13-day seedlings

value: Columbia-0 NRPE1 corresponding wild-type

value: seedlings


title: RxT line in nrpd1-3 mutant background, 13-day seedlings

value: Columbia-0 nrpd1-3 mutant

value: 13-day old

value: small RNA


title: RxT line in NRPD1 corresponding wild-type background, 13-day seedlings

value: Columbia-0 NRPD1 corresponding wild-type


title: RxT line in nrpe1-11 mutant background, 13-day seedlings

value: Columbia-0 nrpe1-11 mutant


title: RxT line in RDR6 corresponding wild-type background, 13-day seedlings

value: Columbia-0 RDR6 corresponding wild-type


title: Canton S, CT56

description:
CS56
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011).  The following parameters were used: "-limitBowtieNU -limitNU 25".

*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.

Genome Build:
CS_CT56.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
CS_CT56.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)

source_name: Adult Drosophila brain, wildtype, CT56


title: DU.GUSxT line,Col-0 13-day seedlings

description: contains 3 techinical replicates

value: Columbia-0 wild type


title: RxT line in RDR2 corresponding wild-type background, 13-day seedlings

value: Columbia-0 RDR2 corresponding wild-type

value: RxT


title: RxT line in rdr6-11 mutant background, 13-day seedlings

value: Columbia-0 rdr6-11 mutant


title: RxT line in rdr2-1 mutant background, 13-day seedlings

value: Columbia-0 rdr2-1 mutant


title: RxT line in DCL3 corresponding wild-type background, 13-day seedlings

value: Columbia-0 DCL3 corresponding wild-type


title: RxT line in DCL4 corresponding wild-type background, 13-day seedlings

value: Columbia-0 DCL4 corresponding wild-type


title: RxT line in dcl4-2 mutant background, 13-day seedlings

value: Columbia-0 dcl4-2 mutant


title: RxT line in dcl3-1 mutant background, 13-day seedlings

value: Columbia-0 dcl3-1 mutant


title: RxT line in ATR corresponding wild-type background, 13-day seedlings

value: Columbia-0 ATR corresponding wild-type


title: RxT line in dcl2-1 mutant background, 13-day seedlings

value: Columbia-0 dcl2-1 mutant

value: seedlings


title: R (DGU.US) line,Col-0 13-day seedlings

value: R

value: 13-day old


title: RxT line in ago4-1 mutant background, 13-day seedlings

value: La-er ago4-1 mutant

value: small RNA


title: RxT line,Col-0 13-day seedlings


title: human DR-GFP/U2OS cells that were transfected with a control plasmid and collected at 20 h post-transfection

description: human DR-GFP/U2OS cells that were transfected with a plasmid having the same vector backbone but missing I-SceI and collected at 20 h post-transfection as control. contains three biogical replicates

source_name: DR-GFP/U2OS cells

tag: cell line


title: human DR-GFP/U2OS cells that were transfected with pCBASce plasmid and collected at 24 h post-transfection

description: contains three biogical replicates

value: transfected with pCBASce plasmid and collected at 24 h post-transfection.


title: mES_Dnmt-TKO_H3K27m3_ChIP-BS

description: 100 ng ChIP DNA or 10 ng MethylCap DNA was first subjected to end-repair in a 30 µl reaction containing 6 units T4 DNA polymerase, 2.5 units DNA Polymerase I (Large Klenow Fragment), 20 units T4 Polynucleotide Kinase (all New England Biolabs), dATP, dCTP, dGTP and dTTP (0.125 mM each), and 1x T4 Ligase buffer with ATP for 30 min at 20C. Illumina sequencing generates sequences corresponding to the 5'-ends of the input DNA fragments. Therefore, fill-in of 5'-overhangs did not alter sequenced DNA methylation patterns. Purification was performed using a standard phenol:chloroform:isoamyl alcohol (25:24:1) protocol and ethanol precipitation. DNA was then adenylated in a 20 µl reaction containing 10 units Klenow Fragment (3'->5' exo-) (New England Biolabs), 0.5 mM dATP and 1x NEB buffer 2 for 30 min at 37C. After phenol extraction and ethanol precipitation, Illumina genomic DNA adapters containing 5-methylcytosine instead of cytosine (atdbio, Southampton), preventing deamination during bisulfite conversion, were ligated. In a 20 µl reaction, DNA was incubated with 1.5 µM preannealed adapters, 2000 units T4 DNA Ligase (NEB) and 1x T4 Ligase buffer with ATP, for 16-20 h at 16C. Adapter-ligated DNA fragments were subsequently purified by phenol extraction and ethanol precipitation, and size-selected on gel. 50 ng sheared and dephosphorylated E-coli K12 genomic DNA was added to adapter-ligated DNA as carrier during size-selection and bisulfite conversion. DNA was run on 2.5% Nusieve 3:1 Agarose (Lonza) gels. Lanes containing marker (50 bp ladder New England Biolabs) were stained with SYBR Green (Invitrogen), and size regions to be excised were marked with toothpicks. To obtain 80-280 bp (low) and 280-430 bp (high) insert sizes, adapter-ligated DNA fragments from 200-400 and 400-550 bp, respectively, were excised. The Illumina adapters cause the fragments to run slower, presumably due to the forked structure. Note that after PCR, dsDNA libraries appear at 140-340 bp and 340-490 bp, in accordance with exact sizes. DNA was isolated from gel using the MinElute Gel Extraction kit (QIAGEN). The low and high libraries were kept separate in subsequent steps. Before proceeding to bisulfite conversion, analytical PCRs were performed to check the libraries. Amplifications were performed in 10 µl reactions containing 0.3 µl template DNA (from 20 µl eluted after size-selection), 0.5 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), Illumina primers LPX 1.1 and 2.1 (0.3 µM each), dNTPs (0.25 mM each), 1x Turbo Cx buffer, under the following thermocycler conditions: 94C for 5 min,  n x (94C for 30 s, 65C for 30 s, 72C for 1 min) and 72C for 7 min. We tested three different cycle numbers (n) - 10, 15 and 20 cycles - and analyzed PCR products on 4-20% TBE Criterion precast gels (BioRad) and subsequent SYBR Green staining. Adapter-ligated and size-selected DNA was subjected to two subsequent 5h bisulfite treatments using the EpiTect Bisulfite kit (QIAGEN) following the manufacturer's protocol for DNA isolated from FFPE tissue samples. After bisulfite conversion, analytical PCRs were performed as before to determine the minimum number of cycles required in the final amplification step for each sample. In this case, tested cycle numbers were several cycles higher as before bisulfite conversion, and 15, 19 and 22 PCR cycles were performed. The minimum cycle number for final large-scale amplification was determined as the lowest cycle number that generated enough PCR product of the desired size range to be visualized on analytical gels as above. Large-scale amplification was performed by 8 reactions of 25 µl, containing 3 µl DNA (from 40 µl eluted after bisulfite conversion, remains were stored at -80C as back-up), 1.25 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), primer LPX 1.1 and 2.1 (0.3 µM each), dNTPs (0.25 mM each), 1x Turbo Cx buffer and thermocycler conditions as above. Amplified libraries were purified with the MinElute PCR Purification kit (QIAGEN), and subsequently purified from gel essentially as described above; whole gels were stained with SYBR Green and no carrier DNA was added. Final libraries were analysed on analytical 4-20% TBE Criterion precast gels (BioRad), and measured by Quant-iT dsDNA HS Assays (Invitrogen). The protocol for preparation of captured DNA for bisulfite deep sequencing was adapted from 27-29. Sequence reads were generated on the Illumina Genome Analyzer IIx using a standard 36-base protocol. After sequencing low and high library reads were combined.

data_processing: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina HiSeq2000 platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Mapping of bisulfite-converted sequence reads was done using a custom-made pipeline. To reduce PCR artifacts, a maximum of three identical sequence reads was allowed. To perform mapping independently of DNA methylation status, sequence reads were in silico bisulfite-converted (C to T), and subsequently mapped to two different in silico converted mm9 genome sequences; one C to T converted genome and one G to A converted genome. Reads mapping to both genomes were discarded, which typically represented a very minor fraction of all reads. Mapping was done using the Burrows-Wheeler Aligner (BWA), with default settings allowing a single mismatch. The obtained mapping positions were used to align unconverted sequence reads with their corresponding unconverted genomic sequence and to subsequently determine the methylation status of each sequenced cytosine within a CpG context, both on the forward strand as well as on the reverse strand.

extract_protocol: ES cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sheared using a Biouptor (Diagenode). Sonicated chromatin was centrifuged for 5 min and then incubated overnight with 2 ug of antibody and protein A/G beads (Santa Cruz). Beads were washed six times with different buffers at 4C: twice with solution of composition 0.1% SDS, 0.1% DOC, 1% Triton, 150 mM NaCl, HEG, once with the solution same as before but with 500 mM NaCl, once with solution of composition 0.25 M LiCl, 0.5% DOC, 0.5% NP-40, HEG and twice with HEG. Precipitated chromatin was eluted with 400 µl of elution buffer (1% SDS, 0.1 M NaHCO3), incubated at 65C for 4 h in the presence of 200 mM NaCl, phenol extracted and precipitated with 20 ug of glycogen at -20C overnight.

value: Embryonic stem cells

value: ChIP-bisulfite sequencing

tag: antibody

tag: antibody vendor

value: Millipore

tag: antibody catalog #

tag: antibody lot #


title: mES_V6.5_H3K27m3_ChIP-BS


title: mES_V6.5_H3K27m3_ChIP

data_processing: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina HiSeq2000 platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse (mm9) reference genome using the Illumina Analysis Pipeline allowing, one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Mus Musculus mm9 genome assembly.

value: ChIP-sequencing


title: human DR-GFP/U2OS cells that were transfected with pCBASce plasmid and collected at 16 h post-transfection

description: contains three biogical replicates

tag: treatment

value: transfected with pCBASce plasmid and collected at 16 h post-transfection.


title: human DR-GFP/U2OS cells that were transfected with pCBASce plasmid and collected at 12 h post-transfection

description: contains three biogical replicates

value: transfected with pCBASce plasmid and collected at 12 h post-transfection.