city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: MeDIP-Seq analysis of breast luminal epithelial cell from RM035 (HS1393) using Illumina Genome Analyzer IIx
library name: HS1393
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: N/A ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM493615_UCSF-UBC.Breast_Luminal_Epithelial_Cells_Individual_2.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.Breast_Luminal_Epithelial_Cells_Individual_2.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of Breast, Luminal_Epithelial Cells, Individual 2 MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment in Breast, Luminal Epithelial Cells, Individual 2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.2858
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

**********************************************************************

ANALYSIS FILE NAME: GSM493615_UCSF-UBC.Breast_Luminal_Epithelial_Cells.MeDIP-Seq.RM035.bed
ANALYSIS ALIAS: HS1393-1_42ENEAAXX-HS1393-1_42F10AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on Breast Luminal Epithelial Cells, Donor RM035 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4246
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4703
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4531
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9867
IROC_PERCENTILE: 91
POISSON_SCORE: 0.7198
POISSON_PERCENTILE: 91

**********************************************************************

ANALYSIS FILE NAME: GSM493615_UCSF-UBC.Breast_Luminal_Epithelial_Cells.MeDIP-Seq.RM035.wig
ANALYSIS ALIAS: HS1393-1_42ENEAAXX-HS1393-1_42F10AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM035 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4222
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BLEC MeDIP 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Luminal Epithelial Cells MeDIP-Seq Donor RM035 EA Release 2

QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.4703
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4531
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9867
IROC_PERCENTILE: 91
POISSON_SCORE: 0.7198
POISSON_PERCENTILE: 91

**********************************************************************

extract_protocol: library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: female

tag: body site

value: Breast

tag: histological type

value: Luminal epithelial cell

tag: is tumor

value: No

value: primary cell

value: breast luminal epithelial cell


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H1 (hESC-01) Cells; renlab.H3K27ac.hESC-01.01

status: Public on Mar 22 2010

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL313
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1596
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM466732_UCSD.H1.H3K27ac.LL313.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC-01.01-renlab.H3K27ac.hESC-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the H1 Cell Line, Library LL313 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5173
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.3355
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3968
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9855
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5188
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM466732_UCSD.H1.H3K27ac.LL313.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC-01.01-renlab.H3K27ac.hESC-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H1 Cell Line, Library LL313 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4477
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K27ac 13
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K27ac Library LL313 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.3355
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3968
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9855
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5188
POISSON_PERCENTILE: 50

**********************************************************************

molecule: genomic DNA

organism: Homo sapiens

source_name: hESC-01; renlab.H3K27ac.hESC-01.01

extract_protocol:
Library construction protocol:
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 25 and 45

tag: medium

value: mTeSER

tag: Sex

value: Male

tag: batch

value: Histone H3K27ac

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: orc1-161_G2_37C_Nucleosomes_rep1-2

status: Public on Mar 19 2010

city: Durham

first: Matthew

middle: Lucas

last: Eaton

state: NC

address: LSRC Room C315, Research Dr

department: Pharmacology & Cancer Biology

institute: Duke University

description: MNase digestion of isogenic orc1-161 temperature sensitive mutant mononucleosomal fragments at heatshock temperature, replicates 1 & 2 combined

data_processing: Mapview alignment files were generated with the program MAQ, which was fed the raw data in the Illumina fastq format, and a build of the S. cerevisiae S288C from SGD (Jan 2006). All of the default options were used, except that the maximum number of allowed mismatches was raised to 3. All further processed data was generated using in-house analysis methods described in the GSE16926_nucleosomes_2009_supp.pdf.

organism: Saccharomyces cerevisiae

growth_protocol: wild-type (W303) and mutant (orc1-161) yeast strains were grown at the permissive temperature (23C) in rich medium for all experiments.

extract_protocol: Mononucleosomes were prepared from 1.5 x 10^9 cells that were cross-linked with .1% formaldehyde for 30 minutes and quenched with 125 mM glycine. After cross-linking, the cells were spheroplasted and treated with 80 units of micrococcal nuclease to generate mononucleosome fragments. 50 ng of isolated mononucleosomal DNA fragments were prepared for sequencing using the genomic DNA sample preparation kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Cells were arrested at G2/M in 10 µg/ml nocodazole for two hours and then shifted to the restrictive temperature (37C) for two hours.

tag: synchronized

value: G2 / nocodazole

tag: temperature

tag: fragmentation

value: micrococcal nuclease


title: WT_G1_37C_Nucleosomes

description: MNase digestion of WT mononucleosomal fragments at heatshock temperature

source_name: WT W303

growth_protocol: Yeast were grown at the permissive temperature (23C) in rich medium for all experiments.

treatment_protocol: Cells were arrested for two hours at G1 in 0.25 µg/ml alpha factor at permissive temperature (23C) and then shifted for two additional hours at restrictive temperature (37C). Mononucleosomes were prepared from cells that were cross-linked with .1% formaldehyde for 30 minutes and quenched with 125 mM glycine. After cross-linking, the cells were spheroplasted and treated with 80 units of micrococcal nuclease to generate mononucleosome fragments.


title: WT_Asynchronous_23C_Nucleosomes

description: MNase digestion of WT mononucleosomal fragments

data_processing: Mapview alignment files were generated with the program MAQ, which was fed the raw data in the Illumina fastq format, and a build of the S. cerevisiae S288C from SGD (released 12/16/2005). All of the default options were used, except that the maximum number of allowed mismatches was raised to 3. All further processed data was generated using in-house analysis methods described in the GSE16926_nucleosomes_2009_supp.pdf.

value: Asynchronous


title: Rattlesnake-big-tg

status: Public on Mar 16 2010

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Rattlesnake, large trigeminal ganglion

library_source: transcriptomic

data_processing: blastx versus Gallus gallus RefSeq v2.1

molecule: polyA RNA

organism: Crotalus atrox

source_name: Rattlesnake, large trigeminal ganglion

extract_protocol: Paraformaldehyde fixation and trizol extraction. Short read RNA sequencing by polyadenylation and circularization: RNA fragments were dephosphorylated, purified by filtration followed by gel purification for ~30 bp fragments, tailed with poly-A polymerase, reverse transcribed with anchored oligo-dT primer, cDNA was circularized

tag: tissue

value: large trigeminal ganglion


title: Rattlesnake-drg

description: Rattlesnake, dorsal root ganglion

source_name: Rattlesnake, dorsal root ganglion

value: dorsal root ganglion


title: Boa-drg

description: Boa, dorsal root ganglion

organism: Corallus hortulana

source_name: Boa, dorsal root ganglion


title: AG18359_Pol_II_ChIPSeq_IgG_Rep2

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

description: Chromatin IP against normal mouse IgG

data_processing: FASTQ files are either the sequence.txt files from the Illumnia pipeline (which exclude low quality reads) or, when available, are generated from the Illumina export.txt files which include all reads. Both types of alignment files, eland_result.txt and eland_multi.txt, are directly out of the Illumnia pipeline and unmodified. The narrowPeak files are the scored results generated from the PeakSeq pipeline (http://www.ncbi.nlm.nih.gov/pubmed/19122651?dopt=Abstract) and formatted in the UCSC narrowPeak format.

organism: Pan troglodytes

source_name: Lymphoblastoid Cells

growth_protocol: Lymphoblastoid cell lines were grown in RPMI-1640 Medium, supplemented with glutamine, 15% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 6-8 x10^5 cells/ml.

extract_protocol: Chomatin immunoprecipitation was performed as previously described (Euskirchen et al. 2007; Rozowsky et al. 2009). 2 x 10^8 cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched by adding glycine to a final concentration of 125 mM. Nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 × 30-s intervals), such that the chromatin fragments ranged from 50-2000kb. Clarified lysates were divided in half and treated overnight at four degrees Celsius with 24μg of either mouse monoclonal 8WG16 antibody (Covance MMS-126R) or normal mouse IgG (Millipore #12-371). Protein-DNA complexes were captured on Protein A agarose beads (Upstate #16-156) and eluted in 1% SDS TE buffer at 65°C. Following cross-link reversal and purification, the ChIP DNA sequencing libraries were generated according to Illumina DNA Sample Kit Instructions (Illumina Part # 0801– 0303). The protocol was modified such that enzymes were obtained from other suppliers, as described in Auerbach et al. 2009.

treatment_protocol: For Pol II ChIP-Seq, cells were not treated prior to cross-linking.

tag: cell line

tag: cell type

value: Lymphoblastoid cell

tag: chip antibody

value: normal mouse IgG


description:
design description: ChIP-Seq input analysis of H1 embryonic stem cell line (HS1348) using Illumina Genome Analyzer IIx
library name: HS1348
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 35.3 ug
SIZE_FRACTION: 80-280 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM450270_UCSF-UBC.H1.Input.TOTAL-hEScd2-2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1348-1_305H8AAXX-HS1348-1_42F2TAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library TOTAL-hEScd2-2 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4312
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0173
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.1575
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.8421
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5711
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM450270_UCSF-UBC.H1.Input.TOTAL-hEScd2-2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1348-1_305H8AAXX-HS1348-1_42F2TAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library TOTAL-hEScd2-2 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4361
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 Input 2
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line ChIP-Seq Input Library TOTAL-hEScd2-2 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0173
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.1575
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.8421
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5711
POISSON_PERCENTILE: 100

**********************************************************************

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: cell line

value: male

tag: body site

value: Embryo ICM

tag: histological type

value: Embryonic stem cell

value: No


title: WT_G2_ORC_rep1-2

description:
ChIP against ORC
GSM424494_acs_locations.bed: a file with our calls for exact ORC positions based on both sequence motifs and the ChIP-seq data (ORC binds a motif called the ACS)

extract_protocol: ChIP extracts were prepared from 5x10^8 cells. An anti-ORC polyclonal antibody was used for the ChIP. 500 ng of the immunoprecipitated DNA was prepared for sequencing using the genomic DNA sample preparation kit (Illumina) according to the manufacturer's instructions and was size-selected (250-350 bp) after the addition of the adapter oligomers and the PCR amplication step.

treatment_protocol: Cells were arrested at G2/M in 10 µg/ml nocodazole for two hours.

tag: antibody

value: polyclonal ORC

value: sonication


title: Rattlesnake-small-tg

description: Rattlesnake, small trigeminal ganglion

source_name: Rattlesnake, small trigeminal ganglion

value: small trigeminal ganglion


title: ORC2_KC167_2 extraction2_seq1 aliquote 1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is ChIP DNA. Antibody information listed below:

official name: dORC2
target name: Drosophila ORC2p
host: Rabbit
antigen: purified full length protein
clonal: Polyclonal
purified: Crude
company: Lab
catalog: Stephen P. Bell MIT
reference: Austin et al 1999

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1    Processed data are obtained using following parameters: read length is 36   ORC_ChIPseq_analysis:DM:1 protocol. Processing and peaking calling for ORC solexa data.

organism: Drosophila melanogaster

source_name: ORC2_KC167_2 extraction2_seq1 channel_1

growth_protocol: Growth of modENCODE cell lines for large scale chromatin extract preparation from asynchronous cultures.

extract_protocol:
Cross linking and chromatin extraction protocol for Drosophila ChIP experiments.
Chromatin IP of a chromatin extract with an antibody.
Generation of a genomic library suitable for Illumina sequencing.

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

tag: genotype

value: se/e

tag: sex

value: Female


title: ORC2_KC167_1 extraction1_seq1 aliquote 1

source_name: ORC2_KC167_1 extraction1_seq1 channel_1


title: WT_G2_37C_Nucleosomes_rep1-2

description: MNase digestion of WT mononucleosomal fragments at heatshock temperature, replicates 1 & 2 combined

treatment_protocol: Cells were arrested at G2/M in 10 µg/ml nocodazole for two hours and then shifted to the restrictive temperature (37C) for two hours. Mononucleosomes were prepared from cells that were cross-linked with .1% formaldehyde for 30 minutes and quenched with 125 mM glycine. After cross-linking, the cells were spheroplasted and treated with 80 units of micrococcal nuclease to generate mononucleosome fragments.

value: G2 / nocodazole

value: micrococcal nuclease


title: ORC2_ML_DmBG3_c2_Input_1 extraction3_seq1 aliquote 1

description: channel ch1 is input DNA;

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: ORC2_KC167_Input_1 extraction3_seq1 aliquote 1

description: channel ch1 is input DNA;


title: MCM_KC167_2 extraction2_seq1 aliquote 1

description:
channel ch1 is ChIP DNA. Antibody information listed below:

official name: Pan MCM2-7 Antibody
target name: MCM2-7 complex
host: Mouse
antigen: MCM2-7 complex Walker B motif
clonal: Monoclonal
purified: Crude
company: Lab
catalog: Anthony Schwacha
reference: PMID: 12403810
short description: Monoclonal antibody against purified yeast MCM complex. Works cross species.

source_name: MCM_KC167_2 extraction2_seq1 channel_1


title: ORC2_ML_DmBG3_c2_1 extraction1_seq1 aliquote 1

description:
channel ch1 is ChIP DNA. Antibody information listed below

official name: dORC2
target name: Drosophila ORC2p
host: Rabbit
antigen: purified full length protein
clonal: Polyclonal
purified: Crude
company: Lab
catalog: Stephen P. Bell MIT
reference: Austin et al 1999


title: ORC2_ML_DmBG3_c2_2 extraction2_seq1 aliquote 1


title: Boa-tg

description: Boa, trigeminal ganglion

source_name: Boa, trigeminal ganglion

value: trigeminal ganglion


title: MCM_KC167_1 extraction1_seq1 aliquote 1

source_name: MCM_KC167_1 extraction1_seq1 channel_1


title: MCM_KC167_Input_1 extraction3_seq1 aliquote 1

description: channel ch1 is input DNA;


title: ORC2_S2_DSRC_Input_1 extraction3_seq1 aliquote 1

description: channel ch1 is input DNA;

value: Male


title: ORC2_S2_DRSC_1 extraction1_seq1 aliquote 1


title: ORC2_S2_DRSC_2 extraction2_seq1 aliquote 1


title: Nonpit-drg

description: Non-pit snakes, dorsal root ganglion

organism:
Pantherophis obsoletus lindheimeri
Masticophis flagellum testaceus

source_name: Non-pit snakes, dorsal root ganglion

value: dorsal root ganglion

tag: synonym

value: Elaphe obsoleta lindheimerii


title: D11

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

country: Australia

institute: QIMR

description:
We sequenced 12 small RNA libraries using Illumina's GAII platform.
Processed data file build: hg18

data_processing: Illumina Pipeline software followed by miRanalyzer for miRNA analysis

molecule: total RNA

source_name: mucosal melanoma

extract_protocol: The small RNA libraries were constructed using a Digital Gene Expression (DGE) Small RNA sample prep kit (Illumina, San Diego, Ca) as per the manufacturer's instructions.

value: secondary mucosal melanoma


title: Nonpit-small-tg

description: Non-pit snakes, small trigeminal ganglion


title: MM426

source_name: secondary cutaneous melanoma

value: secondary cutaneous melanoma


title: Nonpit-big-tg

description: Non-pit snakes, large trigeminal ganglion

value: large trigeminal ganglion


title: MEL202

source_name: primary uveal melanoma

value: primary uveal melanoma


title: MM472

source_name: secondary cutaneous melanoma from a chronically sun-damaged body site


title: Python-drg

description: Python, dorsal root ganglion

organism: Python regius

source_name: Python, dorsal root ganglion


title: D10

source_name: acral melanoma

value: secondary acral melanoma


title: MELB

source_name: melanocyte

value: primary melanocyte


title: Python-tg

description: Python, trigeminal ganglion

source_name: Python, trigeminal ganglion


title: MM603


title: GM19239_CTCF_REP1

status: Public on Mar 15 2010

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: Chromatin IP against CTCF

data_processing:
Sequences from each experiment were aligned to the genome using Maq (Li et al., 2008) and those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes). The resulting digital signal was converted to a continuous wiggle track using F-Seq that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Discrete DNase HS, FAIRE, and ChIP sites (peaks) were identified from DNase/ChIP-seq using F-Seq by setting a Parzen cutoff based on ROC curve analysis using peaks and non-peaks identified from DNase/ChIP-chip using NimbleGen Human ENCODE tiling arrays (1% of the genome).
Regions of enriched signal in either DNaseI HS,  or ChIP experiments. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008b). Significant regions were determined by performing ROC analysis of sequence data using data from the 1% ENCODE arrays, and determining a cut-off value at approximately the 95% sensitivity level. The solid vertical line in the peak represents the point with highest signal. ENCODE Peaks tables contain a p-value for statistical significance. For these data, this was determined by fitting the data to a gamma distribution

source_name: lymphoblastoid cells

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Boyle et al., 2008a, Crawford et al., 2006). Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. DNaseI digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina (Solexa) sequencing. DNase-seq data were verified using material that was hybridized to NimbleGen Human ENCODE tiling arrays (1% of the genome). Multiple independent growths (replicates) were compared to verify the reproducibility of the data.

tag: individual


title: GM19238_CTCF_REP2

description: Chromatin IP against CTCF


title: GM12892_CTCF_REP2

description: Chromatin IP against CTCF


title: GM12892_CTCF_REP1

description: Chromatin IP against CTCF


title: GM12891_CTCF_REP2

description: Chromatin IP against CTCF


title: GM12891_CTCF_REP1

description: Chromatin IP against CTCF


title: GM19238_CTCF_REP1

description: Chromatin IP against CTCF


title: GM19240_CTCF_REP2

description: Chromatin IP against CTCF


title: GM19240_CTCF_REP1

description: Chromatin IP against CTCF


title: GM12878_CTCF_REP1

description: Chromatin IP against CTCF


title: GM12878_CTCF_REP2

description: Chromatin IP against CTCF


title: GM19239_DNAse_REP2

description: DNase-Seq


title: GM19238_DNAse_REP2

description: DNase-Seq


title: GM19239_DNAse_REP1

description: DNase-Seq


title: GM19239_CTCF_REP2

description: Chromatin IP against CTCF


title: MM466


title: GM19238_DNAse_REP1

description: DNase-Seq


title: GM19240_DNAse_REP1

description: DNase-Seq


title: GM19240_DNAse_REP2

description: DNase-Seq


title: GM12892_DNAse_REP2

description: DNase-Seq


title: D20


title: GM12891_DNAse_REP2

description: DNase-Seq


title: AX4-24-whole organism-1

status: Public on Mar 12 2010

city: Houston

first: Anup

last: Parikh

address: One Baylor Plaza

department: Molecular & Human Genetics

institute: Baylor College of Medicine

description:
dd_AX4_all_24_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)

data_processing:
We sequenced the cDNA libraries to 35 bases on an Illumina high-throughput  Illumina Genome Analyzer II using the standard manufacturer’s pipeline (versions 1.2 and 1.3).  The resulting FASTQ files were mapped in multiple steps using a short-read alignment software from Novocraft according to the manufacturer’s default parameters (http://www.novocraft.com).  First the reads were mapped to reference genome. Sequence reads from D. discoideum were mapped to the May 13, 2009 build of D. discoideum from dictyBase (http://dictybase.org), with the second duplicated region of chromosome 2 (nucleotide 3015984 to 3768555) and the latter half of the RDNA palindrome (nucleotide 42801 to 78150) masked.  Sequence reads from D. purpureum were mapped to the D. purpureum genome assembly (manuscript in preparation). Second, all sequences that did not map to the chromosomal sequences were mapped to a library of all possible splice junctions that we have determined using the annotated gene models.  The gene models for D. discoideum are defined by the May 13, 2009 build from dictyBase (http://dictybase.org) and D. purpureum by the published genome annotations (manuscript in preparation). The nucleotide coverage was calculated as the sum of all reads starting at a given position.

File naming convention: [species]_[strain]_[cell type]_[time point]_[biological replicate] where dd = D. discoideum and dp = D. purpureum

-- *.coverage files contain coverage for each nucleotide on the forward (F) and reverse (R) strands across the entire genome.  Gene models can be found in the supplement of the publication.

organism: Dictyostelium discoideum

source_name: AX4 whole organism cell type

growth_protocol: We grew cells to mid-log phase in association with Klebsiella aerogenes bacteria on SM-agar plates. To induce development, we collected the cells, washed them as described, deposited them on nitrocellulose filters and developed them in the dark at 22°C.

extract_protocol: At each time point we collected 1X108 cells directly into 1 ml Trizol reagent (Life Technologies) and extracted total RNA according to the manufacturer’s recommended protocol. To prepare cDNA we subjected 20 µg of total RNA to one round of PolyA selection on oligo(dT) beads (Dynal).  We fragmented 125 ng of the resulting mRNA to an average size of 200 bases using divalent cations (Fragmentation Buffer, Ambion) at 70°C for 5 minutes and terminated the reaction with the stop buffer (Ambion).  We precipitated the fragments by adding NaOAC, pH 5.2, glycogen and 70% (final concentration) Ethanol, washed the precipitate once with 70% ethanol and resuspended it in RNAse free water.  We prepared first-strand cDNA with super script II reverse transcriptase (Invitrogen) and 3µg of random hexamer primers.  We then synthesized second strand cDNA with DNA Polymerase I and RNaseH in a illumina (Illumina) custom buffer.  We purified the products on a QiaQuick PCR column (Qiagen) and eluted them in 30 μl EB buffer (Qiagen).  We further processed the cDNAs using the Genomic DNA Sequencing Sample Prep Kit (Illumina) according to the manufacturer’s recommended protocol.

tag: strain

tag: supporting culture organism

value: Klebsiella aerogenes

tag: developmental time point

value: whole organism

tag: biological replicate

tag: poly selection


title: MM386

tag: cell line


title: NC4-48-prespore-4

description:
dd_NC4_prespore_48_4.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)

source_name: NC4 prespore cell type

tag: cell type

value: prespore


title: NC4-48-prestalk-4

description:
dd_NC4_prestalk_48_4.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)

source_name: NC4 prestalk cell type

value: prestalk


title: NC4-48-prestalk-2

description:
dd_NC4_prestalk_48_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: NC4-48-prespore-2

description:
dd_NC4_prespore_48_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: Liquid_culture_control_RNA-Seq rep 2

status: Public on Mar 13 2010

city: Shenzhen

first: Guangwu

last: Guo

state: Guangdong Province

address: Main Building,Beishan Industrial Zone, Yantian District

department: Bioinformatics center

country: China

institute: Beijing Genomics Institute at Shenzhen

description: sample for paired-end library with insert size of 200 bp which generates 44 bp paired-end reads

data_processing: Alignment:   After removing reads containing sequencing adapters and reads of low quality (reads containing Ns >5), we aligned paired-end reads to the  Aspergillus oryzae genome using SOAP 2 allowing up to 2 mismatches. Reads failed to be mapped were progressively trimmed off 1 base from the 3'-end and mapped to genome again until a match was found. Meanwhile, we set insert of paired reads was 1~5 kilo bases allowing to span introns with varied sizes on genome.

organism: Aspergillus oryzae

source_name: cell in liquid culture

growth_protocol: Aspergillus oryzae RIB40 was got from NITE Biological Resource Center (NBRC) in Japan. The CD medium used has been modified, composed of 0.3% NaNO3, 0.2% KCl, 0.05% MgSO4·7H2O, 0.001% FeSO4·7H2O, 0.1% K2HPO4, 2.0% glucose, pH5.5.

extract_protocol: mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 44 bp of sequence was determined from the both of fragment ends with insert size of 200 ±25 bp

treatment_protocol: 107 spores were inoculated into 30 mL CD medium in 100 mL flask, and were cultivated at 30 oC at 200 rpm until the mid-logarithmic phase (40 h).


title: Solid_culture_ER_stress_RNA-Seq rep 2

source_name: cell under ER stress in solid culture

treatment_protocol: the mycelia together with the cellophane, was transferred to the surface of 2 cm-thick filter paper soaked with 20 mL CD medium which contained 20 mmol/L dithiothreitol (DTT) for induce treatment


title: Solid_culture_control_RNA-Seq rep 2

source_name: cell in solid culture

treatment_protocol: 107 spores were distributed over the CD medium-agar plate which was covered by a layer of cellophane, and were cultivated at 30 oC until the mid-logarithmic phase (40 h)


title: AX4-24-whole organism-2

description:
dd_AX4_all_24_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: MM653

source_name: giant congental nevus

value: primary giant congental nevus


title: GM12892_DNAse_REP1

description: DNase-Seq


title: AX4-20-whole organism-1

description:
dd_AX4_all_20_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-20-whole organism-2

description:
dd_AX4_all_20_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: Liquid_culture_ER_stress_RNA-Seq rep 2

source_name: cell under ER stress in liquid culture

treatment_protocol: For induce treatment, DTT was added to the culture at a final concentration of 20 mmol/L.


title: AX4-16-whole organism-2

description:
dd_AX4_all_16_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: QF1160MB

source_name: melanoblast

value: primary melanoblast


title: AX4-16-whole organism-1

description:
dd_AX4_all_16_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-12-whole organism-2

description:
dd_AX4_all_12_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-12-whole organism-1

description:
dd_AX4_all_12_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: BJ_BRD7KD_+RAS_IPBRD7

status: Public on Mar 14 2010

city: Amsterdam

first: Jarno

last: Drost

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: The Netherlands Cancer Institute

description: IP BRD7

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the unmasked human reference genome (NCBI v36, hg18) using the Illumina Eland program. Only the tags uniquely mapped to the genome with at most two mismatches were retained.

source_name: BJ primary foreskin fibroblasts, BRD7 knockdown IP

growth_protocol: BJ/ET/RASV12ER cells expressing vector, BRD7KD, or p53KD were cultured in the presence of 4OHT.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: The antibody used for the p53 IPs was DO-1 (Santa Cruz Biotechnology), and the one for the BRD7 IPs was produced in-house.

value: BJ

value: foreskin fibroblasts

tag: oncogene expression

tag: vector

value: BRD7 knockdown

tag: sample type

value: control


title: BJ_p53KD_+RAS_IPp53

description: IP p53

source_name: BJ primary foreskin fibroblasts, p53 knockdown IP

value: p53 knockdown


title: BJ_+RAS_IPBRD7

description: IP BRD7

source_name: BJ primary foreskin fibroblasts, wildtype BRD7 IP

value: empty

value: experiment


title: GM12878_CTCF_REP3

description: Chromatin IP against CTCF


title: BJ_+RAS_IPp53

description: IP p53

source_name: BJ primary foreskin fibroblasts, wildtype p53 IP


title: AX4-8-whole organism-2

description:
dd_AX4_all_8_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-4-whole organism-2

description:
dd_AX4_all_4_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-8-whole organism-1

description:
dd_AX4_all_8_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-0-whole organism-2

description:
dd_AX4_all_0_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-0-whole organism-1

description:
dd_AX4_all_0_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: AX4-4-whole organism-1

description:
dd_AX4_all_4_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-48-prestalk-2

description:
dp_dpAX1_prestalk_48_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)

organism: Dictyostelium purpureum

source_name: dpAX1 prestalk cell type


title: dpAX1-48-prespore-2

description:
dp_dpAX1_prespore_48_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)

source_name: dpAX1 prespore cell type


title: dpAX1-48-prestalk-1

description:
dp_dpAX1_prestalk_48_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-24-whole organism-2

description:
dp_dpAX1_all_24_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)

source_name: dpAX1 whole organism cell type


title: dpAX1-48-prespore-1

description:
dp_dpAX1_prespore_48_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-20-whole organism-1

description:
dp_dpAX1_all_20_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-8-whole organism-2

description:
dp_dpAX1_all_8_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-16-whole organism-2

description:
dp_dpAX1_all_16_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-16-whole organism-1

description:
dp_dpAX1_all_16_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-12-whole organism-1

description:
dp_dpAX1_all_12_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-20-whole organism-2

description:
dp_dpAX1_all_20_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-24-whole organism-1

description:
dp_dpAX1_all_24_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-8-whole organism-1

description:
dp_dpAX1_all_8_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-4-whole organism-1

description:
dp_dpAX1_all_4_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-0-whole organism-2

description:
dp_dpAX1_all_0_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-4-whole organism-2

description:
dp_dpAX1_all_4_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-0-whole organism-1

description:
dp_dpAX1_all_0_1.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: dpAX1-12-whole organism-2

description:
dp_dpAX1_all_12_2.coverage
library selection: total RNA was subjected to one round of PolyA selection on oligo(dT) beads (Dynal)


title: H3K4me3_DHT_4h_ChIPSeq

status: Public on Mar 09 2010

first: Housheng

middle: Hansen

last: He

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

institute: UNIVERSITY HEALTH NETWORK

description: Chromatin IP against H3K4me3. Mono-nucleosome level histone mark ChIP-Seq data (Mnase ChIP).

data_processing:
Bed: Sequence reads were obtained and mapped to the human genome (March, 2006) using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the "Nucleosome Positioning from Sequencing (NPS)" algorithm (http://liulab.dfci.harvard.edu/NPS/)
Processed data file build: hg18

source_name: prostate cancer Cells

extract_protocol: Lysates were clarified from MNase digested chromatin and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~220 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were cultured in RPMI 1640 supplemented with 10%  charcoal-stripe FBS for 4 days, and then treated with DHT or Ethanol for 4 or 16 hours

value: LNCaP prostate cancer cell line

value: prostate cancer Cells

tag: passages

tag: agent

value: DHT

tag: time

tag: chip antibody


title: H3K4me2_DHT_4h_ChIPSeq

description: Chromatin IP against H3K4me2. Mono-nucleosome level histone mark ChIP-Seq data (Mnase ChIP).


title: H3K4me2_DHT_16h_ChIPSeq


title: NANOG

status: Public on Mar 06 2010

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: ChIP was performed using commercial antibody

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, hg18) using Eland software with maximal 2 mis-matches.
Peak detection was performed using MACS (Zhang, Y. et al 2008). The binding regions were ranked based on the enrichment of ChIP sequenced tags by comparing each ChIP library to an Input library as a control. Defined the binding peaks as those above the p-value cut-off of 1.00e-05.

source_name: embryonic stem cells

growth_protocol: The hESC lines H1 (WA-01, passage 28) was used for this study. They were cultured feeder free on matri-gel (BD). Condition medium used for culturing human contained 20% KO serum replacement, 1 mM L-glutamine, 1% non-essential amino acids and 0.1 mM 2-mercaptoethanol and additional 8ng/ml of basic fibroblast growth factor (Invitrogen) supplemented to the hESCs unconditioned medium.

extract_protocol: 10ng of ChIP material, respectively, as per manufacturers protocol. Briefly, using the Solexa ChIP Seq DNA sample preparation kit universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing

treatment_protocol: The ES cells were fixed in 1 % formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation

tag: antibody

value: NANOG

value: embryonic stem cell

tag: antibody manufacturer


title: H3K4me2_Vehicle_ChIPSeq


title: ZNF711 in SH-SY5Y

status: Public on Mar 08 2010

city: Copenhagen

first: Daniela

last: Kleine-Kohlbrecher

address: Ole Maaløes vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC

description: chromatin IP against ZNF711

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline version 1.3 allowing up to 1 mismatches in the first 32 bases of the read. Only reads that align uniquely are reported.
Peaks: Peak detection was performed with CisGenome software (http://www.biostat.jhsph.edu/~hji/cisgenome/) as described in Hongkai et al. (2008) Nature Biotechnology, 26: 1293-1300.

source_name: neuroblastoma cell line

growth_protocol: SH-SY5Y cells were routinely cultured on collagen coated tissue culture dishes in DMEM, 10% FBS (Hyclone)

extract_protocol: ChIP analyses were performed as described in Bracken et al. (2006). Genes Dev.1;20(9):1123-36. DNA ffrom ChIP experiments was prepared for sequencing with the Illumina ChIPSeq Sample Prep kit (IP-102-1001). DNA libraries were quantified using a fluorometer (Fluoroscan, Ascent) and diluted to 5-10 pM. Diluted libraries were used directly for cluster generation and sequencing analysis using the Genome Analyzer II (Illumina) following the protocol of the manufacturer. All samples have been sequenced two times (described as s1 and s2 for raw data files). Basecalling and mapping of the 36 bp sequences were done using Illumina's analysis Pipeline v 1.01 for the first sequencing of the PHF8 sample all the other samples were done using v 1.3 allowing up to one mismatch in the first 32 bases of a read against human genome March 2006 release (hg18).

treatment_protocol: no treatment

value: neuroblastoma cell line SH-SY5Y

tag: subclone

value: neuroblast-like subclone of SK-N-SH


title: H3K4me3 in SH-SY5Y

description: chromatin IP against H3K4me3


title: N1_A_p1_1 (Illumina)

status: Public on Mar 04 2010

first: Lukas

last: Habegger

address: 266 Whitney Ave

description: RNA-Seq; polyA selected mRNA

data_processing: Reads were obtained and aligned to the human reference genome (hg18) using BOWTIE for Illumina single-end reads, ELAND for Illumina paired-end reads, and BLAT for the long 454 reads.  Subsequently, the mapped reads were converted into signal track (WIG) files by counting the number of mapped reads at each nucleotide position.  The counts were then normalized by the total number of mapped reads per million.

source_name: Neural differentiation; early initiation

growth_protocol: Two neural differentiation strategies were used. In one approach (A) hESC H1 line was differentiated and cultured using feeder-free chemically defined adherent cell culture system through three stages: N1, an initiation stage; N2, a Neural Progenitor Cell (NPC) stage which produces only neurons upon further differentiation; and N3 which produces both neurons and glial cells. In the second approach (B), neural progenitors (N2-B) were generated from undifferentiated H1 hESCs via embryoid body like neurosphere formation. In each case, standard protocols involving bone morphogenic protein (BMP) signaling antagonists (Noggin) and basic fibroblast growth factor (bFGF) were used

extract_protocol: Solexa sequencing: mRNA was fragmented using 10X Fragmentation Buffer (Ambion) and double-stranded cDNA was synthesized using SuperScript II (invitrogen) reverse transcriptase and random primers. DNA sequencing followed the instructions of the mRNA-Sequencing Sample Prep Kit (Illumina). 454 sequencing: Single-stranded cDNA library was synthesized and adapters were ligated (Supporting Information Appendix) and sequenced using the emPCR II Kit (Amplicon A) and on the 454 Genome Sequencer FLX instrument following the manufacturer’s instructions.  GS FLX Titanium cDNA Libraries were prepared and sequenced at the 454 Life Sciences Sequencing Centre (Branford, CT).

tag: developmental stage

value: early initiation


title: hESC_B_p1_1 (Illumina)

description: RNA-Seq; polyA selected mRNA

source_name: Embryonic stem cells

value: Embryonic stem cells


title: OCT4

value: abcam (AB19857)


title: PHF8 in SH-SY5Y

description: chromatin IP against PHF8


title: N2_A_p1_1 (Illumina)

description: RNA-Seq; polyA selected mRNA

source_name: Neural differentiation; neural progenitors

value: neural progenitors


title: m_Brain_MeCP2_M

city: Edinburgh

first: Adrian

middle: P

last: Bird

state: Midlothian

address: Mayfield Road

department: WTCCB

country: United Kingdom

institute: The University of Edinburgh

description: Chromatin IP against MeCP2

data_processing: Alignment: Single-end sequence reads were mapped to the mouse genome (NCBIm37) using MAQ (http://maq.sourceforge.net/). Reads with a mapping score greater or equal to 30 where retained.

organism: Mus musculus

source_name: Whole Brain

growth_protocol: Whole brains / Cerebellum were disected from C57black/6 mice.

extract_protocol: Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Brains were manually homogenised to a single cells suspension and crosslinked using 1% formaldehyde. Chromatin was sheared using a combination of Micrococcal nuclease and sonication. Protein-DNA complexes were immunoprecipitated with an MeCP2 antibody and the DNA was subsequently extracted.

tag: strain

tag: age

value: 9.5 weeks

tag: chip antibody / mbd affinity column

value: MeCP2 (674 - In house antibody)

tag: tissue

value: whole brain


title: H3K4me3_Vehicle_ChIPSeq

tag: cell line

value: control


title: CTCF

value: CTCF

tag: cell type


title: hESC_A_p1_1 (Illumina)

description: RNA-Seq; polyA selected mRNA


title: N3_A_p1_1 (Illumina)

description: RNA-Seq; polyA selected mRNA

source_name: Neural differentiation; early glial-like

value: early glial-like


title: N2_B_p1_1 (Illumina)

description: RNA-Seq; polyA selected mRNA


title: m_Cerebellum_MBD_M

description: MBD affinity chromatography

source_name: Cerebellum

treatment_protocol: Cerebellum DNA was extracted according to standard protocols. DNA was sheared to approximately 400 bp using sonication. Methylated DNA was purified by two step MBD Affinity Purification as described in Illingworth et al., 2008.

value: 30 weeks

value: Methyl-seq (recombinant human MBD domain)

value: cerebellum


title: Hiranull_ES_H33_EYFP_antiH3K36me3_nChIPSeq

city: New York

first: Aaron

middle: D

last: Goldberg

state: NY

address: 1230 York Avenue - Box 78

department: Laboratory of Chromatin Biology

institute: The Rockefeller University

description:
sample 32
Native chromatin IP (nChIP) against H3K36me3

data_processing: BED files were generated from alignment files by keeping unique reads mapped to a single best-matching location with no more than two mismatches. The UCSC mm9 was used for the alignments.

growth_protocol: For early passages, ES cells were maintained on mitomycin C treated feeders in standard ES cell media, KO-DMEM (Invitrogen 10829-018), 2mM L-glutamine (Sigma G7513) and pen-strep, 15% ES grade fetal bovine serum (Gibco 10439-024), 10-4 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF).  To remove feeders for ChIP or NPC differentiation, ES cells were passaged at least two passages off of feeders on to gelatin-coated plates.  ES cells were differentiated to NPCs by re-plating d7 adherent neural differentiation cultures (typically 2–3 × 10^6 cells) into an uncoated T75 flask in NS-A medium as described (Conti et al., 2005).  To expand NPCs for ChIP, NPCs were cultured on gelatin-coated plates in NeuroCult NSC Basal Medium (Mouse, Stem Cell Technologies) supplemented with 2mM final L-glutamine and pen-strep (Omega Scientific), modified N2 supplement freshly prepared in house as described (Conti et al., 2005), and 10ng/ml of both mouse EGF and human FGF-2 (Peprotech).

extract_protocol: Crosslinking ChIP was performed as described (Lee et al. 2006), with minor modifications as described in Goldberg, et al. 2010. Briefly, ES cells and NPCs were harvested and fixed in 1% paraformaldehyde, pellets flash-frozen in liquid nitrogen, and stored at -80 degrees C.  Chromatin was isolated and sheared to 200-700 bp using a Bioruptor (Diagenode), and ChIP was performed as described (Lee et al. 2006).  Native ChIP was performed as described (Barski et al. 2007), with minor modifications as described in Goldberg, et al. 2010.  Following isolation of ChIP DNA, libraries were prepared for cluster generation as described (Goldberg et al. 2010).  Purified DNA libraries were used for cluster generation on Illumina/Solexa flow cells, and sequencing analysis was performed on an Illumina/Solexa Genome Analyzer 2 following manufacturer protocols.

value: Hira -/- H3.3-EYFP / H3.3B

value: cl34 Hira -/- embryonic stem cells

value: H3K36me3 (Abcam ab9050)


title: Atrxflox_ES_H33_EYFP_Input_nChIPSeq

description:
sample 35
Native chromatin input control

value: Atrxflox H3.3-EYFP / H3.3B

value: Atrxflox embryonic stem cells

value: native ChIP input control. No antibody.


title: ES_H33_EYFP_antiH3K36me3_nChIPSeq

description:
sample 29
Native chromatin IP (nChIP) against H3K36me3

value: C6 embryonic stem cells


title: ES_wild_type_antiHA_control_xChIPSeq

description:
sample 38
Crosslinking chromatin IP (xChIP) against HA in wild-type ES background

value: W9.5 embryonic stem cells

value: anti-HA (12CA5) control. No HA epitope in untagged ES cells


title: Hiranull_ES_H33_EYFP_antiH3K4me1_nChIPSeq

description:
sample 31
Native chromatin IP (nChIP) against H3K4me1

value: H3K4me1 (Abcam ab8895)


title: Atrxnull_ES_H33_EYFP_antiGFP_nChIPSeq

description:
sample 36
Native chromatin IP (nChIP) against H3.3-EYFP

value: Atrxnull H3.3-EYFP / H3.3B

value: Atrxnull embryonic stem cells

value: anti-GFP (Cristea et al., 2005)


title: ES_H33_EYFP_Input_nChIPSeq

description:
sample 27
Native chromatin input control

value: native ChIP input control.  No antibody.


title: ES_H33_EYFP_antiH3K4me1_nChIPSeq

description:
sample 28
Native chromatin IP (nChIP) against H3K4me1


title: ES_H33_HA_input_nChIPSeq

description:
sample 21
Native chromatin input control


title: ES_H32_HA_input_nChIPSeq

description:
sample 25
Native chromatin input control


title: ES_H32_HA_H3K4me3_nChIPSeq

description:
sample 23
Native chromatin IP (nChIP) against H3K4me3

value: H3K4me3 (Abcam ab8580)


title: ES_H32_HA_H3K27me3_nChIPSeq

description:
sample 24
Native chromatin IP (nChIP) against H3K27me3

value: H3K27me3 (Upstate/Millipore #07-449)


title: ES_H33_EYFP_antiGFP_nChIPSeq

description:
sample 26
Native chromatin IP (nChIP) against H3.3-EYFP


title: Atrxflox_ES_H33_EYFP_antiGFP_nChIPSeq

description:
sample 34
Native chromatin IP (nChIP) against H3.3-EYFP


title: Hiranull_ES_H33_EYFP_antiGFP_nChIPSeq

description:
sample 30
Native chromatin IP (nChIP) against H3.3-EYFP


title: ES_H32_HA_antiHA_nChIPSeq

description:
sample 22
Native chromatin IP (nChIP) against H3.3-HA

value: anti-HA (12CA5)


title: Hiranull_ES_H33_EYFP_Input_nChIPSeq

description:
sample 33
Native chromatin input control

value: Hira -/- H3.3-EYFP / H3.3B


title: Atrxnull_ES_H33_EYFP_Input_nChIPSeq

description:
sample 37
Native chromatin input control


title: ES_H33_HA_H3K4me3_nChIPSeq

description:
sample 20
Native chromatin IP (nChIP) against H3K4me3


title: ES_H33_HA_antiHA_nChIPSeq

description:
sample 19
Native chromatin IP (nChIP) against H3.3-HA


title: ESHyb_H31S31_HA_H3K36me3_xChIPSeq

description:
sample 18
Crosslinking chromatin IP (xChIP) against H3K36me3

tag: strain/genotype

value: 129SvJae x M. m. castaneus F1  H3.1S31-HA / H3.3B

value: F1 hybrid "965" embryonic stem cells


title: ESHyb_H33_HA_H3K36me3_xChIPSeq

description:
sample 15
Crosslinking chromatin IP (xChIP) against H3K36me3

value: 129SvJae x M. m. castaneus F1  H3.3-HA / H3.3B

value: H3K36me3 (Abcam ab9050)


title: ESHyb_H31S31_HA_antiHA_xChIPSeq

description:
sample 17
Crosslinking chromatin IP (xChIP) against H3.3-HA


title: ESHyb_H31S31_HA_Input_xChIPSeq

description:
sample 16
Crosslinking chromatin input control

value: x-link ChIP input control.  No antibody.


title: Kc PSC 2

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

description: Chromatin was prepared from Kc cells and ChIP using an antibody against Drosophila PSC was performed.

data_processing:
Reads were filtered with chastity < 0.6, low complexity, and more than 2 N's.
GSE17697_readCounts.200.tab.txt: where each row contains the number of reads per 200bp window in each sample. As the reads are 36-mers, and a minimum overlap of 18 is required, each read is assigned to exactly one window. Reads were mapped to the dm3 version of the Drosophila genome using bowtie allowing for up to two mismatches and retaining all best hits for reads with up to 100 alignments.

source_name: Kc genomic DNA

extract_protocol:
Chromatin fixation and immunoprecipitation were performed essentially as described (Beisel et al. (2007) PNAS 104, 16615-16620). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 200-500 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The Psc antibody was described previously (Strutt, H. & Paro, R. (1997) Mol Cell Biol 17, 6773-6783).
Libraries for Illumina sequencing were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit  (Cat# IP-102-1001) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 18 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer 2 following the manufacturer's protocols.

tag: gender

value: female

value: PSC


title: ESHyb_H33_HA_Input_xChIPSeq

description:
sample 13
Crosslinking chromatin input control


title: ES_H32_HA_H3K36me3_xChIPSeq

description:
sample 6
Crosslinking chromatin IP (xChIP) against H3K36me3

value: C6 embryonic stem cells


title: NP_H33_HA_H3K36me3_xChIPSeq

description:
sample 8
Crosslinking chromatin IP (xChIP) against H3K36me3

source_name: Neural progenitor cells

value: ES-derived neural progenitor cells


title: NP_H33_HA_H3K4me1_xChIPSeq

description:
sample 9
Crosslinking chromatin IP (xChIP) against H3K4me1


title: NP_H32_HA_H3K36me3_xChIPSeq

description:
sample 12
Crosslinking chromatin IP (xChIP) against H3K36me3


title: NP_H33_HA_RNAPII_CTD4H8_xChIPSeq

description:
sample 10
Crosslinking chromatin IP (xChIP) against RNAPII_Ser5p_CTD4H8

value: anti-RNAPII_Ser5p (CTD4H8)


title: ES_H33_HA_RNAPII_CTD4H8_xChIPSeq

description:
sample 4
Crosslinking chromatin IP (xChIP) against RNAPII_Ser5p_CTD4H8


title: germlineless_mononuc_seq

status: Public on Mar 02 2010

city: Chapel Hill

first: Jason

last: Lieb

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

description: sequencing of mononucleosomal DNA

data_processing: Raw coverage tracks: The sequencing was done using Illumina paired end reads technology. All lanes of each replicate were combined and mapped together. The two single reads of each pair were mapped independently to WS170 genome, using a proprietary software (SeqHit) allowing a single mismatch and no gaps. The hits of the non unique reads were extended to a nucleosomes length and their union defined the non unique regions. The pairs of mapped reads that define a valid (up to 200 basepairs length) and unique regions are collected. The raw coverage of a basepair is caluclated by summing up the number of unique reads covering it. Zero value is assigned to unique basepairs that were covered by none.

organism: Caenorhabditis elegans

source_name: young germlineless adults

growth_protocol: Worms were grown in standard S-basal media liquid culture. JK1107 (glp-1(q224) III.) were grown at 15C and bleached for embryos. Embryos were starved to L1 and then fed and shifted to 25C. Germline-less adults were collected over 20uM Nitex membrane, and washed with M9 and PBS. Adults were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as “popcorn” in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/. protocol: Worm germlineless adult soma growth and harvest:JL:5

extract_protocol: Frozen adults (popcorn) were broken into smaller pieces with biopulverizer and ground to a powder with mortar and pestle. The frozen powder was briefly crosslinked 1 minute at room temperature with 1% formaldehyde. Sample was dounced and chromatin was obtained by centrifugation at 4000g. Chromatin was digested with increasing amounts of MNase. Mononucleosomal DNA was purified with Qiagen Gel Extraction kit. For a detailed protocol see http://www.modencode.org/ protocol: Worm adult nucleosome preparation:JL:SE1.    Solexa_Library_Prep DNA was incubated with End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3’ ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and mononucleosome length DNA was recovered from the gel. For a detailed protocol see http://www.modencode.org/ protocol:Solexa Library Preparation:JL:SE1

treatment_protocol: Crosslink frozen worm powder 1 minute at room temperature with PBS containing 1% formaldehyde.

value: adult


title: ES_H33_HA_antiHA_xChIPSeq

description:
sample 1
Crosslinking chromatin IP (xChIP) against H3.3-HA


title: NP_H33_HA_antiHA_xChIPSeq

description:
sample 7
Crosslinking chromatin IP (xChIP) against H3.3-HA


title: ES_H33_HA_H3K4me1_xChIPSeq

description:
sample 3
Crosslinking chromatin IP (xChIP) against H3K4me1


title: NP_H32_HA_antiHA_xChIPSeq

description:
sample 11
Crosslinking chromatin IP (xChIP) against H3.2-HA


title: embryo_mononuc_seq

description: sequencing of mononucleosomal DNA

source_name: mixed stage embryos

growth_protocol: Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 15 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/ protocol:Worm embryo growth and harvest:JL:SE2

extract_protocol: Worm_embryo_nucleosome_preparation_SE1. Cross-linked embryos were treated with chitinase to release eggshell. Blastomeres were dounced and chromatin was obtained by centrifugation at 4000g. Chromatin was digested with increasing amounts of MNase. Mononucleosomal DNA was purified with Qiagen Gel Extraction kit. For a detailed protocol see http://www.modencode.org/: Worm embryo nucleosome preparation:JL:SE1. Solexa_Library_Prep DNA was incubated with End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3’ ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and mononucleosome length DNA was recovered from the gel. For a detailed protocol see http://www.modencode.org/ protocol:Solexa Library Preparation:JL:SE1

treatment_protocol: Crosslink live embryos for 15 min in M9 buffer containing 2% formaldehyde.

value: embryo


title: Kc PSC 1


title: ESHyb_H33_HA_antiHA_xChIPSeq

description:
sample 14
Crosslinking chromatin IP (xChIP) against H3.3-HA


title: Kc PSC 3


title: flowering leaf RNA-Seq data

status: Public on Mar 01 2010

description:
sample for single-end library which generates 35 bp single-end reads
processed_data_file_type: alignment

data_processing: After removing reads containing sequencing adapters and reads of low quality (reads containing Ns >5), we aligned reads to the Indica genome using SOAP allowing up to 2 mismatches. Reads failed to be mapped were progressively trimmed off 1 base from the 3'-end and mapped to genome again until a match was found.

organism: Oryza sativa

source_name: flowering leaf at flowering stage

extract_protocol:
total RNA was diluted and separated into two parts, 20μg for each half. One half was purified with oligo-dT magnetic beads to obtain mRNA (PolyA RNA) .The other half is carried through electrophoreses with denaturing agarose gel and size-selected fragments by cut gel from 200bp to 1kb. Both of halves (mRNA and specific size-range RNA) were mixed and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 35 bp of sequence was determined from the fragment ends.
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.

value: flag leave of Oryza sativa L. ssp. indica cv. 9311


title: small RNA from mixture of  8 tissues

description: this RNA mixture was size-fractionated on a denaturing agarose gel and the 18nt～30nt was obtained from excised gel.

data_processing: Large amount of 35 nt small RNA reads  were subjected to several filtering processes, 1) filter low quality reads; 2) trim 3 prime adaptor sequence by a modified dynamic programming algorithm ; 3) remove adaptor contaminants formed by adaptor ligation; 4) collect short RNAs ranged from 18-30 nt .

source_name: sample pooled from callus,seedling shoot,seedling root,tillering leaf,flowering panicle,flowering leaf,filling panicle and booting panicle

extract_protocol:
2.5μg total RNA from each tissue of callus, seedling shoot, seedling root, tillering leaf, flowering panicle, flowering leaf, filling panicle and booting panicle was diluted and pooled to a mix solution, concentration of 1μg/μl, amounted to 20μl. Afterward, this RNA mix was size-fractionated on a denaturing agarose gel (Novex™ 15% TBE-Urea Gel, Invitrogen) and the 18nt～30nt was obtained from excised gel based on the 10 base pair ladder size standard (Invitrogen). We run gel for 1 hour at 200V. 0.3 M NaCl (Ambion) was utilized to facilitate elution by rotating at room temperature for 4 hours and Spin-X Cellulose Acetate filters (Fisher) was used to separate gel debris. Then, the small RNA was precipitated using 100% ethanol combined with glycogen (Ambion) and acetate sodium (Novagen). Illumina 5’ RNA adapter was ligated to small RNA using 10U of T4 RNA ligase (Promega) and 40U of RNaseOUTTM (Invitrogen) at 4C overnight. Then the small RNA with 5’ adapter was purified by gel extraction as previous step, except the gel band corresponding to 40nt~60nt was cut out and recovered. Subsequently, Illumina 3’ RNA adapter ligation was added as the procedure of 5’ RNA adapter ligation. We used Novex™ 10% TBE-Urea Gel (Invitrogen) to separate RNA, in which ranged from 70nt to 90nt was recovered. The adapter linked RNA was performed to reverse transcription with small RNA RT-primer. After heated to 65°C for 5 minutes, the following reagents was introduced: 10mM dNTP (NEB), 0.1M DTT, 40U RNaseOUTTM (Invitrogen) and 200U of SuperscriptⅡ reverse transcriptase (Invitrogen). This reaction mixture was incubated at 44℃ for 1 hours, then diluted the solution to 50μl. Subsequently, the small RNA derived cDNA was amplified by 15 cycles of PCR reaction. The composition of liquid system and thermo cycling steps were the same as cDNA library procedure except the small RNA PCR primer 1 and small RNA PCR primer 2 replaced the primer1.1 and primer2.1. The products were purified by gel separation with 6% Novex™ TBE gel (Invitrogen) and ～92nt DNA band was cut out and extracted. Finally, the library products were sequenced using the Illumina Genome Analyzer.
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.

value: total RNA from each of 8 tissues was diluted and pooled to a mix solution


title: GAPDH

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing: Sequencing reads were quality trimmed after 3 consecutive nucleotides with quality score less than 10. After quality trimming reads at least 18 nucleotides long were mapped against the human reference genome (hg18 assembly, NCBI build 36) using SHRiMP package [11]  with default settings which allows mapping in SOLiD color space corresponding to dinucleotide encoding of the sequenced DNA. For analysis we used only uniquely placed reads, which were defined as reads having at least two additional mismatches in the second best hit compared to the best hit.

source_name: cell line

extract_protocol: Chromatin was additionally sheared for 6 minutes using Covaris sonicator (6 x 16 mm AFA fiber Tube, duty cycle: 20%, intensity: 5, cycles/burst: 200, frequency sweeping) to obtain suitable shorter fragments (75-125 bp). After fragmentation, fragments were blunt-ended and phosophorylated at the 5'-prime end using the End-it Kit (Epicentre) according to the manufacturer’s instructions. Ligation of double stranded adapters compatible with SOLiD sequencing was performed using Quick ligation kit (New England Biolabs) with 750 mM P1 ds and P2 ds adaptor (Applied Biosystems), 11.7 µl of 2x Quick ligation buffer, 1 µl Quick Ligase (NEB) in total volume of 23.4 µl. Samples were purified using Ampure beads (Agencourt) and run on a native 6% polyacrylamide gel. Fragments ranging from 140 to 180 bp were excised; the piece of gel containing DNA fragments was shredded and dispersed into 400 µl of Platinum PCR Supermix with 750 mM of each P1 and P2 PCR primer, 2,5 U of Pfu (Stratagene) and 5 U Taq (Bioline). Prior to ligation-mediated PCR the sample was incubated at 72O C for 20 minutes in PCR mix to let the DNA diffuse out of the gel and to perform nick translation on non ligated 3'-ends of DNA fragments. After 17 cycles of amplification the library was purified using Ampure beads and was quality checked on 2100 Bioanalyzer (Agilent) for the absence of possible adapter dimers and heterodimers.

value: HeLa


title: BTAF


title: tillering leaf RNA-Seq data

source_name: tillering leaf

value: flag leave at tillering stage

tag: cultivar

value: Oryza sativa L. ssp. indica cv. 9311


title: seedling root RNA-Seq data

source_name: seedling root

value: shoot at seedling stage of 14 days


title: flowering panicle RNA-Seq data

source_name: flowering panicle

value: panicle at flowering stage


title: ES_H32_HA_antiHA_xChIPSeq

description:
sample 5
Crosslinking chromatin IP (xChIP) against H3.2-HA

tag: passages

value: anti-HA (12CA5)


title: booting panicle RNA-Seq data rep13

description:
sample for paired-end library with insert size of 178 bp which generates 75 bp paired-end reads
processed_data_file_type: alignment

data_processing: After removing reads containing sequencing adapters and reads of low quality (reads containing Ns >5), we aligned paired-end reads to the Indica genome using SOAP 1 allowing up to 2 mismatches. Reads failed to be mapped were progressively trimmed off 1 base from the 3'-end and mapped to genome again until a match was found. Meanwhile, we set insert of paired reads was 1~10 kilo bases allowing to span introns with varied sizes on genome.

source_name: booting panicle

extract_protocol:
mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 75 bp of sequence was determined from the both of fragment ends with insert size of 200 ±50 bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.

value: panicle at booting stage


title: seedling shoot RNA-Seq data

source_name: seedling shoot

value: root at seedling stage of 14 days


title: booting panicle RNA-Seq data rep7

description:
sample for paired-end library with insert size of 414 bp which generates 44 bp paired-end reads
processed_data_file_type: alignment

extract_protocol:
mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 44 bp of sequence was determined from the both of fragment ends with insert size of 500 ±50 bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.


title: booting panicle RNA-Seq data rep15


title: booting panicle RNA-Seq data rep10


title: filling panicle RNA-Seq data

source_name: filling panicle at filling stage

value: panicle of Oryza sativa L. ssp. indica cv. 9311


title: booting panicle RNA-Seq data rep9


title: booting panicle RNA-Seq data rep11


title: booting panicle RNA-Seq data rep8


title: ES_H33_HA_H3K36me3_xChIPSeq

description:
sample 2
Crosslinking chromatin IP (xChIP) against H3K36me3

source_name: Embryonic stem cells


title: booting panicle RNA-Seq data rep6


title: booting panicle RNA-Seq data rep3

description:
sample for paired-end library with insert size of 360 bp which generates 44 bp paired-end reads
processed_data_file_type: alignment


title: booting panicle RNA-Seq data rep14


title: booting panicle RNA-Seq data rep4


title: Rice_rdr2

city: Beijing

first: Yijun

last: Qi

address: No.7 Science Park Road,Zhongguancun Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing: The adaptor sequences in Illumina 1G sequencing reads were removed by using ‘‘vectorstrip’’ in the EMBOSS package. The small RNA reads with length of 19–27 nt were mapped to the genome using Blast. small RNAs with match to transgenic inverted-repeat or without perfect match to the genome were removed.

source_name: rdr2-2 seedling

growth_protocol: Rice plants were gorwn in growth chambers with 12-h light/dark cycles, 28 oC during the day and 23 oC during the night.

extract_protocol: Small RNAs were ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified using a pair of Illumina cloning primers and then provided for Illumina sequencing.

treatment_protocol: RNAs were extracted from total extract and immunopurified AGO4 complexes by Trizol reagents. Bigger RNAs were removed by PEG precipitation, and enriched small RNAs were seperated on 15% PAGE/7M Urea gel, and small RNA within the range of 18-28 nt were purified from the gel.

tag: protein complex

value: total extract


title: booting panicle RNA-Seq data rep2


title: Kc RNA

description: contains filtered reads

data_processing: Reads were filtered with chastity < 0.6, low complexity, and more than 2 N's.

source_name: Kc RNA

extract_protocol: Total RNA was isolated from Drosophila Kc cells using Trizol reagent. Purification of mRNA and the generation of cDNA library was performed following the Illumina protocol for mRNA sequencing. Primary sequencing data analysis was done following the Illumina Genome Analyzer software pipeline.

value: female


title: booting panicle RNA-Seq data rep5


title: Callus RNA-Seq data rep12

description:
sample for paired-end library with insert size of 180 bp which generates 75 bp paired-end reads
processed_data_file_type: alignment

source_name: callus

extract_protocol:
mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 75 bp of sequence was determined from the both of fragment ends with insert size of 300 ±25 bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.

value: callus


title: Callus RNA-Seq data rep13


title: Callus RNA-Seq data rep9


title: Callus RNA-Seq data rep10


title: Callus RNA-Seq data rep7


title: booting panicle RNA-Seq data rep1


title: Callus RNA-Seq data rep14


title: Callus RNA-Seq data rep8


title: Callus RNA-Seq data rep6

description:
sample for paired-end library with insert size of 206 bp which generates 39 bp paired-end reads
processed_data_file_type: alignment

extract_protocol:
mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 39 bp of sequence was determined from the both of fragment ends with insert size of 300 ±25 bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.


title: Callus RNA-Seq data rep11


title: Callus RNA-Seq data rep5

description:
sample for paired-end library with insert size of 206 bp which generates 35 bp paired-end reads
processed_data_file_type: alignment

extract_protocol:
mRNA was purified from total RNA with oligo-dT magnetic beads and cDNA was synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 35 bp of sequence was determined from the both of fragment ends with insert size of 300 ±25 bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.


title: Callus RNA-Seq data rep2

description:
sample for paired-end library with insert size of 203 bp which generates 35 bp paired-end reads
processed_data_file_type: alignment

extract_protocol:
total RNA was diluted and separated into two parts, 20μg for each half. One half was purified with oligo-dT magnetic beads to obtain mRNA (PolyA RNA) .The other half is carried through electrophoreses with denaturing agarose gel and size-selected fragments by cut gel from 200bp to 1kb. Both of halves (mRNA and specific size-range RNA) were mixed and cDNA is synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 35 bp of sequence was determined from the both of fragment ends with insert size of 300±25  bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.


title: Callus RNA-Seq data rep3


title: Callus RNA-Seq data rep1


title: Callus RNA-Seq data rep4

description:
sample for paired-end library with insert size of 203 bp which generates 39 bp paired-end reads
processed_data_file_type: alignment

extract_protocol:
total RNA was diluted and separated into two parts, 20μg for each half. One half was purified with oligo-dT magnetic beads to obtain mRNA (PolyA RNA) .The other half is carried through electrophoreses with denaturing agarose gel and size-selected fragments by cut gel from 200bp to 1kb. Both of halves (mRNA and specific size-range RNA) were mixed and cDNA is synthesized with random primer priming.The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 39 bp of sequence was determined from the both of fragment ends with insert size of 300±25  bp
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer’s instructions and stored at -80℃. At the beginning of all below experiments, total RNA was treated for 30 minutes at 37℃ with RNase-free DNase I (New England Biolabs, NEB) to remove residual DNA.


title: Disw1_hybrid1 and hybrid2

city: Rehovot

first: Itay

last: Tirosh

address: herzl

department: Molecular genetics

country: Israel

institute: Weizmann Institute of Science

data_processing: Each read was mapped to only one of the genomes based on genomic differences. The reads from biological replicates were combined and each read location was converted to the estimated center position of the DNA fragment based on the estimated fragment length of each sample (140-160 in each sample). The density of converted read locations was smoothed with a gaussian filter of STD=25. The smoothed data was mapped to the location of ~4000 aligned genes, including 2kb surrounding the start codon of each gene. We used the S.cerevisiae SGD genome last updated at June 2008, and the S.paradoxus contigs from SGD, last updated at October 2003.

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: Mnase-digested genomic DNA

growth_protocol: Cells were grown to OD600 of 0.8-1.0 at 30°C from overnight starter diluted to 100 ml of YPD medium at OD600 of 0.15.

extract_protocol: Similar amounts of DNA from three independent biological repeats were mixed and diluted to 1 ng/ml concentration. The ChIP-Seq DNA Sample Prep Kit (IP-102-1001) and the standard protocol by Illumina were used to create libraries for sequencing, with the modification: the fragments with ligated adaptors were subjected directly to amplification, skipping the gel purification and size selection step. All other steps of cluster formation and sequencing procedure were performed following standard protocols for Illumina GA2 instrument.

treatment_protocol: Formaldehyde solution (37%) was added to final concentration of 1%, followed by shaking at 30 °C for 15 min. The formaldehyde was quenched by adding glycine to 0.125 M and letting to stand at room temperature for 5 min. Cells were collected by centrifugation at 3000 g for 5 min and washed twice with same volume of ice-cold water. At this point pellet can be stored at -80°C. Cells were resuspended in 10 ml Buffer Z (1M sorbitol, 50 mM Tris-HCl pH = 7.5, freshly added 10 mM β- mercaptoethanol), 70 ml of zymolase was added and the cells were incubated at 30°C for 30 min. Then the spheroplasts were collected by centrifugation at 3000g for 10 min, washed with 10 ml Buffer Z and resuspended in 0.5 ml Buffer NP (1M sorbitol, 10 mM Tris- HCl pH = 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, freshly added 1 mM β- mercaptoethanol, NP-40 0.075%, 0.5 mM spermidine). Then the sample was split for 2 aliquots, digested for 20 min at 37°C with 0.5 and 2 units of MNase. The reactions were stopped by addition of 0.1 ml of 5% SDS with 50 mM EDTA to each reaction. Cross-linking was reversed at 65°C for 4 h, samples were diluted with 0.4 ml water and 5 ml of RNase A (10 mg/ml , Sigma) were added. The samples were incubated at 37°C for 1 h, then 5 ml of Proteinase K (20 mg/ml) were added to each sample and were incubated at 65°C for 1 h. The DNA was extracted by phenol-chloroform-isoamyl alcohol (PCI), washed with chloroform-isoamyl alcohol (CI) and precipitated with ethanol. The digestion products were resolved on a 2% agarose gel, and mononucleosomal size band (~150 bp) was isolated by Wizard SV gel clean-up kit (Promega). An additional ethanol precipitation was performed to improve purity of the sample and to concentrate the input DNA.

value: (BY4741 Disw1 X CBS432 ho::nat MATα Disw1 )


title: WT_hybrid

value: (BY4741 X CBS432 ho::nat MATα)


title: Dbre1_parents

description: pool of mono-nucleosome DNA fragments from two yeast species

organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

value: S. cerevisiae (BY4743 Dbre1), S. paradoxus (CBS 432 ho::nat MATα Dbre1)


title: WT_control_hybrid1 and hybrid 2


title: Dgcn5_hybrid1 and hybrid2

value: (BY4741 Dgcn5 X CBS432 ho::nat MATα Dgcn5)


title: Dhtz1_hybrid1 and hybrid2

value: (BY4741 Dhtz1 X CBS432 ho::nat MATα Dhtz1)


title: WT_control_parents1 and parents2

source_name: Mnase-digested naked genomic DNA

value: S. cerevisiae (BY4743), S. paradoxus (CBS 432 ho::nat MATα)


title: WT_parents


title: CAS2

status: Public on Feb 28 2010

city: Ploen

first: Bettina

last: Harr

address: August-Thienemannstrasse 2

country: Germany

institute: Max-Planck-Institute for Evolutionary Biology

description:
sample 3 (CAS2_1), paired with sample 4
sample 4 (CAS2_2), paired with sample 3

data_processing:
Library preparation and deep sequencing using a Genome Analyzer II (Illumina, San Diego, CA) was performed by the National Center for Genome Resources (Santa Fe, NM) following paired-end sequencing and mRNA sequencing protocols from Illumina.
FASTQ files were generated using the Illumina pipeline version 1.0. The program Tophat/Bowtie was used to align the reads to the mouse reference genome [Ensembl Build NCBIM37.50 (mm9, NCBI Build 37)]. The outfiles (in .sam format) were then filtered for reads that matched uniquely in the genome and in the expected "paired-end" fashion.

organism: Mus musculus castaneus

source_name: adult testis

growth_protocol: adult mice were sacrifieced at an age of 6-8 weeks

extract_protocol:
Library construction protocol: Paired-end
We extracted RNA from flash-frozen testis tissue using TRIZOL (Invitrogen, Carlsbad, CA), and isolated mRNA from total RNA using the μMACS mRNA isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Sample integrity of total RNA and mRNA were verified using the RNA 6000 Nano chip kit on an Agilent Technologies 2100 Bioanalyzer (Waldbronn, Germany).
We synthesized cDNA from mRNA using Superscript III reverse transcriptase (Invitrogen) and a 10:1 primer mixture of random dodecamers and oligo(dT)18. The insert size was 200 bp.


title: Disw1_parents1 and parents2

value: S. cerevisiae (BY4743 Disw1), S. paradoxus (CBS 432 ho::nat MATα Disw1)


title: Dhtz1_parents1 and parents2

value: S. cerevisiae (BY4743 Dhtz1), S. paradoxus (CBS 432 ho::nat MATα Dhtz1)


title: small RNAs-parthenogenetic

city: Rennes

first: Stephanie

last: Jaubert

address: domaine de la Motte

country: France

institute: INRA

data_processing: unique_quant.fa includes unredundant sequences with quantification (the postfix number corresponds to the number of times the sequence has been found in the sample). for example : >quant-1_x24329 AAATTCGGTTCTAGAGAGGTTT has been found 24329 times

organism: Acyrthosiphon pisum

source_name: parthenogenetic colony

growth_protocol: The LSR1 clone of the pea aphid was reared and maintained as parthegonetic individuals on the plant vicia fabae at 18°C under 16h photoperiod.

extract_protocol: Total RNA was extracted from a mixed culture of parthenogenetic females of the LSR1 clone [15] of pea aphid using PureZOL RNA Isolation Reagent (Bio-Rad, Hayward CA). The RNA concentration and purity were determined photometrically by measuring absorbance at 260 nm and A260/A280 ratio using the NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies). 40µg of ethanol precipitated RNA was sent in duplicate to Illumina Inc. (Hayward CA) for size fractionation (<50bp) and deep sequencing.


title: Dgcn5_parents1 and parents2

value: S. cerevisiae (BY4743 Dgcn5), S. paradoxus (CBS 432 ho::nat MATα Dgcn5)


title: CAS1

description:
sample 1 (CAS1_1), paired with sample 2
sample 2 (CAS1_2), paired with sample 1


title: MUS1

description:
sample 13 (MUS1.1_1), paired with sample 14
sample 14 (MUS1.1_2), paired with sample 13
sample 15 (MUS1.2_1), paired with sample 16
sample 16 (MUS1.2_2), paired with sample 15

organism: Mus musculus musculus


title: MUS2

description:
sample 17 (MUS2_1), paired with sample 18
sample 18 (MUS2_2), paired with sample 17


title: Drad6_parents

value: S. cerevisiae (BY4743 Drad6), S. paradoxus (CBS 432 ho::nat MATα Drad6)


title: NA18505_2_argonne

city: Chicago

first: Joseph

last: Pickrell

state: IL

institute: University of Chicago

description: RNA-Seq

data_processing: Mapped using MAQ v. 0.6.8

organism: Homo sapiens

source_name: lymphoblastoid cell line

growth_protocol: 37o in RPMI

extract_protocol: Total RNA from HapMap Yoruba lymphoblastoid cell lines was extracted using an RNeasy Mini Kit (Qiagen) and assessed using an Agilent Bioanalyzer. mRNA was then isolated with Dyna1 oligo-dT beads (Invitrogen) from 10 micrograms of total RNA. The mRNA was randomly fragmented using the RNA fragmentation kit from Ambion. First-strand cDNA synthesis was performed using random primers and SuperScriptII reverse-transcriptase (Invitrogen). This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNaseH (Invitrogen).  The short cDNA fragments from each sample were prepared into a library for Illumina sequencing. Briefly, the Illumina adaptor was ligated to the ends of the double-stranded cDNA fragments and a 200 bp size-selection of the final product was performed by gel-excision, following the Illumina-recommended protocol. 200 bp cDNA template molecules with the adaptor attached were enriched by PCR to create the final library.


title: NA18912_argonne

description: RNA-Seq


title: NA18502_2_argonne

description: RNA-Seq


title: NA18856_argonne

description: RNA-Seq


title: NA19102_argonne

description: RNA-Seq


title: NA18856_2_argonne

description: RNA-Seq


title: NA19200_argonne

description: RNA-Seq


title: NA18523_yale

description: RNA-Seq


title: NA18501_argonne

description: RNA-Seq


title: NA19119_argonne

description: RNA-Seq


title: NA19200_2_argonne

description: RNA-Seq


title: NA19137_yale

description: RNA-Seq


title: NA18858_yale

description: RNA-Seq


title: NA18502_2_yale

description: RNA-Seq


title: NA18852_yale

description: RNA-Seq


title: NA19171_argonne

description: RNA-Seq


title: NA18505_2_yale

description: RNA-Seq


title: NA18856_2_yale

description: RNA-Seq


title: NA18501_2_yale

description: RNA-Seq


title: NA18855_yale

description: RNA-Seq


title: NA18912_2_yale

description: RNA-Seq


title: NA18510_argonne

description: RNA-Seq


title: NA19160_2_argonne

description: RNA-Seq


title: NA19200_2_yale

description: RNA-Seq


title: NA19193_argonne

description: RNA-Seq


title: NA18855_argonne

description: RNA-Seq


title: NA18852_argonne

description: RNA-Seq


title: NA18870_argonne

description: RNA-Seq


title: NA18912_2_argonne

description: RNA-Seq


title: NA19171_2_argonne

description: RNA-Seq