title: Histone H3K27ac ChIP-Seq of Fetal Intestine, Large; Histone.DS21780

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21780
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14947
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
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: GSM1058765_UW.Fetal_Intestine_Large.H3K27ac.H-24595.Histone.DS21780.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21780-Histone.DS21780.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Intestine Large, Donor H-24595, 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.16822
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,606,952
FINDPEAKS_SCORE: 0.6263
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.6196
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9995
IROC_PERCENTILE: 92
POISSON_SCORE: 0.662
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058765_UW.Fetal_Intestine_Large.H3K27ac.H-24595.Histone.DS21780.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21780-Histone.DS21780.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, 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.16918
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 9
BROWSER_TRACK_NAME: FIL H3K27ac 95 80
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K27ac Donor H-24595 Library Histone.DS21780 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,606,952
FINDPEAKS_SCORE: 0.6263
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.6196
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9995
IROC_PERCENTILE: 92
POISSON_SCORE: 0.662
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS21780

value: Fetal Intestine, Large

value: Primary Tissue


title: Hirschmanniella_infected_rice_root-time_point_2-replicate_2

status: Public on Jan 10 2013

type: SRA

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

description: Time point 2 = 7 days after inoculation

library_source: non-genomic

data_processing: Reads were mapped to the Oryza sativa subsp. Japonica reference genome (build MSU6.0) in two phases using TopHat (Trapnell et al., 2009, version 1.3.1) and Cufflinks (Trapnell et al., 2010, version 1.0.3). This software requires Samtools (Li et al., 2009, version 0.1.12a) which was downloaded from “http://samtools.sourceforge.net/”. The Bowtie index was constructed with the ‘bowtie-build’ command (Langmead et al., 2009, version 0.12.7) from the chromosomal fasta files at “ftp://ftp.ensemblgenomes.org/pub/release-10/plants/fasta/oryza_sativa/dna/”. In the first phase the reads from all samples were mapped together using TopHat, maximising sensitivity, to create the input file for Cufflinks. The Ensembl reference annotation in GTF format (“ftp://ftp.ensemblgenomes.org/pub/release-10/plants/gtf/oryza_sativa/”) was used to provide established junctions via the ‘–G’ option. Further, standard parameters were used with exception of following options: --bowtie-n, --initial-read-mismatches 1, -g 10, -a 10, -m 1, -i 30, --solexa1.3-quals. The next step consisted of applying Cufflinks to construct a minimal set of transcripts using reference annotation based transcript (RABT) assembly (Roberts et al., 2011), again based on the Ensembl MSU6 GTF annotation file. Standard settings were used with the exception of following options:  -u, -I 500000, --min-intron-length 30. In the second phase all samples were remapped separately using the same TopHat settings with the following two exceptions: the ‘transcripts.gtf’ output from Cufflinks was used to supply junctions and ‘--no-novel-juncs’ was added to prevent TopHat from introducing new sample specific junctions that were not detected in the first phase. All mapped reads were summed per MSU6 gene or nTAR. Processed data file does not include counts for probable nematode transcripts (see Kyndt et al. 2012).

molecule: polyA RNA

organism: Oryza sativa Japonica Group

source_name: Rice root

growth_protocol: Oryza sativa cv. ‘Nipponbare’ (GSOR-100, USDA) was germinated on wet filter paper for 6 days at 30°C and then transferred to SAP-substrate (Reversat et al., 1999) and further grown at 26°C under a 16h/8h light-regime.  The nematodes , originally isolated in the Philippines (M. graminicola) and Myanmar (H. oryzae), were cultured and extracted as described in Kyndt et al. 2012. Five days after transplanting in SAP the plants were inoculated with 250 nematodes per plant for M. graminicola and 400 nematodes per plant for H. oryzae. Control plants were mock-inoculated. One day after inoculation the plants were transferred to a hydroponic culturing system with Hoagland solution (Reversat et al., 1999) to synchronize the infection process. Infected and control tissue was collected at 3 and 7 days after inoculation.

extract_protocol: Approximately two microgram of total RNA from infected and non-infected roots and root tips were used for mRNA-Seq library construction according to the manufacturer’s recommendations (Illumina). The mRNA was isolated from the total RNA using oligo dT-attached magnetic beads and subsequently fragmented using divalent cations under elevated temperature. First-strand cDNA was generated with reverse transcriptase and random primers. After second-strand cDNA synthesis and adaptor ligation, cDNA fragments of approximately 200 bp were isolated by gel electrophoresis. cDNA fragments were amplified by 18 cycles of PCR using the multiplexing primers from the ‘Multiplexing sample preparation kit’. The denatured library was diluted to a final concentration of 6 pM and loaded on a single read flow cell. Multiplexing was applied to minimize lane effects. After cluster generation, the multiplexed library was sequenced on an Illumina Genome Analyzer II (76 cycles).

treatment_protocol: The root (tips) were excised with a scalpel from the remaining root system. In the case of root knot nematode infected plants, where galls were taken as infected tissue, the root tips of uninfected plants were sampled as control tissue (GSE30367). For migratory nematode infection, the whole root tissue, without root tips, was sampled in infected and uninfected plants. For each treatment, two or three biological replicates, with each replicate containing a pool of 6 different plants.

tag: tissue

value: root

tag: strain

value: cv. Nipponbare (GSOR-100)

tag: growth conditions

value: hydroponic culture for 6 days

tag: origin

value: Myanmar

tag: infection

value: Hirschmanniella oryzae

tag: time point

value: 7 days after inoculation


title: Hirschmanniella_infected_rice_root-time_point_2-replicate_1

description: Time point 2 = 7 days after inoculation


title: Hirschmanniella_infected_rice_root-time_point_1-replicate_3

description: Time point 1 = 3 days after inoculation

value: hydroponic culture for 2 days

value: 3 days after inoculation


title: Histone H3K27ac ChIP-Seq of CD3 Primary Cells; Histone.DS21704

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21704
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14895
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6984
****************
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: GSM1058764_UW.CD3_Primary_Cells.H3K27ac.RO_01701.Histone.DS21704.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21704-Histone.DS21704.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on CD3 Primary Cells, Donor RO 01701, 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.16819
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,285,565
FINDPEAKS_SCORE: 0.3229
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3256
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9994
IROC_PERCENTILE: 89
POISSON_SCORE: 0.3736
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058764_UW.CD3_Primary_Cells.H3K27ac.RO_01701.Histone.DS21704.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21704-Histone.DS21704.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from CD3 Primary Cells, Donor RO 01701, 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.16915
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 9
BROWSER_TRACK_NAME: CD3 H3K27ac 01 04
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells Histone H3K27ac Donor RO 01701 Library Histone.DS21704 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,285,565
FINDPEAKS_SCORE: 0.3229
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3256
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9994
IROC_PERCENTILE: 89
POISSON_SCORE: 0.3736
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: flow sorted CD3+ Cells, year 37; Histone.DS21704

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: CD3 Primary Cells

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Male

value: Hispanic

value: Histone H3K27ac

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Invitrogen Dynabeads

value: Active Motif


title: Hirschmanniella_infected_rice_root-time_point_1-replicate_2

description: Time point 1 = 3 days after inoculation

value: root

value: cv. Nipponbare (GSOR-100)

value: Myanmar


title: Hirschmanniella_infected_rice_root-time_point_1-replicate_1

description: Time point 1 = 3 days after inoculation

value: hydroponic culture for 2 days

value: Hirschmanniella oryzae


title: Meloidogyne_infected_rice_root_tip-time_point_2-replicate_1

description: Time point 2 = 7 days after inoculation

source_name: Rice root tip

value: root tip

value: hydroponic culture for 6 days

value: Philippines

value: Meloidogyne graminicola

value: 7 days after inoculation


title: Meloidogyne_infected_rice_root_tip-time_point_1-replicate_3

description: Time point 1 = 3 days after inoculation

value: 3 days after inoculation


title: Meloidogyne_infected_rice_root_tip-time_point_2-replicate_2

description: Time point 2 = 7 days after inoculation


title: Histone H3K4me1 ChIP-Seq of Fetal Intestine, Small; Histone.DS22555

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22555
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14910
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14909
****************
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: GSM1058776_UW.Fetal_Intestine_Small.H3K4me1.H-24595.Histone.DS22555.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22555-Histone.DS22555.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Intestine Small, Donor H-24595, 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.16840
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,419,517
FINDPEAKS_SCORE: 0.3469
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.3929
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9881
IROC_PERCENTILE: 68
POISSON_SCORE: 0.517
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058776_UW.Fetal_Intestine_Small.H3K4me1.H-24595.Histone.DS22555.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22555-Histone.DS22555.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Intestine Small, Donor H-24595, 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.16936
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 9
BROWSER_TRACK_NAME: FIS H3K4me1 95 55
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small Histone H3K4me1 Donor H-24595 Library Histone.DS22555 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,419,517
FINDPEAKS_SCORE: 0.3469
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.3929
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9881
IROC_PERCENTILE: 68
POISSON_SCORE: 0.517
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Small primary tissue, day 108; Histone.DS22555

value: Fetal Intestine, Small

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 108

value: Male

value: Histone H3K4me1

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry


title: Meloidogyne_infected_rice_root_tip-time_point_2-replicate_3

description: Time point 2 = 7 days after inoculation

value: root tip

value: cv. Nipponbare (GSOR-100)


title: Histone H3K36me3 ChIP-Seq of Fetal Muscle, Leg; Histone.DS22560

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22560
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14959
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1058773_UW.Fetal_Muscle_Leg.H3K36me3.H-24644.Histone.DS22560.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22560-Histone.DS22560.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16836
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,987,056
FINDPEAKS_SCORE: 0.3187
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3244
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9833
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5345
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058773_UW.Fetal_Muscle_Leg.H3K36me3.H-24644.Histone.DS22560.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22560-Histone.DS22560.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16932
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 9
BROWSER_TRACK_NAME: FML H3K36me3 44 60
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K36me3 Donor H-24644 Library Histone.DS22560 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,987,056
FINDPEAKS_SCORE: 0.3187
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3244
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9833
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5345
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS22560

value: Fetal Muscle, Leg

value: day 110

value: Female

value: Histone H3K36me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Active Motif


title: Mock_infected_rice_root-time_point_2-replicate_2

description: Time point 2 = 7 days after mock inoculation

value: root

value: hydroponic culture for 6 days

value: mock

value: 7 days after inoculation


title: Meloidogyne_infected_rice_root_tip-time_point_1-replicate_2

description: Time point 1 = 3 days after inoculation

value: hydroponic culture for 2 days

value: Philippines

value: Meloidogyne graminicola

value: 3 days after inoculation


title: Meloidogyne_infected_rice_root_tip-time_point_1-replicate_1

description: Time point 1 = 3 days after inoculation

value: root tip


title: Mock_infected_rice_root-time_point_1-replicate_1

description: Time point 1 = 3 days after mock inoculation

value: cv. Nipponbare (GSOR-100)


title: Mock_infected_rice_root-time_point_1-replicate_2


title: Mock_infected_rice_root-time_point_2-replicate_1


title: Mock_infected_rice_root_tip-time_point_2-replicate_2


title: Mock_infected_rice_root_tip-time_point_1-replicate_3


title: Mock_infected_rice_root_tip-time_point_2-replicate_1


title: Mock_infected_rice_root_tip-time_point_2-replicate_3


title: NAc_saline_rep2

city: Farmington

first: Jodi

last: Eipper-Mains

state: CT

address: 263 Farmington Ave.

department: Genetics & Developmental Biology

institute: University of Connecticut Health Center

library_source: transcriptomic

data_processing:
Sequences and quality scores were extracted from image files using GAPipeline software v1.0 or v1.3.2.
Sequences were aligned to the Mus musculus genome (2007, mm9; NCBI Build 37) using Bowtie v0.12.7 permitting multi-alignment and allowing up to two mismatches. Ambiguous alignments were resolved using the Spliced Paired-end Aligner Perl script (Brooks et al. 2011).
Normalized mRNA expression was calculated as RPKM (reads per kilobase gene model per million mapped reads) (Mortazavi et al. 2008) from aligned sequence reads.
Z-scores were computed from frequency data using the following equation: (x − μ)/ σ; x, sample frequency; μ, mean across all samples; σ, standard deviation across all samples.
Gene expression data (Z-scores) were hierarchically clustered using Gene Cluster v3.0; heat maps were generated using Java Treeview v1.1.6r2.
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each replicate and composite files of all RPKM values.

organism: Mus musculus

source_name: Nucleus accumbens

growth_protocol: Adult male C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME; 2–5months old) were group-housed in the animal facility at the University of Connecticut Health Center on a 12h light/dark cycle (lights, 0700–1900h) and handled in accordance with Institutional Animal Care and Use Committee guidelines. After acclimation for 1 week, animals were handled for 1min/day for 2–3days prior to injections. On each treatment day, animals were allowed to acclimate to the behavior room for 45–60min before beginning injections.

extract_protocol:
Nucleus accumbens punches were taken from individual mice (at least eight animals/treatment group). Total RNA was prepared using TRIzol. Total RNA used for NAc library preparation consisted of equal amounts of RNA from eight individual mice for each treatment. One Saline, one Cocaine and one 8-day Withdrawal mRNA-Seq library was prepared from each pooled RNA sample according to manufacturer’s specifications (Illumina, San Diego, CA, USA). Briefly, total RNA was treated with DNase I; poly(A)+ RNA purified using Dynal magnetic beads (Invitrogen) was fragmented by partial alkaline hydrolysis (Ambion, Grand Island, CA, USA) and reverse-transcribed using random primers and SuperScript II (Invitrogen). cDNA was size-selected (∼200bp insert) on 2% agarose gels.
Libraries were prepared for sequencing using the Paired-End DNA Sample Prep Kit (Illumina). Nucleus accumbens libraries were sequenced in nine lanes (three technical replicates per sample) on an Illumina GAIIx using a 37-cycle paired-end sequencing protocol.

treatment_protocol: Animals were given Saline (10 ml/kg/day) or Cocaine (10 or 20mg/kg/day) intraperitoneally for 7days and locomotor activity was monitored daily using a 15′′ × 15′′ Plexiglas chamber; after the seventh injection, locomotor activity was threefold higher in mice receiving Cocaine than in mice receiving Saline. Animals were sacrificed by decapitation 24h after the final injection with the exception of mice in the Withdrawal groups, which were kept in the home cage for 8 days after the final Cocaine dose prior to tissue harvest.

value: Nucleus accumbens

tag: treatment

value: Saline


title: Histone H3K27me3 ChIP-Seq of Fetal Intestine, Large; Histone.DS22553

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22553
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14944
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
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: GSM1058768_UW.Fetal_Intestine_Large.H3K27me3.H-24595.Histone.DS22553.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22553-Histone.DS22553.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Intestine Large, Donor H-24595, 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.16878
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,453,627
FINDPEAKS_SCORE: 0.0668
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1387
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9724
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2469
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1058768_UW.Fetal_Intestine_Large.H3K27me3.H-24595.Histone.DS22553.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22553-Histone.DS22553.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, 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.16974
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 9
BROWSER_TRACK_NAME: FIL H3K27me3 95 53
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K27me3 Donor H-24595 Library Histone.DS22553 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,453,627
FINDPEAKS_SCORE: 0.0668
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1387
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9724
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2469
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS22553

value: Fetal Intestine, Large

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 108

value: Male

value: Histone H3K27me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Millipore


title: Histone H3K27me3 ChIP-Seq of Fetal Muscle, Leg; Histone.DS22559

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22559
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14962
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1058770_UW.Fetal_Muscle_Leg.H3K27me3.H-24644.Histone.DS22559.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22559-Histone.DS22559-Histone.DS22559.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16868
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,170,133
FINDPEAKS_SCORE: 0.2562
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3437
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9433
IROC_PERCENTILE: 72
POISSON_SCORE: 0.4734
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058770_UW.Fetal_Muscle_Leg.H3K27me3.H-24644.Histone.DS22559.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22559-Histone.DS22559-Histone.DS22559.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16964
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 9
BROWSER_TRACK_NAME: FML H3K27me3 44 59
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K27me3 Donor H-24644 Library Histone.DS22559 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,170,133
FINDPEAKS_SCORE: 0.2562
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3437
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9433
IROC_PERCENTILE: 72
POISSON_SCORE: 0.4734
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS22559

value: Fetal Muscle, Leg

value: day 110

value: Female

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


title: Mock_infected_rice_root_tip-time_point_1-replicate_2

value: root tip

value: cv. Nipponbare (GSOR-100)

value: hydroponic culture for 2 days

value: mock

value: 3 days after inoculation


title: Mock_infected_rice_root_tip-time_point_1-replicate_1


title: Sample 20 shoot microRNA HLS As(III) 80 uM 24 h

status: Public on Jan 09 2013

city: Guangzhou

first: Lujun

last: Yu

state: Guandong

address: xingangxilu 135

country: China

institute: Sun Yat-sen University

data_processing: RNA-Seq tag mapping to the rice reference genome  Pair-end mRNA sequence tags were mapped to Nipponbare rice genome by BWA (Li & Durbin, 2009) with the default parameters. Read counts used in expression analyses were based on the subset of uniquely aligned reads that also overlapped the genomic spans of the TIGR6.1 gene model. Gene expression levels within a given sample were normalized using values for a gene's uniquely aligned read counts per kilobase of exon model per million reads (RPKM), uniquely aligning within each sample.   Bioinformatics for gene functional annotation   Z-score was determined based on the RPKM according to the following formula: Z = (X-μ)/σ, where X is the RPKM of a gene for a specific tissue / timepoint, and μ and σ are the mean transcript expression and standard deviation of a gene across all samples, respectively. All calculations and plots were performed in R language (Severin et al., 2010). DEGseq was used for the identification of differentially expressed genes (P < 0.001) (Wang et al., 2010). In addition, we have made a special effort to compare the GO terms of each gene were annotated based on the integrated information from TIGR6.1 and AgriGo database (Du et al., 2010). Pathway information for gene models was retrieved from Kyoto Encyclopedia of Genes and GenomesKEGG database (KEGG; http://www.genome.jp/kegg/) (Kanehisa & Goto, 2000).   miRNA processing  miRNA analysis was based on retrieved results from DSAP websites (Huang et al., 2010). Custom R scripts were used for clustering and graphical representation. Rice miRNA-targets pairs information of computational prediction and degradome-seq data was download from RMRD (Lindow et al., 2007; Zhang et al., 2010) and starBase (Yang et al., 2011). Taking into account the fact that miRNA may down-regulate the expressional level of its target mRNA (Rhoades et al., 2002), there should be a negative correlation between miRNA and target mRNA expression profiles. We computed the expressional correlation between the miRNAs and target mRNA (Wang & Li, 2009). The miRNA-mRNA pairs were considered to be biological relevance if Pearson correlation coefficients between them were in the range from -1 to -0.5.

molecule: total RNA

source_name: shoot

growth_protocol: Seedlings were grown in 1/2 Hoagland nutrient solution at 28°C day/ 25°C night with a photoperiod of 16 h light (9:00-0:59) and 8 h night (1:00-8:59) in the green house.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs) to remove contaminated genomic DNA. mRNA was isolated from total RNA using Dynabeads oligo(dT) (Invitrogen). First- and second-strand cDNA were generated using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction according to the illuminaIllumina paired-end sample preparation protocol, using custom multiplex indexed Solexa adaptors and sequenced as 75 × 2 using the Illumina GA Genome Analyzer paired-end pipeline.

treatment_protocol: For As(III) treatments, 14-d-old rice seedlings were exposed to sodium arsenite (20 and 80 μm) at 9:00, and materials were harvested at 0, 6 and 24 h after treatment.

value: Nipponbare

value: shoot

value: As(III) 80 uM

tag: time

tag: development stage


title: Sample 19 shoot microRNA LLS As(III) 20 uM 24 h

value: As(III) 20 uM


title: Sample 18 shoot microRNA HSS As(III) 80 uM 6 h

value: 6 h


title: Sample 16 shoot microRNA CKS As(III) 20/80 uM 0 h

value: control for As(III) 20/80 uM

value: 0 h


title: Sample 15 root microRNA HLR  As(III) 80 uM 24 h

source_name: root

value: root


title: Sample 14 root microRNA LLR  As(III) 20 uM 24 h


title: Sample 13 root microRNA HSR As(III) 80 uM 6 h


title: Sample 12 root microRNA LSR  As(III) 20 uM 6 h


title: Sample 9 shoot mRNA LLS_1 As(III) 20 uM 24 h


title: Sample 8 shoot mRNA HSS_1 As(III) 80 uM 6 h


title: Sample 6 shoot mRNA CKS_1 As(III) 20/80 uM 0 h


title: Sample 7 shoot mRNA LSS_1 As(III) 20 uM 6 h


title: Sample 5 root mRNA HLR_1 As(III) 80 uM 24 h


title: Sample 4 root mRNA LLR_1 As(III) 20 uM 24 h


title: Sample 1 root mRNA CKR_1 As(III) 20/80 uM 0 h


title: Sample 10 shoot mRNA HLS_1 As(III) 80 uM 24 h


title: Sample 2 root mRNA LSR_1 As(III) 20 uM 6 h


title: Dox- (without doxycycline chow)

city: changchun

first: zhong

middle: q

last: p

address: nenu

institute: Mouse Uterus

description: Doxjian (Dox-)

data_processing:
Baescalls performed using Illumina CASAVA 1.7software
To produce total clean tags, adaptor only, low quality sequences and tags with copy number less than 2 were removed.
The copy number corresponding to each  gene was counted and standardized. Clean tags were calculated and normalized to Transcripts Per Million (TPM) for comparison between samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene ID, gene symbol, gene expression level and GO analysis, for each Sample

source_name: Uterus

extract_protocol:
Total RNA was isolated from 3 uteri of Dox+ and Dox- at G2.5 using RNAisoTM Plus. For RNA library construction and deep sequencing, equal amounts of total RNA from three individual Dox+ and Dox- uteri were pooled. The mRNAs were purified from 6 μg of total RNA using Oligo (dT) magnetic beads and fragmented into small pieces using divalent cations under elevate tempreture using Illumina’s kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Double transgenic mice (VEGFtetO/tetO/beta-AKtg/wt)

value: uterus

tag: age

value: gestation day 2.5

tag: genotype

value: VEGF-repression


title: LH AML cells 955

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

description:
flowcell id: C02D3ACXX
lane: 1

data_processing:
Reads were created by CASAVA 1.8 from the HiSeq2000, and these are all reads which pass filter
Reads were filtered from the adapter sequences using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website (2011) (http://sourceforge.net/projects/theflexibleadap/).
Reads were aligned to whole genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool with a maximum of 2 mismatches in a directional manner and only uniquely aligning reads were retained.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 20 phred quality score and the base position should have at least 10X coverage. Only CpG dinucleotides that satisfy these coverage and quality criteria were retained for subsequent analysis. *myCpG.txt files are constructed for each CpG position in the genome. The file contains location of the CpG, total read coverage on the C base, percentage of bisulfite converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The pipeline that aligns and calls for methylation percentage per base is available at http://code.google.com/p/amp-errbs
Genome_build: mm9
Supplementary_files_format_and_content: myCpG.txt = tab delimited file with the following column heades: chrBase chr base strand coverage freqC freqT

source_name: LH AML cells

extract_protocol: ERRBS libraries were constructed as described in 18. Akalin A et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia. PLOS Genetics 8, in press (2012).

tag: cell type

value: MLL-AF9 transformed hematopoietic stem cells (HSC)

value: Acute Myeloid Leukemia


title: LH AML cells 459

description:
flowcell id: BC0N3YACXX
lane: 5


title: LH AML cells 460

description:
flowcell id: BC0N3YACXX
lane: 6


title: LH AML cells 956

description:
flowcell id: C02D3ACXX
lane: 2


title: LG AML cells 950

description:
flowcell id: D0BA7ACXX
lane: 5

source_name: LG AML cells

value: MLL-AF9 transformed granulocyte macrophage progenitors (GMP)


title: LG AML cells 949

description:
flowcell id: AC0BCKACXX
lane: 2


title: Dox+ (with doxycycline chow)

description: Doxjia (Dox+)

tag: tissue

value: VEGF-normal (wild type)


title: Sample 17 shoot microRNA LSS As(III) 20 uM 6 h

tag: strain


title: LG AML cells 499

description:
flowcell id: BC0N3YACXX
lane: 7


title: Input_CT18_ChIPSeq

status: Public on Jan 08 2013

city: Cambridge

first: Akhilesh

middle: Basi

last: Reddy

address: Hills Road

department: Institute of Metabolic Science

country: United Kingdom

institute: University of Cambridge

description: Chromatin IP against Input

data_processing:
Alignment: Paired-end sequence reads (50bp length) were aligned with BOWTIE using a pre-built UCSC mm9 index.
Peaks: Cisgenome (2-sample comparison) was used for peak detection using a window size of 100 and a FDR of 0.1 (10%). Output peak files are in ".bar" format and converted into .txt files.

source_name: Liver tissue

extract_protocol:
Liver tissue (30mg per final ChIP) was rapidly chopped into small (approx. 5 mm x 5mm x 2.5mm cubes) whilst defrosting using a sterile scalpel and immediately submerged in 4% formaldehyde (Sigma) and incubated at room temperature with gentle shaking for 10 mins. Glycine (1.25M) was added to a final concentration of 125 mM and incubated for a further 10 mins to quench the formaldehyde. Tissue was then dounce homogenised briefly to break up the tissue and then passed through a 100 µm cell strainer (BD Biosciences) and a cell suspension harvested. The cells were washed in ice cold phosphate-buffered saline (PBS) and then incubated with 2ml Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40, Roche Complete Protease Inhibitor Cocktail) at 4oC for 15 mins to release nuclei. After spinning down, pelleted nuclei were then lysed with 1ml RIPA Buffer (1xPBS, 1% NP40, 0.5% Sodium Deoxycholate, 0.1% SDS, Roche Complete Protease Inhibitor Cocktail) and incubated for a further 15 mins at 4oC. Chromatin was sheared using a Diagenode Bioruptor at 4oC, using conditions optimised to produce 150-300bp fragments with the use of 15 ml Falcon tubes holding 2ml of lysate each (30 cycles of 30 secs on HIGH, 30 secs OFF). Sheared chromatin was transferred to 1.5 ml microcentrifuge tubes and spun at 14,000 rpm for 15 min at 4°C to pellet debris. Cleared supernatants were transferred to clean microcentrifuge tubes and 100 µl from each sample lysate was saved for use as an input control for sequencing and to check fragment size distribution.
For each liver from n=4 animals per time-point, duplicate ChIPs were performed with each antibody. ChIP-grade antibodies were purchased from Abcam (UK): anti-H3K4me3 (ab8580), anti-H3K9me3 (ab8898) and anti-Histone H3 (ab1791). 50 µl of Protein G magnetic beads (Dynal/Invitrogen) were washed three times (in 1 ml 1XPBS/1% BSA) and then incubated with 5 µg antibody in 300 µl volumes (diluted in PBS/BSA) for 4 hours at 4oC on a rotator. Excess / non-specifically bound antibody was removed by washing a further three times in PBS/BSA. The beads were then added to 900 µl of sheared chromatin in 1.5 ml DNA Lo-bind tubes (Eppendorf) and incubated at 4oC overnight with gentle rotation. Beads were washed six times in 1 ml LiCl Wash Buffer (100 mM Tris, 500 mM LiCl, 1% NP40, 1% Sodium Deoxycholate) for 3 min each, followed by a brief wash in Tris-EDTA (TE) buffer, pH 7.4. The beads were then suspended in TE, transferred to a clean microcentrifuge tube, and TE was removed. 200 ul of IP Elution Buffer (1% SDS and 100 mM NaHCO3) was added at room temperature and then the beads were incubated for 45 mins at 65oC with continuous shaking on a thermomixer (at 800 rpm). The eluate was then removed from the beads and incubated overnight at 65oC to reverse cross-linking. DNA was extracted using a Qiagen Minelute PCR purification kit (using 12 ul of Buffer EB to elute DNA) and then quantified using Picogreen assays (Invitrogen) in a microplate as per the manufacturer's instruction. Input chromatin was reverse cross-linked in parallel and assayed with a Nanodrop spectrophotometer (because of the much higher DNA concentration) and a sample was run on a 2% agarose gel to check fragment size distributions were correct.
Samples were prepared for sequencing on an Illumina Genome Analyzer II following the manufacturer's recommended library preparation protocol using 50 ng of ChIPed DNA, except that a custom adapter was used, the PCR was performed using indexed adapters and a high-efficiency amplification step, and the size selection step was performed after the PCR. The average insert length was 200bp and SD = 50.

treatment_protocol: Liver tissue was harvested from 4 adult male C57Bl/6 mice (Harlan-Olac, UK) once every 6 hours on the second cycle after transfer from 12L:12DR (stably entrained for 4 weeks) to DR:DR (L, light [220 µW cm-2] and DR, dim red light [< 5 µW cm-2]) and immediately frozen and then stored at -80°C prior to use.

value: Liver

tag: chip antibody


title: Sample 11 root microRNA CKR  As(III) 20/80 uM 0 h

value: Nipponbare


title: Input_CT6_ChIPSeq

description: Chromatin IP against Input


title: H3Pan_CT18_ChIPSeq

description: Chromatin IP against H3Pan


title: Input_CT12_ChIPSeq

description: Chromatin IP against Input


title: Input_CT0_ChIPSeq

description: Chromatin IP against Input


title: H3K9me3_CT18_ChIPSeq

description: Chromatin IP against H3K9me3


title: H3K4me3_CT18_ChIPSeq

description: Chromatin IP against H3K4me3


title: H3K9me3_CT0_ChIPSeq

description: Chromatin IP against H3K9me3


title: H3K9me3_CT6_ChIPSeq

description: Chromatin IP against H3K9me3


title: Sample 3 root mRNA HSR_1 As(III) 80 uM 6 h


title: H3K4me3_CT12_ChIPSeq

description: Chromatin IP against H3K4me3


title: H3Pan_CT0_ChIPSeq

description: Chromatin IP against H3Pan


title: H3K4me3_CT0_ChIPSeq

description: Chromatin IP against H3K4me3


title: fetal CEC 2

city: Los Angeles

first: Kevin

last: Huang

state: CA

address: Gonda BLDG Rm. 6554, P.O.Box 957088

institute: UCLA

data_processing:
each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.
For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: filtered and normalized RPKM table

source_name: corneal endothelial cells

growth_protocol: Adult cornea samples (age 31, 56, and 64 years old) were obtained from normal subjects who donated to the eye bank in UCLA Jules Stein Eye Institute. Fetal CEC samples were dissected from fetal ocular samples (16-18 weeks of gestation) provided by UCLA department of Pathology & laboratory and approved by UCLA IRB. The whole corneal endothelial layers were carefully peeled off under dissecting microscope and were immediately lyses in reagents for RNA purification.

extract_protocol:
RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer
RNA-Seq library construction followed the protocol described in illumina TruSeq™ RNA Sample Preparation Guide.  Library construction was started with 100ng total RNA, via poly-T oligo-attached magnetic beads to purify the poly-A containing mRNA molecules. RNA fragments were reverse transcribed into first stand cDNA, follwed by synthesis  second strand cDNA. After end repaired with a single ‘A’ base, cDNAs were ligated with different adapters for PCR amplification. After amplified for 15 cycles, the concentration of product was tested by the Qubit Fluorometer (Invitrogen, USA).

value: corneal endothelial cells

value: gestation age 16-18wk


title: H3Pan_CT6_ChIPSeq

description: Chromatin IP against H3Pan


title: fetal CEC 1


title: adult CEC 40


title: DS011_MCF-7_foxm1_DMSO_4

status: Public on Jan 07 2013

first: Dario

last: Beraldi

address: Robinson Way

institute: Cambridge Research Institute

data_processing:
Basecalls were performed using CASAVA version 1.7.
ChIP-Seq reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.6, March 2008) using bwa 0.6.1 with default settings.
Reads mapped with MAPQ < 15 were filtered out. Reads overlapping regions producing aspecific binding were also removed (regions obtained from http://hgdownload-test.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/wgEncodeDukeRegionsExcluded.bed).
Peaks were identified with MACS 1.4.1 using as a control file the input library matched by the same cell line as the treatment library.
Genome_build: hg18
Supplementary_files_format_and_content: Files produced by MACS that report peak positons and statistics. File description adapted from MACS manual (http://liulab.dfci.harvard.edu/MACS/00README.html): NAME_peaks.txt is a tab-delimited text file that contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. Information includes: chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region (e.g., pvalue =1e-10, then this value should be 100), fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage. Coordinates are 1-based, which is different from BED format.

source_name: MCF-7 breast adenocarcinoma cells, control, FOXM1 ChIP

growth_protocol: Human MCF-7 and MDA-MB-231 cell lines were obtained from the ECACC (European Collection of Animal Cell Cultures) and grown in DMEM supplemented with 10% FBS.

extract_protocol: 6 x 15cm2 plates were used per IP protocol. IP was carried out as described in Schmidt et al. (2009) (PMID 19275939). In brief, cells were cross-linked using 1% formaldehyde for 10 min at RT, reaction was quenched with 1/20th volume 2.5M Glycine and cell pellets were collected after scraping plates. Nuclear lysates were prepared by lysing with LB1 (50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X plus PI) 10 min at 4°C and LB2 (10mM Tris-HCl, pH8.0, 200mM NaCl, 1mM EDTA, 0.5M EGTA plus PI) 5 min at 4°C, followed by sonication in LB3 (10mM Tris-HCl, pH8.0, 100mM NaCl, 1mM EDTA, 0.5M EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine plus PI) using a diagnode sonicator to give a fragment size of ~200-300bp. Sonicated lysate was combined with 100ul protein-A magnetic beads preloaded with 10ug anti-FOXM1 antibody (Santa Cruz Biotechnology, USA; cat no. sc-502; lot no. D0110) O/N at 4°C. Beads were washed X6 in RIPA buffer (50mM HEPES pH7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and DNA was eluted for 16 hr at 65°C in elution buffer (50mM Tris-HCl, pH8.0, 10mM EDTA, 1% SDS). Extracted DNA was treated with RNase A for 30 min at 37°C, followed by Proteinase K for 1 hr at 55°C, and DNA was purified by phenol-chloroform extraction. DNA was prepared for Illumina library construction by repair with Klenow and T4 polymerase, A-tailing with Klenow exo-polymerase and attachment of adapters (diluted 1:20) using DNA ligase. Adapter-ligated fragments were amplified by PCR using phusion polymerase (12 cycles), and ~200-300 bp fragments were extracted by gel purification. Library size and quantity were determined by Bioanalyzer.

treatment_protocol: Cells were grown to 60% confluence, and then treated with Thiostrepton (10μM) or DMSO (0.1%) for 4 hr.

value: ER-positive breast adenocarcinoma cells

value: DMSO

tag: replicate


title: adult CEC 39


title: DS008_MDA-MB-231_foxm1_Thiostrepton_2

source_name: MDA-MB-231 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP

value: ER-negative breast adenocarcinoma cells

value: thiostrepton


title: DS007_MDA-MB-231_foxm1_DMSO_2

source_name: MDA-MB-231 breast adenocarcinoma cells, control, FOXM1 ChIP


title: DS012_MCF-7_foxm1_Thiostrepton_4

source_name: MCF-7 breast adenocarcinoma cells, thiostrepton, FOXM1 ChIP


title: adult CEC 33


title: DS004_MCF-7_foxm1_Thiostrepton_2


title: NAc_withdrawal_rep3

value: Nucleus accumbens

value: Withdrawal


title: DS005_MDA-MB-231_foxm1_DMSO_1


title: DS003_MCF-7_foxm1_DMSO_2


title: DS002_MCF-7_foxm1_Thiostrepton_1


title: H3K9me3_CT12_ChIPSeq

description: Chromatin IP against H3K9me3


title: DS001_MCF-7_foxm1_DMSO_1


title: Post-diff mRNA-seq TAF7L (C2C12.TAF7L cells)

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

description:
Post-diff mRNA-seq TAF7L (C2C12 cells)
Sample name: HY-RS6

data_processing:
Peak calling methods: To accurately identify significant binding positions across the genome, we incorporated two peak calling methods, as described previously (May et al., 2012). First, we used MACS (Zhang et al., 2008) (version 1.4, with default settings except: --nomodel --shiftsize=110 --pvalue=1e-2 --mfold=10,10000 --slocal=2000 --llocal=20000), with an FDR significant threshold of 0.05 (using IgG ChIP as a control). Second, we applied the Grizzly peak fitting algorithm (Harrison et al., 2011), which uses a model-based iterative approach to accurately identify multiple binding loci at every enriched region. Peaks were then associated with the nearest TSS (using gene annotation from UCSC, version mm9), and classified as promoter peaks (up to 500bp from start site), proximal enhancer peaks (larger than 500bp and less than 5Kb), distal enhancer peaks (less than 50 Kb from TSS), or none (further away than any start site). Peaks are summarized in the following format: (1) position (2) chromosome (3) from position (4) to position (5) max coverage (6) total coverage (7) peaks (8) their respective heights (9) threshold for stopping criterion.  Note: There are some runs with no or very few peaks called.
Digital gene expression of mRNA-seq: The reads were than mapped to the mouse transcriptome (created using UCSC table browser, version mm9, on February 2012), using TopHat (Trapnell et al., 2009), version v1.4.0., using default parameters. We then applied cufflinks (Trapnell et al., 2010), version v1.3.0, using the default parameters except: --max-mle-iterations 1, to estimate the digital expression levels at each transcript. Due to the high number of sequence reads, these steps were done in seven batches of 25 million reads each, per sample.
Genome_build: UCSC mm9 [MGSCv37]
Supplementary_files_format_and_content: Peak calling output files (.xls; intersection of MACS and Grizzly Peak fitting algorithms).
Supplementary_files_format_and_content: Adipose_mRNA_ChIP.xlsx and Adipose_mRNA_ChIP.txt are large tables summarizing ChIP binding at promoters, proximal or remote for every data/gene, as well as gene expression levels and ratios.  These two files are mostly identical: the binary excel format  is ideal for visualizations and the text version suitable for automated parsing. The files were generated using my MATLAB programs, then curated manually.

source_name: C2C12.TAF7L mouse cells

growth_protocol:
Cell culture protocol: C3H10T1/2, C2C12 cells were cultured in high glucose DMEM with 10% fetal bovine serum at 10% CO2.
Adipogenesis protocol: For adipogenesis, cells were grown to confluence in medium containing 10% fetal bovine serum. At confluence, cells were exposed to induction medium containing dexamethasone (1uM), IBMX(0.1mM), insulin(5ug/ml) and rosiglitazone(1uM), and 10% FBS. 3 days later, cells were further cultured in DMEM containing insulin (5ug/ml) and rosiglitazone (1uM) until they were ready for collection.

extract_protocol:
Total RNA from cultured cells or mouse tissues was isolated using QIAGEN RNeasy Plus mini columns according to the manufacturer’s instructions (Qiagen, MA).
mRNA-seq libraries preparation and deep sequencing: Total RNAs were extracted from C3H10T1/2 cells and adipocytes, differentiated shTAF7L-C3H10T1/2 cells, differentiated C2C12.CNTL and C2C12.TAF7L cells by RNeasy Plus Mini Kit (Qiagen), 8ug of each sample was used to purify mRNA and subsequently converted into to mRNA-seq library using mRNA-Seq Sample Prep Kit (Illumina).
Preparation of the ChIP-seq and mRNA-seq libraries on the DNA samples of the immunoprecipitation from antibodies and IgGs and mRNA extracted from different cells precisely followed the instructions from Illumina (Illumina Inc.), qualities of the libraries were assessed by 2100 Bioanalyzer and then subjected to ultra-high throughput sequencing.

value: C2C12.TAF7L cells


title: H3K4me3_CT6_ChIPSeq

description: Chromatin IP against H3K4me3


title: DS018_MCF-7_foxm1_Thiostrepton_7


title: Post-diff mRNA-seq (Adipocytes)

description:
Post-diff mRNA-seq (Adipocytes)
Sample name: HY-RS2

source_name: adipocytes differentiated from C3H10T1/2 mouse cells

value: adipocytes differentiated from C3H10T1/2 cells


title: Post-diff mRNA-seq shTAF7L (Adipocytes)

description:
Post-diff mRNA-seq shTAF7L (Adipocytes)
Sample name: HY-RS3

source_name: adipocytes differentiated from shTAF7L-treated C3H10T1/2 mouse cells

value: adipocytes differentiated from shTAF7L-treated C3H10T1/2 cells


title: Post-diff mRNA-seq (C2C12.CNTL cells)

description:
Post-diff mRNA-seq (C2C12 cells)
Sample name: HY-RS5

source_name: C2C12.CNTL mouse cells

value: C2C12.CNTL cells


title: H3Pan_CT12_ChIPSeq

description: Chromatin IP against H3Pan


title: DS017_MCF-7_foxm1_DMSO_7


title: TAF7L ChIP-seq (10T1/2)

description:
TAF7L ChIP-seq (10T1/2)
Sample name: HY_TAF7L_Pre

source_name: C3H10T1/2 mouse cells

extract_protocol:
Antibody production and purification, antibodies: A fragment of the TAF7L gene corresponding to residues 500-600 was cloned into the pGEX-4T-1 vector carrying a GST tag. GST-TAF7L was expressed and purified from E.coli and injected into rabbits. Bleeds were collected after three boosts and TAF7L antibodies were tested and confirmed by in vitro transcribed and translated TAF7L and mouse testis whole protein extracts from wild-type and TAF7L knockout mice. The antisera obtained were affinity-purified using antigen immobilized on Affigel 10/15 resin (Bio-rad). For Pol II antibody, monoclonal anti-Pol II (8WG16) was concentrated from hybridoma supernatant with Protein A Sepharose Beads (GE Healthcare).
ChIP, ChIP libraries preparation, and deep sequencing (ChIP-seq): Fix C3H10T1/2 cells and differentiated adipocytes with 1% formaldehyde for 10 mins at room temperature then use 0.125M glycine to stop the crosslinking for an additional 5 mins. Collect cells and extract nuclei with extraction buffer. The chromatin obtained from C3H10T1/2 cells and adipocytes was fragmented to sizes ranging from 175 to 250 bp using a Covaris-S2 (Covaris, Inc.) sonicator for a total processing time of 40 min (20s on, 20s off). 900 µg of the chromatin was used in each immunoprecipitation reaction as previously described (Liu et al., 2011), with the Pol II, TBP, PPARγ and TAF7L antibodies, mouse and rabbit IgG as negative controls respectively. We prepared the IgG abs in-house from mice and rabbits and concentrated with Protein A Sepharose Beads (GE Healthcare).
Preparation of the ChIP-seq and mRNA-seq libraries on the DNA samples of the immunoprecipitation from antibodies and IgGs and mRNA extracted from different cells precisely followed the instructions from Illumina (Illumina Inc.), qualities of the libraries were assessed by 2100 Bioanalyzer and then subjected to ultra-high throughput sequencing.

value: C3H10T1/2 cells

value: TAF7L (in-house)


title: TBP ChIP-seq (10T1/2)

description:
TBP ChIP-seq (10T1/2)
Sample name: HY_TBP_Pre

value: anti-TBP (abcam 62126)


title: Pparg ChIP-seq (Adipocytes)

description:
Pparg ChIP-seq (Adipocytes)
Sample name: HY_Pparg_Post

value: PPARγ (sc-7196)


title: DS006_MDA-MB-231_foxm1_Thiostrepton_1


title: TAF7L ChIP-seq (Adipocytes)

description:
TAF7L ChIP-seq (Adipocytes)
Sample name: HY_TAF7L_Post


title: GEK-49

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Eugenia uniflora

source_name: leaf

growth_protocol: Adult individual

extract_protocol: Total RNA was isolated from the leaf material using CTAB method (Gambino et al.,  2008) and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. One mRNA library was constructed and it was sequenced by Illumina HiSeq2000. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.

tag: sample

value: single

value: adult

value: leaf


title: Pparg ChIP-seq (10T1/2)

description:
Pparg ChIP-seq (10T1/2)
Sample name: HY_Pparg_Pre


title: PolII ChIP-seq (Adipocytes)

description:
PolII ChIP-seq (Adipocytes)
Sample name: HY_PolII_Post

value: Pol II (monoclonal 8GW16, protein-A purified)


title: PolII ChIP-seq (10T1/2)

description:
PolII ChIP-seq (10T1/2)
Sample name: HY_PolII_Pre


title: IgG ChIP-seq (10T1/2)

description:
Input ChIP-seq (10T1/2)
Sample name: HY_PI_Pre

value: IgG (in-house)


title: IgG ChIP-seq (Adipocytes)

description:
Input ChIP-seq (Adipocytes)
Sample name: HY_PI_Post


title: input_control_S2-PH_ChIPSeq

status: Public on Jan 04 2013

first: Nicole

last: Follmer

state: MA

address: 16 Divinity Avenue

institute: Harvard University

data_processing:
Alignment: Sequenced reads were aligned to the D. melanogaster genome (dm3) using Bowtie 1.1.2 (Langmead, B. et al., 2009) with the paramters -n 2 -m 1  --best --strata through Galaxy (Blankenberg, D. et al., 2010; Goecks, J. et al., 2010; Giardine, B. et al., 2005).
Peaks: peak detection was performed using the Model-Based Analysis of ChIP-Seq (MACS, version 1.0.1) through Galaxy using --tsize 36, --gsize 120000000 --bw 200 --nomodel --shiftsize 100.  Peaks were filtered to retain peaks with a false discovery rate of 5% or below for all samples except for mitotic PH.  Peaks on chromosome U and Uextra were removed.
Genome_build: dm3
Supplementary_files_format_and_content: Wig files were generated using MACS (version 1.0.1) and represent shifted tag counts for every 10bp.  Wig files were normalzed by reads per million (RPM).  Bed files contain a score that is given by -10*LOG10(pvalue).

organism: Drosophila melanogaster

source_name: S2 cell line

growth_protocol: Drosophila S2 cells were grown in ESF921 medium (Expression Systems) at 27°C

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine.  Cells were stained with antibodies to either anti-H3S10p (colchicine-treated cells) or anti-H3 (asynchronous cultures) that were either FITC-conjugated or treated with a FITC-conjugated secondary antibody and FACS sorted to collect FITC positive cells. Nuclear lysates were sonicated to generate 300-600 bp DNA fragments. Chromatin was incubated overnight with antibody against PSC at 4°C (S2 cells) or without antibody (S2-PH cells). Chromatin was precipitated with streptavidin-coated beads for 2 hours at 4°C. After washing and eluting from beads the crosslinking was reversed and DNA was isolated. Eluted DNA and input DNA was sheared with a Bioruptor (Diagenode) to give ~180bp fragments.  Libraries were generated by the BioMicroCenter (MIT) using the SPRI-works system.

treatment_protocol: for mitotic samples S2 or S2-PH cells were treated with 350ng/ml (880nM) colchicine for 15hrs.

tag: cell line

value: S2 experssing biotin-PH

tag: facs sorting antibody

tag: cell cycle profile

value: asynchronous


title: WT_rep2

status: Public on Jan 06 2013

city: Bucheon

first: Joo-Young

last: Lee

state: Gyonggi

address: 43-1 Yokgok2-dong

department: Department of Biotechnology

country: South Korea

institute: The Catholic University of Korea

data_processing:
Xpression (https://depts.washington.edu/cshlab/html/rnaseq.html) was used for RNA-Seq data processing.
Xpression was used for filtering and trimming reads.
Reference files for the genome sequence being queried, Corynebacterium glutamicum ATCC13032 genome (BX927147.1) were uploaded.
Raw sequencing reads (FASTQ) were processed by Xpression and only the uniquely mapped reads were subjected to further analysis.
The number of reads overlapping each gene was recorded and normalized based on reads per kilobase per million (RPKM) uniquely mapped reads.
genome build: BX927147.1
Supplementary_files_format_and_content: wig

organism: Corynebacterium glutamicum ATCC 13032

source_name: bacterial cells

growth_protocol: Cells were grown in a 500 ml baffled flask containing 50 ml MCGC minimal medium. Actively growing cells (OD600nm = 3) were harvested by centrifugation, and the pellets were used for RNA.

extract_protocol:
Total RNA was harvested from C. glutamicum cells using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and NucleoSpin® (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions with the following modifications. Cells were harvested by centrifugation, resuspended in TRIzol® reagent, and transferred to a vial containing Lysing Matrix B® (MP Biomedicals, Solon, OH, USA) for lysis. The suspension was centrifuged, and the supernatant was applied to a NucleoSpin® RNA II kit for purification.
Library construction protocol: First and second strand cDNA synthesis was carried out using the Ovation® Prokaryotic RNA-Seq System (NuGEN Technologies Inc., San Carlos, CA, USA), and NuGEN’s Encore NGS Library System was applied to construct the cDNA library for the Illumina Genome Analyzer II platform.

treatment_protocol: The wild-type strain grown (OD600=3.0) under no stress condition and HA strain grown (OD600=3.0) under 10 mM H2O2 condition in MCGC minimal medium were harvested for RNA isolation.

tag: genotype/variation

value: wild-type

tag: condition

value: MCGC


title: Pre-diff mRNA-seq (10T1/2)

description:
Pre-diff mRNA-seq (10T1/2)
Sample name: HY-RS1


title: input_mitotic_S2-PH_ChIPSeq

value: mitotic


title: HA+H2O2_rep1

value: 10 mM H2O2 adapted (HA)

value: MCGC+10 mM H2O2


title: MNase-seq replicate

city: Daejeon, Seoul

first: kwoneel

last: kim

address: Gwahangno, Yuseong gu

institute: KAIST

data_processing:
MNase-1.bed; genome build: sacCer2
Sequence reads were mapped to the yeast genome (NCBI June 2008) by means of the Illumina sequencing pipeline. The sequencing tags were extended to the average size of fragments in the library (150 bp)

organism: Saccharomyces cerevisiae

source_name: yeast extract

growth_protocol: Yeast cells were grown in YPD to an A600 OD of 1.5 at 200 rpm. Cells were fixed in 1% formaldehyde, and incubated for 30 minutes at room temperature, shaking, at 200 rpm. 2.5 M glycine was added to a final concentration of 125 mM to quench the formaldehyde. Cell pellet was resuspended in 10ml b-ME buffer (200mM EDTA, 0.7 M b-mercaptoethanol). After 30min of incubation at 30C, cell pellet were precipitated by 5 min of centrifugation at 3000 rpm

extract_protocol: Mononucleosomal DNA fragments were sequenced by Illumina Genome Analyzer, subjected to 36 cycles of single-read sequencing.

treatment_protocol: Spheroplast preparation was conducted at 30C for30 minutes in 10ml lyticase lysis buffer (1M sorbitol. 50mM Tris, pH 7.8; 5mM b-ME) using 10000 units of Lyticase (Sigma). After digesting cell walls, spheroplasts were spun down, washed twice with 1 M sorbitol. DNA digestion was conducted at 37C for 20 minutes in 1.6 ml of digestion buffer (1M sorbitol, 50mM NaCl, 10mM Tris-HCl at pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 1mM b-mercaptoethanol, 0.5mM spermidine and 0.075% v/v NP40). 400uL aliquots of spheroplasts were digested with 3.5 units of MNase (Sigma). Reaction was stopped by the addition of MNase stop buffer (5% SDS, 250mM EDTA). Samples were treated with 5uL of proteinase K (20mg/mL) at 37C for 5 hours, then phenol:chloroform extracted, ethanol precipitated, treated with RNase A, and precipitated with ethanol.Digested DNA was purified and separated on a 1.5% agarose gel, and mononucleosomal DNA (~147 bp) was cut out of the gel.

value: yeast cells


title: PH_control_S2-PH_ChIPSeq

value: none (streptavidin-coated beads used to pulldown biotinlyated PH)


title: input_mitotic_S2 ChIPSeq replicate 2


title: PH_mitotic_S2-PH_ChIPSeq


title: E14_IgG

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

description: Precipitation of chromatin using IgG.

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: mm9
Supplementary_files_format_and_content: Wig files generated by MACS were normalized to sequencing depth and converted to bigWig format using UCSC wigToBigwig tool.

source_name: E14 ES cells

growth_protocol: ES cell lines were grown on 0.1% gelatinaized tissue culture dishes in DMEM in presence of  15% Serum and Leukemia inhibitory factor.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Exponentially growing ES cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using proteinA coupled beads and recovered DNA was used for hightrouput sequencing.

value: E14 ES cells

value: Anti-IgG (IgG from rabbit serum, Sigma-Aldrich, catalog# I5006)


title: MNase-seq

data_processing:
MNase.bed; genome build: sacCer2
Sequence reads were mapped to the yeast genome (NCBI June 2008) by means of the Illumina sequencing pipeline. The sequencing tags were extended to the average size of fragments in the library (150 bp)


title: input_control_S2 ChIPSeq replicate 2


title: input_control_S2 ChIPSeq replicate 1


title: PSC_control_S2_ChIPSeq replicate 2

value: PSC custom made rabbit polyclonal antibody that was affinity purified (described in Francis et al., 2009. PMID:19303136)


title: E14_Ogt

description: Precipitation of chromatin using a specific antibody against OGT.

value: Anti-OGT (O-Linked N-Acetylglucosamine Transferase antibody sold, Abcam, catalog# ab50273)


title: WT_rep1


title: input_mitotic_S2 ChIPSeq replicate 1


title: PSC_control_S2_ChIPSeq replicate 1


title: PSC_mitotic_S2_ChIPSeq replicate 2


title: PSC_mitotic_S2_ChIPSeq replicate 1


title: 8-202

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_24hrPostCIDR_30.counts.txt: bt4

organism: Bos taurus

source_name: Cervix

growth_protocol: The estrous cycles of Limousin heifers (n = 30) were synchronized by insertion of a controlled internal drug release (CIDR) device (1.94 g progesterone; Pfizer Animal Health) placed into the vagina for 8 days. A 0.5 mg intramuscular injection of a prostaglandin F2α (PG) analogue (PG, Estrumate, Shering-Plough Animal Health, Hertfordshire, UK) was administered 1 day before CIDR removal.  Heifers were checked for standing  estrus  and only those exhibiting  estrus  (Day 0) were used.

extract_protocol: The standard Illumina protocol for generating single read RNAseq data was followed. Version 2 illumina sequencing kits were used.

treatment_protocol: Cervical tissues were collected at slaughter from heifers 12h after CIDR removal (Group 1: CIDR + 12 h, n = 6), 24h after CIDR removal (Group 2: CIDR + 24 h, n = 6), at the onset of  estrus  (Group 3: Estrus, n = 4), 12 h after the onset of  estrus  (Group 4:  estrus  + 12 h, n = 5), 48 h after the onset of  estrus  (Group 5: Estrus+48h, n = 4) and on day 7 after the onset of  estrus  (Group 6: Luteal phase, n = 5).

tag: Stage

tag: animaltype

value: Heifer

tag: animalid

tag: timepoint


title: 7-132

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostOestrus_25.counts.txt: bt4


title: 8-174

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostCIDR_29.counts.txt: bt4


title: 7-287

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostOestrus_27.counts.txt: bt4


title: 5-122

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostCIDR_23.counts.txt: bt4


title: 7-232

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_24hrPostCIDR_26.counts.txt: bt4


title: 95-237

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostCIDR_28.counts.txt: bt4


title: 7-258

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_48hrPostOestrus_24.counts.txt: bt4


title: 2-081

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_48hrPostOestrus_22.counts.txt: bt4


title: 75-237

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Oestrus_21.counts.txt: bt4

value: Oestrus


title: 9-212

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Oestrus_19.counts.txt: bt4


title: 8-142

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_48hrPostOestrus_18.counts.txt: bt4


title: 7-302

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_24hrPostCIDR_17.counts.txt: bt4


title: 73-237

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Oestrus_20.counts.txt: bt4


title: 6-076

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostOestrus_16.counts.txt: bt4


title: 6-155

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostCIDR_13.counts.txt: bt4


title: 5-001

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_48hrPostOestrus_10.counts.txt: bt4


title: 4-037

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_24hrPostCIDR_9.counts.txt: bt4


title: 5-062

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_24hrPostCIDR_11.counts.txt: bt4


title: 8-178

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Luteal_14.counts.txt: bt4

value: Luteal


title: 3-235

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Luteal_8.counts.txt: bt4


title: 4-154

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostCIDR_15.counts.txt: bt4


title: 6-086

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_24hrPostCIDR_5.counts.txt: bt4


title: 5-091

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Luteal_12.counts.txt: bt4


title: TBP ChIP-seq (Adipocytes)

description:
TBP ChIP-seq (Adipocytes)
Sample name: HY_TBP_Post

data_processing:
Peak calling methods: To accurately identify significant binding positions across the genome, we incorporated two peak calling methods, as described previously (May et al., 2012). First, we used MACS (Zhang et al., 2008) (version 1.4, with default settings except: --nomodel --shiftsize=110 --pvalue=1e-2 --mfold=10,10000 --slocal=2000 --llocal=20000), with an FDR significant threshold of 0.05 (using IgG ChIP as a control). Second, we applied the Grizzly peak fitting algorithm (Harrison et al., 2011), which uses a model-based iterative approach to accurately identify multiple binding loci at every enriched region. Peaks were then associated with the nearest TSS (using gene annotation from UCSC, version mm9), and classified as promoter peaks (up to 500bp from start site), proximal enhancer peaks (larger than 500bp and less than 5Kb), distal enhancer peaks (less than 50 Kb from TSS), or none (further away than any start site). Peaks are summarized in the following format: (1) position (2) chromosome (3) from position (4) to position (5) max coverage (6) total coverage (7) peaks (8) their respective heights (9) threshold for stopping criterion.  Note: There are some runs with no or very few peaks called.
Digital gene expression of mRNA-seq: The reads were than mapped to the mouse transcriptome (created using UCSC table browser, version mm9, on February 2012), using TopHat (Trapnell et al., 2009), version v1.4.0., using default parameters. We then applied cufflinks (Trapnell et al., 2010), version v1.3.0, using the default parameters except: --max-mle-iterations 1, to estimate the digital expression levels at each transcript. Due to the high number of sequence reads, these steps were done in seven batches of 25 million reads each, per sample.
Genome_build: UCSC mm9 [MGSCv37]
Supplementary_files_format_and_content: Peak calling output files (.xls; intersection of MACS and Grizzly Peak fitting algorithms).
Supplementary_files_format_and_content: Adipose_mRNA_ChIP.xlsx and Adipose_mRNA_ChIP.txt are large tables summarizing ChIP binding at promoters, proximal or remote for every data/gene, as well as gene expression levels and ratios.  These two files are mostly identical: the binary excel format  is ideal for visualizations and the text version suitable for automated parsing. The files were generated using my MATLAB programs, then curated manually.

value: adipocytes differentiated from C3H10T1/2 cells

value: anti-TBP (abcam 62126)


title: 4-126

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_48hrPostOestrus_2.counts.txt: bt4


title: 7-049

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Oestrus_6.counts.txt: bt4


title: 1-131

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Luteal_1.counts.txt: bt4


title: 6-282

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_Luteal_4.counts.txt: bt4


title: 3T3-2hrs-severe-HS-Riboseq

status: Public on Jan 03 2013

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

institute: Technion

data_processing: RNAseq: mapping was performed using bowtie v. 12.3 with the following parameters: "-m 1 --best --strata -m 1 -n 2 --best --strata --sam" with a sam format output. reads were uniquely mapped to the mm9 genome, with the addition of splice junctions and ribosomal RNA. the 2 ends of each library were further combined to a single sam file.  RNA Seq bowtie files for the combined replicates of control, HS8M, and HS2S are provided as supplementary files on the Series record.

source_name: 3T3 cells

extract_protocol: RNAseq- RNAeasy for RNA extraction and standard illumina PE including size selection. Riboseq - RNA extraction and library prepration as described in Ingolia et al. Science, 2009

treatment_protocol: Mild HS: 8 hours in 42 deg C, Severe HS: 2 hours in 44 deg C.

tag: treatment

value: severe heat shock

value: 3T3 cells

tag: assay type

value: Riboseq


title: 3T3-Control-Riboseq

value: control


title: Pancreatic Islets paternal T2D

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

institute: Institute of Zoology, Chinese Academy of Sciences

description: Immunoprecipitation using antibodies against 5mC followed by deep sequencing

data_processing:
Basecalls performed using CASAVA version 1.4, with default parameters.
MeDIP-Seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2.
Peaks were called using PeaksFind version 2.2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited excel files include peak scores for each sample

source_name: Pancreatic Islets

growth_protocol: Male F0 founders were weaned from mothers at 3 weeks of age, and sibling males were put into cages with high-fat diet (33% energy as fat) or control diet until 12 weeks of age, at which point mice fed with HFD were injected intraperitoneally with a low dose of STZ and kept on the same diet for 4 weeks. Fasting blood glucose was examined each week post-STZ for 4 weeks, and only glucose level at 7~11 mM was considered as T2D. Females were always raised on standard diet. At 16 weeks, male F0 founders were mated with females. After 1 or 2 days, males were removed, and pregnant females were left alone until their litters were 3 weeks of age. Pancreatic islets were collected from 6 control and 6 T2D offspring. Sperm were collected from 6 control and 6 T2D male F0 founders.

extract_protocol:
For pancreatic islets, genomic DNA was extracted by DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's instructions. For sperm, caudal epididymis was dissected from sacrificed animals, punctured, and incubated for 30 minutes in M2 media (Sigma) at 37 C. Supernatant was removed, pelleted (3,000g for 5 minutes), and washed 2× with PBS, 1× in water, and incubated in Somatic Cell Lysis buffer, and then subjected to DNeasy Blood & Tissue Kit (Qiagen). The 5mC antibody was included in the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode), with the Cat. No. of mc-magme-048.
Lysates were clarified from sonicated nuclei 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 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.

treatment_protocol: Paternal T2D vs control, the pancreatic islets or sperm methylome was analysed through MeDIP-Seq.

value: ICR

value: Pancreatic Islets

tag: age

value: 3 weeks

value: paternal T2D


title: 3T3-2hrs-severe-HS-RNAseq

value: polyA selected RNA


title: Sperm paternal control

source_name: Sperm

tag: tissue

value: Sperm

value: 16 weeks

value: paternal control


title: Sperm paternal T2D

tag: strain


title: 3T3-8hrs-mild-HS-RNAseq

value: mild heat shock


title: 3T3-2hrs-severe-HS-Riboseq-rep2


title: 3T3-8hrs-mild-2hrs-severe-HS-Riboseq

value: mild followed by severe heat shock