title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Adrenal Gland Tissue; renlab.H3K36me3.STL003AD.01.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY287
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13346
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
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: GSM956015_UCSD.Adrenal_Gland.H3K36me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003AD.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adrenal Gland H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Adrenal Gland, Donor STL003, 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.16377
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: 17,094,595
FINDPEAKS_SCORE: 0.0764
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.2648
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8739
IROC_PERCENTILE: 14
POISSON_SCORE: 0.447
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM956015_UCSD.Adrenal_Gland.H3K36me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003AD.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Adrenal Gland, Donor STL003, 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.16531
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: AG H3K36me3 03 87
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Histone H3K36me3 Donor STL003 Library AY287 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,094,595
FINDPEAKS_SCORE: 0.0764
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.2648
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.8739
IROC_PERCENTILE: 14
POISSON_SCORE: 0.447
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adrenal Gland tissue; renlab.H3K36me3.STL003AD.01.01

tag: sample common name

value: Adrenal Gland

value: Histone H3K36me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Celeg-3-ST-RPF

status: Public on Jun 21 2013

type: SRA

city: Stanford

first: Michael

last: Stadler

state: CA

address: 300 Pasteur Dr.

department: Pathology

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Library strategy: RPF
Basecalls performed standard Illumina software
Reads that map multiply to the genome were removed
Remaining reads were mapped to the CDS sequences + 18 nucleotides of genomic flanking regions using Bowtie v0.12.7
Raw counts for each experiment were determined from mappings
Normalization, fold-change, and significance calculations performed using DESeq (Anders and Huber 2010) software package in R.
Genome_build: WS234
Supplementary_files_format_and_content: Matrix of normalized counts, fold change, and statistical output for genes listed by their associated protein name.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: population-whole animal

growth_protocol: 36 million embryos were grown in S-complete liquid media at 20 C. Animals were starved for 24 hours and either harvested by freezing in liquid nitrogen (diapause animals) or fed for three hours with E. coli HB101 at 15 mg/mL.

extract_protocol:
Total mRNA was isolated using Ambion's micro-poly(A) purist kit, fragmented by alkali and heat, followed by library preparation. Ribosome profiling was carried out as described in Ingolia et al (2009) with modifications as Stadler and Fire (2011).
Libraries were constructed using the circligase protocol as described in Ingolia et al. (2009) with modifications described in Stadler and Fire (2013).

tag: developmental stage

value: L1 diapause

tag: batch

tag: strain

tag: rna subtype

value: ribosome protected fragments


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Lung Tissue; renlab.H3K36me3.STL002LG.01.01

status: Public on Jun 22 2013

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY314
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13350
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12247
****************
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: GSM956014_UCSD.Lung.H3K36me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002LG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Lung H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Lung, Donor STL002, 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.16460
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: 21,157,704
FINDPEAKS_SCORE: 0.3415
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3792
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9927
IROC_PERCENTILE: 76
POISSON_SCORE: 0.51
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM956014_UCSD.Lung.H3K36me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002LG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Lung H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Lung, Donor STL002, 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.16614
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: Lung H3K36me3 02 14
BROWSER_TRACK_DESCRIPTION: UCSD Lung Histone H3K36me3 Donor STL002 Library AY314 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,157,704
FINDPEAKS_SCORE: 0.3415
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3792
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9927
IROC_PERCENTILE: 76
POISSON_SCORE: 0.51
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: sample alias

value: Lung

tag: molecule

value: genomic DNA

tag: disease

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Lung Tissue; renlab.H3K27ac.STL001LG.01.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY361
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13948
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13947
****************
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: GSM1013123_UCSD.Lung.H3K27ac.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001LG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Lung H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Lung, Donor STL001, 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.16409
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: 11,748,736
FINDPEAKS_SCORE: 0.5433
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5582
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9977
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6034
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1013123_UCSD.Lung.H3K27ac.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL001LG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Lung H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Lung, Donor STL001, 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.16563
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: Lung H3K27ac 01 61
BROWSER_TRACK_DESCRIPTION: UCSD Lung Histone H3K27ac Donor STL001 Library AY361 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,748,736
FINDPEAKS_SCORE: 0.5433
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5582
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9977
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6034
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: Histone H3K27ac

value: Active Motif


title: Veh_ChIP

city: Chicago

first: Thien

last: Le

state: IL

institute: University of Chicago

data_processing:
Peak-calling software: QuEST
Genome_build: hg18
Supplementary_files_format_and_content: BED file

source_name: ChIP'ed DNA

extract_protocol:
On 15-cm plates, C4-12/Flag.ERβ cells were treated with 10nM E2 for 1 hour then crosslinked with 1% formaldehyde. Cells were lysed with 1mL of ChIP-lysis buffer (50mM Tris pH 7.4, 100mM NaCl, 0.1% SDS, 1% Triton-X, 0.5% NP40, PICIII) and sonicated for 10 cycles, each of which was 10 seconds. The lysate was collected and incubated with 30uL Protein G Plus-Agarose (Santa Cruz) preimmuned with 10ug anti-Flag M2 antibodies (Sigma) to capture protein-DNA complex overnight in ChIP-lysis buffer. The Protein G beads were washed once with ChIP-wash buffer I (20mM Tris pH 8.1, 150mM NaCl, 0.1% SDS, 1% Triton X, 2mM EDTA), once with ChIP-wash buffer II (20mM Tris pH 8.1, 500mM NaCl, 0.1% SDS, 1% Triton X, 2mM EDTA), once with ChIP-wash buffer III (10mM Tris pH 8.1, 250mM LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA), and twice with TE buffer. The protein-DNA complexes were eluted with ChIP-elution buffer (100mM NaHCO3, 1% SDS). The crosslinking was reversed by incubating samples at 65oC overnight. After treatment of RNase A and Proteinase K, the inputs and immunoprecipitated samples were extracted once with phenol/chloroform, once with chloroform, and precipitated in ethanol. The genomic DNA precipitate was suspended in 20uL nuclease-free water.
Illumina ChIP-seq kit

tag: ChIP

value: anti-Flag M2 (Sigma)

tag: treatment

value: Vehicle

tag: cell line


title: Celeg-1-ST-RPF

value: L1 diapause

value: ribosome protected fragments


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Sigmoid Colon Tissue; renlab.H3K36me3.STL003SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY278
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13340
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11872
****************
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: GSM956016_UCSD.Sigmoid_Colon.H3K36me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003SG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Sigmoid Colon, Donor STL003, 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.16428
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: 19,423,133
FINDPEAKS_SCORE: 0.293
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3409
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9852
IROC_PERCENTILE: 63
POISSON_SCORE: 0.4733
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956016_UCSD.Sigmoid_Colon.H3K36me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL003SG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Sigmoid Colon, Donor STL003, 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.16582
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: SC H3K36me3 03 78
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K36me3 Donor STL003 Library AY278 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,423,133
FINDPEAKS_SCORE: 0.293
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3409
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9852
IROC_PERCENTILE: 63
POISSON_SCORE: 0.4733
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Sigmoid Colon tissue; renlab.H3K36me3.STL003SG.01.01

value: Sigmoid Colon

value: genomic DNA

value: Shin Lin, Stanford University

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Histone H3K36me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Celeg-3-FED-mRNA

data_processing:
Basecalls performed standard Illumina software
Reads that map multiply to the genome were removed
Remaining reads were mapped to the CDS sequences + 18 nucleotides of genomic flanking regions using Bowtie v0.12.7
Raw counts for each experiment were determined from mappings
Normalization, fold-change, and significance calculations performed using DESeq (Anders and Huber 2010) software package in R.
Genome_build: WS234
Supplementary_files_format_and_content: Matrix of normalized counts, fold change, and statistical output for genes listed by their associated protein name.

value: L1 fed 3 hours

value: total mRNA


title: Celeg-2-FED-mRNA


title: Celeg-1-FED-mRNA


title: Reference Epigenome: ChIP-Seq Input from Human Lung Tissue; renlab.Input.STL002LG.02.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY296
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13367
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12247
****************
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: GSM956031_UCSD.Lung.Input.STL002.AY296.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002LG.01.01-renlab.Input.STL002LG.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Lung Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Lung, Donor STL002, 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.16477
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: 15,548,306
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0725
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9494
IROC_PERCENTILE: 45
POISSON_SCORE: 0.0923
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM956031_UCSD.Lung.Input.STL002.AY296.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL002LG.01.01-renlab.Input.STL002LG.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Lung Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Lung, Donor STL002, 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.16631
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: Lung Input 02 96
BROWSER_TRACK_DESCRIPTION: UCSD Lung ChIP-Seq Input Donor STL002 Library AY296 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,548,306
FINDPEAKS_SCORE: 0.0063
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.0725
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9494
IROC_PERCENTILE: 45
POISSON_SCORE: 0.0923
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Lung

value: iron deficiency, bipolar

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Small Bowel Tissue; renlab.H3K4me1.STL001SB.01.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Small Bowel Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK328
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13121
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
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: GSM956019_UCSD.Small_Intestine.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001SB.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Small Intestine H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Small Intestine, Donor STL001, 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.16395
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: 18,438,254
FINDPEAKS_SCORE: 0.1119
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2465
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.8955
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4056
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM956019_UCSD.Small_Intestine.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001SB.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Small Intestine, Donor STL001, 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.16549
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: SI H3K4me1 01 28
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K4me1 Donor STL001 Library AK328 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,438,254
FINDPEAKS_SCORE: 0.1119
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2465
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.8955
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4056
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Small Intestine tissue; renlab.H3K4me1.STL001SB.01.01

value: Small Intestine

value: genomic DNA

value: Shin Lin, Stanford University

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: Histone H3K4me1


title: Celeg-2-FED-RPF

value: L1 fed 3 hours

value: ribosome protected fragments


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Ovary Tissue; renlab.H3K27ac.STL002OV.01.01

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY308
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13361
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
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: GSM956009_UCSD.Ovary.H3K27ac.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002OV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Ovary H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Ovary, Donor STL002, 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.16432
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: 16,625,765
FINDPEAKS_SCORE: 0.3756
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4351
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9914
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4951
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM956009_UCSD.Ovary.H3K27ac.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.STL002OV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Ovary H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Ovary, Donor STL002, 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.16586
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: Ovary H3K27ac 02 08
BROWSER_TRACK_DESCRIPTION: UCSD Ovary Histone H3K27ac Donor STL002 Library AY308 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,625,765
FINDPEAKS_SCORE: 0.3756
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4351
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9914
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4951
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Ovary

value: iron deficiency, bipolar

value: Primary Tissue

value: Autopsy

value: Histone H3K27ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Celeg-2-ST-mRNA

value: L1 diapause

value: total mRNA


title: Celeg-1-ST-mRNA


title: shRxr_UT

city: Amsterdam

first: Prashanth Kumar

last: Bajpe

address: Plesmanlaan 121

department: Molecular Carcinogenesis

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequence reads were mapped to mm9 using tophat version 1.4 with parameters --library-type fr-unstranded, -G (GTF Ensembl version 64), -M and --transcriptome-index
Readcounts were obtained by counting the number of reads per gene using HTSeq-count. These readcounts were normalized to 10 million reads per sample and log2 transformed.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including normalized and log2 transformed values for each sample.

organism: Mus musculus

source_name: mouse teratocarcinoma cells

growth_protocol: F9 cells were cultured on gelatin-treated tissue culture plastic in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 8% heat-inactivated charcoal stripped fetal calf serum (FCS), penicillin and streptomycin.

extract_protocol:
Total RNA was isolated from RA treated and untreated control, Ctbp2 and Rxr knock down cells and converted into a library of template molecules suitable for subsequent cluster generation using the reagents provided in the Illumina ® TruSeq™
Total mRNA of each sample was converted into a library of template molecules suitable for subsequent cluster generation using the reagents provided in the Illumina ® TruSeq™ RNA Sample Preparation Kit, following the manufacture protocol. Sequence reads were generated using Illumina HiSeq 2000 with TruSeqTM v3 reagent kits and software.

treatment_protocol: F9 control, Ctbp2 and Rxr knock down cells were cultured in  Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 8% heat-inactivated charcoal stripped fetal calf serum (FCS), penicillin and streptomycin.  48 hours before harvest the cells were untreated or treated with 1 uM al-trans Retinoic Acid.

tag: cell type

value: teratocarcinoma F9 cells

tag: treatments

value: UT-Untreated

tag: expression

value: shRxr


title: shCtbp2_UT


title: shCtbp2_RA

value: RA-al-trans Retinoic Acid induced


title: shGFP_RA

value: shGFP


title: Cbrigg-1-FED-RPF

organism: Caenorhabditis briggsae

value: L1 fed 3 hours


title: Cbrigg-3-FED-RPF

value: ribosome protected fragments


title: Cbrigg-2-FED-RPF


title: Cbrigg-2-ST-RPF


title: shGFP_UT


title: Cbrigg-3-FED-mRNA


title: Cbrigg-3-ST-RPF


title: Cbrigg-1-ST-RPF


title: Cbrigg-2-FED-mRNA


title: E2_ChIP

value: anti-Flag M2 (Sigma)

value: 10nM E2


title: M-P4h_r3_HiSeq

city: Charlotte

first: Zhengchang

last: Su

state: NC

address: 9201 University City Blvd

department: Bioinformatics and Genomics

institute: UNC Charlotte

description: processed data file: M-P4h.plus.BigWig, M-P4h.minus.BigWig

data_processing:
Merge the replicates for each sample. For example, for sample HS15min, merge HS15min_r1.HiSeq.fastq.gz, HS15min_r2.HiSeq.fastq.gz and HS15min_r3.HiSeq.fastq.gz to one fastq file
Sequenced reads were trimmed for adaptor sequence, then mapped to E. coli K12 genome using bowtie v0.12.7 with parameters bowtie -t -v 3 -m 1 --best -S -p 2
Transform the mapped file format from sam to sorted bam which are later tranfered to bigWig, and separated by the strand (plus and minus).
Genome_build: Escherichia coli K12 str MG1655
Supplementary_files_format_and_content: BigWig files for whole-genome reads coverage (including number of mapped reads) for each sample. Each sample has two files, one for plus strand, and the other for minus strand. Therefore, there are 14 BigWig files for 7 samples.

organism: Escherichia coli

source_name: E. coli cells_M-P4h

extract_protocol:
Total RNA was isolated using a RiboPureTM -Bacteria Kit (Ambion) following the manufacturer’s instructions. Once isolated, ~10μg total RNA was treated with 8 units DNase (Invitrogen) twice to remove genomic DNA.
To enrich mRNAs and other transcripts, majority of rRNAs were removed from the DNase-treated total RNA using a MICROBExpress kit (Ambion) following the manufacturer’s instructions.
For the Illumina GAII platform, the directional RNA-seq libraries were constructed by following an Illumina’s instruction using their Small RNA Sample Prep Kit with some modifications. For the HiSeq 2000 platform, the directional RNA-seq libraries were constructed using Illumina’s TruSeq Small RNA Sample Prep Kit.

tag: substrain

tag: culture/growth condition

value: MOPS-P 4h


title: Methionine.8.2

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

description: preimplantation embryos

data_processing:
Reads were mapped to the reference genome (bosTau7) using the software package Tophat (v2.0.4).
Sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.0.2) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.0.2) was used for merging together each of the assemblies with the reference bovine annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty) developed by Simon Anders at EMBL (Heidelberg, Germany).
Genome_build: Baylor Btau_4.6.1/bosTau7
Supplementary_files_format_and_content: Tab-delimited text files include locus, gene name, and number of mapped reads.

organism: Bos taurus

extract_protocol:
Embryo pools underwent RNA extraction and amplification using RNaqueous Micro (Life Technologies) and subsequently amplified using the MessageAmp II aRNA amplification kit (Life Technologies).
Libraries of amplified RNA for each pool were prepared following the Illumina mRNA-Seq protocol. Sequencing libraries were created from 50 ng samples and sequenced with Illumina’s HiSeq 2000 at the University of Wisconsin-Madison Biotechnology Center.

tag: tissue

value: IVF embryos

tag: breed

value: Holstein

value: Methionine


title: LB(OD=0.87)

source_name: E. coli cells_LB(OD=0.87)


title: RPC128-FLAG IP_Nutrient Starvation_Replicate2

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

country: United Kingdom

institute: MRC Human Genetics Unit, The University Of Edinburgh

data_processing:
Reads with phred score < 20 on 80% of the bases were filtered out with FASTX toolkit V0.0.13
Reads aligned to yeast genome using Bowtie 0.12.8 allowing unique alignments with 3 mismatches and taking the best stratum.
Reads are extended to ChIP fragment size (180bp)
Read coverage at each position in the genome is scaled to 1 million and normalized to total number of reads in the library.
Coverage at each base is bundled as .bedGraph files.
Genome_build: sacCer3
Supplementary_files_format_and_content: BEDGRAPH

organism: Saccharomyces cerevisiae

source_name: Log-phase cells shifted to 0.15X YEP minus carbon source (4hours)

growth_protocol: RPC128-FLAG strain grown up to A600~0.8 in YEP medium at 30C.

extract_protocol: ChIP was performed as described earlier(Arimbasseri A.G and Bhargava P, Mol. Cell. Biol. April 2008 vol. 28 no. 8 2598-2607). Libraries for ChIP sequencing were constructed according to the Illumina ChIP Seq library protocol. Briefly, DNA was subjected to a series of enzymatic reactions that repair frayed ends, phosphorylate the fragments, add a single nucleotide A overhang and ligate adaptors (Illumina ChIP Seq Library preparation kit. lot# 6961486 ). The libraries were enriched using PCR, cleaned using Agencourt Ampure XP beads (Beckman Coulter) and size selected using a 2 % Low melting agarose gel. The prepared libraries were quantified using Nanodrop Spectrophotometer and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent).

treatment_protocol: Cells fixed with 1% HCHO and quenched with 0.125M Glycine.

tag: antibody

value: ANTI-FLAG M2 Affinity Gel (Sigma)


title: Cbrigg-1-FED-mRNA

tag: developmental stage

tag: batch


title: Celeg-3-ST-mRNA

tag: strain

tag: rna subtype


title: RPC128-FLAG MOCK_Nutrient Starvation

value: Sepharose® CL-4B (Sigma)


title: Methionine.7.2

description: preimplantation embryos


title: Methionine.7.1

description: preimplantation embryos


title: Cbrigg-3-ST-mRNA

value: L1 diapause


title: RPC128-FLAG MOCK_Normal Growth

source_name: Log-phase cells


title: Cbrigg-2-ST-mRNA

value: total mRNA


title: Methionine.6.2

description: preimplantation embryos


title: shRxr_RA

value: teratocarcinoma F9 cells


title: HS15min_r3_GAII

description: processed data file: HS15min.plus.BigWig, HS15min.minus.BigWig

source_name: E. coli cells_HS15min

value: Heatshock 15min


title: Methionine.6.1

description: preimplantation embryos


title: RPC128-FLAG IP_Normal Growth_Replicate2


title: RPC128-FLAG IP_Nutrient Starvation_Replicate1


title: RPC128-FLAG IP_Normal Growth_Replicate1


title: Cbrenn-3-FED-RPF

organism: Caenorhabditis brenneri


title: Crem-3-FED-RPF

organism: Caenorhabditis remanei


title: Cbrenn-2-FED-RPF


title: Crem-2-FED-RPF


title: Cbrigg-1-ST-mRNA


title: Methionine.8.1

description: preimplantation embryos


title: Crem-1-FED-RPF


title: Control.4.2

description: preimplantation embryos

value: Control


title: Cbrenn-1-FED-RPF


title: Crem-3-ST-RPF


title: Control.4.1

description: preimplantation embryos


title: Methionine.5.1

description: preimplantation embryos


title: Control.3.2

description: preimplantation embryos


title: Cbrenn-2-ST-RPF


title: Crem-1-ST-RPF


title: Crem-2-ST-RPF


title: Cbrenn-1-ST-RPF


title: Control.3.1

description: preimplantation embryos


title: Cbrenn-3-ST-RPF


title: Crem-2-FED-mRNA


title: Control.2.1

description: preimplantation embryos


title: Control.2.2

description: preimplantation embryos


title: Methionine.5.2

description: preimplantation embryos


title: Cbrenn-2-FED-mRNA


title: Control.1.2

description: preimplantation embryos


title: Crem-3-FED-mRNA


title: Control.1.1

description: preimplantation embryos


title: Crem-1-FED-mRNA


title: Crem-2-ST-mRNA


title: Cbrenn-2-ST-mRNA


title: M-P4h_r2_HiSeq


title: Crem-1-ST-mRNA


title: M-P4h_r1_HiSeq


title: M-P2h_r2_HiSeq

description: processed data file: M-P2h.plus.BigWig, M-P2h.minus.BigWig

source_name: E. coli cells_M-P2h

value: MOPS-P 2h


title: Cbrenn-1-ST-mRNA


title: M-P2h_r1_HiSeq


title: HS60min_r2_HiSeq

description: processed data file: HS60min.plus.BigWig, HS60min.minus.BigWig

source_name: E. coli cells_HS60min

value: Heatshock 60min


title: Cbrenn-1-FED-mRNA

value: L1 fed 3 hours


title: HS30min_r2_HiSeq

description: processed data file: HS30min.plus.BigWig, HS30min.minus.BigWig

source_name: E. coli cells_HS30min

value: Heatshock 30min


title: Cbrenn-3-FED-mRNA


title: HS30min_r1_HiSeq


title: M-P0h_r2_HiSeq

description: processed data file: M-P0h.plus.BigWig, M-P0h.minus.BigWig

source_name: E. coli cells_M-P0h

value: MOPS-P 0h


title: HS15min_r2_HiSeq


title: M-P0h_r1_HiSeq


title: E2_2

description: GROseq - Global run-on followed by sequencing

data_processing:
Alignment: Short-reads were aligned to the human reference genome (hg18, NCBI36), including autosomes, X-chromosome, and one complete copy of an rDNA repeat (GenBank ID: U13369.1). The SOAP2 software package was used to align reads with the following options: (1) all non-unique mappings were removed (-r 0), (2) three mismatches were allowed in each mapped read (-v 3), (3) low-quality reads with more than 10 ambiguous bases were removed (-N 10), and (4) for reads failing to align over the entire length of the read, the first 32 bp was used (-l 32). SOAP2 output was processed using custom Perl scripts, and imported into R for most the analysis.  In order to identify E2-regulated genes, we focused on RefSeq-annotated genes, counting reads in a fixed window between +1 kb and +13 kb relative to the transcription start site of each gene, so as to avoid possible complications introduced by paused polymerases, and to allow easy side-by-side comparison among samples. The normalized expression value of 1e-5 (normalized against the sample total read counts) was used as the threshold to select genes for further analyses. Comparing E2 treated samples versus vehicle treated samples, genes with FC>1.2 were considered upregulated; those with FC<0.8 were considered downregulated.
Genome_build: hg18
Supplementary_files_format_and_content: txt: read locations, count reads

source_name: Immortalized human breast cancer cells

extract_protocol:
After 1 hour of E2 or Vehicle treatment, nuclei from C4-12/Flag-ERβ cells were extracted and processed with nuclear run-on assay.
Run-on RNA was ligated with adapters and reverse transcribed to generate cDNA library.

value: 10nM E2

tag: replicate


title: HS15min_r1_HiSeq


title: HS60min_r1_HiSeq


title: Veh_2

value: Vehicle


title: Cbrenn-3-ST-mRNA


title: T7107_S

status: Public on Jun 20 2013

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: In the processed data file the values for each chromosome were generated by dividing by 0.58.

data_processing:
Sequence reads were mapped to the S. cerevisiae reference genome using BioScope (version 1.3.1).
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating (alpha factor arrested or G2 phase) sample for each strain.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor. This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).
Genome_build: sacCer1
Supplementary_files_format_and_content: Wig file containing normalised replication profile.

source_name: T7107 genomic DNA from S phase cells

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to SOLiD instructions.

tag: relevant genotype

value: MATa; RAD5; BUD4; leu2; ura3; trp1; ade2; his3

tag: growth protocol

value: Cells were harvested from mid-log phase cultures grown in rich medium.

tag: treatment protocol

value: Cells were sorted by DNA content, selecting (S phase and) G2 phase cells


title: T9475_G2

source_name: T9475 genomic DNA from G2 phase cells

value: MATa/MATalpha; RAD5/RAD5; BUD4/BUD4; leu2/leu2; ura3/ura3; trp1/trp1; ade2/ade2;, his3/his3

value: Cells were sorted by DNA content, selecting S phase (and G2 phase) cells.


title: T9475_S

description: In the processed data file the values for each chromosome were generated by dividing by 0.379.

source_name: T9475 genomic DNA from S phase cells


title: T7107_G2

source_name: T7107 genomic DNA from G2 phase cells


title: Testis mmu ts m

city: Cambridge

first: Magali

last: Soumillon

state: MA

address: Divinity Avenue 7

institute: Harvard University, HSCRB

description: C57BL/6 mouse

data_processing:
The basecalling was performed with Ibis (Kircher et al, 2009). The quality values are given in the phred-33 format, for all samples.
RNA‐seq reads were processed, mapped and counted as previously described (Brawand et al. 2011).
RNA-Seq reads were aligned with TopHat version 1.4.0 and Bowtie version 0.12.5. Command line for TopHat: tophat -p 4 -o -a 8 -i 40 -m 1 -I 1000000 -F 0 --coverage-search --microexon-search.
The genome-wide read coverage was determined using the "wiggles" utility in TopHat.
Expression levels for Ensembl-annotated genes were estimated with Cufflinks 2.0.0, using all reads, with the multi-read correction embedded in Cufflinks. Cufflinks command line: cufflinks -q  -G Transcripts_ProteinCoding.gtf -p 4 --library-type fr-secondstrand --multi-read-correct. For expression level computation, GTF files were retrieved from Ensembl 62, and filtered to retain only transcripts annotated as "protein-coding" for protein-coding genes (all transcripts were kept for other gene biotypes).
Genome_build: mm9
Supplementary_files_format_and_content: .FPKM files contain expression levels quantified with Cufflinks; the columns are tab-separated. .wig files contain genome-wide read coverage statistics, in bedGraph format, obtained with the "wiggles" utility in TopHat.

molecule: polyA RNA

source_name: Testis

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Strand‐specific RNA-seq  libraries  were  prepared  for  mouse  brain,  liver and testis  according  to  the  Directional  mRNA‐seq  Library  Prep Pre‐Release Protocol from Illumina.  Each  of  these libraries were sequenced (76 cycles, single‐end) in three lanes using the Illumina Genome Analyzer IIx platform, yielding  a  total  of  ∼900  million  reads  (mean  of  ∼114  million  reads  per sample).

value: Testis

tag: Sex

value: male

tag: age

value: 11 weeks


title: Spermatids cs mmu sd m

description: In house, C57BL7/6 colonies

data_processing:
The basecalling was performed with Ibis (Kircher et al, 2009). The quality values are given in the phred-33 format, for all samples.
RRBS reads  were  mapped  onto  the  mouse  genome  using  the  BSMAP mapping  tool,  which  was  specifically  designed  for  bisulfite  sequence  mapping  (Xi  and  Li  2009).  Percentages of DNA  methylation  levels  based  on  bisulfite  conversation  yield  were  computed  at  the  single  nucleotide  scale  for positions  represented  by  at  least  10X  coverage  of  uniquely  mapped  reads.
Reads were  mapped  onto  the  mouse  genome  using  Bowtie  (Langmead et  al.  2009).  We then  determined  the  coverage  per  base  for  each  sample  by  restricting  our  data  to  16  million randomly  resampled  uniquely  mapped  reads.
Genome_build: mm9
Supplementary_files_format_and_content: *MethylationCount.tab is a tab delimited file containing DNA methylation levels based on bisulfite conversation at the single nucleotide scale for positions represented by at least 10X  of coverage. *.cov is a tab delimited file containing the coverage per base for each sample by restricting our data to 16 million randomly resampled uniquely mapped reads.

source_name: Spermatids

extract_protocol:
see Smith et al. 2009 and Bernstein  et  al.  2005
For RRBS, two sets of DNA methylation bisulfite sequencing libraries (differing by their insert sizes) were generated, using a previously described protocol (Smith et al. 2009), for the 5 mouse samples (brain, liver, testis, spermatocyte and spermatid). These libraries were sequenced (38 and 76 cycles, respectively) on the Illumina Genome Analyzer IIx platform, yielding a total of ∼322 million reads (mean of  ∼64  million  reads  per  sample). For ChIP-seq, Chromatin immunoprecipitation  with  antibodies  against  H3K4me2  was  carried  out  as  previously  described (Bernstein  et  al.  2005), for  the  same  samples  for  which DNA  methylation  data  were produced.  Sequencing libraries  were  prepared  according  to  the  Illumina  protocol  for  ChIP  sequencing  and sequenced  (38  cycles)  using  the  Illumina  Genome  Analyzer  IIx  platform,  yielding  a  total  of  ∼131  million  reads (mean:  ∼26  million  reads  per  sample).

tag: cell type

value: Spermatids

tag: chip antibody


title: Spermatocytes cs mmu sc m

description: In house, C57BL7/6 colonies

source_name: Spermatocytes

value: Spermatocytes


title: Liver mmu lv m

description: C57BL/6 mouse

source_name: Liver

value: Liver


title: Crem-3-ST-mRNA

source_name: population-whole animal

value: L1 diapause

value: total mRNA


title: Brain mmu br m

description: C57BL/6 mouse

source_name: Brain

value: Brain


title: Liver cs mmu lv m

description: In house, C57BL7/6 colonies


title: Testis cs mmu ts m

description: In house, C57BL7/6 colonies


title: Spermatids rrbs mmu sd m

description: In house, C57BL7/6 colonies


title: Spermatocytes rrbs mmu sc m

description: In house, C57BL7/6 colonies


title: Brain cs mmu br m

description: In house, C57BL7/6 colonies


title: Liver rrbs mmu lv m

description: In house, C57BL7/6 colonies


title: Testis rrbs mmu ts m

description: In house, C57BL7/6 colonies


title: Brain rrbs mmu br m

description: In house, C57BL7/6 colonies


title: Spermatids mmu sd m

description: C57BL/6 mouse

extract_protocol:
Total RNA was extracted using the Trizol (Invitrogen) procedure or RNAeasy/RNAeasy Lipid/miRNeasy (Qiagen) column purification kits. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Strand‐specific RNA-seq  libraries  were  prepared  for  five  different  testis  cell types (sertoli, spermatogonia, spermatocyte, spermatid and spermatozoa)  according  to  the  Directional  mRNA‐seq  Library  Prep Pre‐Release Protocol from Illumina.  Each  of  these libraries were sequenced (76 cycles, single‐end) in three lanes using the Illumina Genome Analyzer IIx platform, yielding  a  total  of  ∼900  million  reads  (mean  of  ∼114  million  reads  per sample).

value: Male


title: Spermatocytes mmu sc m

description: C57BL/6 mouse


title: Spermatozoa mmu sz m

description: C57BL/6 mouse

source_name: Spermatozoa

value: Spermatozoa


title: Sertoli cells mmu sl m

description: C57BL/6 mouse

source_name: Sertoli cells

value: Sertoli cells

value: 3 weeks


title: CTCF BxC

city: London

first: Rebecca

middle: J

last: Oakey

address: Great Maze Pond

department: Medical and Molecular Genetics

institute: King's College London

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
CTCF_BxC_dupmark.bam: mm9

source_name: whole brain

extract_protocol: Illumina ChIP-seq library prep kit (inputs) and NEBNext Chip-seq library prep kit (CTCF and Rad21)

value: brain

tag: genotype

value: wild type

value: CTCF

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot #


title: input CTCF CxB

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
iCTCF_CxB_dupmark.bam: mm9

tag: tissue

value: IgG


title: input CTCF BxC

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
iCTCF_BxC_dupmark.bam: mm9


title: Rad21 CxB

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
Rad21_CxB_dupmark.bam: mm9

value: Abcam


title: input rad21 CxB

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
iRad21_CxB_dupmark.bam: mm9


title: input Rad21 BxC

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
iRad21_BxC_dupmark.bam: mm9


title: mRNA-seq Puro

city: Basel

first: Andreas

middle: R

last: Gruber

address: Klingelbergstrasse 50-70

department: Biozentrum

country: Switzerland

institute: University of Basel

description: None strand-specific mRNA-seq in puromycin treated HeLa cells

data_processing:
For iCLIP samples, first seven nucleotides were trimmed because of bad quality scores prior to mapping to the genome.
Read processing and mapping to the human genome was done with the CLIPZ server (www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Research 2011, 39:D245 (PMID 21087992)).
Genome_build: hg19; UCSC Feb. 2009
Supplementary_files_format_and_content: BED file with uniquely mapped iCLIP sites and uniquely mapped mRNA-seq reads

source_name: HeLa

growth_protocol: HeLa cells were cultivated in Dulbecco’s Modified Eagle Media (DMEM) supplemented with 100 U/mL Penicillin, 100 mg/mL Streptomycin and 10 % fetal calf serum (FCS) in ten 150 cm2 dishes until 80% confluency (corresponding to a total of 8 x 107 cells).

extract_protocol:
Cells were subjected to 150 mJ/cm2 UV-C light. After irradiation cells were scrapped off the dishes in PBS. Cell pellets were shock frozen in liquid nitrogen and stored at –80 °C until use. After thawing on ice, cells were lysed in hypotonic gentle lysis buffer for 20 min. The cell lysate was cleared by centrifugation at 4 °C and 13,000 g for 15 min
We then employed the steps of nuclease digestion, primer ligation and blotting of immunoprecipitated complexes to nitrocellulose from the iCLIP method, to minimize cloning of background RNA. Immunoprecipitation (IP) was performed with UPF1-specific antibodies. The cDNA library preparation was performed according to the iCLIP protocol (Konig et al., 2010)

treatment_protocol: For the iCLIP2 Puro experiment, puromycin (Calbiochem) was added to a final concentration of 60.6 mM 6 h before crosslinking.

tag: cell line

value: HeLa

tag: treated with

value: puromycoin


title: CTCF CxB

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
CTCF_CxB_dupmark.bam: mm9

tag: strain


title: Rad21 BxC

data_processing:
Alignments: reads were aligned to mm9 using novoalign. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard.
Genome Build:
Rad21_BxC_dupmark.bam: mm9


title: iCLIP1 UT

description: iCLIP of Upf1 in untreated HeLa cells

data_processing:
library strategy: iCLIP-seq
For iCLIP samples, first seven nucleotides were trimmed because of bad quality scores prior to mapping to the genome.
Read processing and mapping to the human genome was done with the CLIPZ server (www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Research 2011, 39:D245 (PMID 21087992)).
Genome_build: hg19; UCSC Feb. 2009
Supplementary_files_format_and_content: BED file with uniquely mapped iCLIP sites and uniquely mapped mRNA-seq reads

source_name: HeLa_iCLIP UT

value: none (untreated)

tag: antibody

tag: antibody vendor

value: Bethyl

tag: antibody cat. #


title: iCLIP2 Puro

description: iCLIP of Upf1 in puromycoin treated HeLa cells

source_name: HeLa_iCLIP puro


title: mRNA-seq UT

description: None strand-specific mRNA-seq in untreated HeLa cells


title: shControl for shHEB

city: New York

first: Yanwen

last: Jiang

state: NY

institute: Weill Cornell Medical College

description: shControl for shHEB

data_processing:
Raw sequence reads were aligned with TopHat to the reference genome (hg19).
The aligned reads were processed with an in-house program to remove PCR duplicates.
The RPKM value for each gene were calculated following published methods (http://woldlab.caltech.edu/~alim/RNAseq/).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown with RPMI 1640 medium (Invitrogen) plus 10% fetal bovine serum (FBS; Gemini Bio-Products) and penicillin-streptomycin (Invitrogen) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted with TRIzol Reagent according to the manufacturer’s protocol (Invitrogen). One μg of total RNA was treated with DNase I (Qiagen), purified and tested for integrity on the Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina). Briefly, mRNA was selected by using magnetic polydT beads and then fragmented. First-strand synthesis was performed using Superscipt II (Invitrogen). After second-strand synthesis a paired-end library was prepared following the Illumina protocol including end-repair, A-tailing, adaptor ligation, and library enrichment.  Final products were verified using the Agilent 2100 Bioanalyzer. Each library was loaded onto an Illimina pair-end flowcell at a concentation of 7.5 pM (one library per lane), and sequenced for 50 cycles at each end with Illumina HiSeq2000.

treatment_protocol: Kasumi-1 cells were infected with the shRNA-expressing lentiviruses in the presence of 8 μg/ml polybrene (Sigma-Aldrich) for 24 hours and then selected with 1 μg/ml puromycin (Sigma-Aldrich). The cells were harvested for RNA purification at 4 days post-infection.

value: Hematopoietic

tag: tumor stage

value: Acute myeloid leukemia

tag: gene knockdown


title: shControl for shHEB+shE2A

description: shControl for shHEB+shE2A


title: iCLIP2 UT

description: iCLIP of Upf1 in untreated HeLa cells


title: shHEB+shE2A

value: HEB/TCF12 and E2A/TCF3


title: shLMO2


title: shLDB1


title: shHEB

description: shHEB


title: shControl for shAML1-ETO, shE2A, shLYL1, shLDB1 and shLMO2


title: shLYL1


title: Spermatogonia mmu sg m

description: C57BL/6 mouse

source_name: Spermatogonia

value: Spermatogonia

tag: Sex

value: Male

value: 6 days


title: Input DNA for HEB and E2A ChIP-seq

data_processing:
Sequence reads were aligned to the human reference genome (hg18) using ELAND.
After filtering clonal reads, uniquely aligned reads were then used to perform peak-calling and flowing analyses by ChIPseeqer (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml).
Genome_build: hg18

source_name: Input DNA for HEB and E2A ChIP-seq

extract_protocol:
Kasumi-1 cells were first dual cross-linked with 2 mM disuccinimidyl glutarate and 1% formaldehyde and then lysed with buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA and 1% SDS). Cell lysates were subjected to sonication, dilution with buffer (16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS and 1.1% Triton X-100) and then immunoprecipitation using the indicated antibodies. After extensive washing, ChIP DNA samples were purified with QIAquick PCR Purification Kit (Qiagen).
ChIP-Seq libraries were constructed following the Illumina protocol. Briefly, end-repair, “A” addition, and adaptor ligation steps were performed on 10 ng ChIP or Input DNA. Adaptor-ligated DNA with a size between 200 to 300 bp was selected and amplified to generate a sequencing library. 8 pM of sequencing library was applied to Illumina Single-Read flowcell for cluster generation on cBot. Finally, clusters were sequenced on the Illumina Genome Analyzer II to generate 36-bp short sequence reads.

value: Kasumi-1 cells


title: Input DNA for LMO2 ChIP-seq

source_name: Input DNA for LMO2 ChIP-seq


title: E2A ChIP-seq

source_name: E2A ChIP-seq

value: anti-E2A (Santa Cruz; sc-763)


title: Non-infected total RNA

first: Pavel

last: Morozov

department: Tuschl Lab

institute: Rockefeller University

description: Barcoded sample, single HiSeq sequencing lane.

data_processing:
Alignment was performed using Bowtie2 (Langmead and Salzberg, 2012) and standalone BLAST (NCBI).
Annotation was accomplished using custom Perl scripts with the following reference sequence sources: ACMPNV genome (Ayres et al., 1994), D. melanogaster genome (FB2013_03, except for rRNA which was added from ENTREZ NCBI), and an internally curated human tRNA database (based originally on (Lowe and Eddy, 1997)).
Genome_build: FlyBase FB2013_03 (Drosophila melanogaster)
Supplementary_files_format_and_content: Tab-delimited text files containing sequences and counts. See the GSE48076_README.txt file for details.

organism: Trichoplusia ni

source_name: cell culture, non-infected

growth_protocol: Approximately 1 million High Five (T. ni) uninfected or infected (with AGO1 baculovirus) cells were used for RNA isolation.

extract_protocol:
Standard Trizol (Invitrogen) RNA extraction, per manufacturer's instructions. Additionally, 10 μg of purified hAGO proteins were subjected to Trizol RNA extraction.
Barcoded small RNA sequencing was performed essentially as described (Hafner et al., 2011 (PMID 21775473)). RNA inputs of 2 μg (from T. ni cells) or 20 ng (AGO-isolated RNAs) were used per sample.

treatment_protocol: Baculovirus infection for recombinant protein expression.

value: Hive Five

tag: infection

tag: rna source

value: total RNA


title: Infected total RNA

source_name: cell culture, AGO1 baculovirus infected

value: AGO1 baculovirus


title: AML1-ETO ChIP-seq

source_name: AML1-ETO ChIP-seq

tag: chip antibody

value: anti-ETO (home made, antigen-purified)


title: AGO1-isolated RNA

source_name: cell culture, purified AGO1

value: purified AGO1 protein


title: Input DNA for AML1-ETO ChIP-seq

source_name: Input DNA for AML1-ETO ChIP-seq


title: AGO2-isolated RNA

source_name: cell culture, purified AGO2

value: AGO2 baculovirus

value: purified AGO2 protein


title: CEP4A

city: Augusta

first: Mingqiang

last: Ren

state: GA

address: 1120 15th Street

department: Cancer Center

institute: Georgia Regents University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using CLC Genomics Workbench.
The transcript expression levels were determined in terms of number of reads per kilobase per million (RPKM) and compared between sorted normal myeloid (Gr1+Mac1+) cells and sorted leukemic myeloid cells, using CLC Genomics Workbench software.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

source_name: Mac+Gr1+B220+ AML cells

extract_protocol:
Cells from bone marrows and spleens were FACS sorted into TRIzol LS for isolation of total RNA. The cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: bone marrow and spleen

tag: age

value: 10-12 months

tag: cell type

value: Mac+Gr1+B220+ AML cells


title: BM4

source_name: normal Gr1+Mac1+ myeloid cells

value: bone marrow

value: normal Gr1+Mac1+ myeloid cells


title: HEB ChIP-seq

source_name: HEB ChIP-seq

value: Hematopoietic

value: Acute myeloid leukemia

value: anti-HEB (Santa Cruz; sc-357)


title: shAML1-ETO


title: shE2A


title: Snord116del_RNA-seq_Zt16_1

city: Davis

first: Weston

last: Powell

address: 3426 Tupper Hall

department: MMI

institute: UC Davis

description:
Sample 14
processed data file: RNAseq030113.txt (available on Series records)

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
RNA-seq reads were aligned to the mm9 genome assembly using TopHat v2.0.5 with options --library-type fr-firststrand -p 2 -G Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf
Differential transcript abundance was called using cuffdiff v2.0.2 with options -p 2 -L WT,Snord116del --FDR 0.05  -u --library-type fr-firststrand Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf.
Genome_build: mm9
Supplementary_files_format_and_content: Differential transcript abundance

growth_protocol: B6(Cg)-Snord116tm1.1Uta/J (Snord116del) and WT C57BL/6J mice were obtained from Jackson Labs (Bar Harbor, ME) and housed in a 24-hour light/dark cycle (6am-6pm light, 6pm-6am dark), temperature controlled room and fed a standard diet of Picolab mouse chow 20 (PMI international, St. Louis, MO).

extract_protocol:
For RNA-seq: Mouse brain cortex was dissected on ice and placed in RNALater (Ambion). RNA was isolated using manufacturer's protocol for RNEasy Mini Kit (Qiagen part #:74101) following tissue homogenization with a Qiashredder (Qiagen part #: 79654).
For RNA-seq: Libraries were prepared according to Nugen's protocol accompanying the Encore Complete RNA-seq DR Multiplex system 1-8 (Part #: 0333-32).  The libraries were analyzed on a Bioanalyzer, and submitted to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries were sequenced on the Hi-Seq 2000 following the manufacturer's protocols.

tag: genotype/variation

value: Snord116del (+/-)

value: adult

value: brain cortex

tag: time of day


title: BM3

tag: tissue


title: Snord116del_RNA-seq_Zt16_2

description:
Sample 15
processed data file: RNAseq030113.txt (available on Series records)


title: WT_RNA-seq_Zt16_2

description:
Sample 13
processed data file: RNAseq030113.txt (available on Series records)

value: wild type


title: WT_RNA-seq_Zt6_2

description:
Sample 8
processed data file: RNAseq030113.txt (available on Series records)


title: CEP5A


title: Snord116del_RNA-seq_Zt6_1

description:
processed data file: RNAseq.txt (available on Series records)
Sample 10

data_processing:
Basecalls performed using Illumina CASAVA_v1.8.0
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2-2.0.0-beta6 with default settings and option -p 2.
Peaks were called using MACS14 v.1.4.2 with options -f BAM --bw 1000 -s 50 -g mm.
Output peak file from MACS was filtered using Excel sort on FDR to exclude peaks with FDR >1, and Excel sort on fold enrichment to exclude peaks with fold enrichment <20.  Excel spreadsheet was converted to .bed file using command line $ tr '\r' '\n' <excel_peaks.txt >peaks.bed.
RNA-seq reads were aligned to the mm9 genome assembly using TopHat v2.0.5 with options --library-type fr-firststrand -p 2 -G Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf
Differential transcript abundance was called using cuffdiff v2.0.2 with options -p 2 -L WT,Snord116del --FDR 0.015  -u --library-type fr-firststrand Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf.
Genome_build: mm9
Supplementary_files_format_and_content: .bed files represent peaks called using MACS14 and filtered for FDR and fold enrichment from input for samples WT_116HG_ChIRP-seq_1, WT 116HG_ChIRP-seq_2, WT_NSC_ChIRP-seq, Snord116del_116HG_ChIRP-seq, Snord116del_NSC_ChIRP-seq.
Supplementary_files_format_and_content: RNAseq.txt is automatic output from cuffdiff gene level.

source_name: Snord116del_brain cortex_RNA-seq

extract_protocol:
Mouse brain cortex was dissected on ice and placed in RNALater (Ambion). RNA was isolated using manufacturer's protocol for RNEasy Mini Kit (Qiagen part #:74101) following tissue homogenization with a Qiashredder (Qiagen part #: 79654).
Libraries were prepared according to Nugen's protocol accompanying the Encore Complete RNA-seq DR Multiplex system 1-8 (Part #: 0333-32).  The libraries were analyzed on a Bioanalyzer, and submitted to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries were sequenced on the Hi-Seq 2000 following the manufacturer's protocols.


title: WT_RNA-seq_Zt6_1

description:
processed data file: RNAseq.txt (available on Series records)
Sample 7

source_name: WT_brain cortex_RNA-seq


title: Input_ChIRP-seq

description: Sample 6

extract_protocol:
Tissue was crosslinked in 1% formaldehyde, homogenized, and lysates clarified by sonication. lncRNA:DNA was isolated using biotin oligo probes and streptavidin beads. DNA was purified with phenol:chloroform extraction and resuspended in H2O.
Libraries were prepared according to Nugen's protocol accompanying the Ovation Ultralow DR Multiplex System 1-8 (Part# 0330). The libraries were analyzed on a Bioanalyzer, and submitted to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries were sequenced on the Hi-Seq 2000 following the manufacturer's protocols.

value: brain

tag: oligo set


title: LMO2 ChIP-seq

source_name: LMO2 ChIP-seq

tag: cell line

value: Kasumi-1 cells

value: anti-LMO2 (Abcam; ab81988)


title: Snord116del_116HG_ChIRP-seq

description: Sample 4

tag: strain

value: custom 116HG oligos


title: WT_116HG_ChIRP-seq rep2

description: Sample 3


title: WT_NSC_ChIRP-seq

description: Sample 2

value: custom NSC oligos


title: EFG1s_1_reads

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

description:
EFG1 smooth mutant Sample 1
processed_data_file: cuffdiff_WT_vs_EFG1concentric.txt

data_processing:
basecalling with CASAVA v1.8
fastq files were demultiplexed using the three barcodes (AGCTAT, CGATCT, GCTAGT), with an error tolerance of 1 in 6 bases. 1% of reads with >1 mismatch with the barcodes were discarded.
demultiplexed fastq files were aligned to the C. parapsilosis genome using TopHat 1.4, using strand-specific option for dUTP
BAM files were processed with CuffDiff 2.0.1 using geometric mean normalization and multi-read correction to improve accuracy for reads mapping to multiple genomic regions. Repetitive regions with high read representation (rDNA locus and TEF1/TEF2 genes) were masked. Only annotated features were used to determine differential expression.
Supplementary_files_format_and_content: 2 raw cuffdiff outputs (gene_exp.diff) for 1) wild type vs. EFG1 smooth and 2) wild type vs. EFG1 concentric mutants
Supplementary_files_format_and_content: The gene_exp.diff output files from Cuffdiff 2.0.1, comparing the wild type replicates with the EFG1 mutants; used geometric mean normalization a multi-read correction for reads mapping on multiple locations. The first lines include a legend for the headers (the header line is the original from Cuffdiff). Only genes with "yes" in the "significant" column were considered.

organism: Candida parapsilosis

source_name: efg1 mutant_smooth

growth_protocol: Cells were grown overnight from single colonies in 5 ml YPD (1% Yeast Extract, 2% Peptone, 2% Glucose; FormediumTM) at 30°C . They were diluted in 50 ml fresh YPD to an A600 of 0.2, and grown to an A600 of 1

extract_protocol: mRNA purified from total RNA using oligo dT Dynabeads (Invitrogen) was fragmented to an average size of 200 nucleotides by a 5 minute heat treatment (70°C) with a buffered zinc solution (Fragmentation Reagent, Ambion). Fragmentation of mRNA was stopped using an EDTA based Stop buffer (Ambion). Fragmented mRNA was incubated with 3 μg Random Hexamer Primers at 65°C for 5 min. First strand cDNA synthesis was carried out using 1 x First Strand Buffer (Invitrogen), 10 mM DTT, 500 μM dNTP mix (Invitrogen), 20 Units RNaseOUT and 200 units SuperScriptTM II Reverse Transcriptase (Invitrogen). For strand-specific library generation, unincorporated dNTPs were subsequently removed using G-50 Micro Columns (GE Healthcare). Second strand cDNA was generated using 1x Second Strand Buffer, 300 μM dNTP mix, 2 units RNaseH, 50 units DNA Polymerase I (NEB), while a 300 μM dUTP mix was used instead of a dNTP mix for the generation of a strand specific library. This material was used for library preparation. For strand-specific libraries, DNA fragments were blunted in an End Repair reaction using T4 DNA Polymerase, Klenow DNA Polymerase and T4 Polynucleotide Kinase, after which a single ‘A’ base was added to the 3’ end using dATP and Klenow Exo Fragment. To allow multiplexing of samples 6-nt barcoded Illumina compatible adapters (AGCTAT, CGATCT, GCTAGT) were ligated to the ends of the DNA fragments, in place of the commercially supplied adapters (PMID:18794863). Fragments of approximately 200-250 base pairs were purified from a 2% Agarose Gel. The second strand containing uridine was removed by treatment with 1 unit Uracil N-glycosylase (UNG) in TE Buffer at 37°C for 15 min. In all cases, purified adapter ligated DNA templates were then amplified through PCR enrichment, using PCR primers (Illumina), a dNTP mix, Phusion Polymerase (NEB) and 16 cycles of PCR. All libraries were quantified using a Qubit® Fluorometer (Invitrogen) and assessed on a 2% agarose gel. Amplified libraries were loaded on a flow cell. Sequencing was carried out in-house by running at least 36 cycles on an Illumina Genome Analyzer IIx according to manufacturer’s instructions, resulting in read lengths of approximately 42 bases.

value: efg1 deletion

tag: phenotype

value: smooth

tag: growth phase

value: log phase


title: EFG1s_2_reads

description:
EFG1 smooth mutant Sample 2
processed_data_file: cuffdiff_WT_vs_EFG1concentric.txt


title: EFG1c_1_reads

description:
EFG1 concentric mutant Sample 1
processed_data_file: cuffdiff_WT_vs_EFG1smooth.txt

source_name: efg1 mutant_concentric

value: concentric


title: WT_3_reads

description:
Wildtype Sample 3
processed_data_file: cuffdiff_WT_vs_EFG1smooth.txt
processed_data_file: cuffdiff_WT_vs_EFG1concentric.txt

source_name: wild type_concentric


title: WT_RNA-seq_Zt6_3

description:
Sample 9
processed data file: RNAseq030113.txt (available on Series records)


title: Snord116del_RNA-seq_Zt6_2

description:
processed data file: RNAseq.txt (available on Series records)
Sample 11


title: EFG1_ip3

description: Sample 6

data_processing:
basecalling with CASAVA v1.8
fastq reads mapped to C. parapsilosis genome with BWA
BAM files used for peak calling with MACS 1.4, genome size = 12600000, keep duplicate reads = auto
MACS peaks filtered (max False Discovery Rate: 5%)
filtered peaks and WIG files from MACS processed with Peak Splitter to get subpeaks, valley cutoff = 0.1
subpeaks' low coverage extremities shortened with a custom Java script,coverage  threshold = 0.5 of coverage at subpeak summit
shortened subpeaks assigned to C. parapsilosis coding genes using a custom Python pipeline. Peaks were not assigned were covering an entire coding sequence or when located 3' to two genes, on the sense and antisense strands.
summit fold change was calculated for each shortened subpeak as ratio of read coverage in the sample at summit position from Peak Splitter and coverage in the control in the corresponding position
summit fold change values lower than 2.0 were ignored
gene assignments supported by only 1 on 3 samples were discarded
results were ranked in decreasing order by Summit Fold Change for sample 1, then sample 2, then sample 3
in case of divergent promoters only one of the two corresponding genes has values in the final table
Genome_build: parapsilosis_genome.fasta (available on a Series records)
Supplementary_files_format_and_content: The 'EFG1chipseq_assignments.txt' file includes information on our ChIP-seq analysis. The first lines include a legend. Promoter region type (column 3) has been determined with a script: divergent promoters are regions in 5 prime to both a sense and an antisense coding gene. A distinction was made between genes predicted to be regulated by EFG1 and promoters: genes were sorted by decreasing order of summit fold change for sample 1, then for sample 2 then for sample 3, then for gene identifier; in case of divergent promoters, values were kept for only one of the two genes.

growth_protocol: Cells were grown from single colonies overnight in 5 ml YPD (1% Yeast Extract, 2% Peptone, 2% Glucose; FormediumTM) at 30°C . They were diluted in 50 ml fresh YPD to an A600 of 0.2, and grown to an A600 of 1

extract_protocol: Libraries were generated according to the protocol Preparing Samples for ChIP Sequencing of DNA (Illumina Guide Part # 11257047 Rev. A). The library preparation methodology of end repair to create blunt ended fragments, addition of 3’- A overhang for efficient adapter ligation, ligation of the SR adapters (Illumina Single Read Adapters (FC-102-1003) - aliquots kindly provided by A. Lohan), size selection of adapter ligated material was carried out utilizing enzymes indicated in the protocol. All enzymes for library generation were purchased from New England Biolabs (Ipswitch, MA, USA). A limited 18 cycle amplification of size selected libraries was carried out.  To eliminate adapter -dimers libraries were further sized selected a  2.5% TAE agarose gels. Purified libraries were quantified using a Qubit™ fluorometer (Invitrogen, Carlsbad, CA, USA) and a Quant-iT™ double-stranded DNA High-Sensitivity Assay Kit (Invitrogen, Carlsbad, CA, USA). Clustering and sequencing of the material was carried out as per manufacturers instructions on the Illumina GAIIx platform in the UCD Conway Institute (UCD, Dublin Ireland).

treatment_protocol: 1% formaldehyde was added to cultures and samples were incubated at room temperature for 30 min, shaking at 50 rpm. 125mM glycine was added to each sample and left incubate for 5 min at room temperature, shaking at 50 rpm. Cells were centrifuges and collected. Samples were sonicated using a Biorupter™ (Diagenode) for 15 min at 30 s intervals at high power setting in an ice bath. The ice was then changed and the sonication was repeated. Input samples before the addition of antibody were used as control. Regions bound to Efg1 were immunoprecipitated using a mouse monoclonal antibody (Myc-tag 9B11, Cell Signaling).


title: EFG1c_3_reads

description:
EFG1 concentric mutant Sample 3
processed_data_file: cuffdiff_WT_vs_EFG1smooth.txt


title: WT_1_reads

description:
Wildtype Sample 1
processed_data_file: cuffdiff_WT_vs_EFG1smooth.txt
processed_data_file: cuffdiff_WT_vs_EFG1concentric.txt


title: WT_2_reads

description:
Wildtype Sample 2
processed_data_file: cuffdiff_WT_vs_EFG1smooth.txt
processed_data_file: cuffdiff_WT_vs_EFG1concentric.txt


title: EFG1c_2_reads

description:
EFG1 concentric mutant Sample 2
processed_data_file: cuffdiff_WT_vs_EFG1smooth.txt


title: Snord116del_NSC_ChIRP-seq

description: Sample 5


title: EFG1_input2

description: Sample 3

value: Myc-Tag (9B11) Mouse mAB

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat. #

tag: chip antibody lot #


title: EFG1_input3

description: Sample 5


title: WT_RNA-seq_Zt16_1

description:
Sample 12
processed data file: RNAseq030113.txt (available on Series records)


title: EFG1_input1

description: Sample 1


title: EFG1_ip2

description: Sample 4


title: Ecoli_dFNR_rep2_anaerobic

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: This sample is of ∆fnr Escherichia coli MG1655 K-12. It is the second of two ∆fnr biological replicates used in this experiment, each from separate cultures.

data_processing:
Resulting reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle & Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
Genome Build:
FNR-_Anaerobic_RNAseq_B_Tag_Count.txt: U00096.2
FNR-_Anaerobic_RNAseq_B_WIG.wig: U00096.2

organism: Escherichia coli str. K-12 substr. MG1655star

source_name: Escherichia coli MG1655 K-12 dFNR (PK4854)

growth_protocol: Escherichia coli MG1655 K-12 WT and ∆fnr were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Ref).

extract_protocol: The RNAs were chemically fragmented using RNA Fragmentation Reagents (Ambion) to the size range of 200-250 bp using 1x fragmentation solution for 5 minutes at 70°C (Ambion).  Double stranded cDNA was generated using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) following the manufacturer’s protocol.  The Illumina Paired End Sample Prep kit was used for Illumina RNA-seq library creation using the manufacturer’s instructions.  Briefly, the fragmented cDNA was end repaired, ligated to Illumina specific adapters and amplified with 10 cycles of PCR using the TruSeq SR Cluster Kit (v2).  Single-end 36 bp reads were generated by sequencing on the Illumina Genome Analyzer IIx, using the TruSeq SBS Kit (v5) following the manufacturer’s protocol.

treatment_protocol: Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (ref). Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop. To enrich for mRNA, the 23S and 16S rRNA were removed using the Ambion MICROBExpress kit (Ambion) following manufacturer’s guidelines, except the total RNA was incubated with the rRNA oligonucleotides for one hour instead of 15 minutes.

tag: genoype

value: dFNR

value: lacking FNR protein

tag: growth condition

value: anaerobic


title: BM2

value: BALB/c

value: bone marrow

value: 10-12 months

value: normal Gr1+Mac1+ myeloid cells


title: EFG1_ip1

description: Sample 2


title: Ecoli_wild-type_rep1_anaerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.

data_processing:
Resulting reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle & Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
Genome Build:
WT_Anaerobic_RNAseq_A_Tag_Count.txt: U00096.2
WT_Anaerobic_RNAseq_A_WIG.wig: U00096.2

source_name: Escherichia coli MG1655 K-12 WT

value: Wild-Type

value: normal


title: Ecoli_dFNR_rep1_anaerobic

description: This sample is of ∆fnr Escherichia coli MG1655 K-12. It is the first of two ∆fnr biological replicates used in this experiment, each from separate cultures.

data_processing:
Resulting reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle & Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
Genome Build:
FNR-_Anaerobic_RNAseq_A_Tag_Count.txt: U00096.2
FNR-_Anaerobic_RNAseq_A_WIG.wig: U00096.2


title: Ecoli_wild-type_rep2_anaerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

data_processing:
Resulting reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle & Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
Genome Build:
WT_Anaerobic_RNAseq_B_Tag_Count.txt: U00096.2
WT_Anaerobic_RNAseq_B_WIG.wig: U00096.2


title: σ70 IP ChIP-seq Anaerobic B

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
Genome_build: U00096.2

source_name: Anaerobic Cultures

growth_protocol: Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

extract_protocol: DNA were submitted to the Joint Genome Institute for ChIP-seq library preparation.  Samples were sheared to 200-500 nt during the IP process to facilitate library preparation.  All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting either 275 bp fragments (s70 libraries).  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  A single read, 36 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. Basecalling was performed using the standard Illumina Pipeline version 1.6.

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

tag: antibody

value: RNA Polymerase σ70 monoclonal antibody from NeoClone (W0004)

value: Wild Type K-12

value: Anaerobic Cultures


title: INPUT DNA B

source_name: Aerobic Cultures

value: INPUT

value: Aerobic Cultures