title: Whole Genome Shotgun Bisulfite Sequencing of Pancreas Cells from Human STL002; methylC-seq_STL002PA-01b

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Pancreas Cells from Human STL002
Library name: methylC-seq_STL002PA-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18869
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Pancreas

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

value: Female

value: Caucasian

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 uM


title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL002; methylC-seq_STL002GA-01b

status: Public on Dec 12 2013

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL002
Library name: methylC-seq_STL002GA-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18868
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14004
****************
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: Various levels of processed data files will be made available as this project proceeds.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Library construction protocol: One ug of genomic DNA was extracted from frozen ground tissue using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA).  Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 25 ul 2x KAPA HiFi HotStart Uracil+ReadyMix, 2.5 ul Primer 1, 2.5 ul Primer 2 (50 ul final). The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 4-8 cycles of 98C 15 sec, 60C 30 sec and 72C 4 min, ending with one 72C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

tag: sra sample accession

tag: disease

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Gastric

value: Autopsy

value: 1 ug

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT


title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL002; methylC-seq_STL002FT-01b

description:
sample_term_id: UBERON_0001013
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL002
Library name: methylC-seq_STL002FT-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18867
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15439
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

tag: sample alias

value: Adipose

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

value: Female

value: Caucasian

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles


title: Suspension cells

status: Public on Dec 13 2013

city: Brisbane

first: Peter

middle: Richard

last: Sternes

state: Queensland

address: John Hines Building, University of Queensland, St Lucia

department: School of Agriculture and Food Science

country: Australia

institute: University of Queensland

description: small RNA

library_source: transcriptomic

data_processing:
Sequencing adapter primers (proprietary) were trimmed using UNIX shell scripting
Sense and antisense matches to known tRNA, rRNA and chloroplast sequences from Rfam, Genomic tRNA, EMBL release 95 and SILVA rRNA databases were removed using UNIX shell scripting
Sequences were counted and displayed as tab delimited files containing a count and the unique sequence per line, using UNIX shell scripting
Supplementary_files_format_and_content: Tab delimited text files containing counts of trimmed and filtered small RNA sequences

molecule: total RNA

organism: Saccharum sp.

source_name: Suspension cells grown in a liquid cell culture

extract_protocol:
Total RNA was isolated using TRIsure reagent (Bioline) as per the manufacturer's intstructions
Libraries were constructed using the TruSeq Small RNA kit (Illumina)

tag: cultivar

tag: tissue

value: suspension cells

tag: tissue type

value: cultured


title: Whole Genome Shotgun Bisulfite Sequencing of Esophagus Cells from Human STL002; methylC-seq_STL002EG-01b

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Esophagus Cells from Human STL002
Library name: methylC-seq_STL002EG-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18866
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14001
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Esophagus

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 uM


title: m_2_1_i7

city: Davis

first: Danielle

middle: G

last: Lemay

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

data_processing:
FASTQ files were de-multiplexed to assign the 100bp reads to the originating sample
Reads were first trimmed to remove adaptor sequences using Scythe [17] and then adaptively trimmed for quality on both the 5’ and 3’ ends using Sickle [18]
Resulting reads were checked for quality using FastQC
The rhesus macaque genome assembly rheMac2 was indexed using Bowtie
Reads were then mapped to the indexed genome using TopHat
Transcript abundances were estimated as fragments per kilobase of exon per million fragments mapped (FPKMs) using Cufflinks and all MMUL1.0 Ensembl transcripts from the Ensembl database, release 67
Genome_build: rheMac2
Supplementary_files_format_and_content: Tab-delimited text file contains FPKMs for each transcript in each sample

organism: Macaca mulatta

source_name: Macaque milk

extract_protocol:
RNA was extracted using the Qiagen Universal Kit (Qiagen, Netherlands), followed by treatment with DNAse. RNA yield and quality (260/280 nm, 260/230 nm) were measured by Nanodrop spectrophotometry (Thermo Fisher Scientific Inc., Wilmington, DE). RNA integrity was assessed with an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocol with polyA selection

tag: time point (days post-partum)

value: Fat

tag: animal id


title: m_2_1_i6


title: m_2_1_i12


title: m_2_1_i5

value: Cells


title: Sample_264G45LB

city: Pullman

first: Devendra

middle: H

last: Shah

state: WA

address: #402, Bustad Hall

department: Veterinary Microbiology and Pathology

institute: Washington State University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (single-end) were mapped to S. Enteirtidis  whole genome (AM933172) using CLC-Bio Workbench version 5.0 with following parameters: minimum of 75 bp wihth allowance up to two mismatches and >90% of the each reads length had to map to the reference sequence to be considred as mapped reads.
Genes with zero reads were removed and the total raw read counts were used for data analysis using EdgeR and DESeq statistical packages for differential gene expression analysis
Genome_build: GenBank: AM933172.1
Supplementary_files_format_and_content: Tab-delimited text file includes total raw read counts values for all samples

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: poultry-associated field strains of S. Enteritidis grown in laboratory media at avian body temperature (42°C)_LP

growth_protocol: S. Enteritidis strains were grown at avian bpdy temperature (42C) in luria bertani broth

extract_protocol:
Bacterial cells wer epelleted and RNA was extracted using Ribopure Bacterial Kit (Ambion, USA), DNAse treated and ribosomal RNA was removed using DNS protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment

tag: strain

tag: phenotype

value: Low-pathogenic (LP)

tag: phenotype id

tag: serovar

value: Enteritidis


title: m_2_1_i2

value: Bx


title: m_2_1_i4


title: m_2_1_i13


title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL001; methylC-seq_STL001RV-01b

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL001
Library name: methylC-seq_STL001RV-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18862
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; methylC-seq_STL001RV-01b

value: Shin Lin, Stanford University

value: Primary Tissue

value: Right Ventricle

value: Autopsy

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

value: Male

value: Caucasian and African American

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 ug

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT


title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL002; methylC-seq_STL002AD-01b

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL002
Library name: methylC-seq_STL002AD-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18864
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13995
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Adrenal Gland tissue; methylC-seq_STL002AD-01b

value: iron deficiency, bipolar

value: Adrenal Gland

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

value: Female

value: Caucasian

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 uM


title: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL001; methylC-seq_STL001SX-01b

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL001
Library name: methylC-seq_STL001SX-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18863
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15438
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Spleen tissue; methylC-seq_STL001SX-01b

value: Shin Lin, Stanford University

value: Primary Tissue

value: Spleen

value: Autopsy

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

value: Male

value: Caucasian and African American

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles


title: m_4_3_i15

value: Fat


title: m_4_3_i13

value: Cells


title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL001; methylC-seq_STL001GA-01b

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL001
Library name: methylC-seq_STL001GA-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18859
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Gastric

value: 1 ug

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix


title: m_4_3_i14


title: Whole Genome Shotgun Bisulfite Sequencing of Lung Cells from Human STL001; methylC-seq_STL001LG-01b

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Lung Cells from Human STL001
Library name: methylC-seq_STL001LG-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18860
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
****************

source_name: Lung tissue; methylC-seq_STL001LG-01b

value: Shin Lin, Stanford University

value: Primary Tissue

value: Lung

value: Autopsy

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

value: Male

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 uM


title: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL001; methylC-seq_STL001PO-01b

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL001
Library name: methylC-seq_STL001PO-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18861
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; methylC-seq_STL001PO-01b

value: Psoas Muscle

value: Caucasian and African American

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 ug


title: m_4_3_i6


title: m_4_3_i5

value: Fat


title: m_4_3_i2

value: Cells


title: m_4_3_i4


title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL001; methylC-seq_STL001FT-01b

description:
sample_term_id: UBERON_0001013
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL001
Library name: methylC-seq_STL001FT-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18858
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15437
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Shin Lin, Stanford University

value: Primary Tissue

value: Adipose

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix


title: m_3_3_i19

value: Bx


title: Reference Epigenome: ChIP-Seq Input from Human Esophagus Tissue; renlab.Input.STL002EG.03.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY310
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18778
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14001
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

value: iron deficiency, bipolar

value: Esophagus

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: m_3_3_i18


title: m_4_3_i16


title: m_3_3_i14

value: Cells


title: Reference Epigenome: ChIP-Seq Input from Human Aorta Tissue; renlab.Input.STL002AO.02.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY312
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18780
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Shin Lin, Stanford University

value: Primary Tissue

value: Aorta


title: Reference Epigenome: ChIP-Seq Input from Human Right Ventricle Tissue; renlab.Input.STL001RV.02.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY340
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18805
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.Input.STL001RV.02.01

value: Right Ventricle

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

value: Male

value: Caucasian and African American


title: m_3_3_i7

value: Fat


title: m_3_3_i16


title: Reference Epigenome: ChIP-Seq Input from Human Gastric Tissue; renlab.Input.STL001GA.02.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY342
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18807
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Gastric

value: Autopsy


title: Reference Epigenome: ChIP-Seq Input from Human Psoas Muscle Tissue; renlab.Input.STL001PO.02.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY339
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18803
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; renlab.Input.STL001PO.02.01

value: Psoas Muscle


title: m_3_3_i13

value: Bx


title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL002; methylC-seq_STL002AO-01b

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL002
Library name: methylC-seq_STL002AO-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18865
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Aorta tissue; methylC-seq_STL002AO-01b

value: iron deficiency, bipolar

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

value: Female

value: Caucasian

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 ug

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 uM


title: m_4_3_i7

value: Bx


title: m_3_3_i12

value: Fat


title: m_3_3_i5

value: Cells


title: m_4_3_i12


title: m_3_3_i4


title: m_3_3_i2


title: m_2_3_i19


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Sigmoid Colon Tissue; renlab.H3K4me3.STL003SG.02.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY337
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18798
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
****************

source_name: Sigmoid Colon tissue; renlab.H3K4me3.STL003SG.02.01

value: Shin Lin, Stanford University

value: Primary Tissue

value: Sigmoid Colon

value: Autopsy

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

value: Male

value: Caucasian

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Spleen Tissue; renlab.H3K9me3.STL001SX.02.01

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY362
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18822
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15438
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Spleen

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

value: Caucasian and African American

value: Histone H3K9me3

value: Abcam


title: m_2_3_i18

value: Fat


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Small Intestine Tissue; renlab.H3K4me3.STL002SB.02.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Small Intestine Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY355
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18816
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14055
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Small Intestine tissue; renlab.H3K4me3.STL002SB.02.01

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Small Intestine

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

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Pancreas Tissue; renlab.H3K4me3.STL002PA.02.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY333
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18796
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Pancreas

value: Autopsy

value: Caucasian

value: Histone H3K4me3

value: Biorupter


title: m_2_3_i16


title: m_3_3_i15

value: Cells


title: m_2_3_i14


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Esophagus Tissue; renlab.H3K4me3.STL002EG.02.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY330
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18790
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14001
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Esophagus

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: m_2_3_i13

value: Bx


title: m_2_3_i12


title: Reference Epigenome: ChIP-Seq H3K4me3 from Human Right Ventricle Tissue; renlab.H3K4me3.STL001RV.02.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq H3K4me3 from Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY349
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18826
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.H3K4me3.STL001RV.02.01

value: Shin Lin, Stanford University

value: Right Ventricle

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

value: Male

value: Caucasian and African American


title: m_2_3_i5


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Spleen Tissue; renlab.H3K4me3.STL001SX.02.01

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY360
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18820
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15438
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Primary Tissue

value: Spleen


title: m_2_3_i7

value: Fat


title: m_2_3_i4


title: m_2_3_i2


title: m_2_3_i6


title: m_4_2_i15


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Aorta Tissue; renlab.H3K4me3.STL002AO.02.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY328
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18788
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Aorta

value: Autopsy

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

value: Female

value: Caucasian

value: Histone H3K4me3


title: m_4_2_i16


title: m_4_2_i14


title: m_4_2_i12

value: Cells


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Gastric Tissue; renlab.H3K4me3.STL001GA.02.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY331
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18792
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Gastric

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq H3K27me3 from Human Right Ventricle Tissue; renlab.H3K27me3.STL003RV.02.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq H3K27me3 from Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY348
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18854
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.H3K27me3.STL003RV.02.01

value: Shin Lin, Stanford University

value: Primary Tissue

value: Right Ventricle

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

value: Male

value: Histone H3K27me3

value: Active Motif


title: m_2_3_i15


title: m_4_2_i7

value: Bx


title: m_3_3_i6


title: m_4_2_i6


title: m_4_2_i5

value: Fat


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Small Intestine Tissue; renlab.H3K27me3.STL002SB.02.01

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Small Intestine Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY353
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18814
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14055
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Small Intestine tissue; renlab.H3K27me3.STL002SB.02.01

value: iron deficiency, bipolar

value: Small Intestine

value: Autopsy

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

value: Female

value: Caucasian


title: m_4_2_i2

value: Cells


title: m_4_2_i4


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Pancreas Tissue; renlab.H3K27me3.STL002PA.03.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY325
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18786
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Pancreas

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: m_3_2_i19


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Human Lung Tissue; renlab.H3K4me3.STL001LG.02.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY332
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18794
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
****************

value: Shin Lin, Stanford University

value: Primary Tissue

value: Lung

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

value: Male

value: Caucasian and African American

value: Histone H3K4me3

value: Millipore


title: m_3_2_i15


title: m_3_2_i18


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Esophagus Tissue; renlab.H3K27me3.STL002EG.02.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY322
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18784
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14001
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Esophagus

value: Autopsy

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

value: Histone H3K27me3

value: Active Motif


title: m_4_2_i13

value: Cells


title: m_3_2_i6


title: m_3_2_i16

value: Fat


title: m_3_2_i5


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Aorta Tissue; renlab.H3K27me3.STL002AO.02.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY320
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18776
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Aorta

value: Female

value: Caucasian

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: m_3_2_i14


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Psoas Muscle Tissue; renlab.H3K27me3.STL001PO.02.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY338
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18800
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; renlab.H3K27me3.STL001PO.02.01

value: Shin Lin, Stanford University

value: Primary Tissue

value: Psoas Muscle

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

value: Male

value: Caucasian and African American


title: m_3_2_i13

value: Bx


title: m_3_2_i2


title: m_2_2_i19


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Spleen Tissue; renlab.H3K27me3.STL001SX.02.01

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY358
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18818
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15438
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Spleen

value: Autopsy

value: Histone H3K27me3

value: Active Motif


title: m_2_2_i16

value: Fat


title: Reference Epigenome: ChIP-Seq H3K27me3 from Human Right Ventricle Tissue; renlab.H3K27me3.STL001RV.02.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq H3K27me3 from Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY348
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18824
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.H3K27me3.STL001RV.02.01

value: Right Ventricle


title: m_2_2_i14

source_name: Macaque milk

value: Cells


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.STL001GA.02.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY347
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18812
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Gastric

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms


title: m_2_2_i13


title: m_2_2_i12


title: m_3_2_i12


title: m_3_2_i4


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue; renlab.H3K27ac.STL002AO.02.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY316
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18782
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Aorta

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

value: Female

value: Caucasian

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue; renlab.H3K27ac.STL001PO.02.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY346
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18809
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; renlab.H3K27ac.STL001PO.02.01

value: Psoas Muscle

value: Autopsy

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

value: Male

value: Caucasian and African American

value: Active Motif


title: m_2_2_i6

value: Fat


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Right Atrium Tissue; renlab.H3K27me3.STL003RA.02.01

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Right Atrium Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY837
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17511
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11888
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Atrium tissue; renlab.H3K27me3.STL003RA.02.01

value: Right Atrium

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

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms


title: m_2_2_i18


title: m_2_2_i4

value: Cells


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Lung Tissue; renlab.H3K27me3.STL002LG.02.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY834
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17513
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
****************

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Lung

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

value: Female


title: m_2_2_i15


title: m_4_1_i15


title: m_4_1_i16


title: m_4_1_i13


title: m_4_1_i14


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Thymus Tissue; renlab.H3K27me3.STL01TH.01.01

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY838
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17509
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Thymus

value: Autopsy

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

value: magnetic anti-rabbit

value: 5 micrograms


title: m_3_2_i7

value: Fat


title: m_2_2_i7


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Adrenal Gland Tissue; renlab.H3K27me3.STL003AD.03.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY833
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17519
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
****************

source_name: Adrenal Gland tissue; renlab.H3K27me3.STL003AD.03.01

value: Adrenal Gland

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

value: Male

value: Caucasian

value: Active Motif


title: m_2_2_i2

value: Bx


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Ovary Tissue; renlab.H3K27me3.STL002OV.02.01

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY836
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17515
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
****************

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Ovary

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms


title: m_2_2_i5

value: Cells


title: m_4_1_i4


title: Whole genome sequencing of STL011 donor; STL011_genome

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: Whole genome sequencing of STL011 donor
Library name: STL011
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18174
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.18173
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: STL011 is a sample that is part of Roadmap Epigenome Project; STL011_genome

extract_protocol: Library construction protocol: Two µg of genomic DNA was extracted from ground, frozen tissue using the DNeasy Blood and Tissue kit (Qiagen, Valencia, CA). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 300-400 bp, followed by library preparation using the TruSeq DNA Sample Prep kit (Illumina, San Diego, CA) as per manufacturer's instructions. The library was run on a 2% agarose gel and gel size selected to 400-500 bp using the MinElute Gel Extraction kit (Qiagen).

tag: sample common name

value: Spleen

value: coronary artery disease. No history of hypertension or diabetes

value: Liver

value: Primary Tissue

value: Autopsy

value: Whole Genome Sequencing

value: Qiagen DNeasy Blood and Tissue kit, performed as per manufacturer's instructions

value: Covaris S2

value: 400 bp target peak size, 2 cycles


title: m_4_1_i5

value: Fat


title: Whole genome sequencing of STL003 donor; STL003_genome

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: Whole genome sequencing of STL003 donor
Library name: STL003
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17995
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.17994
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: STL003 is a sample that is part of Roadmap Epigenome Project; STL003_genome

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

value: Male

value: Caucasian


title: m_4_1_i7

value: Bx


title: m_3_1_i19


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Pancreas Tissue; renlab.H3K27me3.STL002PA.02.01

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Pancreas Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY134
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18745
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Pancreas

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

value: Female

value: Histone H3K27me3

value: Biorupter

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Right Ventricle Tissue; renlab.H3K27ac.STL003RV.02.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18743
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.H3K27ac.STL003RV.02.01

value: Primary Tissue

value: Right Ventricle

value: Autopsy

value: Histone H3K27ac

value: 500 micrograms


title: m_3_1_i16

value: Fat


title: m_4_1_i2

value: Cells


title: m_3_1_i14


title: m_4_1_i6


title: m_3_1_i18


title: m_3_1_i15


title: Whole genome sequencing of STL002 donor; STL002_genome

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: Whole genome sequencing of STL002 donor
Library name: STL002
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17812
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.17811
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: STL002 is a sample that is part of Roadmap Epigenome Project; STL002_genome

value: Spleen

value: iron deficiency, bipolar

value: Caucasian

value: Whole Genome Sequencing

value: Qiagen DNeasy Blood and Tissue kit, performed as per manufacturer's instructions

value: Covaris S2

value: 400 bp target peak size, 2 cycles


title: m_3_1_i12


title: Whole genome sequencing of STL001 donor; STL001_genome

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: Whole genome sequencing of STL001 donor
Library name: STL001
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.17653
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.17652
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: STL001 is a sample that is part of Roadmap Epigenome Project; STL001_genome

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


title: m_3_1_i7


title: m_4_1_i12


title: m_3_1_i5


title: m_3_1_i2

value: Bx


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue; renlab.H3K27ac.STL003AD.02.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY176
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15830
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
****************

source_name: Adrenal Gland tissue; renlab.H3K27ac.STL003AD.02.01

value: Adrenal Gland

value: Primary Tissue

value: Autopsy

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

value: Biorupter

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: m_2_1_i18

value: Fat


title: Whole Genome Shotgun Bisulfite Sequencing of Bladder Cells from Human STL001; methylC-seq_STL001BL-01c

description:
sample_term_id: UBERON_0001255
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Bladder Cells from Human STL001
Library name: methylC-seq_STL001BL-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15836
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: Library construction protocol: One µg of genomic DNA was extracted from frozen ground tissue using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16degC for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA).  Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 25 µl 2x KAPA HiFi HotStart Uracil+ReadyMix, 2.5 µl Primer 1, 2.5 µl Primer 2 (50 µl final). The thermocycling parameters were: 95degC 2 min, 98degC 30 sec, then 4-8 cycles of 98degC 15 sec, 60degC 30 sec and 72degC 4 min, ending with one 72degC 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: Bladder

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: 200 bp, 3 cycles

value: 1 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: polyA RNA sequencing of STL002 Sigmoid Colon Cells; polyA-RNA-seq_STL002SG_r1a

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL002 Sigmoid Colon Cells
Library name: polyA-RNA-seq_STL002SG_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15455
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15440
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Sigmoid Colon tissue; polyA-RNA-seq_STL002SG_r1a

extract_protocol: Library construction protocol: Four µg of total RNA was extracted from frozen cell pellets using the RNeasy Mini Kit (Qiagen, Valencia, CA). PolyA RNA was isolated from total RNA using Dynabeads oligo(dt)25 (Invitrogen). PolyA selected RNA was eluted in 2x Superscript III buffer supplemented with 10mM DTT and was fragmented by incubation at 94°C for 4 minutes. First-strand cDNA was synthesized with the following reaction composition: 0.5 µL random hexamer, 0.5 µL RNase Out, 1 µL DTT (100 mM), 0.5 µL dNTP (25 mM), 0.5 µL SuperScript III (20 µL final). The reaction was incubated at 25°C for 10 min then 50°C for 50 min.  Single-stranded cDNA was isolated by purification with RNAClean XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing second-strand was synthesized with the following reaction: 1.5 µL NEBuffer 2 (NEB), 1 µL dNTP mix (10 mM dATP, dCTP, dGTP, and dUTP), 0.2 µL RNase H, 1 µL DNA Polymerase I (E. coli) (New England Biolabs) (15 µL final). The reaction was incubated at 16°C for 2.5 hours. The dUTP-containing cDNA was isolated by purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing cDNA was then end repaired and a 3'A base was added. TruSeq adapters (Illumina, San Diego, CA) were ligated to the dUTP-containing cDNA at 16°C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated cDNA was isolated by two rounds of purification with AMPure XP beads. The dUTP-containing strands were digested at 37°C for 30 min with uracil DNA glycosylase (Enzymatics). Adapter-ligated, single-stranded DNA molecules were enriched by 10 cycles of PCR with the following reaction composition: 5 µL TruSeq PCR Primer Cocktail (Illumina), 25 µL TruSeq PCR Master Mix (Illumina) (50 µL final). The thermocycling parameters were: 98°C 30 sec, then 10-15 cycles of 98°C 10 sec, 60°C 30 sec and 72°C 30 sec, ending with one 72°C 5 min step. The reaction products were purified using AMPure XP beads.

value: Sigmoid Colon

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: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: m_3_1_i4

value: Cells


title: m_2_1_i16

value: Fat


title: m_3_1_i6


title: m_2_1_i19


title: m_2_1_i15


title: m_2_1_i14


title: IN3 (Internode 3)

description: small RNA

source_name: Pooled internode 3 tissue from 3 independent field grown sugarcane plants

value: internode 3

value: vegetative


title: m_3_1_i13

value: Bx


title: Whole Genome Shotgun Bisulfite Sequencing of Bladder Cells from Human STL001; methylC-seq_STL001BL-01a

description:
sample_term_id: UBERON_0001255
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Bladder Cells from Human STL001
Library name: methylC-seq_STL001BL-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14779
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14777
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: Library construction protocol: One µg of genomic DNA was extracted from frozen ground tissue using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair and addition of a 3'A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16degC for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA).  Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 25 µl 2x KAPA HiFi HotStart Uracil+ReadyMix, 2.5 µl Primer 1, 2.5 µl Primer 2 (50 µl final). The thermocycling parameters were: 95degC 2 min, 98degC 30 sec, then 4-8 cycles of 98degC 15 sec, 60degC 30 sec and 72degC 4 min, ending with one 72degC 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: Bladder

tag: molecule

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian and African American

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 µl PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole Genome Shotgun Bisulfite Sequencing of Liver Cells from Human STL011; methylC-seq_STL011LI-01a

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Liver Cells from Human STL011
Library name: methylC-seq_STL011LI-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.14780
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14778
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Liver tissue; methylC-seq_STL011LI-01a

value: Adult Liver

value: genomic DNA

value: coronary artery disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Liver

value: Autopsy

value: coronary artery disease. No history of hypertension or diabetes.

value: Caucasian

value: 16degC for 16 hours with T4 DNA ligase (New England Biolabs)


title: RFX2KD_2

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

description: Animal cap with RFX2 morpholino treatment, total poly-(A) RNAs, rep 2

data_processing:
Filter out all reads with no-call (‘N’) and low complexity (reads without all 4 bases).
Take reads that both paired-end reads are passed the above condition.
Map to constructed X. laevis gene model (‘Oktoberfest’ version; longest transcript per gene loci) with bowtie1, then calculate RPKM (read counts per kb per 1 million of reads), Calculate FDR with edgeR.
genome_build: X. laevis draft genome (JGI v6.0), X. laevis gene model (Oktoberfest)
supplementary_files_format_and_content: Tab-delimited text file includes RPKM values, fold-change and FDR

molecule: polyA RNA

organism: Xenopus laevis

extract_protocol: Total RNA isolated from 100 animal caps from X. laevis (stage 20)

value: Animal cap

value: RFX2 knockdown


title: RFX2KD_1

description: Animal cap with RFX2 morpholino treatment, total poly-(A) RNAs, rep 1


title: RFX2GFP

description: ChIP-seq with RFX2-GFP construct

data_processing:
Filter out all reads with no-call (‘N’) and low complexity (reads without all 4 bases).
Map to draft X. laevis genome (6.0) with bowtie1, call peaks with MACS.
genome_build: X. laevis draft genome (JGI v6.0), X. laevis gene model (Oktoberfest)
supplementary_files_format_and_content: MACS1 peaks

source_name: ChIP-seq with RFX2-GFP construct

extract_protocol: ChIP-seq assays were performed with stage 20 X. laevis embryos, injected with in vitro transcribed mRNA coding for either GFP-Rfx2 or GFP alone. Samples were crosslinked with 1% formaldehyde for 1 hour and the reaction stopped by adding glycine (to 125mM) for 10 min. Embryos were rinsed with PBS and resuspended in lysis buffer with protease inhibitor cocktail (Roche). Chromatin was sonicated to an average size of 200 to 600 base pair using a Branson 450 Sonifier, then immunoprecipitated using protein G magnetic beads (Invitrogen) coupled to 5μg α-GFP antibody (ab290) at 4°C overnight. Magnetic beads were washed, the bound chromatin eluted, and crosslinks reversed. ChIP DNA was extracted with phenol-chloroform and purified with a QIAquick PCR Purification Kit (Qiagen).

value: Epithelial tissue

tag: chip antibody

value: α-GFP antibody (ab290)

value: RFX2-GFP expression


title: polyA RNA sequencing of STL003 Small Bowel Cells; polyA-RNA-seq_STL003SB_r1a

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL003 Small Bowel Cells
Library name: polyA-RNA-seq_STL003SB_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15454
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11844
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Small Intestine tissue; polyA-RNA-seq_STL003SB_r1a

value: Small Intestine

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

value: Male

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: Hdc negative cells

city: Worcester

first: Daniel

middle: R

last: Caffrey

state: MA

address: 364 Plantation St

institute: UMASS Medical School

data_processing:
Sequence reads were aligned to the genome using TopHat version 2.0.07
Gene level read counts were calculated with HTSeq-count
Genome_build: NCBI m37 (UCSC MM9, Ensembl 64)
Supplementary_files_format_and_content: Gene count files were generated with the HTSeq-count program.

organism: Mus musculus

source_name: stomach corpus epithelium

extract_protocol:
Qiagen Rneasy mini kit from Qiagen
Truseq RNA kit from Illumina

tag: cell type

value: Hdc-CFP depleted stomach corpus epithelial cells.

tag: genotype

value: Hdc-CFP transgenic


title: Ctrl_1

description: Wild-type animal cap, total poly-(A) RNAs, rep 1

value: Animal cap

value: wild-type


title: Hdc1

value: sorted stomach Hdc-CFP+ cells


title: H3K4me3_ChIPSeq

status: Public on Dec 11 2013

city: Milano

first: Stefano

last: Casola

state: Select a State or Province

address: Via Adamello 16

country: Italy

institute: IFOM

data_processing:
RTA 1.17.20.0-64 bit
FastQ files were filtered using fastX toolkit (version 0.0.13.2). The following filters were applied: trimming of nucleotides from the most right position if median quality score across reads smaller than 20 (Phred 33 code); clipping on both side if adapters were identified by fastqc; elimination of reads with more than 20% of nucleotide presenting a quality score below 20
ChIP-sequencing were aligned to the mm9 genome using bowtie 0.12.8. Configuration:maximum number of mismatches = 2; reports max 1 alignment; discard reads with more than 1 alignment
Duplicated reads were removed using samtools rmdup (version 0.1.18)
Peaks were called using MACS (version 1.4.0), with default parameters for H3K4me3, and with the addition of --nomodel --nolambda for the H3K27me3. Only peaks with a p-val below 10e-10 were retained.
Genome_build: mm9
Supplementary_files_format_and_content: wig and bed files generated with bowtie and macs

source_name: Germinal Center

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3- (C36B11, Cell Signaling) or H3K4me3- (04-745, Millipore) specific antibodies.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sorted GC B cells (CD19+CD38loCD95hi) were obtained from pools of C57BL/6 mice sacrificed 7d after intraperitoneal immunization with 1 x 10^8 sheep red blood cells/mouse in PBS.

value: Sorted Germinal Center B cells

value: H3K4me3 (MC315, Millipore)


title: WT ESCs (GEI-38)

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: small RNA-seq

data_processing:
ncPRO-seq pipeline v1.4.1 has been used for the complete analysis of the libraries (Chen C., Servant N. et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: The processed files correspond to distinct sequences and the associated counts

source_name: ESC E14

growth_protocol: Male E14 Embryonic Stem (ES) cell line and Dicer_KO were cultured in Dulbecco’s Modified Eagle Media (DMEM) (Invitrogen), containing 15% FCS (Bio West), 1000 U/ml LIF (Chemicon), 0.1 mM beta-mercaptoethanol (Invitrogen), 0.05 mg/ml of streptomycin (Invitrogen) and 50 U/ml of penicillin (Invitrogen) on a gelatin-coated support in the absence of feeder cells. The culture medium was changed daily. All cells were grown at 37°C in 8% CO2.

extract_protocol:
Trizol extraction for Total RNA
Total cellular RNA samples (5-10 μg), prepared using Trizol reagent (MRC Molecular Research Center), were processed into sequencing libraries using adapted Illumina protocols for Solexa technology and sequenced by Fasteris ((http://www.fasteris.com, Switzerland).

value: embryonic stem cells

value: WT


title: DCR-/- (GEI-39)

description: small RNA-seq

source_name: DCR-/- ESC

value: DCR -/-


title: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL002; methylC-seq_STL002PO-01b

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL002
Library name: methylC-seq_STL002PO-01b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18870
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14050
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; methylC-seq_STL002PO-01b

tag: sra sample accession

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Psoas Muscle

value: Autopsy

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

value: Female

value: Caucasian

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: 200 bp, 3 cycles

value: 1 ug

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >The adapter-ligated, bisulfite converted DNA was used in a 50 ul PCR reaction

value: KAPA HiFi HotStart Uracil+ ReadyMix

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 uM


title: Sample_A1

city: Baronissi

first: Maria Rosaria

last: De Filippo

address: Via Allende 1

institute: University of Salerno

data_processing:
Basecalls was performed using CASAVA version 1.8
Adapter sequence was removed using  PERL script named "Adapter_trim.pl" downloaded from miRTools and held in iMir package.
To predict novel miRNAs iMir uses miRDeep2, while miRAnalyzer version 0.3 was used for the identification of known miRNAs.
Differential expression analisys of known miRNAs was done using DESEQ 1.0.6 package from R Bioconductor setting a p-value ≤ 0.05 and a fold-change ≤-1.5 and ≥1.5
Target prediction was performed using Target Scan and microRNA.org.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files represent known mature miRNAs. They were generated using miRAnalyzer version 0.3 and then filtered for readcount cut-off  ≥5.

source_name: Exponentially growing

growth_protocol: MCF-7 cells were either maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% FBS, antibiotics (100U/ml penicillin, 100mg/ml streptomycin, 250ng/ml Amfotericin-B), 50µg/ml G418 (standard growth conditions) or hormone deprived (starvation). Starvation was performed by culturing in DMEM w/o phenol red and 5% Dextran Coated Charcoal stripped serum (DCC-FBS) for 5 days, as described earlier.

extract_protocol: Total RNA was extracted from MCF-7 wt using the standard RNA Extraction method with TRI Reagent  (Sigma) method. 7.5μg of total RNA was used in a library preparation according to the Illumina TruSeq small RNA sample preparation protocol.

tag: cell line

value: breast cancer


title: Sample_A3


title: CtrlGFP

description: ChIP-seq control

source_name: ChIP-seq control

value: Epithelial tissue

value: α-GFP antibody (ab290)

value: GFP expression


title: Sample_A2


title: Sample_B2

source_name: growth-arrested


title: Sample_B1


title: Sample_B3


title: Ctrl_2

description: Wild-type animal cap, total poly-(A) RNAs, rep 2

value: Animal cap

value: wild-type


title: HadjurLab-HiC-mAST-Rad21-WT+AdCre, replicate 1

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

data_processing:
Read alignment was done by using Bowtie v1.0.0 with the parameters as "-n 3 -a -m 1 --best --strata".
Genome_build: mm9
Supplementary_files_format_and_content: The tab-delimited text file summaries alignment results for all samples.

source_name: astrocytes

growth_protocol: Cells were grown in serum-free media containing EGF+FGF (for NSCs) or BMP+FGF (for ASTs) and Laminin

extract_protocol:
Cells were treated with accutase and immediately fixed with 1% formaldehyde before proceeding with Hi-C protocol.The PE library preparations for the HiC were also done according to illuminas PE kit procedure.
Ligated material was sonicated, enriched for biotinylated ligation junctions and PE sequencing adapters were added according to Illumina standard protocols

treatment_protocol: To delete Rad21, cells were grown in OHT for 48hr (for NSCs) or AdCre for 96hr (for ASTs)

value: astrocytes

tag: genotype/variation

value: wild type


title: HadjurLab-HiC-mAST-Rad21-WT, replicate 1


title: E36_Eed_-/-_H3

city: Milan

first: Sri Ganesh

last: Jammula

institute: IFOM-IEO

description: Chromatin precipitatin using a specific antibody against H3

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie. The alignments were performed allowing zero to two mismatches and keeping only the reads that align to unique positions in the genome.
Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: mm9

source_name: E36 ES cells

growth_protocol: ES cell lines were grown on 0.1% gelatinized tissue culture dishes in GMEM supplemented with 15% fetal calf serum, 2 mM glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin, 0.1 mM non-essential aminoacids, 1 mM Na-Pyruvate, 50 μM β-mercaptoethanol-phosphate-buffered saline and Leukemia Inhibitory Factor.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the Illumina ChIPSeq Sample Prep kit (IP-102-1001) and multiplexing oligonucleotide kit (PE-400-1001).

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

tag: antibody vendor/catalog/lot


title: HadjurLab-HiC-mAST-Rad21-deleted, replicate 2

value: deleted--mutant


title: H3K27me3_ChIPSeq

value: Sorted Germinal Center B cells

value: H3K27me3 (C36B11; Cell Signaling)


title: E36_Eed_+/+_H3


title: Input DNA


title: HadjurLab-HiC-mAST-Rad21-floxed, replicate 1

value: floxed--conditional mutants


title: HadjurLab-HiC-mAST-Rad21-floxed, replicate 2


title: HadjurLab-HiC-mNSC-Rad21-WT+OHT, replicate 1

source_name: neural stem cells

value: neural stem cells


title: HadjurLab-HiC-mAST-Rad21-deleted, replicate 1


title: HadjurLab-HiC-mNSC-Rad21-floxed-G1, replicate 1


title: HadjurLab-RNASeq-mAST-Rad21-deleted-96hr, replicate 2

data_processing:
Read alignment using TopHat v2.0.4 (underleying Bowtie 2.0.0.7 and Samtools 0.1.18.0) with the parameters as "-g 1 --library-type fr-secondstrand --no-coverage-search".
Transcript assembly using Cufflinks v2.0.2 with the parameters as "--library-type fr-secondstrand".
Genome_build: mm9
Supplementary_files_format_and_content: The tab-delimited text file includes RPKM values for each samples.

source_name: astrocyte

growth_protocol: Cells were grown in serum-free media containing BMP+FGF and Laminin

extract_protocol:
RNA was extracted using qiagen RNAeasy columns. Cells were treated with accutase, washed and immediately flash frozen. RNA was prepared using standard protocols and only high quality RNA (RIN>8) was used downstream.
RNA was fragmented, PE adapters were ligated and libraries amplified according to the Illumina TruSeq protocol

treatment_protocol: To delete Rad21, cells were treated with AdCre for 72 or 96hr

value: astrocyte

tag: time point


title: HadjurLab-HiC-mNSC-Rad21-deleted, replicate 1


title: HadjurLab-HiC-mNSC-Rad21-floxed, replicate 2


title: HadjurLab-HiC-mNSC-Rad21-deleted, replicate 2


title: HadjurLab-RNASeq-mAST-Rad21-floxed-96hr, replicate 1

value: floxed--conditional mutant


title: HadjurLab-RNASeq-mAST-Rad21-deleted-72hr, replicate 2


title: HadjurLab-RNASeq-mAST-Rad21-deleted-96hr, replicate 1


title: HadjurLab-HiC-mNSC-Rad21-floxed, replicate 1


title: HadjurLab-HiC-mNSC-Rad21-WT, replicate 1


title: HadjurLab-RNASeq-mAST-Rad21-floxed-96hr, replicate 2


title: HadjurLab-RNASeq-mAST-Rad21-deleted-72hr, replicate 1


title: HadjurLab-RNASeq-mAST-Rad21-floxed-72hr, replicate 2


title: HadjurLab-RNASeq-mAST-Rad21-floxed-72hr, replicate 1


title: HadjurLab-ChIPSeq-mNSC-INPUT 1

data_processing:
Read alignment using Bowtie v1.0.0 with the parameters as "-n 3 -a -m 1 --best --strata".
Peak calling using MACS v2.0.9 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The encodePeak files were generated using MACS.

source_name: neural stem cell

extract_protocol:
DNA was extracted using phenol chlorophorm. Cells were accutased, washed and immediately fixed with 1% formaldehyde. Chromatin was sonicated and immunoprecipitated with Rad21 antibody and PGS beads.
Immunoprecipitated material was ligated to PE adapters. Libraries were amplified, checked on Bioanalyser and sequenced.

treatment_protocol: cells did not undergo any treatments

value: neural stem cell

tag: antibody


title: HadjurLab-ChIPSeq-mAST-INPUT 3


title: E14_H3

source_name: E14 ES cells


title: E14_H3K27me2

description: Chromatin precipitatin using a specific antibody against H3K27me2

value: Cell Signaling/No 9728S/Lot 1


title: E14_H3K27me1

description: Chromatin precipitatin using a specific antibody against H3K27me1

value: Cell Signaling/No 07-448/Lot 24439


title: Wil-2 root, biological replicate 2

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
Barcode for sample: TGCT
wil-2_root_br2
polyA RNA

data_processing:
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol and base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with TopHat 2.0.9, Bowtie2 2.1.0, SAMtools 0.1.19-44428cd, and Cufflinks 2.1.1 for calculation of gene expression levels (the TAIR10 annotation was used for assessing gene expression).
Genome_build: TAIR10
Supplementary_files_format_and_content: A single text file per sample with the output of Cufflinks 2.1.1. The files are tab-delimited.

organism: Arabidopsis thaliana

source_name: 10-day-old root, Wil-2

growth_protocol: Plants were germinated on plates and grown for 10 days under standard long day conditions (16 hours light 8 hours dark, at 20C).

extract_protocol:
Tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7, page 13.
Illumina non-strand-specific (a minor adaptation of the Illumina mRNA-seq methods as reported by Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7, page 13).

tag: accession

tag: tissue

value: whole root

tag: age

value: 10 days

tag: replicate

value: biological replicate 2


title: Zu-0 root, biological replicate 2

description:
Barcode for sample: TGCT
zu-0_root_br2
polyA RNA

source_name: 10-day-old root, Zu-0


title: Ws-0 root, biological replicate 2

description:
Barcode for sample: TGCT
ws-0_root_br2
polyA RNA

source_name: 10-day-old root, Ws-0


title: Zu-0 root, biological replicate 1

description:
Barcode for sample: GTAT
zu-0_root_br1
polyA RNA

value: biological replicate 1


title: Tsu-0 root, biological replicate 2

description:
Barcode for sample: GTAT
tsu-0_root_br2
polyA RNA

source_name: 10-day-old root, Tsu-0


title: Wu-0 root, biological replicate 2

description:
Barcode for sample: CATT
wu-0_root_br2
polyA RNA

source_name: 10-day-old root, Wu-0


title: HadjurLab-ChIPSeq-mAST-Rad21 IP 4

tag: antibody vendor/catalog#

value: Abcam 992


title: Wil-2 root, biological replicate 1

description:
Barcode for sample: TGCT
wil-2_root_br1
polyA RNA


title: Po-0 root, biological replicate 1

description:
Barcode for sample: TGCT
po-0_root_br1
polyA RNA

source_name: 10-day-old root, Po-0


title: Rsch-4 root, biological replicate 2

description:
Barcode for sample: ACGT
rsch-4_root_br2
polyA RNA

source_name: 10-day-old root, Rsch-4


title: Oy-0 root, biological replicate 1

description:
Barcode for sample: CATT
oy-0_root_br1
polyA RNA

source_name: 10-day-old root, Oy-0


title: Po-0 root, biological replicate 2

description:
Barcode for sample: TGCT
po-0_root_br2
polyA RNA


title: Rsch-4 root, biological replicate 1

description:
Barcode for sample: ACGT
rsch-4_root_br1
polyA RNA


title: Sf-2 root, biological replicate 1

description:
Barcode for sample: CATT
sf-2_root_br1
polyA RNA

source_name: 10-day-old root, Sf-2


title: Ler-0 root, biological replicate 2

description:
Barcode for sample: TGCT
ler-0_root_br2
polyA RNA

source_name: 10-day-old root, Ler-0


title: Oy-0 root, biological replicate 2

description:
Barcode for sample: GTAT
oy-0_root_br2
polyA RNA