title: Whole Genome Shotgun Bisulfite Sequencing of Sigmoid Colon Cells from Human STL003; methylC-seq_STL003SG-01a

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Sigmoid Colon Cells from Human STL003
Library name: methylC-seq_STL003SG-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13795
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11872
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010989_UCSD.Sigmoid_Colon.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003SG-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Sigmoid Colon Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Sigmoid Colon, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18760
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SC BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,398,174,906
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.26
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

source_name: Sigmoid Colon tissue; methylC-seq_STL003SG-01a

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets 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 100-150 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: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl 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.

value: Sigmoid Colon

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian

value: DNA Methylation

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 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: Stratagene Pfu Turbo Cx

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

value: 25 µM


title: miRNA_P7_metastasis

status: Public on Sep 18 2013

type: SRA

city: Berlin

first: Michal

middle: Ruth

last: Schweiger

address: Ihnestrasse 63-73

department: Lehrach

country: Germany

institute: Max Planck Institute For Molecular Genetics

description: total RNA, small RNA fraction

library_source: transcriptomic

data_processing:
Illumina Casava1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped hg19 whole genome using bwa 0.5.9-r16 with default parameters for the small RNA fraction experiments (Sample 1 – 24) and TopHat v1.3.3 with parameters -u -N --max-bundle-length 350000000 --max-bundle-frags 50000000 and using Ensembl v64 transcripts as template for all total RNA Seq experiments (Sample 25 – 36)
to obtain the .MirBase15.stat files mapped reads where counted for each miRNA if a read overlapped the miRNAs coordinates from miRbase 15 db by at least one base
to obtain the .geneExp.txt files, cuffdiff was called on the tophat pipeline output using the parameters  --max-bundle-frags 10000000 -L Benign,Tumor,Metastase -N -r
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each miRNA or gene

molecule: total RNA

organism: Homo sapiens

source_name: metastasis biopsy, lymph node

extract_protocol:
RNA was harvested using Trizol reagent including a DNase digestion step with the RNase-free DNase set from Qiagen. For RNA sequencing rRNA substraction was performed with the RiboMinus™ Human/Mouse Transcriptome Isolation Kit SmallRNA.
cDNA library preparation, and sequencing was performed by Illumina’s DGE smallRNA sample and Illumina’s RNA-Seq prep kit following the manufacturer’s instructions with 2 ug of total RNA for the construction of mRNA sequencing libraries and 10 ug total RNA for the preparation of small RNA sequencing libraries.

tag: subject

tag: tissue

value: metastasis biopsy, lymph node

tag: Sex

value: female

tag: disease state

value: metastasis

tag: age

tag: microsatellite status

value: MSS


title: Whole Genome Shotgun Bisulfite Sequencing of Right Ventricle Cells from Human STL003; methylC-seq_STL003RV-01a

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_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 STL003
Library name: methylC-seq_STL003RV-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13794
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM1010988_UCSD.Right_Ventricle.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003RV-01a-methylC-seq_STL003RV-01b-methylC-seq_STL003RV-01d-methylC-seq_STL003RV-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Right Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Right Ventricle, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18750
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: RV BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,080,014,270
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.03
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010988, GSM1059433, GSM1120337, GSM1120336 (thus .wig files on these records are identical)

molecule: genomic DNA

source_name: Right Ventricle tissue; methylC-seq_STL003RV-01a

tag: sample alias

tag: sample common name

value: Right Ventricle

tag: molecule

value: genomic DNA

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian

value: DNA Methylation

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

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT


title: mRNA_P3_tumor

description: total RNA

source_name: colorectal biopsy, colon ascendens

value: colorectal biopsy, colon ascendens

value: male

value: tumor

value: MSI


title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL001; methylC-seq_STL001SB-01c

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL001
Library name: methylC-seq_STL001SB-01c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15839
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1120321_UCSD.Small_Intestine.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001SB-01a-methylC-seq_STL001SB-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Small Intestine Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Small Intestine, Donor STL001 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18761
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SI BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,419,291,562
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.12
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM983646, GSM1120321 (thus .wig files on these records are identical)

source_name: Small Intestine tissue; methylC-seq_STL001SB-01c

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: Small Intestine

tag: sra sample accession

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

value: Caucasian and African American

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: 25 µM


title: miRNA_P6_metastasis

description: total RNA, small RNA fraction

source_name: metastasis biopsy, liver

value: metastasis biopsy, liver

value: female

value: metastasis

value: MSS


title: miRNA_P6_normal

description: total RNA, small RNA fraction

value: colorectal biopsy, colon ascendens

value: benign


title: miRNA_P6_tumor

description: total RNA, small RNA fraction

value: tumor


title: Whole Genome Shotgun Bisulfite Sequencing of Gastric Cells from Human STL003; methylC-seq_STL003GA-01a

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 STL003
Library name: methylC-seq_STL003GA-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13790
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010984_UCSD.Gastric.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003GA-01a-methylC-seq_STL003GA-01d-methylC-seq_STL003GA-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Gastric Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Gastric, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18747
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Gastric BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Gastric Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,235,431,773
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010984, GSM1120333, GSM1120332 (thus .wig files on these records are identical)

value: Gastric

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian

value: DNA Methylation

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

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

value: Stratagene Pfu Turbo Cx

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


title: Whole Genome Shotgun Bisulfite Sequencing of Fat Cells from Human STL003; methylC-seq_STL003FT-01a

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 STL003
Library name: methylC-seq_STL003FT-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13789
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11859
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010983_UCSD.Adipose_Tissue.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003FT-01d-methylC-seq_STL003FT-01a-methylC-seq_STL003FT-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Adipose Tissue Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Adipose Tissue, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18763
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AT BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Adipose Tissue Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 666,743,193
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120331, GSM1010983, GSM1120330 (thus .wig files on these records are identical)

value: Adipose Tissue

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: 25 µM


title: Whole Genome Shotgun Bisulfite Sequencing of Adrenal Cells from Human STL003; methylC-seq_STL003AD-01a

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 STL003
Library name: methylC-seq_STL003AD-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13787
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010981_UCSD.Adrenal_Gland.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AD-01a-methylC-seq_STL003AD-01c-methylC-seq_STL003AD-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Adrenal Gland Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Adrenal Gland, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18751
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AG BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,008,110,717
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010981, GSM1120324, GSM1120325 (thus .wig files on these records are identical)

source_name: Adrenal Gland tissue; methylC-seq_STL003AD-01a

value: Adrenal Gland

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian


title: Whole Genome Shotgun Bisulfite Sequencing of Thymus Cells from Human STL001; methylC-seq_STL001TH-01a

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Thymus Cells from Human STL001
Library name: methylC-seq_STL001TH-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13785
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
****************

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

ANALYSIS FILE NAME: GSM1010979_UCSD.Thymus.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001TH-01a-methylC-seq_STL001TH-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Thymus Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Thymus, Donor STL001 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18749
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Thymus BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Thymus Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,247,539,549
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.28
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010979, GSM1120322 (thus .wig files on these records are identical)

source_name: Thymus tissue; methylC-seq_STL001TH-01a

value: Thymus

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

value: Caucasian and African American

value: DNA Methylation

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

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

value: Stratagene Pfu Turbo Cx

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


title: miRNA_P5_tumor

description: total RNA, small RNA fraction

source_name: colorectal biopsy, colon

value: colorectal biopsy, colon

value: female

value: tumor

value: MSI


title: miRNA_P5_metastasis

description: total RNA, small RNA fraction

value: metastasis biopsy, lymph node

value: metastasis


title: Whole Genome Shotgun Bisulfite Sequencing of Ovary Cells from Human STL002; methylC-seq_STL002OV-01a

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Ovary Cells from Human STL002
Library name: methylC-seq_STL002OV-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13786
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010980_UCSD.Ovary.Bisulfite-Seq.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL002OV-01a-methylC-seq_STL002OV-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Ovary Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Ovary, Donor STL002 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18755
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Ovary BS 02
BROWSER_TRACK_DESCRIPTION: UCSD Ovary Bisulfite-Seq Donor STL002 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,339,301,372
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1010980, GSM1120323 (thus .wig files on these records are identical)

source_name: Ovary tissue; methylC-seq_STL002OV-01a

value: Ovary

value: genomic DNA

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: 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: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001; methylC-seq_STL001LV-01a

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL001
Library name: methylC-seq_STL001LV-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13784
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010978_UCSD.Left_Ventricle.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001LV-01a-methylC-seq_STL001LV-01c-methylC-seq_STL001LV-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Left Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Left Ventricle, Donor STL001 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18757
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: LV BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,277,811,198
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.03
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

SPECIAL NOTE: generated from combined data in GSM1010978, GSM1120319, GSM1120320 (thus .wig files on these records are identical)

source_name: Left Ventricle tissue; methylC-seq_STL001LV-01a

value: Left Ventricle

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: Standard fragment express, 6 cycles

value: 5 µg

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

value: Stratagene Pfu Turbo Cx

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


title: miRNA_P7_tumor

description: total RNA, small RNA fraction

value: colorectal biopsy, colon ascendens

value: female

value: tumor

value: MSS


title: miRNA_P4_metastasis

description: total RNA, small RNA fraction

value: metastasis biopsy, liver

value: metastasis


title: miRNA_P4_tumor

description: total RNA, small RNA fraction

source_name: colorectal biopsy, rectum/sigma

value: colorectal biopsy, rectum/sigma


title: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003; methylC-seq_STL003RA-01a

description:
sample_term_id: UBERON_0002078
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Right Atrium Cells from Human STL003
Library name: methylC-seq_STL003RA-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13793
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
****************

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

ANALYSIS FILE NAME: GSM1010987_UCSD.Right_Atrium.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003RA-01d-methylC-seq_STL003RA-01a-methylC-seq_STL003RA-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Right Atrium Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Right Atrium, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18762
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: RA BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Atrium Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,302,897,809
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.18
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120335, GSM1010987, GSM1120334 (thus .wig files on these records are identical)

source_name: Right Atrium tissue; methylC-seq_STL003RA-01a

value: Right Atrium

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian

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: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: miRNA_P4_normal

description: total RNA, small RNA fraction

value: female

value: benign

value: MSS


title: Whole Genome Shotgun Bisulfite Sequencing of Psoas Cells from Human STL003; methylC-seq_STL003PO-01a

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 STL003
Library name: methylC-seq_STL003PO-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13792
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010986_UCSD.Psoas_Muscle.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003PO-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Psoas Muscle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Psoas Muscle, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18748
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PM BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,493,677,815
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.04
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Psoas Muscle tissue; methylC-seq_STL003PO-01a

value: Psoas Muscle

value: genomic DNA

value: DNA Methylation

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

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

value: Stratagene Pfu Turbo Cx

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


title: miRNA_P3_metastasis

description: total RNA, small RNA fraction

value: metastasis biopsy, liver

value: male

value: metastasis

value: MSI


title: miRNA_P2_tumor

description: total RNA, small RNA fraction

source_name: colorectal biopsy, coecum

value: colorectal biopsy, coecum

value: tumor


title: miRNA_P3_normal

description: total RNA, small RNA fraction

value: colorectal biopsy, colon ascendens

value: benign


title: miRNA_P2_metastasis

description: total RNA, small RNA fraction

value: MSS


title: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL003; methylC-seq_STL003LV-01a

description:
sample_term_id: UBERON_0002084
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Left Ventricle Cells from Human STL003
Library name: methylC-seq_STL003LV-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13686
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11885
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983650_UCSD.Left_Ventricle.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003LV-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Left Ventricle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Left Ventricle, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18759
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: LV BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,415,935,850
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.01
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Left Ventricle tissue; methylC-seq_STL003LV-01a

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets 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 100-150 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: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 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: Left Ventricle

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian

value: DNA Methylation

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: 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 Lung Cells from Human STL002; methylC-seq_STL002LG-01a

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 STL002
Library name: methylC-seq_STL002LG-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13683
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12247
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983647_UCSD.Lung.Bisulfite-Seq.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL002LG-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Lung Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Lung, Donor STL002 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18764
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Lung BS 02
BROWSER_TRACK_DESCRIPTION: UCSD Lung Bisulfite-Seq Donor STL002 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,523,404,047
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Lung tissue; methylC-seq_STL002LG-01a

value: Lung

value: iron deficiency, bipolar

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

value: Female

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

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

value: Stratagene Pfu Turbo Cx


title: miRNA_P1_tumor

description: total RNA, small RNA fraction

source_name: colorectal biopsy, sigma

value: colorectal biopsy, sigma

value: male

value: tumor

value: MSS


title: Whole Genome Shotgun Bisulfite Sequencing of Esophagus Cells from Human STL003; methylC-seq_STL003EG-01a

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 STL003
Library name: methylC-seq_STL003EG-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13685
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11826
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983649_UCSD.Esophagus.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003EG-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Esophagus Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Esophagus, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18753
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Esophagus BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,343,065,144
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.22
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Esophagus

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian

value: DNA Methylation

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


title: optimized ligation for mouse heart miRNAs

city: Boulder

first: Zhaojie

last: Zhang

state: CO

address: 2300 Arapahoe Ave

institute: University of Colorado at Boulder

description: no barcode

data_processing:
adaptor removal with self-written python scripts
miRNA mapping with BLAST, parameters: -m 8
BLAST results parsing and miRNA counts with self-written python scripts
Genome_build: Mouse miRNA sequences from Mirbase.org
Supplementary_files_format_and_content: .xls file containing counts assigned to each miRNA

organism: Mus musculus

source_name: mouse heart

growth_protocol: Mice were housed in the Mouse Facility under standard conditions.

extract_protocol:
RNA was extracted from cells with the use of Trizol according to the Trizol manufacturer's instructions. Synthetic miRNAs were chemically synthesized by ThermoFisher according to published mouse miRNA sequences.
An improved Ligation-based small RNA cloning protocol based on the Illumina protocol for small RNA cloning. Two adaptors (3' adaptor and 5' adaptor) were ligated to small RNAs followed by RT-PCR and gel-purification. Then purified PCR products were sent out for sequencing.

value: mouse heart

tag: strain


title: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL001; methylC-seq_STL001SB-01a

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Small Bowel Cells from Human STL001
Library name: methylC-seq_STL001SB-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13682
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983646_UCSD.Small_Intestine.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001SB-01a-methylC-seq_STL001SB-01c.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Small Intestine Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Small Intestine, Donor STL001 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18761
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SI BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,419,291,562
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.12
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM983646, GSM1120321 (thus .wig files on these records are identical)

source_name: Small Intestine tissue; methylC-seq_STL001SB-01a

value: Small Intestine

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

value: Caucasian and African American

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

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

value: Stratagene Pfu Turbo Cx

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole Genome Shotgun Bisulfite Sequencing of Pancreas Cells from Human STL003; methylC-seq_STL003PA-01a

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 STL003
Library name: methylC-seq_STL003PA-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13687
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11847
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983651_UCSD.Pancreas.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003PA-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Pancreas Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Pancreas, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18754
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Pancreas BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,365,896,804
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.18
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Pancreas

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian

value: DNA Methylation

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

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


title: miRNA_P1_metastasis

description: total RNA, small RNA fraction

data_processing:
Illumina Casava1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped hg19 whole genome using bwa 0.5.9-r16 with default parameters for the small RNA fraction experiments (Sample 1 – 24) and TopHat v1.3.3 with parameters -u -N --max-bundle-length 350000000 --max-bundle-frags 50000000 and using Ensembl v64 transcripts as template for all total RNA Seq experiments (Sample 25 – 36)
to obtain the .MirBase15.stat files mapped reads where counted for each miRNA if a read overlapped the miRNAs coordinates from miRbase 15 db by at least one base
to obtain the .geneExp.txt files, cuffdiff was called on the tophat pipeline output using the parameters  --max-bundle-frags 10000000 -L Benign,Tumor,Metastase -N -r
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each miRNA or gene

value: metastasis biopsy, liver

value: male

value: metastasis

value: MSS


title: Whole Genome Shotgun Bisulfite Sequencing of Aorta Cells from Human STL003; methylC-seq_STL003AO-01a

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 STL003
Library name: methylC-seq_STL003AO-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13684
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983648_UCSD.Aorta.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003AO-01a-methylC-seq_STL003AO-01f-methylC-seq_STL003AO-01e-methylC-seq_STL003AO-01c-methylC-seq_STL003AO-01d.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Aorta Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Aorta, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18752
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Aorta BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,368,332,289
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.14
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM983648, GSM1120329, GSM1120328, GSM1120326, GSM1120327 (thus .wig files on these records are identical)

source_name: Aorta tissue; methylC-seq_STL003AO-01a

value: Aorta

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

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

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: Stratagene Pfu Turbo Cx

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


title: miRNA_P1_normal

description: total RNA, small RNA fraction

value: colorectal biopsy, sigma

value: benign


title: Whole Genome Shotgun Bisulfite Sequencing of Sigmoid Colon Cells from Human STL001; methylC-seq_STL001SG-01a

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole Genome Shotgun Bisulfite Sequencing of Sigmoid Colon Cells from Human STL001
Library name: methylC-seq_STL001SG-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13681
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983645_UCSD.Sigmoid_Colon.Bisulfite-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL001SG-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Sigmoid Colon Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Sigmoid Colon, Donor STL001 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18758
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SC BS 01
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Bisulfite-Seq Donor STL001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,542,229,729
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.16
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

source_name: Sigmoid Colon tissue; methylC-seq_STL001SG-01a

value: Sigmoid Colon

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

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

value: 25 µM


title: miRNA_P5_normal

description: total RNA, small RNA fraction

value: colorectal biopsy, colon

value: female

value: MSI


title: Whole Genome Shotgun Bisulfite Sequencing of Spleen Cells from Human STL003; methylC-seq_STL003SX-01a

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 STL003
Library name: methylC-seq_STL003SX-01a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13688
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11852
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM983652_UCSD.Spleen.Bisulfite-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_STL003SX-01a.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of Spleen Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Spleen, Donor STL003 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18756
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Spleen BS 03
BROWSER_TRACK_DESCRIPTION: UCSD Spleen Bisulfite-Seq Donor STL003 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,270,611,083
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Spleen tissue; methylC-seq_STL003SX-01a

value: Spleen

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

value: Caucasian

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

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

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

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: Stratagene Pfu Turbo Cx

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


title: optimized ligation for synthetic miRs with worm total RNA, rep2

description: no barcode

source_name: chemically synthesized miRNAs

tag: sample type

value: synthetic miRNAs


title: optimized ligation for synthetic miRs with worm total RNA, rep1

description: no barcode


title: optimized ligation for synthetic miRs with let-7 gradient, rep2

description: no barcode


title: optimized ligation for mouse brain miRNAs

description: no barcode

source_name: mouse brain

value: mouse brain


title: optimized ligation for synthetic miRs, rep2

description: no barcode


title: optimized ligation for synthetic miRs with let-7 gradient, rep1

description: no barcode


title: optimized ligation for synthetic miRs, rep 1

description: no barcode


title: use of splint ligation in cloning synthetic miRs

description: This sample consists of 2 replicates. One with barcode('CGTCAA') and one with barcode('CTGATT') after the miRNAs' reads for demultiplexing.


title: miRNA_P3_tumor

description: total RNA, small RNA fraction

source_name: colorectal biopsy, colon ascendens

value: colorectal biopsy, colon ascendens

value: male

value: tumor

value: MSI


title: synthetic miRs cloned with the previous method

description:
The previous method" means "Illumina protocol for small RNA cloning, version1.5
barcode ('CAG') in the 5' end of the reads before the miRNAs' reads for demultiplexing


title: mouse hair follicle matrix miRs cloned with the previous method

description: The previous method" means "Illumina protocol for small RNA cloning, version1.5

source_name: mouse hair follicles

value: hair follicles


title: use of Thermostable ligase in cloning synthetic miRs

description: This sample consists of 2 replicates. One with barcode('TAGCTA') and one with barcode('TGATGT') after the miRNAs' reads for demultiplexing.


title: A37G total RNA 0.1 ppm Se

status: Public on Sep 17 2013

city: Salt Lake City

first: Michael

middle: T

last: Howard

state: UT

department: Human Genetics

institute: University of Utah

description: mRNA

data_processing:
base calling was done with the standard Illumina  pipeline
Sequence reads were trimmed for adaptor sequences, and aligned using bowtie (alignment parameters -m1 -v2 -a --best --strata) to a mm9 RefSeq mRNA database in which each transcript with multiple isoforms was reduced to a single entry corresponding to the longest isoform. For Selenoprotein analysis, a data base of selenoprotein mRNAs was created from RefSeq entries and ribosome protected or mRNA sequences were aligned individually using the same bowtie parameters.
Reads per kilobase per million mapped reads (RPKM for total RNA RPFKM for ribosome protected fragments) in each experiment were determined for entire mRNAs, for coding sequences (excluding the first 15 and last 3 codons). For selenoproteins, coding sequences upstream of the UGA-Sec codon and downstream of the UGA-Sec codon were also examined and assigned RPKM values.
Genome_build: RefSeq July 2008 release
Supplementary_files_format_and_content: RPKM

source_name: Liver

extract_protocol:
Livers were excised, flash frozen in liquid nitrogen, and homogenized in the presence of cycloheximide using a bead mill. Ribo-Seq samples were treated with Rnase 1 and monosomes isolated by ultracentrifugation. Ribosome protected fragments and total mRNA were isolated using Trizol reagent.
TruSeq small RNA Sample Kit

tag: transgene

value: Contains 20 copies TrspA37G

value: 3 weeks

tag: treatment

value: 6 week diet 0.1 ppm selenium


title: Wt total RNA 2.0 ppm Se

description: mRNA

value: FVB/N

value: 6 week diet 2.0 ppm selenium


title: A37G total RNA 2.0 ppm Se

description: mRNA


title: A37G total RNA 0 ppm Se

description: mRNA

value: 6 week diet 0 ppm selenium


title: Wt total RNA 0.1 ppm Se

description: mRNA


title: A37G Ribo-Seq 2.0 ppm Se

description: Ribosome protected mRNA


title: Wt total RNA 0 ppm Se

description: mRNA


title: Wt Ribo-Seq 0 ppm Se

description: Ribosome protected mRNA


title: Wt Ribo-Seq 0.1 ppm Se

description: Ribosome protected mRNA


title: Wt Ribo-Seq 2.0 ppm Se

description: Ribosome protected mRNA


title: Activated B-cells from individual B5, day 16

city: Baltimore

first: Kasper

middle: Daniel

last: Hansen

state: Maryland

address: 615 N Wolfe St. E3527

department: Biostatistics

institute: Johns Hopkins

data_processing:
Basecalls performed using CASAVA 1.8.1
Reads were aligned to bisulfite-treated genome with the Bsmooth pipeline, version 0.4.5-beta, with --bscpg option
The Bsmooth alignment pipeline used Bowtie 2.0.0-beta8 with --ignore-quals option
Only summarized data with a quality score greater than 20 was used. Data was processed using the Bsmooth function from the bsseq package from Bioconductor. Each sample was processed twice, one for small scale smoothing (used to find small DMRs, parameters were h = 1000, ns = 70) and once for large scale smoothing (used to find large hypomethylated blocks, parameters were h=20000,ns=500)
Only CpGs which had at least 2 samples with a coverage of 2 or more in each of the following 3 group (B1,B2,B3 activation), (B1,B2,B3 resting) and (B1,B2,B3 transformed)
Genome_build: human NCBI genome build 37, lambda phage (gi|9626243|ref|NC_001416.1|) and EBV virus (gi|86261677|emb|AJ507799.2|)
Supplementary_files_format_and_content: Rows are CpGs, columns are as follows: chr (chromosome) and pos (position) is genomic location. Cov is the number of reads covering the CpG and M is the number of reads covering the CpGs, supporting methylation. smallSmooth and largeSmooth are smoothed values for small and large scale smoothing.

source_name: Activated B-cells_day 16

extract_protocol:
Epicentre Masterpure DNA isolation kit
Bisulfite converted Illumina TruSeq DNA library

treatment_protocol: Cells were either resting, CD40 activated or EBV transformed

tag: individual/donor id

tag: sample group

value: CD40 activation

tag: time point

value: day16 following CD40 activation


title: EBV transformed B-cells from Individual B4, 3 weeks post infection

source_name: EBV transformed B-cells_3 weeks post infection

value: EBV transformation into LCL

value: week3 following EBV infection


title: Activated B-cells from individual B4, week 3

source_name: Activated B-cells_week 3

value: week3 following CD40 activation


title: Activated B-cells from individual B5, week 3


title: Activated B-cells from individual B4, day 16


title: miRNA_P2_normal

description: total RNA, small RNA fraction

source_name: colorectal biopsy, coecum

tag: subject

tag: tissue

value: colorectal biopsy, coecum

value: benign

value: MSS


title: EBV transformed B-cells from Individual B1

source_name: EBV transformed B-cells

value: week6 following EBV infection


title: Resting B-cells from individual B3

source_name: Resting B-cells

value: Resting


title: Activated B-cells from individual B3

source_name: Activated B-cells

value: day6 following CD40 activation


title: Resting B-cells from individual B1


title: Activated B-cells from individual B1


title: A37G Ribo-Seq 0.1 ppm Se

description: Ribosome protected mRNA

value: Contains 20 copies TrspA37G


title: EBV transformed B-cells from Individual B3


title: Salmonella-infected control_rep2

status: Public on Sep 16 2013

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

country: Netherlands

institute: Institute of Biology, Leiden University

description: Sample 7

data_processing:
Image analysis and base calling was done by the Illumina HCS version 1.15.1
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Zv9_63) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Danio_rerio.Zv9.63.dna.toplevel downloaded from http://www.ensembl.org/info/data/ftp/index.html
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos were snap frozen in liquid nitrogen and kept at -80°C. Total RNA was isolated using the miRNeasy Mini kit (Qiagen) with an on-column DNA purification with RNase Free DNase set (Qiagen). RNA quality of samples for RNAseq analysis was checked with an Agilent Bioanalyzer 2100 using the RNA 6000 Nano series Kit (Agilent, Santa Clara, CA, USA). All samples had a RNA integrity value (RIN) of 10.
A total of 3 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 2 x 50 nucleotides.

treatment_protocol: Morpholino oligonucleotides (GeneTools) were diluted to the desired concentration in 1× Danieau buffer (58 mM NaCl, 0.7 mM KCl, 0.4 mM MgSO4, 0.6 mM Ca(NO3)2, 5.0 mM HEPES; pH 7.6) containing 1% phenol red (Sigma-Aldrich) and approximately 1 nl was injected at the 1-2 cell stage using a Femtojet injector (Eppendorf). Morpholinos for miR-146a (5’ACCATCTATGGAATTCAGTTCTCAG3’) and miR-146b (5’GACACCCTTGGAATTCAGTTCTCAA3’) target the miRNA guide strand and were used in combination, at a concentration of 0.75 mM for each morpholino. As a control the standard control morpholino from GeneTools was used as previously described (Kanwal et al., 2013, J. Immunol. 190:1631-45. At 28 h postfertilization (hpf), embryos were injected with S. typhimurium SL1027 or mock-injected with PBS (phosphate buffered saline) into the caudal vein close to the urogenital opening and pools of 20–40 embryos were collected at 8 hours post infection (hpi). Two independent experiments were performed for RNAseq analysis of biological duplicates.

tag: tag

value: zebrafish embryo

tag: injected with

value: control morpholino at 1-cell stage

tag: genotype/variation

value: wild type (control)

tag: infected with

value: S. typhimurium at 28 hpf

value: 8 hpi


title: Salmonella-infected miR-146 knockdown_rep2

description: Sample 8

source_name: zebrafish embryo_Salmonella-infected miR-146 knockdown

value: miR-146a and miR-146b morpholino at 1-cell stage

value: miR-146 knockdown


title: uninfected control_rep2

description: Sample 5

source_name: zebrafish embryo_uninfected control

value: PBS (mock) at 28 hpf


title: Salmonella-infected miR-146 knockdown_rep1

description: Sample 4


title: uninfected miR-146 knockdown_rep2

description: Sample 6

source_name: zebrafish embryo_uninfected miR-146 knockdown


title: EBV transformed B-cells from Individual B4, 16 days post infection

source_name: EBV transformed B-cells_16 days post infection

value: EBV transformation into LCL

value: day16 following CD40 activation


title: Salmonella-infected control_rep1

description: Sample 3


title: uninfected miR-146 knockdown_rep1

description: Sample 2


title: RNAseq L3 KLE2 homo Rep3

city: New York

first: Sevinc

last: Ercan

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

data_processing:
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.0.2 using default parameters supplying gene annotations.
supplementary_files_format_and_content: FPKM text file contains the FPKM values for each gene for each replicate.
Genome_build: WS220

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole worms

extract_protocol:
RNA was extracted by freeze cracking embryos by freezein gin liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA was cleaned up through Qiagen RNeasy column.
mRNA was purified from ~0.5-1 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212

treatment_protocol: ~500 heterozygote and homozygote early L3 worms were hand picked and resuspended in 1 ml of Trizol and frozen at -80C.

tag: developmental stage


title: RNAseq L3 KLE2 homo Rep1


title: RNAseq L3 KLE2 homo Rep2


title: uninfected control_rep1

description: Sample 1


title: Input N2 L3 Rep1 ChIPSeq

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 0.12.7 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.141 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.141 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks per subunits, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
To get final peak sets representing condensinI-IDC and condensinII, we used a sliding window across the genome. Each base pair covered by at least two of the three non-SMC subunits (DPY-26, DPY-28, and CAPG-1 for condensinI-IDC, CAPG-2, HCP-6, and KLE-2 for condensinII) was included in the final peak set.
supplementary_files_format_and_content: Wig files were generated using MACS version 1.4.141, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position.
supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.141 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Genome_build: WS220

growth_protocol: N2 L3 worms were obtained by growing synchronous culture in liquid media.

extract_protocol:
Frozen Larva were broken into pieces using cryo-mixer mill, and crosslinked with 1% formaldehyde for 10 minutes. The worms were collected by centrifugation, were washed with and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of larva extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Larva were frozen in to "popcorn" by dripping into liquid nitrogen, and stored at -80C until extract preparation.

tag: antibody

value: None (input)


title: KLE2 N2 L3 Rep4 ChIPSeq

tag: matching input

value: KLE-2 SDQ3898 Rabbit polyclonal is against the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: Input N2 L3 Rep2 ChIPSeq


title: Resting B-cells from individual B2


title: EBV transformed B-cells from Individual B2


title: RNAseq L3 KLE2 het Rep2


title: KLE2 N2 L3 Rep3 ChIPSeq


title: KLE2 N2 L3 Rep2 ChIPSeq

value: KLE-2 SDQ3942 Rabbit polyclonal is against the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: RNAseq L3 KLE2 het Rep3


title: KLE2 N2 L3 Rep1 ChIPSeq


title: RNAseq L3 KLE2 het Rep1


title: PQN85 TY1072 Rep3 ChIPSeq

description:
Sample name: PQN85_TY1072_MxEmb_Rep3
PQN85_TY1072_Mxemb_average_var.wig.gz
PQN85_TY1072_Mxemb_peaks.bed

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 0.12.7 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.141 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.141 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks per subunits, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
To get final peak sets representing condensinI-IDC and condensinII, we used a sliding window across the genome. Each base pair covered by at least two of the three non-SMC subunits (DPY-26, DPY-28, and CAPG-1 for condensinI-IDC, CAPG-2, HCP-6, and KLE-2 for condensinII) was included in the final peak set.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.0.2 using default parameters supplying gene annotations.
Genome_build: WS220
Supplementary_files_format_and_content: Wig files were generated using MACS version 1.4.141, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position.
Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.141 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Supplementary_files_format_and_content: FPKM text file contains the FPKM values for each gene for each replicate.

growth_protocol: Mixed stage embryos (wild type N2) were isolated by bleaching gravid adults grown in liquid or plates at 20C temperature.

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

value: embryo

value: PQN-85 SDQ4481 Rabbit polyclonal is against the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: Input Rep20 ChIPSeq

description: Sample name: Input_TY1072_MxEmb_Rep20


title: KLE2 TY1072 Rep2 ChIPSeq

description:
Sample name: KLE2_TY1072_MxEmb_Rep2
KLE2_TY1072_Mxemb_average_var.wig.gz
KLE2_TY1072_MxEmb_peaks.bed


title: KLE2 TY1072 Rep1 ChIPSeq

description:
Sample name: KLE2_TY1072_MxEmb_Rep1
KLE2_TY1072_Mxemb_average_var.wig.gz
KLE2_TY1072_MxEmb_peaks.bed


title: Input Rep19 ChIPSeq

description: Sample name: Input_TY1072_MxEmb_Rep19


title: Input Rep7 ChIPSeq


title: Input Rep6 ChIPSeq


title: Input Rep5 ChIPSeq


title: RNAseq Rep4

extract_protocol:
RNA was extracted by freeze cracking embryos five times, and by Trizol isolation according to the manufacturer's (Invitrogen) protocol. The remaining RNA was cleaned up through Qiagen RNeasy column.
mRNA was purified from 5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212

treatment_protocol: Packed embryos were resuspended in 10V of Trizol and frozen at -80C.


title: Input Rep17 ChIPSeq


title: RNAseq Rep5


title: Input Rep4 ChIPSeq


title: Input Rep3 ChIPSeq


title: RNAseq Rep3


title: RNAseq Rep2


title: Input Rep1 ChIPSeq


title: Input Rep2 ChIPSeq


title: Input Rep18 ChIPSeq


title: Input Rep16 ChIPSeq


title: PQN85 Rep2 ChIPSeq

description:
PQN85_N2_Mxemb_average.wig
PQN85_N2_Mxemb_peaks.bed


title: MIX1 Rep5 ChIPSeq

description:
MIX1_N2_Mxemb_average.wig
MIX1_N2_MxEmb_peaks.bed

value: MIX-1 SDQ3892 Rabbit polyclonal is against the antigen MHIKSIHLDGFKSYQKHTDILDFSPTFNAITGYNGSGKSNILDSICFIMGINKLDNIRAKSMHELISHGGTKAIVQVRFDNTDKRCSPFGMEHLDEIVVQ May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: PQN85 Rep1 ChIPSeq


title: Input Rep15 ChIPSeq


title: MIX1 Rep4 ChIPSeq


title: Input Rep14 ChIPSeq


title: MIX1 Rep3 ChIPSeq

value: MIX-1 SDQ4107 Rabbit polyclonal is against the antigen MHIKSIHLDGFKSYQKHTDILDFSPTFNAITGYNGSGKSNILDSICFIMGINKLDNIRAKSMHELISHGGTKAIVQVRFDNTDKRCSPFGMEHLDEIVVQ. May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"


title: Input Rep13 ChIPSeq


title: MIX1 Rep2 ChIPSeq


title: Input Rep12 ChIPSeq


title: KLE2 Rep2 ChIPSeq

description:
KLE2_N2_Mxemb_average.wig
KLE2_N2_Mxemb_peaks.bed


title: Input Rep11 ChIPSeq


title: MIX1 Rep1 ChIPSeq

value: MIX-1 JL0004 Rabbit polyclonal to 837-1244 aa. (PMID:19853451) is against the antigen 837-1244 aa


title: KLE2 Rep1 ChIPSeq


title: Input Rep9 ChIPSeq


title: Input Rep8 ChIPSeq


title: HTZ Rep1 ChIPSeq

value: HTZ1 BK00001 mouse ascites polyclonal against HTZ-1 specific C-terminal peptide N-PGKPGAPGQGPQ-C (PMID:18787694)


title: RNAseq Rep1

extract_protocol:
RNA was extracted by freeze cracking embryos by freezein gin liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA RNA was cleaned up through Qiagen RNeasy column.
mRNA was purified from 5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212


title: IgG Rep2 ChIPSeq

description:
IgG_N2_Mxemb_average.wig
IgG_N2_Mxemb_peaks.bed

value: Rabbit IgG, Abcam antibody catalog number ab46540