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| Status |
Public on Oct 13, 2009 |
| Title |
Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r1c |
| Sample type |
SRA |
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| Source name |
Whole genome shotgun bisulfite sequencing of the IMR90 cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell_type: IMR90 cells
molecule: genomic DNA
disease: None
biomaterial_provider: ATCC
biomaterial_type: Cell Line
line: IMR90
lineage: NA
batch: Replicate 1
differentiation_stage: Fetal lung fibroblast
differentiation_method: NA
passage: 4
medium: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)
Sex: Female
experiment_type: DNA Methylation
extraction_protocol: Qiagen DNeasy mini kit, performed as per manufacturer's instructions'
extraction_protocol_type_of_sonicator: Diagenode Bioruptor
extraction_protocol_sonication_cycles: 20 cycles of: 30 seconds on high power, 2 minutes off
dna_preparation_initial_dna_qnty: 5 µg
dna_preparation_fragment_size_range: 50-500 bp
dna_preparation_adaptor_sequence: A: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B: 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT
dna_preparation_adaptor_ligation_protocol: Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina
dna_preparation_post-ligation_fragment_size_selection: Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments
bisulfite_conversion_protocol: Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol
bisulfite_conversion_percent: 99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample
library_generation_pcr_template_conc: One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction
library_generation_pcr_polymerase_type: Stratagene Pfu Turbo Cx
library_generation_pcr_thermocycling_program: 95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min
library_generation_pcr_number_cycles: 4
library_generation_pcr_f_primer_sequence: 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
library_generation_pcr_r_primer_sequence: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
library_generation_pcr_primer_conc: 25 µM
library_generation_pcr_product_isolation_protocol: Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Genomic DNA was purified from IMR90 human embryonic stem cells, sheared by sonication to 50-500 bp, ligated to methylated single-end Illumina adaptors, fragments of 140-210 bp isolated after agarose gel electrophoresis, bisulfite converted, amplified by PCR and sequenced using the Illumina Genome Analyzer II according to manufacturer's instructions
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
sample_term_id: EFO_0001196
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Library name: methylC-seq_imr90_r1c
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1114
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
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| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM432689_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r1c.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line, Library methylC-seq_imr90_r1c 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.5118
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 2
BROWSER_TRACK_NAME: IMR90 BS 1c
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Library methylC-seq_imr90_r1c EA Release 2
QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED: 17
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.47
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 88
**********************************************************************
ANALYSIS FILE NAME: GSM432689_UCSD.IMR90.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_imr90_r1a-methylC-seq_imr90_r1b-methylC-seq_imr90_r1c-methylC-seq_imr90_r2a-methylC-seq_imr90_r2b-methylC-seq_imr90_r2c.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of IMR90 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the IMR90 Cell Line combined libraries 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.5128
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 2
BROWSER_TRACK_NAME: IMR90 BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Bisulfite-Seq Combined Libraries methylC-seq_imr90_r1a EA Release 2
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.4
SPECIAL NOTE: generated from combined data in GSM432687, GSM432688, GSM432689, GSM432690, GSM432691, GSM432692 (thus .wig files on these records are identical)
**********************************************************************
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| Submission date |
Jul 23, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSD AND SALK |
| Organization name |
University of California, San Diego
|
| Street address |
Health Sciences Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92092 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
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| Relations |
| SRA |
SRX006785 |
| BioSample |
SAMN00004463 |
| Named Annotation |
GSM432689_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r1c.wig.gz |
| Named Annotation |
GSM432689_UCSD.IMR90.Bisulfite-Seq.combined.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM432689_UCSD.IMR90.Bisulfite-Seq.combined.wig.gz |
222.4 Mb |
(ftp)(http) |
WIG |
| GSM432689_UCSD.IMR90.Bisulfite-Seq.methylC-seq_imr90_r1c.wig.gz |
39.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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