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Sample GSM432689 Query DataSets for GSM432689
Status Public on Oct 13, 2009
Title Whole genome shotgun bisulfite sequencing of the IMR90 cell line; methylC-seq_imr90_r1c
Sample type SRA
 
Source name Whole genome shotgun bisulfite sequencing of the IMR90 cell line
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.
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
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer II
 
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
****************
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
 
Platform ID GPL9115
Series (1)
GSE16256 UCSD Human Reference Epigenome Mapping Project
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 SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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