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Sample GSM670069 Query DataSets for GSM670069
Status Public on Mar 31, 2011
Title Bisulfite-Seq analysis of RRBS596 derived from human Fib27 cells; RRBS596
Sample type SRA
 
Source name human primary fibroblasts; RRBS596
Organism Homo sapiens
Characteristics sample alias: hFib_27_p7
sample common name: Primary Fibroblast Cell Line
lineage: mesoderm
medium: 10% KOSR (Invitrogen)
molecule: genomic DNA
disease: none
passage: 7
line: Fib27
differentiation_method: NA
batch: NA
biomaterial_type: Cell Line
differentiation_stage: undifferentiated
Sex: Female
biomaterial_provider: Harvard University
bisulfite_conversion_protocol: 2x5hrs Epitect Kit
dna_preparation_initial_dna_qnty: 20 ng
extraction_protocol_sonication_cycles: NA
dna_preparation_adaptor_ligation_protocol: T4 Ligase (2,000U/ul) 16C o/n
dna_preparation_adaptor_sequence: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT
library_generation_pcr_r_primer_sequence: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
dna_preparation_post-ligation_fragment_size_selection: 180-360/120-240
bisulfite_conversion_percent: >99%
extraction_protocol: Standard Protocol (Smith et al., Methods 48, 226-232)
library_generation_pcr_primer_conc: 25uM
dna_preparation_fragment_size_range: 90-270/30-150
experiment_type: DNA Methylation
library_generation_pcr_thermocycling_program: Smith et al., Methods 48, 226-232
library_generation_pcr_product_isolation_protocol: Gel size selection
library_generation_pcr_f_primer_sequence: 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
library_generation_pcr_template_conc: NA
library_generation_pcr_polymerase_type: Pfu Turbo Cx hot start
library_generation_pcr_number_cycles: 15
extraction_protocol_type_of_sonicator: NA
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: Smith et al., Methods 48, 226-232
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina Genome Analyzer IIx
 
Description sample_term_id: CL_0000057
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS596
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6099
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6166
****************
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: GSM670069_BI.Primary_Fibroblast.RRBS.RRBS595-596.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS595-RRBS596.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of Primary Fibroblast Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the Primary Fibroblast Cell Line, Libraries RRBS595-596 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.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6843
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: PF RRBS 95
BROWSER_TRACK_DESCRIPTION: BI Primary Fibroblast Cell Line RRBS Libraries RRBS595-596 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.64

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

 
Submission date Feb 07, 2011
Last update date May 15, 2019
Contact name BROAD INSTITUTE
E-mail(s) rharris1@bcm.tmc.edu
Organization name Broad Institute
Street address -
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL10999
Series (1)
GSE25247 BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS in human subject
Relations
SRA SRX041115
BioSample SAMN00205696
Named Annotation GSM670069_BI.Primary_Fibroblast.RRBS.RRBS595-596.wig.gz

Supplementary file Size Download File type/resource
GSM670069_BI.Primary_Fibroblast.RRBS.RRBS595-596.wig.gz 12.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data not provided for this record
Processed data provided as supplementary file
Raw data are available in SRA

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