|
Status |
Public on Oct 03, 2012 |
Title |
Bisulfite-Seq analysis of RRBS_Lib 267 and 277 derived from human mid frontal lobe cells; RRBS_Lib 267 and RRBS_Lib 277 |
Sample type |
SRA |
|
|
Source name |
specified brain region obtained by post-mortem collection in a longitudinal study; RRBS_Lib 267 and RRBS_Lib 277
|
Organism |
Homo sapiens |
Characteristics |
sample alias: 218 sample common name: Brain, Mid Frontal Lobe collection_method: Post-Mortem donor_health_status: no AD evident at demise molecule: genomic DNA disease: no AD evident at demise tissue_type: Mid Frontal Lobe donor_ethnicity: NA donor_sex: Male biomaterial_type: Primary Tissue tissue_depot: Brain donor_id: 149 biomaterial_provider: Rush University Medical Center donor_age: 81.0 Years bisulfite_conversion_protocol: 2x5hrs Epitect Kit dna_preparation_initial_dna_qnty: 30-300 ng extraction_protocol_sonication_cycles: NA dna_preparation_adaptor_ligation_protocol: T4 Ligase (2,000U/ul) 16C o/n dna_preparation_adaptor_sequence: Illumina TruSeq adapter library_generation_pcr_r_primer_sequence: Illumina TruSeq primer dna_preparation_post-ligation_fragment_size_selection: 120-400 bisulfite_conversion_percent: 99.5% extraction_protocol: Standard Protocol (Smith et al., Methods 48, 226-232) library_generation_pcr_primer_conc: 25uM dna_preparation_fragment_size_range: 30-280 experiment_type: DNA Methylation library_generation_pcr_thermocycling_program: Smith et al., Methods 48, 226-232 library_generation_pcr_product_isolation_protocol: SPRI Beads library_generation_pcr_f_primer_sequence: Illumina TruSeq primer pair library_generation_pcr_template_conc: NA library_generation_pcr_polymerase_type: Pfu Turbo Cx hot start library_generation_pcr_number_cycles: 11-15 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 HiSeq 2000 |
|
|
Description |
sample_term_id: UBERON_0006483 assay_term_id: OBI_0001862 nucleic_acid_term_id: SO_0000352 Design description: RRBS REMC Sequencing on Illumina Library name: RRBS_Lib 267 and RRBS_Lib 277 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11780 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448 **************** 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: GSM916085_BI.Brain_Mid_Frontal_Lobe.RRBS.149.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: RRBS_Lib 267-RRBS_Lib 277.hg19.level.2.release.8 ANALYSIS TITLE: Methylation Proportion Graphs of Brain Mid Frontal Lobe RRBS Data ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Brain Mid Frontal Lobe, Donor 149 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.13907 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 8 BROWSER_TRACK_NAME: BMFL RRBS 49 67 BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 59,549,360 NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.75 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 15 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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|
|
Submission date |
Apr 16, 2012 |
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 |
GPL11154 |
Series (1) |
GSE17312 |
BI Human Reference Epigenome Mapping Project |
|
Relations |
BioSample |
SAMN00691461 |
SRA |
SRX142817 |
Named Annotation |
GSM916085_BI.Brain_Mid_Frontal_Lobe.RRBS.149.wig.gz |