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| Status |
Public on Sep 13, 2012 |
| Title |
Bisulfite-Seq analysis of WGBS_Lib 10 derived from human hippocampus middle cells; WGBS_Lib 10 |
| Sample type |
SRA |
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| Source name |
specified brain region obtained by post-mortem collection in a longitudinal study; WGBS_Lib 10
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: 223
sample common name: Brain, Hippocampus Middle
collection_method: Post-Mortem
donor_health_status: no AD present
molecule: genomic DNA
disease: no AD present
tissue_type: Hippocampus Middle
donor_ethnicity: NA
donor_sex: Male
biomaterial_type: Primary Tissue
tissue_depot: Brain
donor_id: 150
biomaterial_provider: Rush University Medical Center
donor_age: 73.0 Years
bisulfite_conversion_protocol: 2x5hrs Epitect Kit
dna_preparation_initial_dna_qnty: 5 ug
extraction_protocol_sonication_cycles: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes
dna_preparation_adaptor_ligation_protocol: T4 Ligase (2,000U/ul) 16C o/n
dna_preparation_adaptor_sequence: Illumina paired end adapter
library_generation_pcr_r_primer_sequence: PE1.0
dna_preparation_post-ligation_fragment_size_selection: 270-370
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: 150-250
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: PE2.0
library_generation_pcr_template_conc: NA
library_generation_pcr_polymerase_type: Pfu Turbo Cx hot start
library_generation_pcr_number_cycles: 5-8
extraction_protocol_type_of_sonicator: Covaris S2 (TM)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_term_id: EFO_0000530
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 10
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11649
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9760
****************
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: GSM916050_BI.Brain_Hippocampus_Middle.Bisulfite-Seq.150.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 10.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Brain Hippocampus Middle Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from Brain Hippocampus Middle, Donor 150 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.13766
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 8
BROWSER_TRACK_NAME: BHM BS 50 10
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,406,121,847
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.01
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 17
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
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| Organization name |
Broad Institute
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| Street address |
-
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE17312 |
BI Human Reference Epigenome Mapping Project |
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| Relations |
| Reanalyzed by |
GSE46644 |
| BioSample |
SAMN00857851 |
| Named Annotation |
GSM916050_BI.Brain_Hippocampus_Middle.Bisulfite-Seq.150.wig.gz |
| SRA |
SRX533049 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM916050_BI.Brain_Hippocampus_Middle.Bisulfite-Seq.150.wig.gz |
206.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
| Raw data are available in SRA |
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