|
| Status |
Public on Oct 03, 2012 |
| Title |
Bisulfite-Seq analysis of RRBS_Lib 140 and RRBS_Lib 136 derived from human BM-MSC cells; RRBS_Lib 140 and RRBS_Lib 136 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; RRBS_Lib 140 and RRBS_Lib 136
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: 77
sample common name: Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
donor_health_status: healthy
molecule: genomic DNA
disease: none
markers: NA
culture_conditions: Medium: DMEM/FBS; Differentiation Method: adherence
passage_if_expanded: NA
cell_type: BM-MSC
donor_ethnicity: NA
donor_sex: Unknown
biomaterial_type: Primary Cell Culture
donor_id: 59
biomaterial_provider: Rikshospitalet University Hospital
donor_age: NA
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: 150-400
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: EFO_0000586
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 140 and RRBS_Lib 136
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11786
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5948
****************
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: GSM916091_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.RRBS.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 140-RRBS_Lib 136.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 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.13908
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: BMDMSC RRBS 59 36
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 136 and RRBS_Lib 140 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 128,444,247
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.78
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.79
**********************************************************************
|
| |
|
| Submission date |
Apr 16, 2012 |
| Last update date |
Jan 29, 2015 |
| 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 |
SAMN00205684 |
| Named Annotation |
GSM916091_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.RRBS.59.wig.gz |
