|
| Status |
Public on Oct 03, 2012 |
| Title |
Bisulfite-Seq analysis of RRBS_Lib 116 and 120 derived from human chondrogenic dif cells; RRBS_Lib 116 and RRBS_Lib 120 |
| Sample type |
SRA |
| |
|
| Source name |
chondrocytes derived via in vitro culture from mesenchymal stem cells; RRBS_Lib 116 and RRBS_Lib 120
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: 79
sample common name: Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
donor_health_status: healthy
molecule: genomic DNA
disease: none
markers: NA
culture_conditions: Medium: NA; Differentiation Method: alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)
passage_if_expanded: NA
cell_type: chondrogenic dif cells
donor_ethnicity: NA
donor_sex: Unknown
biomaterial_type: Primary Cell Culture
donor_id: 57
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: 150-490
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: CL_0000138
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 116 and RRBS_Lib 120
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11778
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
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: GSM916083_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.RRBS.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS_Lib 116-RRBS_Lib 120.hg19.level.2.release.8
ANALYSIS TITLE: Methylation Proportion Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 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.13900
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: CfBMDMSC RRBS 57 16
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 57 Library RRBS_Lib 116 and RRBS_Lib 120 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,445,038
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.83
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.89
**********************************************************************
|
| |
|
| 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 |
SAMN00205685 |
| Named Annotation |
GSM916083_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.RRBS.57.wig.gz |
