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| Status |
Public on Mar 26, 2014 |
| Title |
Bisulfite-Seq analysis of RRBS_Lib 362 derived from human stomach mucosa cells; RRBS_Lib 362 |
| Sample type |
SRA |
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| Source name |
Primary stomach mucosal tissue; RRBS_Lib 362
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| Organism |
Homo sapiens |
| Characteristics |
sra sample accession: SRS255288
collection_method: Surgery
donor_health_status: NK stomach mucosa, stomach rmvd as part of pancr. CA
disease: NK stomach mucosa, stomach rmvd as part of pancr. CA
tissue_type: Stomach Mucosa
donor_ethnicity: Caucasian
donor_sex: Male
biomaterial_type: Primary Tissue
tissue_depot: Stomach
donor_id: 157
biomaterial_provider: MGH
donor_age: 59.0 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: 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
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Smith et al., Methods 48, 226-232
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_term_id: UBERON_0001199
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 362
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19070
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
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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 |
Various levels of processed data files will be made available as this project proceeds.
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| Submission date |
Mar 25, 2014 |
| Last update date |
Jan 29, 2015 |
| 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 |
| BioSample |
SAMN00691466 |
| Supplementary data files not provided |
| Raw data provided as supplementary file |
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