|
| Status |
Public on Mar 26, 2014 |
| Title |
Bisulfite-Seq analysis of RRBS_Lib 361 derived from human colonic mucosa cells; RRBS_Lib 361 |
| Sample type |
SRA |
| |
|
| Source name |
Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; RRBS_Lib 361
|
| Organism |
Homo sapiens |
| Characteristics |
sra sample accession: SRS406758
collection_method: Surgery
donor_health_status: NL colonic mucosa, colon rmvd as part of abmnl Sarc
disease: NL colonic mucosa, colon rmvd as part of abmnl Sarc
tissue_type: Colonic Mucosa
donor_ethnicity: Caucasian
donor_sex: Female
biomaterial_type: Primary Tissue
tissue_depot: Colon
donor_id: 155
biomaterial_provider: MGH
donor_age: 56.0 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
|
| 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_0000317
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS_Lib 361
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.19069
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.14740
****************
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 |
Various levels of processed data files will be made available as this project proceeds.
|
| |
|
| Submission date |
Mar 25, 2014 |
| 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 |
SAMN01997267 |
