|
| Status |
Public on Jul 18, 2013 |
| Title |
ChIP-Seq analysis of WCE in human angular gyrus cells; DNA_Lib 708 |
| Sample type |
SRA |
| |
|
| Source name |
specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 708
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: 221
sample common name: Brain, Angular Gyrus
collection_method: Post-Mortem
donor_health_status: no AD evident at demise
molecule: genomic DNA
disease: no AD evident at demise
tissue_type: Angular gyrus
donor_ethnicity: NA
donor_sex: Male
biomaterial_type: Primary Tissue
tissue_depot: Brain
donor_id: 149
biomaterial_provider: Rush University Medical Center
donor_age: 81.0 Years
extraction_protocol_sonication_cycles: 1
chip_protocol_chromatin_amount: standard
extraction_protocol: cell/nuclei lysis
experiment_type: ChIP-Seq Input
chip_protocol: Input
extraction_protocol_type_of_sonicator: Branson
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 708
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8621
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9456
****************
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: GSM772931_BI.Brain_Angular_Gyrus.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 635-DNA_Lib 708.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Brain Angular Gyrus, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17305
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
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.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,076,686
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.0064
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0428
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM772931_BI.Brain_Angular_Gyrus.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 635-DNA_Lib 708.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Brain Angular Gyrus, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17488
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
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: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BAG Input 49 35
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 635 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,076,686
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.0064
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0428
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Aug 03, 2011 |
| Last update date |
May 15, 2019 |
| 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 |
SAMN00691469 |
| Named Annotation |
GSM772931_BI.Brain_Angular_Gyrus.Input.149.wig.gz |
| SRA |
SRX532972 |
