|
| Status |
Public on Jul 07, 2012 |
| Title |
Reference Epigenome: ChIP-Seq Input from Neural Progenitor Cells; renlab.Input.NPC.04.01 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.Input.NPC.04.01
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: NPC-07
sample common name: H1 Derived Neuronal Progenitor Cultured Cells
molecule: genomic DNA
disease: None
biomaterial_provider: James Thomson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: Embryonic stem cell differentiated into neural progenitor cells
differentiation_method: Publication in progress
passage: 30
medium: Publication in progress
Sex: Male
batch: NPC-7
experiment_type: ChIP-Seq Input
extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
extraction_protocol_type_of_sonicator: Biorupter
extraction_protocol_sonication_cycles: 80
chip_protocol: Input
chip_protocol_chromatin_amount: 500 micrograms
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK407
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13085
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956029_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Input.AK407.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.NPC.04.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK407, 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.16388
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: 36,184,641
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0089
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.0
IROC_PERCENTILE: 21
POISSON_SCORE: 0.0855
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
ANALYSIS FILE NAME: GSM956029_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Input.AK407.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.NPC.04.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK407, 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.16542
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: HDNP Input 07
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK407 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,184,641
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0089
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.0
IROC_PERCENTILE: 21
POISSON_SCORE: 0.0855
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
|
| |
|
| Submission date |
Jul 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSD AND SALK |
| Organization name |
University of California, San Diego
|
| Street address |
Health Sciences Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92092 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX157647 |
| BioSample |
SAMN01085431 |
| Named Annotation |
GSM956029_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Input.AK407.wig.gz |
