description:
design description: miRNA-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (m01580) using Illumina Genome Analyzer IIx
library name: m01580
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9.3
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.08 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM751287_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01580-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 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.9536
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,926,129
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 87.55
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

ANALYSIS FILE NAME: GSM751287_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01580-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9551
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,926,129
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 87.55
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

ANALYSIS FILE NAME: GSM751287_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01580-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9566
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NGED smRNA 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Donor HuFNSC02 Library M01580-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,926,129
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 87.55
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

value: Ganglionic eminence neurosphere culture

value: primary cell culture


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in hESC H9 Cells; renlab.H3K14ac.hESC.H9.01.01

status: Public on Jul 06 2011

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K14ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK380
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7643
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM752964_UCSD.H9.H3K14ac.SK380.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H9.01.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K14ac ChIP-Seq on H9 Cell Line, Library SK380, 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.10471
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,208,595
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.06
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.16
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.85
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM752964_UCSD.H9.H3K14ac.SK380.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H9.01.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K14ac ChIP-Seq read mappings from the H9 Cell Line, Library SK380, 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.10544
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 5
BROWSER_TRACK_NAME: H9 H3K14ac 80
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K14ac Library SK380 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,208,595
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.06
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.16
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.85
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

molecule: genomic DNA

organism: Homo sapiens

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K14ac.hESC.H9.01.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

value: H9 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

tag: medium

value: mTeSER

tag: Sex

value: Female

tag: batch

value: Histone H3K14ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: miRNA-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (m01586) using Illumina Genome Analyzer IIx
library name: m01586
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN n/a
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.032 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM751284_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01586-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Brain Germinal Matrix, Donor HuFGM02 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.9535
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,086,312
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 65.99
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.892

**********************************************************************

ANALYSIS FILE NAME: GSM751284_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01586-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Brain Germinal Matrix, Donor HuFGM02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9550
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,086,312
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 65.99
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.892

**********************************************************************

ANALYSIS FILE NAME: GSM751284_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01586-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9565
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: BGM smRNA 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix smRNA-Seq Donor HuFGM02 Library M01586-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,086,312
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 65.99
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.892

**********************************************************************

molecule: total RNA

extract_protocol: library construction protocol: Refer to document 'miRNA3 - Plate Format miRNA Library Construction' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

tag: body site

value: Brain

tag: histological type

value: Germinal matrix tissue

tag: is tumor

value: No

value: primary tissue

value: brain (germinal matrix) tissue


description:
design description: miRNA-Seq analysis of cortex neural stem and progenitor cells from HuFNSC01 (m01577) using Illumina Genome Analyzer IIx
library name: m01577
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9.5
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.44 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM751282_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01577-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.9541
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,528,237
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.33
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.999

**********************************************************************

ANALYSIS FILE NAME: GSM751282_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC01.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01577-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9556
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,528,237
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.33
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.999

**********************************************************************

ANALYSIS FILE NAME: GSM751282_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01577-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9571
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NCD smRNA 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived smRNA-Seq Donor HuFNSC01 Library M01577-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,528,237
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.33
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.999

**********************************************************************

value: female

value: Cortex neurosphere culture

value: primary cell culture

tag: cell type

value: cortex neural stem and progenitor cells


description:
design description: miRNA-Seq analysis of cortex neural stem and progenitor cells from HuFNSC03 (m01587) using Illumina Genome Analyzer IIx
library name: m01587
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 8
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 3.432 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM751288_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01587-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC03 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.9528
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,180,987
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.78
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

ANALYSIS FILE NAME: GSM751288_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC03.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01587-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC03 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9543
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,180,987
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.78
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

ANALYSIS FILE NAME: GSM751288_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01587-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC03 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9558
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NCD smRNA 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived smRNA-Seq Donor HuFNSC03 Library M01587-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,180,987
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.78
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************


description:
design description: miRNA-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC01 (m01578) using Illumina Genome Analyzer IIx
library name: m01578
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9.1
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 4.072 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM751281_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01578-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.9531
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 3,918,576
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.78
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

ANALYSIS FILE NAME: GSM751281_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC01.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01578-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9546
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 3,918,576
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.78
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

ANALYSIS FILE NAME: GSM751281_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01578-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9561
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NGED smRNA 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Donor HuFNSC01 Library M01578-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 3,918,576
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 88.78
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.998

**********************************************************************

value: Ganglionic eminence neurosphere culture


description:
design description: miRNA-Seq analysis of cortex neural stem and progenitor cells from HuFNSC02 (m01579) using Illumina Genome Analyzer IIx
library name: m01579
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9.1
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 3.232 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM751280_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01579-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 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.9542
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,270,388
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.9
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.999

**********************************************************************

ANALYSIS FILE NAME: GSM751280_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01579-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9557
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,270,388
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.9
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.999

**********************************************************************

ANALYSIS FILE NAME: GSM751280_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01579-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9572
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: NCD smRNA 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived smRNA-Seq Donor HuFNSC02 Library M01579-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,270,388
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.9
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.999

**********************************************************************


description:
design description: miRNA-Seq analysis of brain (germinal matrix) tissue from HuFGM01 (m01576) using Illumina Genome Analyzer IIx
library name: m01576
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 6.1
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.552 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM751283_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01576-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Brain Germinal Matrix, Donor HuFGM01 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.9530
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,496,398
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 59.64
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.892

**********************************************************************

ANALYSIS FILE NAME: GSM751283_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM01.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01576-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Brain Germinal Matrix, Donor HuFGM01 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9545
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,496,398
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 59.64
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.892

**********************************************************************

ANALYSIS FILE NAME: GSM751283_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01576-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Brain Germinal Matrix, Donor HuFGM01 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9560
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: BGM smRNA 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix smRNA-Seq Donor HuFGM01 Library M01576-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,496,398
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 59.64
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: 0.892

**********************************************************************


title: G4A2-Notch1

city: Boston

first: James

last: Zou

state: MA

address: 185 Cambridge St.

institute: Harvard University

description: Notch1 Chromatin IP

data_processing: Allignment: human sequence reads were mapped to hg18 and mouse sequence reads were mapped to mm9 using Illumina Genome Analyzer Pipeline allowing 2 mismatches

organism: Mus musculus

source_name: G4A2: Notch1 Chromatin IP

growth_protocol: CUTLL1, T6E, and G4A2 cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, penicillin and streptomycin; T6E cell medium was additionally supplemented with 1 mM sodium pyruvate and 5Î¼M 2-mercaptoethanol.

extract_protocol: Cells were cross-linked with 1% Formaldehyde for 10 minutes. Cell DNA was sonicated to an average size of ~500bp. Antibodies were incubated with lysates overnight at 40C. libraries were constructed per the Illumnia ChIP DNA library preparation kit.

tag: cell line

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte

tag: antibody

value: Rabbit anti Notch1


title: G4A2-RBPJ

description: RBPJ Chromatin IP

source_name: G4A2: RBPJ Chromatin IP

value: Rabbit anti RBPJ


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in BMP4 Mesendoderm Cells; renlab.H3K4me2.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK164
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7819
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
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: GSM752982_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K4me2.AK164.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.BMP4M.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK164, 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.10463
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,509,838
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.41
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.46
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.52

**********************************************************************

ANALYSIS FILE NAME: GSM752982_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K4me2.AK164.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.BMP4M.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK164, 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.10536
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 5
BROWSER_TRACK_NAME: HBDM H3K4me2 64
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K4me2 Library AK164 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,509,838
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.41
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.46
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.52

**********************************************************************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K4me2.BMP4M.02.01

tag: sample alias

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 20 and 30

value: Male

value: Histone H3K4me2

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: G4A2-Input

description: input

source_name: G4A2: input

value: T lymphoblastic leukemia/lymphoma


title: T6E-Input

description: Input

source_name: T6E: Input

value: T lymphocyte


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me1 in IMR90 Cells; renlab.H3K9me1.IMR90.02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me1 in IMR90 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: SK12
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7802
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2019
****************
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: GSM752987_UCSD.IMR90.H3K9me1.SK12.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me1.IMR90.02.01-renlab.H3K9me1.IMR90.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me1 ChIP-Seq on IMR90 Cell Line, Library SK12, 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.10477
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,349,476
NUMBER_OF_H3K9me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.19
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.31
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.93
IROC_PERCENTILE: 100
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

ANALYSIS FILE NAME: GSM752987_UCSD.IMR90.H3K9me1.SK12.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me1.IMR90.02.01-renlab.H3K9me1.IMR90.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK12, 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.10550
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 5
BROWSER_TRACK_NAME: IMR90 H3K9me1 12
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9me1 Library SK12 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,349,476
NUMBER_OF_H3K9me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.19
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.31
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.93
IROC_PERCENTILE: 100
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K9me1.IMR90.02.01

tag: sample common name

value: IMR90 Cell Line

value: ATCC

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female

value: Histone H3K9me1

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in hESC H9 Cells; renlab.H3K4ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK379
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7641
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
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: GSM752976_UCSD.H9.H3K4ac.SK379.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC.H9.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on H9 Cell Line, Library SK379, 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.10452
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,464,100
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.04
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.75
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.83

**********************************************************************

ANALYSIS FILE NAME: GSM752976_UCSD.H9.H3K4ac.SK379.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC.H9.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the H9 Cell Line, Library SK379, 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.10525
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 5
BROWSER_TRACK_NAME: H9 H3K4ac 79
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4ac Library SK379 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,464,100
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.04
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.75
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.83

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4ac.hESC.H9.02.01

value: H9 Cell Line

tag: molecule

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Histone H3K4ac

value: Upstate


title: T6E-Notch1

description: Notch1 Chromatin IP

source_name: T6E: Notch1 Chromatin IP

tag: disease

value: T lymphoblastic leukemia/lymphoma

value: Rabbit anti Notch1


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me1 in IMR90 Cells; renlab.H3K9me1.IMR90.01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me1 in IMR90 Cells. Sequencing was done on the Illumina Genome Analyzer II platform.
Library name: LL237
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7798
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM752986_UCSD.IMR90.H3K9me1.LL237.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me1.IMR90.01.01-renlab.H3K9me1.IMR90.01.01-renlab.H3K9me1.IMR90.01.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me1 ChIP-Seq on IMR90 Cell Line, Library LL237, 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.10491
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,433,504
NUMBER_OF_H3K9me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.19
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.34
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.92
IROC_PERCENTILE: 50
POISSON_SCORE: 0.45
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

ANALYSIS FILE NAME: GSM752986_UCSD.IMR90.H3K9me1.LL237.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me1.IMR90.01.01-renlab.H3K9me1.IMR90.01.01-renlab.H3K9me1.IMR90.01.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL237, 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.10564
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 5
BROWSER_TRACK_NAME: IMR90 H3K9me1 37
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9me1 Library LL237 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,433,504
NUMBER_OF_H3K9me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.19
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.34
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.92
IROC_PERCENTILE: 50
POISSON_SCORE: 0.45
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K9me1.IMR90.01.01

value: IMR90 Cell Line

tag: line

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in iPS 19.11 Cells; renlab.H3K36me3.iPS-19.11.02.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK472
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7781
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7659
****************
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: GSM752974_UCSD.iPS_DF_19.11.H3K36me3.SK472.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.iPS-19.11.02.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on iPS DF 19.11 Cell Line, Library SK472, 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.10479
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,651,514
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.12
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.26
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.91
IROC_PERCENTILE: 41
POISSON_SCORE: 0.43
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM752974_UCSD.iPS_DF_19.11.H3K36me3.SK472.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.iPS-19.11.02.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the iPS DF 19.11 Cell Line, Library SK472, 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.10552
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 5
BROWSER_TRACK_NAME: iD19.11 H3K36me3 72
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Histone H3K36me3 Library SK472 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,651,514
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.12
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.26
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.91
IROC_PERCENTILE: 41
POISSON_SCORE: 0.43
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K36me3.iPS-19.11.02.01

value: iPS DF 19.11 Cell Line

value: James Thomson Laboratory

tag: lineage

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: mTeSR

value: Male

value: Histone H3K36me3


title: T6E-RBPJ

description: RBPJ Chromatin IP

source_name: T6E: RBPJ Chromatin IP

value: T lymphocyte

value: Rabbit anti RBPJ


title: H3K9me3_G1EER4_ChIPSeq_rep2

status: Public on Jul 05 2011

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description: Chromatin IP against H3K9me3

data_processing: Alignment: Sequencing reads were mapped to the mouse genome (mm8 assembly) using the program Efficient Local Alignment of Nucleotide Data (ELAND) or Bowtie.

source_name: G1E-ER4+E2 cells

growth_protocol: G1E and G1E-ER4 cells were grown in IMDM media with 15% fetal calf serum 2U/ml erythropoietin (Amgenâs EpoGen) and 50ng/ml stem cell factor. Erythroid cells were obtained by enriching fresh E14.5 fetal liver preps for Ter119-positive cells using an anti-Ter119 antibody coupled to magnetic beads (StemCell EasySep Kit #18554).

extract_protocol:
For ChIP-seq, ChIP DNA or input DNA was amplified by Illumina ChIP-Seq library preparation kit. To prepare the sequencing libraries, the ChIP DNA fragments were repaired to generate blunt ends, with a single A nucleotide adding to each end. Double-stranded Illumina adaptors were ligated to both ends of the fragments. Ligation products were amplified by 18 cycles of PCR, and the PCR products between 200 and 400 bp were gel purified. The quality of the library was evaluated by qPCR and bio-analyzer to make sure it meets the requirements by Illumina.
For DNase-seq, nuclei isolated from G1E and G1E-ER4+E2 cells were lightly digested with DNaseI to expose regions hypersensitive to the enzyme. Digested ends of the DNA were ligated to a biotinylated and phosphorylated linker and enriched on streptavidin-coated DynaI beads. This was followed by MmeI restriction enzyme digestion, which cuts 20 bases downstream of the recognition site contained within the biotinylated linker. A second linker was ligated to the MmeI cut sites and ligation-mediated polymerase chain reaction performed prior to being sequenced.

treatment_protocol: G1E-ER4 cells were induced in the presence of 10^(-8) mol/L (beta)-estradiol for 24 hours.

tag: developmental stage/cell type

value: recapitulated erythroid differentiation after induction by estradiol treatment for 24hr.


title: ChIPinput_Ter119+_Seq

description: Chromatin IP input

source_name: Ter119+ cells

tag: strain

value: Mouse fetal liver cells with the late erythroid differentiation marker Ter119; primary erythroblasts

tag: chip antibody target


title: TAL1_Ter119+_ChIPSeq_rep1

description: Chromatin IP against TAL1

value: Santa Cruz Biotechnology

value: unknown


title: GATA1_Ter119+_ChIPSeq_rep1

description: Chromatin IP against GATA1


title: H3K9me3_G1EER4_ChIPSeq_rep1

description: Chromatin IP against H3K9me3


title: H3K27me3_G1EER4_ChIPSeq_rep1

description: Chromatin IP against H3K27me3


title: H3K4me3_G1EER4_ChIPSeq_rep1

description: Chromatin IP against H3K4me3


title: GATA2_G1EER4_ChIPSeq_rep2

description: Chromatin IP against GATA2


title: GATA2_G1EER4_ChIPSeq_rep1

description: Chromatin IP against GATA2


title: TAL1_G1EER4_ChIPSeq_rep1

description: Chromatin IP against TAL1


title: H3K27me3_G1E_ChIPSeq_rep2

description: Chromatin IP against H3K27me3

source_name: G1E cells

tag: genotype/variation

value: Erythroid committed, immature progenitor murine cell line

value: Millipore


title: H3K27me3_G1E_ChIPSeq_rep1

description: Chromatin IP against H3K27me3


title: H3K4me1_G1E_ChIPSeq_rep1

description: Chromatin IP against H3K4me1

value: Abcam


title: H3K4me3_G1E_ChIPSeq_rep1

description: Chromatin IP against H3K4me3


title: GATA2_G1E_ChIPSeq_rep1

description: Chromatin IP against GATA2


title: GATA2_G1E_ChIPSeq_rep2

description: Chromatin IP against GATA2


title: TAL1_G1E_ChIPSeq_rep1

description: Chromatin IP against TAL1


title: TAL1_G1E_ChIPSeq_rep2

description: Chromatin IP against TAL1


title: ChIPinput_G1E_Seq

description: Chromatin IP input


title: DNase_G1EER4_seq

description: DNase-seq for DNase hypersensitive sites


title: DNase_G1E_seq


title: GATA1_Ter119+_ChIPSeq_rep2

description: Chromatin IP against GATA1


title: H3K27me3_G1EER4_ChIPSeq_rep2

description: Chromatin IP against H3K27me3


title: GATA1_G1EER4_ChIPSeq_rep2

description: Chromatin IP against GATA1


title: H3K4me1_G1EER4_ChIPSeq_rep2

description: Chromatin IP against H3K4me1


title: TAL1_Ter119+_ChIPSeq_rep2

description: Chromatin IP against TAL1


title: H3K9me3_G1E_ChIPSeq_rep2

description: Chromatin IP against H3K9me3


title: TAL1_G1EER4_ChIPSeq_rep2

description: Chromatin IP against TAL1


title: H3K4me3_G1EER4_ChIPSeq_rep2

description: Chromatin IP against H3K4me3


title: H3K9me3_G1E_ChIPSeq_rep1

description: Chromatin IP against H3K9me3


title: H3K4me1_G1E_ChIPSeq_rep2

description: Chromatin IP against H3K4me1


description:
design description: miRNA-Seq analysis of fetal brain tissue from HuFNSC02 (m01582) using Illumina Genome Analyzer IIx
library name: m01582
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN n/a
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 0.904 ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM751285_UCSF-UBC.Fetal_Brain.smRNA-Seq.HuFNSC02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01582-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Fetal Brain smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Fetal Brain, Donor HuFNSC02 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.9539
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,559,789
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.88
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.996

**********************************************************************

ANALYSIS FILE NAME: GSM751285_UCSF-UBC.Fetal_Brain.smRNA-Seq.HuFNSC02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01582-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Fetal Brain smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Fetal Brain, Donor HuFNSC02 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9554
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,559,789
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.88
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.996

**********************************************************************

ANALYSIS FILE NAME: GSM751285_UCSF-UBC.Fetal_Brain.smRNA-Seq.HuFNSC02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M01582-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Fetal Brain, Donor HuFNSC02 were processed into density graphs of raw signal representing the aligned read density. If a read maps to more than one location, the density of that read at a specific location is calculated as 1/(number of mappings).
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.9569
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FB smRNA 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Fetal Brain smRNA-Seq Donor HuFNSC02 Library M01582-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,559,789
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 90.88
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.996

**********************************************************************

tag: submitted sample id

tag: Sex

value: female

value: Brain

value: Brain tissue

value: No

value: primary tissue

value: fetal brain tissue


title: H3K4me1_G1EER4_ChIPSeq_rep1

description: Chromatin IP against H3K4me1


title: hMADS3 AD0 (1) Adapter B

status: Public on Jul 04 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: hMADS3 AD0

data_processing:
AB Small RNA pipeline v5.0 matching versus human mirbase v16, normalization to 1.000.000 miRNAs count in each sample
processed data: RNA pipeline v5.0 count file

source_name: hMADS3 AD0

growth_protocol: Undifferentiated cells were maintained in DMEM (low glucose) containing 10% FBS

extract_protocol:
SREK kit by Applied Biosystems (life technologies)
Libraries were constructed either with adapter set A (for sequencing microRNA from the 5' to 3' end) or with adapter set B (for sequencing microRNA from the 3' to the 5' end). The sequence of adaptor A and B sequenced in the reads are the same: CGCCTTGGCCGTACAGCAG (330201030313112312 in colorspace).
Libraries were size selected on acrylamide gels (110 to 140 nucleotides)

treatment_protocol: Differentiation medium was composed of: DMEM/Ham’s F12 media supplemented with 10 µg/ml transferrin, 0.86 µM insulin, 0.2 nM triiodothyronine, 1 µM dexamethasone, 100 µM isobutyl-methylxanthine and 1 µM rosiglitazone. Three days after first exposure, the medium was changed and dexamethasone and isobutyl-methylxanthine were omitted.

value: hMADS

tag: amount (ng)

tag: concentration sample (ng/µl)

tag: library concentration (pm)

tag: rin number


title: hMADS3 AD3 (2) Adapter A

description: hMADS3 AD3

source_name: hMADS3 AD3

tag: cell type


title: hMADS3 AD3 (1) Adapter B

description: hMADS3 AD3


title: hMADS3 AD8 (2) Adapter A

description: hMADS3 AD8

source_name: hMADS3 AD8


title: hMADS3 AD3 (1) Adapter A

description: hMADS3 AD3


title: hMADS3 AD8 (1) Adapter B

description: hMADS3 AD8


title: hMADS3 AD3 (2) Adapter B

description: hMADS3 AD3


title: Human_H

status: Public on Jul 01 2011

city: Huntsville

first: Jason

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

description: Reduced Representation Bisulfite Sequencing (MspI digest)

data_processing: To analyze the sequence data, a reference genome is created that contains only the 36 base pairs adjacent to every MspI site and every C in those sequences is changed to T. A converted sequence read file is then created by changing each C in the original sequence reads to a T. The converted sequence reads are aligned to the converted reference genome, and only reads that map uniquely to the reference genome are kept. Once reads are aligned the percent methylation is calculated for each CpG using the original sequence reads. The percent methylation and number of reads is reported for each CpG.

source_name: Leukocyte

extract_protocol: RRBS library construction starts with MspI digestion of genomic DNA , which cuts at every CCGG regardless of methylation status. Klenow exo- DNA Polymerase is then used to fill in the recessed end of the genomic DNA and add an adenosine as a 3prime overhang. Next, a methylated version of the Illumina paired-end adapters is ligated onto the DNA. Adapter ligated genomic DNA fragments between 105 and 185 basepairs are selected using agarose gel electrophoresis and Qiagen Qiaquick Gel Extraction Kit. The selected adapter-ligated fragments are treated with sodium bisulfite using the Zymo Research EZ DNA Methylation Gold Kit, which converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Bisulfite treated DNA is amplified in a final PCR reaction which has been optimized to uniformly amplify diverse fragment sizes and sequence contexts in the same reaction. During this final PCR reaction uracils are copied as thymines resulting in a thymine in the PCR products wherever an unmethylated cytosine existed in the genomic DNA.

tag: family relationship

value: Unrelated


title: hMADS3 AD0 (2) Adapter B

description: hMADS3 AD0


title: Human_F

value: Son


title: hMADS3 AD0 (2) Adapter A

description: hMADS3 AD0


title: Human_G


title: hMADS3 AD0 (1) Adapter A

description: hMADS3 AD0


title: hMADS3 AD8 (1) Adapter A

description: hMADS3 AD8


title: hMADS3 AD8 (2) Adapter B

description: hMADS3 AD8


title: Human_E


title: Human_D

value: Father


title: Human_C

value: Mother


title: H3K4me3_G1E_ChIPSeq_rep2

description: Chromatin IP against H3K4me3


title: Human_B

value: Paternal Grandmother


title: Human_A

value: Maternal Grandmother


title: RBPJ ChIP-seq 2

description:
RBPJ Chromatin IP
Lymphoblastoid cell line

data_processing: Allignment: Sequence reads were mapped to hg.18 using Illumina Genome Analyzer Pipeline allowing 2 mismatches

source_name: IB4 cells

growth_protocol: IB4 LCLs,were grown in RPMI media (Invitrogen) supplemented with 10% fetal plex (Gemini), glutamine. The cells were maintained at 3x105/ml

extract_protocol: IB4 cells were cross-linked with 1% Formaldehyde at 370C for 10 minutes. Cell DNA was sonicated to an average size of ~500bp. Rabbit anti EBNA2 or RBPJ were incubated with lysates overnight at 40C. Salmon sperm DNA protein A agarose beads (Millipore) were added to the lysate and incubated at 40C for 1 hour. After extensive wash, DNA was eluted from the agarose beads, crossliking reversed at 650C for 4 hours, and DNA further purified using PCR columns (Qiagen). ChIP-seq DNA sample preparation kits  were used to prepared ChIP-seq libraries (Illumina).

tag: cell line

value: EBV immotalized lymphocyte

tag: antibody

value: Rabbit anti RBPJ


title: Input 1

description:
Lymphoblastoid cell line
Input


title: RBPJ ChIP-seq 1


title: Input 2

description:
Lymphoblastoid cell line
Input


title: EBNA2 ChIP-seq 1

description:
EBNA2 Chromatin IP
Lymphoblastoid cell line

value: Rabbit anti EBNA2


title: EBNA2 ChIP-seq 2