description:
design description: miRNA-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL04 (m09074) using Illumina HiSeq 2000
library name: m09074
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: RQS 5.2
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.7825 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: GSM1127152_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09074-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Chorion Smooth, Donor CTL04 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.19972
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,839,331
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.29
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.529

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

ANALYSIS FILE NAME: GSM1127152_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09074-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Chorion Smooth, Donor CTL04 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.19995
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 9
BROWSER_TRACK_NAME: PCS smRNA 04 74
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth smRNA-Seq Donor CTL04 Library m09074 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,839,331
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.29
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.529

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

ANALYSIS FILE NAME: GSM1127152_UCSF-UBC.Placenta_Chorion_Smooth.smRNA-Seq.CTL04.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09074-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Chorion Smooth smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Chorion Smooth, Donor CTL04 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.20018
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,839,331
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 92.29
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.529

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


status: Public on Sep 24 2014

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: miRNA-Seq analysis of placenta (villi) tissue from CTL03 (m09070) using Illumina HiSeq 2000
library name: m09070
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: RQS 4.4
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.4848 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: GSM1127155_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09070-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Villi, Donor CTL03 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.19970
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,655,458
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.95
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.672

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

ANALYSIS FILE NAME: GSM1127155_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09070-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Placenta Villi, Donor CTL03 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.19993
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 9
BROWSER_TRACK_NAME: PV smRNA 03 70
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Villi smRNA-Seq Donor CTL03 Library m09070 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,655,458
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.95
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.672

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

ANALYSIS FILE NAME: GSM1127155_UCSF-UBC.Placenta_Villi.smRNA-Seq.CTL03.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09070-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Placenta Villi smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Placenta Villi, Donor CTL03 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.20016
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,655,458
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 89.95
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.672

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

molecule: total RNA

organism: Homo sapiens

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

tag: body site

value: Placenta

tag: histological type

value: Villi tissue

tag: is tumor

value: No

value: primary tissue

value: placenta (villi) tissue


description:
design description: miRNA-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC03 (m05800) using Illumina HiSeq 2000
library name: m05800
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 7.6
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 6.224 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: GSM1127115_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05800-1.hg19.level.1.release.9
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 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.19971
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,361,269
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 98.01
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127115_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05800-1.hg19.level.2.release.9
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 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.19994
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 9
BROWSER_TRACK_NAME: NGED smRNA 03 00
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Donor HuFNSC03 Library m05800 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,361,269
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 98.01
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127115_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC03.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05800-1.hg19.level.2.tag.release.9
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 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.20017
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,361,269
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 98.01
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Brain

value: Ganglionic eminence neurosphere culture

value: primary cell culture

tag: cell type


description:
design description: miRNA-Seq analysis of foreskin fibroblast from skin03 (m05797) using Illumina HiSeq 2000
library name: m05797
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: 3.033 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: GSM1127116_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.smRNA-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05797-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.19977
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,598,112
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 91.84
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127116_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.smRNA-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05797-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.20000
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 9
BROWSER_TRACK_NAME: PFF smRNA 03 97
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells smRNA-Seq Donor skin03 Library m05797 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,598,112
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 91.84
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127116_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.smRNA-Seq.skin03.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05797-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Fibroblast Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin03 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.20023
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,598,112
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 91.84
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: NA

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

tag: Sex

value: male

value: Penis

value: Fibroblast

value: foreskin fibroblast


description:
design description: miRNA-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (m05802) using Illumina HiSeq 2000
library name: m05802
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 8.7
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.639 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: GSM1127114_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC04.m05802.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05802-1.hg19.level.1.release.9
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 HuFNSC04 Library m05802 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.19979
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,401,114
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 97.52
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127114_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC04.m05802.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05802-1.hg19.level.2.release.9
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 HuFNSC04 Library m05802 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.20002
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 9
BROWSER_TRACK_NAME: NGED smRNA 04 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Donor HuFNSC04 Library m05802 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,401,114
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 97.52
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127114_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC04.m05802.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05802-1.hg19.level.2.tag.release.9
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 HuFNSC04 Library m05802 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.20025
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,401,114
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 97.52
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: miRNA-Seq analysis of UCSF-4 embryonic stem cell line (m05795) using Illumina HiSeq 2000
library name: m05795
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 9.2
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 1.941 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: GSM1127112_UCSF-UBC.UCSF-4star.smRNA-Seq.m05795.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05795-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on the UCSF-4* Cell Line, Library m05795 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.19976
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,606,997
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 74.48
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127112_UCSF-UBC.UCSF-4star.smRNA-Seq.m05795.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05795-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4* Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from the UCSF-4* Cell Line, Library m05795 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.19999
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 9
BROWSER_TRACK_NAME: UCSF4* smRNA 95
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line smRNA-Seq Library m05795 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,606,997
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 74.48
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127112_UCSF-UBC.UCSF-4star.smRNA-Seq.m05795.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05795-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of UCSF-4* Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on the UCSF-4* Cell Line, Library m05795 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.20022
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,606,997
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 74.48
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: cell line

tag: line

value: female

value: Embryo ICM

value: Embryonic stem cell


description:
design description: miRNA-Seq analysis of foreskin keratinocyte from skin02 (m05804) using Illumina HiSeq 2000
library name: m05804
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 8.4
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.414 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: GSM1127113_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m05804-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.19983
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,858,015
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 81.41
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127113_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m05804-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.20006
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 9
BROWSER_TRACK_NAME: PFK smRNA 02 04
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin02 Library m05804 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,858,015
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 81.41
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127113_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin02.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m05804-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02 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.20029
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,858,015
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 81.41
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Keratinocyte

value: foreskin keratinocyte


title: U2AF1_Q157R

status: Public on Sep 23 2014

city: Seattle

first: Janine

middle: O

last: Ilagan

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina Casava1.82 software used for basecalling.
Reads were mapped to the UCSC hg19 (NCBI GRCh37) human genome assembly using Bowtie (Langmead et al. 2009), RSEM (Li and Dewey 2011), and TopHat (Trapnell et al. 2009)
Genome_build: hg19
Supplementary_files_format_and_content: .txt files report expression abundance measurements

source_name: erythroleukemia cells

extract_protocol:
Cells were sorted and expanded over a week, RNA were harvested using Trizol reagent. Illumino TruSeq RNA Sample Prep Kit (Cat#RS-122-2001)
RNA libraries were prepared for sequencing using standard Illumina protocols with a few modification.  After adapter ligation, AMPure XP Beads were used to select 100 – 400 bp DNA fragments by varying bead-to-library volume ratios. 0.5X beads were added to the sample library to select for fragments < 400 bp followed by 1X beads to select for > 100 bp fragments. DNA fragments were amplified using 15 cycles of PCR and separated by 2% agarose gel electrophoresis. DNA fragments (300 bp) were purified using the Qiagen MinElute gel extraction kit.

tag: cell line

value: K562 erythroleukemia cell line

tag: genotype/variation


title: U2AF1_Q157P


title: CTCF_ChIPSeq_Control

city: Duarte

first: Dustin

middle: E

last: Schones

address: 1500 Duarte Rd

department: Cancer Biology

institute: City of Hope

library_source: genomic

data_processing:
basecalling have been done by CASAVA-1.8.2
Histone modification ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 "–strata –best –n 1 –m 1 -3 10" for sequence by Illumina HiSeq 2500 because Fastqc checked last 10 bases are not good in quality, otherwise "–strata –best –n 1 –m 1"). CTCF ChIP-seq data have been aligned to human hg19 by bowtie ( version 1.0.0 –strata –best –n 1 –m 1 )
H3K4me3, H3K9ac, CTCF peaks have been called by MACS (1.4.2 version 20120305, default parameters) take correspond input sequence as control.
H3K9me2 and H3K27me3 domains have been called by RSEG (version 0.4.8-rc) with binsize 10kb and 5kb respectively
Genome_build: hg19

molecule: genomic DNA

source_name: BEAS-2B cells

growth_protocol: Immortalized human Bronchial Epithelial Cells (Beas-2B) were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro) supplemented with 1% Penicillin Streptomycin and 10% Fetal Bovine Serum (Atlanta Biologicals) at 37° C and 5 % CO2.

extract_protocol:
For ChIP, untreated and NiCl2 exposed BEAS-2B cells were crosslinked with 1% formaldehyde for 10 minutes at 25°C and sonicated to obtain 200-500 base pair fragments. ChIP was performed using ChIP grade antibodies against H3K9me2 (Abcam, ab1220), H3K27me3 (Millipore, 07-449), H3K4me3 (Millipore, 07-473), H3K9ac (Abcam, ab4441) and CTCF (Active Motif, 61311).
ChIP-Seq libraries were prepared using Illumina TruSeq ChIP sample preparation Kit (IP-202-1024), according to manufacturer’s protocol.

treatment_protocol: For exposing cells to nickel, NiCl2  (Sigma N6136) was added to the media at a concentration of 500 mM and the cells were cultured for 72 hours.

tag: treatment

tag: time point (hours)

tag: chip antibody

value: CTCF (Active Motif, 61311)


description:
design description: miRNA-Seq analysis of foreskin keratinocyte from skin03 (m05798) using Illumina HiSeq 2000
library name: m05798
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: 2.126 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: GSM1127111_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05798-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.19962
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,010,720
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 86.99
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127111_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05798-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.19985
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 9
BROWSER_TRACK_NAME: PFK smRNA 03 98
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin03 Library m05798 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,010,720
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 86.99
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127111_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.smRNA-Seq.skin03.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05798-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.20008
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,010,720
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 86.99
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: No


description:
design description: miRNA-Seq analysis of cortex neural stem and progenitor cells from HuFNSC04 (m05801) using Illumina HiSeq 2000
library name: m05801
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: 2.085 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: GSM1127110_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05801-1.hg19.level.1.release.9
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 HuFNSC04 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.19963
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,272,658
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 97.35
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127110_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05801-1.hg19.level.2.release.9
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 HuFNSC04 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.19986
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 9
BROWSER_TRACK_NAME: NCD smRNA 04 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived smRNA-Seq Donor HuFNSC04 Library m05801 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,272,658
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 97.35
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127110_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.smRNA-Seq.HuFNSC04.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05801-1.hg19.level.2.tag.release.9
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 HuFNSC04 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.20009
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,272,658
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 97.35
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Cortex neurosphere culture

value: cortex neural stem and progenitor cells


description:
design description: miRNA-Seq analysis of UCSF-4 embryonic stem cell line (m05796) using Illumina HiSeq 2000
library name: m05796
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: 2.527 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: GSM1127109_UCSF-UBC.UCSF-4star.smRNA-Seq.m05796.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05796-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on the UCSF-4* Cell Line, Library m05796 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.19978
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,211,292
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 74.05
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127109_UCSF-UBC.UCSF-4star.smRNA-Seq.m05796.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05796-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4* Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from the UCSF-4* Cell Line, Library m05796 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.20001
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 9
BROWSER_TRACK_NAME: UCSF4* smRNA 96
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line smRNA-Seq Library m05796 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,211,292
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 74.05
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127109_UCSF-UBC.UCSF-4star.smRNA-Seq.m05796.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M05796-1.hg19.level.2.tag.release.9
ANALYSIS TITLE: Sequence Tag Counts of UCSF-4* Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on the UCSF-4* Cell Line, Library m05796 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.20024
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,211,292
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 74.05
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA

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


title: U2AF1_S34Y


title: U2AF1_S34F


description:
design description: miRNA-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (m09087) using Illumina HiSeq 2000
library name: m09087
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 8.7
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 2.639 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: GSM1127153_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC04.m09087.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09087-1.hg19.level.1.release.9
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 HuFNSC04 Library m09087 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.19981
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,430,441
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 96.4
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127153_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC04.m09087.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09087-1.hg19.level.2.release.9
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 HuFNSC04 Library m09087 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.20004
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 9
BROWSER_TRACK_NAME: NGED smRNA 04 87
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived smRNA-Seq Donor HuFNSC04 Library m09087 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,430,441
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 96.4
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127153_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.smRNA-Seq.HuFNSC04.m09087.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: m09087-1.hg19.level.2.tag.release.9
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 HuFNSC04 Library m09087 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.20027
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,430,441
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 96.4
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Brain

value: Ganglionic eminence neurosphere culture


title: U2AF1_WT


title: siU2AF1

value: U2AF1 knockdown


title: siSCR

value: scramble (knockdown control)


title: WBC-2

status: Public on Sep 22 2014

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with mouse genome version mm9 and transcriptome defined by the mm9 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The mm9 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: mm9

organism: Mus musculus

source_name: single mouse white blood cell

extract_protocol:
Single cell were individually micromanipulated using an Eppendorf TransferMan NK 2 micromanipulator and ejected into PCR tubes containing RNA protective lysis buffer (10X PCR Buffer II, 25mM MgCl2, 10% NP40, 0.1 M DTT, SUPERase-In, Rnase Inhibitor, 0.5 uM UP1 Primer, 10mM dNTP and Nuclease-free water) and immediately flash frozen in liquid nitrogen. Single cells were then thawed for reverse transcription without further purification given they were individual single cells.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.

tag: tissue

value: single mouse white blood cell


title: WBC-11


title: WBC-8


title: WBC-3


title: WBC-9


title: WBC-12


title: Twi1p-bound 16-32-nt small RNAs fromGIW1 KO cells at 3 hpm

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Following the removal of the adapter sequences from the sequence reads, we removed reads containing any non-A/C/G/T bases; reads from rRNAs, tRNA, snRNAs, and the mitochondrial genome; and reads from mixed phiX174 phage DNA. Then, sequences from 26-32 nt RNAs were used as scnRNAs. Data processing was performed with custom Perl programs. The programs are available upon request.
Supplementary_files_format_and_content: Length distribution of Twi1p-bound scnRNAs

organism: Tetrahymena thermophila

source_name: Conjugating cells at 3 hpm

growth_protocol: Cells were grown in SPP medium containing 2 % proteose peptone, at 30 °C. For conjugation, growing cells (~5-7 x 105/ml) of two different mating types were washed, pre-starved (~12-24 hr) and mixed in 10 mM Tris (pH 7.5) at 30 °C.

extract_protocol:
2,000,000 cells were lysed by sonication in 1 ml lysis buffer A [20 mM Tris pH 7.5, 100mM NaCl, 2 mM MgCl2, 2 mM CaCl2, 1% Tween 20, 0.1 mM PMSF, 1x complete protease inhibitor cocktail (Roche) and 0.4 U/ml RNasin (Promega)]. Twi1p complex was immunoprecipitated using anti-Twi1p (Aronica et al., 2008) antibody, respectively. RNA was extracted by TRIzol.
RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24, , except 16- and 32-nt RNAs were used as size markers for the gel extraction steps.

tag: strain

value: GIW1 KO

tag: developmental stage

value: Conjugating cells at 3 hpm

tag: ip antibody

tag: ip antibody ref.

value: Aronica et al., 2008

tag: molecule subtype

value: 16-32-nt RNAs


title: WBC-5


title: Twi1p-bound 16-32-nt small RNAs from wild-type cells at 3 hpm

value: wild-type


title: WBC-4


title: TuMP7-10h

source_name: mouse pancreatic tumor

value: mouse pancreatic tumor


title: TuMP7-10g


title: WBC-7


title: WBC-10


title: WBC-1


title: TuMP4-10h


title: TuMP7-10c


title: TuMP7-10e


title: TuMP7-10f


title: TuMP7-10d


title: TuMP7-10b


title: TuMP4-10g


title: TuMP7-10a


title: TuMP4-10e


title: TuMP4-10f


title: TuMP4-10d


title: WBC-6


title: TuMP4-10c


title: TuMP4-10b


title: Wt, no Pi, 30min

city: rehovot

first: Noam

last: Vardi

address: herzel 235

department: molecular genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
RNA reads were aligned to the yeast strain S288C R64 reference genome using BOWTIE. Each read contains an unique molecular identidier (UMI) of 4 basepairs. Identical mRNA reads with the same UMI were discarded from the analysis to neutrilize  PCR amplification biases,
50 base pares single reads are in the R1.fastq.gz files. UMI reads are in the matching R2.fastq.gz.files. Fastq.gz.10Indices files are combined R1 and R2 files as produced by the illumina machine
Number of reads for each gene was normalized by the total number of reads and multiplied by 10^6.  Genes that obtained below ten reads were discarded from the analysis.
After alignment to the genome read number per sample was calculated samples that had less than 5*10^5 reads were discarded from the analysis in order to prevent an artificial enrichment for highly expressed genes. The expression at those time points was calculated as the mean between the 2 closest time points in the time course.
Genome_build: S288C R64
Supplementary_files_format_and_content: excel files containing the log2 number of reads in each time point.

organism: Saccharomyces cerevisiae

source_name: Wt_no Pi_30min

growth_protocol: Wild type cells were grown over night at high Phosphate medium , washed and transferred to no phosphate medium. Sample were taken every 15 minuets for 6 hours

extract_protocol:
RNA was extracted using nucleospin® 96 RNA kit Cells lysis was done in a 96 well plate by adding 450 µl of lysis buffer containing 1M sorbitol (SIGMA-ALDRICH), 100mM EDTA and 0.45µl lyticase (10IU/µl). The plate was incubated in 30°C of 30' in order to break the cell wall, then centrifuged for 10' at 2500rpm, and the soup was transfer to a new 96 well plate, that provided by the nucleospin® 96 RNA kit. From that stage on the extraction continued using this kit
cDNA was made for each sample. The cDNA of each samples were run in the Illumina HiSeq 2500

treatment_protocol: cells were harevested and frozen in liquid nitrogen

tag: strain background

value: wild type

tag: time after transfer to no-phosphate medium


title: TuMP3-10f


title: TuMP3-10b


title: TuMP2-10g


title: TuMP3-10c


title: TuMP3-100a


title: TuMP4-10a


title: TuMP3-100b


title: TuMP3-10g


title: TuMP2-10c


title: TuMP2-10e


title: TuMP2-10d


title: TuMP2-10b


title: TuMP2-100a


title: TuGMP3-7-051413

source_name: single cancer cell from the primary pancreatic tumor in a mouse


title: TuGMP3-8-051413

value: single cancer cell from the primary pancreatic tumor in a mouse


title: TuGMP3-5-051413


title: TuGMP3-6-051413


title: TuMP2-10a


title: TuGMP3-4-051413


title: TuGMP3-31-051413


title: TuGMP3-34-051413


title: TuGMP3-26-051413


title: TuGMP3-25-051413


title: TuGMP3-24-051413


title: TuMP3-10a


title: TuMP2-10f


title: TuMP3-10d


title: TuMP3-10e


title: TuMP2-100b


title: TuGMP3-20-051413


title: TuGMP3-22-051413


title: TuGMP3-2-051413


title: TuGMP3-15-051413


title: TuGMP3-14-051413


title: TuGMP3-19-051413


title: TuGMP3-17-051413


title: TuGMP3-35-051413


title: TuGMP3-16-051413


title: nb508-15

source_name: single cell from NB508 mouse pancreatic cancer cell line


title: nb508-9

value: single cell from NB508 mouse pancreatic cancer cell line


title: nb508-8


title: nb508-16


title: nb508-6


title: nb508-4


title: nb508-2


title: TuGMP3-1-051413


title: nb508-3


title: nb508-5


title: nb508-11


title: nb508-13


title: nb508-12


title: nb508-10


title: nb508-14


title: nb508-1


title: MP7-9

source_name: single cell circulating in mouse blood enriched for tumor cells


title: MP7-8

value: single cell circulating in mouse blood enriched for tumor cells


title: MP7-7


title: MP7-42


title: MP7-4


title: MP7-40


title: MP7-37


title: MP7-34


title: MP7-41


title: MP7-31


title: MP7-33


title: MP7-3


title: MP7-30


title: MP7-13


title: MP7-25


title: MP7-20


title: MP7-1


title: MP7-21


title: MP7-16


title: MP7-29


title: MP6-9


title: nb508-7


title: MP6-4


title: MP6-7


title: MP6-6


title: MP6-20


title: MP6-5


title: MP6-3


title: MP6-21


title: MP6-2


title: MP6-19


title: MP6-18


title: MP6-16


title: MP6-15


title: MP6-10


title: MP4-8


title: MP6-11


title: MP4-7


title: MP4-6


title: MP7-18


title: MP7-12


title: MP4-4


title: MP4-31


title: MP4-20


title: MP4-22


title: MP4-29


title: MP4-3


title: MP4-28


title: MP4-14


title: MP4-17


title: MP4-1


title: MP3-8


title: MP4-13


title: MP3-3


title: MP3-5


title: MP6-17


title: MP3-9


title: MP3-21


title: MP3-2


title: MP3-15


title: MP2-4


title: MP3-17


title: MP2-24


title: MP2-32


title: MP2-21


title: MP2-20


title: MP2-2


title: MP2-30


title: MP4-24


title: MP4-32


title: MP2-18


title: MP2-11


title: MP2-17


title: HP3_1

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The file platform.xls gives the genes corresponding to the row IDs in readCounts.xls.

source_name: circulating pancreas tumor cell

extract_protocol:
Blood specimens from 3 patients with PDAC were subjected to microfluidic depletion of RBCs and CD45 and CD66b-positive WBCs, leaving single CTCs and small CTC-clusters in the final product (pubmed ID 23552373). The product containing enriched cells was collected in a 35mm petri dish and viewed using a Nikon Eclipse Ti inverted fluorescent microscope. Cells of interest were identified based on intact cellular morphology and lack of labeling with anti-CD45 magnetic beads. These target cells were individually micromanipulated with a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator and ejected into PCR tubes containing RNA protective lysis buffer and immediately flash frozen in liquid nitrogen.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

tag: patient

value: circulating pancreas tumor single cell in lysis buffer


title: MEF-9

source_name: single mouse embryonic fibroblast cell

value: single mouse embryonic fibroblast cell


title: HP2_3

tag: cell type


title: HP2_2


title: HP1_2


title: MEF-8


title: MEF-7


title: MEF-6


title: HP1_3


title: MP2-1


title: MEF-5


title: MP2-26


title: MP2-36