description:
design description: miRNA-Seq analysis of breast progenitor enriched cell from RM080 (m00740) using Illumina Genome Analyzer IIx
library name: m00740
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A 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: GSM669588_UCSF-UBC.Breast_Stem_Cells.smRNA-Seq.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00740-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Breast Stem Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast Stem Cells, Donor RM080 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.9540
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,613,874
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 46.42
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669588_UCSF-UBC.Breast_Stem_Cells.smRNA-Seq.RM080.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00740-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Breast Stem Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast Stem Cells, Donor RM080 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.9555
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,613,874
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 46.42
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669588_UCSF-UBC.Breast_Stem_Cells.smRNA-Seq.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00740-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Breast Stem Cells, Donor RM080 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.9570
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: BSC smRNA 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Stem Cells smRNA-Seq Donor RM080 Library M00740-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,613,874
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 46.42
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

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/)

value: Progenitor enriched cell

value: No

value: breast progenitor enriched cell


status: Public on Sep 02 2011

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 breast myoepithelial cell from RM080 (m00739) using Illumina Genome Analyzer IIx
library name: m00739
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A 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: GSM669587_UCSF-UBC.Breast_Myoepithelial_Cells.smRNA-Seq.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00739-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast Myoepithelial Cells, Donor RM080 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.9534
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,513,327
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 53.94
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669587_UCSF-UBC.Breast_Myoepithelial_Cells.smRNA-Seq.RM080.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00739-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Breast Myoepithelial Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast Myoepithelial Cells, Donor RM080 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.9549
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,513,327
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 53.94
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669587_UCSF-UBC.Breast_Myoepithelial_Cells.smRNA-Seq.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00739-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Breast Myoepithelial Cells, Donor RM080 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.9564
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: BMC smRNA 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Myoepithelial Cells smRNA-Seq Donor RM080 Library M00739-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,513,327
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 53.94
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: total RNA

organism: Homo sapiens

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Breast

tag: histological type

value: Myoepithelial cell

tag: is tumor

value: primary cell

value: breast myoepithelial cell


title: ES Timepoint, TAF3 Control, PE, replicate 2

city: Berkeley

first: Devin

last: Scannell

address: 378 Stanley Hall #3220

institute: UC Berkeley

description:
polyA RNA
Paired-end reads.

data_processing: Sequence reads were mapped to mm9 using TopHat v1.1.1 with default parameters.

organism: Mus musculus

source_name: Embryonic stem cells, TAF3 control

growth_protocol: ES cells were cultured on 0.1% gelatin-coated plates in the absence of feeder cells. The ES cell medium was prepared by supplementing knockout DMEM (Invitrogen) with 15% FBS, 1mM glutamax, 0.1mM nonessential amino acids, 1mM sodium pyruvate, 0.1mM 2-mercapodhanol and 1000 units of LIF (Millipore).

extract_protocol: As per vendor protocol. Paired-end (PE)  library insert (all) mean=240bp, sd=30bp.

treatment_protocol: Samples were infected with lentiviral vectors expressing either anti-TAF3 (KO) or non-target (Control) shRNA constructs. ES samples were harvested after 72 hours, while EB samples were stimulated to differentiate (by withdrawl of LIF) and sampled either 3 or 6 days later.

tag: strain

tag: cell type

value: embryonic stem cells

tag: genotype

value: TAF3 WT

tag: timepoint

value: ES


description:
design description: miRNA-Seq analysis of peripheral cd8 naive from TC014 (m00737) using Illumina Genome Analyzer IIx
library name: m00737
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A 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: GSM669585_UCSF-UBC.CD8_Naive_Primary_Cells.smRNA-Seq.TC014.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00737-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on CD8 Naive Primary Cells, Donor TC014 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.9532
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,387,066
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 54.76
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669585_UCSF-UBC.CD8_Naive_Primary_Cells.smRNA-Seq.TC014.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00737-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of CD8 Naive Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on CD8 Naive Primary Cells, Donor TC014 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.9547
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,387,066
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 54.76
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669585_UCSF-UBC.CD8_Naive_Primary_Cells.smRNA-Seq.TC014.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00737-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from CD8 Naive Primary Cells, Donor TC014 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.9562
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: CD8N smRNA 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC CD8 Naive Primary Cells smRNA-Seq Donor TC014 Library M00737-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,387,066
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 54.76
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Blood

value: CD8 naive cell


description:
design description: miRNA-Seq analysis of peripheral cd4 memory from TC014 (m00736) using Illumina Genome Analyzer IIx
library name: m00736
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A 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: GSM669584_UCSF-UBC.CD4_Memory_Primary_Cells.smRNA-Seq.TC014.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00736-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on CD4 Memory Primary Cells, Donor TC014 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.9537
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,237,972
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 55.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669584_UCSF-UBC.CD4_Memory_Primary_Cells.smRNA-Seq.TC014.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00736-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of CD4 Memory Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on CD4 Memory Primary Cells, Donor TC014 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.9552
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,237,972
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 55.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669584_UCSF-UBC.CD4_Memory_Primary_Cells.smRNA-Seq.TC014.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00736-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from CD4 Memory Primary Cells, Donor TC014 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.9567
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: CD4M smRNA 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC CD4 Memory Primary Cells smRNA-Seq Donor TC014 Library M00736-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,237,972
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 55.43
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: CD4 memory cell


title: EB Day6 Timepoint, TAF3 Control, replicate 1

description:
polyA RNA
Single read.

source_name: Embryoid body day 6, TAF3 control

value: embryoid body day 6


title: EB Day6 Timepoint, TAF3 KO, replicate 1

description:
polyA RNA
Single read.

source_name: Embryoid body day 6, TAF3 KO

value: TAF3 KO


title: ES Timepoint, TAF3 KO, PE, replicate 1

description:
polyA RNA
Paired-end reads.

source_name: Embryonic stem cells, TAF3 KO


title: ES Timepoint, TAF3 Control, PE, replicate 1

description:
polyA RNA
Paired-end reads.


title: EB Day3 Timepoint, TAF3 KO, replicate 2

description:
polyA RNA
Single read.

source_name: Embryoid body day 3, TAF3 KO

value: embryoid body day 3


title: EB Day6 Timepoint, TAF3 Control, replicate 2

description:
polyA RNA
Single read.


title: ES Timepoint, TAF3 Control, replicate 2

description:
polyA RNA
Single read.


title: ES Timepoint, TAF3 KO, replicate 2

description:
polyA RNA
Single read.


title: EB Day3 Timepoint, TAF3 KO, replicate 1

description:
polyA RNA
Single read.


title: TBP/PolII Mock IP, ES Cells

library_source: genomic

data_processing: Sequence reads were mapped to mm9 using vendor software (Eland) with default parameters.

molecule: genomic DNA

source_name: Embryonic stem cells, TBP/PolII mock

extract_protocol:
Chromatin Immunoprecipitation (ChIP) was performed according to (Boyer et al., 2006) with minor modifications. Briefly, cross-linked ES cell (D3) chromatin was sheared using the Covaris S2 system to a size range of 100bp~400bp. Immunoprecipitation was conducted with either a specific antibody (custom-made except for anti-TBP (Abcam ab62126)) or mock IgG-conjugated Protein A (rabbit and guinea pig) or G (mouse) Sepharose beads (GE Healthcare). The reverse cross-linking was performed at 70oC overnight. After RNAse A and Proteinase K treatment, sample was deproteinized with UltraPure Phenol:Chloroform:Isoamyl Alcohol (Invitrogen) and further purified with the Qiaquick PCR purification kit (Qiagen).

About 10ng of ChIP-enriched DNA (DNA concentration was measured with Quant-iT PicoGreen dsDNA Reagent (invitrogen)) was converted to ChIP-Seq library using the ChIP-Seq DNA Sample Prep Kit (Illumina; IP-102-1001).

tag: chip antibody

value: mock IgG


title: PolII Treatment IP, ES Cells

source_name: Embryonic stem cells, PolII ChIP

value: anti-PolII


title: ES Timepoint, TAF3 Control, replicate 1

description:
polyA RNA
Single read.


title: TBP Treatment IP, ES Cells

source_name: Embryonic stem cells, TBP ChIP

value: anti-TBP

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: antibody lot#


title: TAF1 Mock IP, ES Cells

source_name: Embryonic stem cells, TAF1 mock


title: ES Timepoint, TAF3 KO, PE, replicate 2

description:
polyA RNA
Paired-end reads.


description:
design description: miRNA-Seq analysis of breast luminal epithelial cell from RM080 (m00738) using Illumina Genome Analyzer IIx
library name: m00738
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A 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: GSM669586_UCSF-UBC.Breast_Luminal_Epithelial_Cells.smRNA-Seq.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00738-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Breast Luminal Epithelial Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast Luminal Epithelial Cells, Donor RM080 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.9533
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,708,500
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 58.24
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669586_UCSF-UBC.Breast_Luminal_Epithelial_Cells.smRNA-Seq.RM080.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00738-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Breast Luminal Epithelial Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Breast Luminal Epithelial Cells, Donor RM080 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.9548
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,708,500
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 58.24
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669586_UCSF-UBC.Breast_Luminal_Epithelial_Cells.smRNA-Seq.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00738-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Luminal Epithelial Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Breast Luminal Epithelial Cells, Donor RM080 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.9563
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: BLEC smRNA 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Luminal Epithelial Cells smRNA-Seq Donor RM080 Library M00738-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 2,708,500
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 58.24
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: female

value: Breast

value: Luminal epithelial cell

value: No

value: breast luminal epithelial cell


description:
design description: miRNA-Seq analysis of peripheral mononuclear cell from TC014 (m00734) using Illumina Genome Analyzer IIx
library name: m00734
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A 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: GSM669582_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.smRNA-Seq.TC014.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00734-1.hg19.level.1.release4
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC014 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.9529
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,330,677
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 49.06
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669582_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.smRNA-Seq.TC014.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00734-1.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of Peripheral Blood Mononuclear Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC014 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.9544
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,330,677
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 49.06
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM669582_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.smRNA-Seq.TC014.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: M00734-1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC014 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.9559
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: PBM smRNA 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells smRNA-Seq Donor TC014 Library M00734-1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 1,330,677
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 49.06
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Peripheral blood mononuclear cell

value: primary cell


title: TAF3 Mock IP, ES Cells

source_name: Embryonic stem cells, TAF3 mock

value: embryonic stem cells


title: EB Day6 Timepoint, TAF3 KO, replicate 2

description:
polyA RNA
Single read.


title: O. glaberrima leaf mRNA library

status: Public on Sep 01 2011

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Leaf and panicle tissue was collected from greenhouse grow plants.  Leaf material was collected at the 4-5 leaf stage

data_processing: unique reads wrere tallied

organism: Oryza glaberrima

source_name: Leaf

extract_protocol: Total RNA was extracted from the tissue using TRIzol. The sRNA libraries were constructed using the protocol published by Lu et al., Methods (2007). The mRNA libraries were constructed according to Illumina's instructions accompanying the mRNA-Seq Sample Prep Kit (Catalog # RS-930-1001).

tag: cultivar

tag: tissue

value: Leaf


title: O. glaberrima leaf sRNA library


title: EB Day3 Timepoint, TAF3 Control, replicate 2

description:
polyA RNA
Single read.

source_name: Embryoid body day 3, TAF3 control

value: TAF3 WT


title: TAF3 Treatment IP, ES Cells

source_name: Embryonic stem cells, TAF3 ChIP


title: O. glaberrima root mRNA library

description: Root tissue was collected from plants grown in liquid media.

source_name: Root

value: Root


title: O. glaberrima panicle mRNA library

description: Panicle tissue was collected from  panicles where the top half was flowering, and the lower half had unopened

source_name: Panicle

value: Panicle


title: EB Day3 Timepoint, TAF3 Control, replicate 1

description:
polyA RNA
Single read.

value: embryoid body day 3


title: O. glaberrima panicle sRNA library


title: ES Timepoint, TAF3 KO, replicate 1

description:
polyA RNA
Single read.

value: TAF3 KO

value: ES


title: ID2-H3K4me1-0h.new, biological replicate 2

city: La Jolla

first: Yin

middle: Chun

last: Lin

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: UCSD

description: Chromatin IP against H3K4me1 of uninduced Id2-HPC, biological replicate #2.

data_processing:
Fastq files were generated by CASAVA.
Alignment: Reads were aligned to the mouse mm8 genome (NCBI Build 36) using Bowtie.  Only reads that mapped to a single, unique position were used for downstream analysis.
Custom HOMER software was used for downstream analysis (HOMER, available at http://biowhat.ucsd.edu/homer/).

source_name: Uninduced Id2-HPC cells, 0h, H3K4me1 ChIP

growth_protocol: Cells were cultured in IMDM medium supplemented with 10% FCS/2% PSG/B-me and IL7, Flt3-ligand, and SCF cytokines on S17 feeder cells.

extract_protocol: Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3â end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size selected from a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or IIx following the manufacturer's protocols.

treatment_protocol: None.

tag: genetic background

value: human ID2 transgenic

value: multipotent hematopoietic stem cells (HPCs)

tag: hpc induction

value: uninduced

tag: antibody catalog#


title: ID2-H3K4me1-120h.new, biological replicate 2

description: Chromatin IP against H3K4me1 of induced CD19+ B cells, biological replicate #2.

source_name: Id2-HPC cells induced under B-cell conditions, Cd19+, 120h, H3K4me1 ChIP

growth_protocol: Cells were cultured for up to 5 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL-7 and SCF cytokines on S17 feeder cells in the presence of 1 ug/mL doxycycline, or alternatively, in alpha-MEM medium in the presence of cytokines and on Tst-4 stromal cells.

value: Cd19+ B cells

value: B-cell conditions

tag: induction duration

value: 120 hrs

value: Abcam


title: ID2-HPC Input

description: Input from uninduced Id2-HPC.

source_name: Uninduced Id2-HPC cells, input


title: ID2-H3K4me1-48h.new, biological replicate 2

description: Chromatin IP against H3K4me1 of induced B cells (48 hours), biological replicate #2.

source_name: Id2-HPC cells induced under B-cell conditions, 48h, H3K4me1 ChIP

growth_protocol: Cells were cultured for up to 2 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL-7 and SCF cytokines on S17 feeder cells in the presence of 1 ug/mL doxycycline, or alternatively, in alpha-MEM medium in the presence of cytokines and on Tst-4 stromal cells.

value: B cells

value: 48 hrs


title: ID2-H3K4me1-Myeloid.new, biological replicate 2

description: Chromatin IP against H3K4me1 of induced myeloid cells, biological replicate #2.

source_name: Id2-HPC cells induced under myeloid conditions, H3K4me1 ChIP

growth_protocol: Cells were cultured for up to 6 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL3, Flt3L, GMCSF and MCSF cytokines.

value: myeloid cells

value: myeloid conditions


title: ID2-H3K4me1-120h, biological replicate 1

description: Chromatin IP against H3K4me1 of induced CD19+ B cells, biological replicate #1.


title: TAF1 Treatment IP, ES Cells

source_name: Embryonic stem cells, TAF1 ChIP

value: embryonic stem cells


title: O. glaberrima root sRNA library

value: Root


title: ID2-H3K4me1-0h, biological replicate 1

description: Chromatin IP against H3K4me1 of uninduced Id2-HPC, biological replicate #1.


title: ID2-H3K4me3-Myeloid

description: Chromatin IP against H3K4me3 of induced myeolid cells.

source_name: Id2-HPC cells induced under myeloid conditions, H3K4me3 ChIP

value: Millipore


title: ID2-H3K4me1-48h, biological replicate 1

description: Chromatin IP against H3K4me1 of induced B cells (48 hours), biological replicate #1.


title: human sperm donor 2 bs seq reads

city: Los Angeles

first: Andrew

middle: D

last: Smith

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

description:
Bisulfite converted
PE illumina adaptors were used, ligated libraires were amplified according the maunfacturers instruction.
200-400bp insert size

data_processing: human sequence mapped to hg18 and chimp to panTro2 (bed and wig files)

source_name: Sperm

extract_protocol: Standard illumina genomic library

treatment_protocol: Bisulfite treated genomic DNA

value: Sperm

tag: individual

value: donor 2


title: ID2-H3K4me3-120h

description: Chromatin IP against H3K4me3 of induced Cd19+ B cells.

source_name: Id2-HPC cells induced under B-cell conditions, Cd19+, 120h, H3K4me3 ChIP


title: ID2-H3K4me3-0h

description: Chromatin IP against H3K4me3 of uninduced Id2-HPC.

source_name: Uninduced Id2-HPC cells, 0h, H3K4me3 ChIP


title: human sperm donor 1 bs seq reads

value: donor 1


title: ID2-H3K4me1-Myeloid, biological replicate 1

description: Chromatin IP against H3K4me1 of induced myeloid cells, biological replicate #1.

value: human ID2 transgenic


title: chimp sperm donor 2 bs seq reads

organism: Pan troglodytes


title: MCF7_pe_35bp

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

institute: University of Michigan

description: Illumina_Pipeline_Version:GAPipeline-1.1rc1p4

data_processing: Reads were processed using the ChimeraScan pipeline.  Reads were initially aligned with Bowtie to a combined reference consisting of human genome build hg19 (UCSC) and the knownGene transcript sequences (UCSC, Oct, 2010).  Sets of initially aligned concordant reads are provided as BAM files.  The chimera candidates are provided in the paired BED format defined by the BEDTools software.  Extra fields are described in the ChimeraScan manual (http://chimerascan.googlecode.com).

molecule: polyA RNA

extract_protocol: Messenger RNA (1 microgram) was fragmented at 70 °C for 2 min in a fragmentation buffer (Ambion) and converted to single- stranded cDNA using SuperScript II reverse transcriptase (Invitrogen), followed by second-strand cDNA synthesis using Escherichia coli DNA polymerase I (Invitrogen). The double- stranded cDNA was further processed by Illumina mRNA- sequencing Prep kit. Briefly, double-stranded cDNA was end repaired by using T4 DNA polymerase and T4 polynucleotide kinase, monoadenylated using a Klenow DNA polymerase I (3' to 5' exonucleotide activity), and ligated with adaptor oligo mix (Illumina) using T4 DNA ligase. The adaptor-ligated cDNA library was then fractioned on a 4% agarose gel, and a smear corresponding to 300 nt was excised, purified, and PCR amplified (15 cycles) by Pfu polymerase (Stratagene). The PCR product was again size selected on a 4% agarose gel by cutting out the library smear at 300 base pairs. The library was then purified with the Qiaquick Minelute PCR Purification Kit (Qiagen) and quantified with the Agilent DNA 1000 kit on the Agilent 2100 Bioanalyzer following the manufacturer's 'instructions. Library (10 nM) was used to prepare flowcells with 100,000-130,000 clusters per lane for analysis on the Illumina Genome Analyzer II.

tag: cell line

tag: read type (single/paired-end)

tag: ets fusion status

tag: read length

tag: insert size (bp)

tag: insert size standard deviation (bp)


title: VCaP_pe_53bp

value: VCaP

value: ETS+


title: LNCaP_pe_34bp

value: LNCaP


title: Transcriptome sequence of Hevea brasiliensis

city: Beijing

first: lili

last: hao

address: Beichen west road

country: China

institute: BIG

data_processing:
Filter Dirty Raw Reads: Raw reads that only have 3' adaptor fragments should be removed before data analysis
Clean Reads:Reads after filtering dirty raw reads, on which all following analysis are based
Assembly:Transcriptome de novo assembly is carried out with short reads assembling program - SOAPdenovo (Li, Zhu et al. 2009). SOAPdenovo firstly combines reads with certain length of overlap to form longer fragments without N, which are called contigs. Then the reads are mapped back to contigs; with paired-end reads it is able to detect contigs from the same transcript as well as the distances between these contigs. Next, SOAPdenovo connects the contigs using N to represent unknown sequences between each two contigs, and then Scaffolds are made. Paired-end reads are used again for gap filling of scaffolds to get sequences with least Ns and cannot be extended on either end. Such sequences are defined as Unigenes. When multiple samples from a same species are sequenced, Unigenes from each sample's assembly can be taken into further process of sequence splicing and redundancy removing with sequence clustering software to acquire non-redundant Unigenes as long as possible. In the final step, blastx alignment (evalue < 0.00001) between Unigenes and protein databases like nr, Swiss-Prot, KEGG and COG is performed, and the best aligning results are used to decide sequence direction of Unigenes. If results of different databases conflict with each other, a priority order of nr, Swiss-Prot, KEGG and COG should be followed when deciding sequence direction of Unigenes. When a Unigene happens to be unaligned to non of the above databases, a software named ESTScan (Iseli, Jongeneel et al. 1999) will be introduced to predict its coding regions as well as to decide its sequence direction. For Unigenes with sequence directions, we provide their sequences from 5' end to 3' end; for those without any direction we provide their sequences from assembly software.

organism: Hevea brasiliensis

source_name: letex and leaf

growth_protocol: H. brasiliensis cultivar Reyan 7-33-97 grown at the Experimental Station of theRubber Research Institute of the Chinese Academy of Tropical Agricultural Sciences

extract_protocol:
Total RNA were isolated latex and leaf according to previously described (Tang et al., 2007). RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies). Beads with Oligo(dT) were used to isolate poly(A) mRNA after total RNA (QIAGEN GmbH, Hilden, Germany). Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Taking these short fragments as templates, the first-strand cDNA was synthesized by using random hexamer-primer and Superscript™ Ⅲ (Invitrogen™, California, USA). The second-strand cDNA was synthesized using buffer, dNTPs, RNaseH and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit (QIAGEN GmbH, Hilden, Germany) and resolved with EB buffer for end reparation and adding poly(A). Then the short fragments were connected with sequencing adapters. After agarose gel electrophoresis, the suitable fragment was selected for the PCR amplification as templates.

average insert size: 200bp

treatment_protocol: untreatment

tag: strain


title: 503_control

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing: Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not pass Illumina quality control, do not have the 3'-adaptor, contain N, or have length less than 17nt were removed. The processed files are named as "prefix"_uniq.txt, where "prefix" is the prefix of the file that contains raw data.  The first column in a processed file contains clean reads, and the second column contains the number of copies of the reads in the library.

organism: Vigna unguiculata

source_name: adult plants

growth_protocol: 30-day-old plants grown in greenhouse at 35°C during day and 18°C during night, with natural day length

extract_protocol: Total RNA was isolated from leaves and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 20 to 30 nt were excised and ligated to a preadenylated 3' adaptor and a 5’- adaptor using T4 RNA ligase. Ligation products were purified in polyacrylamide gels, followed by RT-PCR. The small RNA libraries were sequenced by the UCR core facility.

treatment_protocol: plants of two genotypes are each grown under two kinds of conditions: control (well-watered) and drought (ψw=-1.5Mpa)

value: leaves

tag: treatment

value: control


title: 503_drought

value: drought


title: CB46_control


title: CB46_drought


title: USC_ChipSeq_K562_H3K27me3B_UCDavis

status: Public on Aug 31 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

value: immortalized cell line

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: line

tag: cell organism

value: human

tag: cell description

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: rabbit monoclonal

tag: antibody targetdescription

value: Histone H3 (tri-methyl K27) marks repressed chromatin regions

tag: antibody vendorname

value: Cell Signaling

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: replicate

tag: replicate description

value: tier 1


title: SP

city: Nanjing

first: Wenwu

last: Ye

address: Department of Plant Pathology, Nanjing Agricultural University

institute: Nanjing Agricultral University, China

description: Digital gene expression tag profiling

data_processing: Illumina Pipeline Software version 1.0 was used for data processing. Raw sequences have 3' adaptor fragments as well as a few low-quality sequences and several types of impurities. Raw sequences were transformed into clean 21 bp (CATG+17bp) tags by the following steps: (1) 3' adaptor sequence was trimmed, resulting in 21 bp tags from 35 bp, of raw sequence (2) empty reads were removed (reads with only 3' adaptor sequences but no tags); (3) low quality tags were removed (tags with ambiguous base calls); (4) tags of unusual length were removed, leaving only tags of 21 bp; (5) non-redundant tags were removed (each tag needs to be detected at least twice to be considered reliable).

organism: Phytophthora sojae

source_name: zoosporangia

growth_protocol: P. sojae reference strain P6497 (race 2) was used in this research. Mycelia (MY) were cultivated in 10% V8 liquid medium at 25ºC in darkness for 48h, then blotted dry with absorbent paper and preserved in liquid nitrogen for RNA isolation. Zoosporangia (SP) were induced by repeatedly washing 48- to 72-hour-old mycelial mats with sterile distilled water at 25ºC in darkness until sporangia formed abundantly. Zoospores (ZO) were released by placing the zoosporangial mycelial mat into 10 ml sterile distilled water at 5-10ºC for 10-15 min, then at 25ºC for 10-30 min. The zoospores were then concentrated by centrifugation at 2,000 rpm at 0ºC to a concentration of >150 zoospores /µl then preserved in liquid nitrogen for RNA isolation. The zoospores were counted under microscope based on 2µl sucked zoospore suspension sample and estimated from the average of three repeats. Cysts (CY) were produced by vortexing the zoospores suspension at room temperature for 30 seconds, then collected by centrifugation at 2,000 rpm at 0ºC and preserved in liquid nitrogen for RNA isolation. Germinating cysts (GC) were obtained by cultivating cysts with 5% V8 liquid medium at 25ºC, 150 rpm for 1h, then harvesting them by centrifugation at 2,000 rpm at 0ºC. For mycelia infection (IF1.5h- IF24h), the soybean cultivar Williams, which is susceptible to P6497, was grown in a greenhouse at 22-28ºC and used at the second leaf stage. Soybean leaves were treated with 0.05% v/v solution of tween 20 to improve wetting. A mycelial mat was washed with sterile distilled water and then laid on and sandwiched between upper surfaces of two leaves at 25ºC respectively for 1.5h, 3h, 6h, 12h, 24h after infection. For the 1.5 h and 3 h time points, the mycelial mat was carefully peeled from the leaves and preserved in liquid nitrogen. For the later time points, the regions of the leaves in contact with the mycelia were excised together with the mycelia and preserved in liquid nitrogen.

extract_protocol: Tag library preparation for the samples was performed in parallel using Illumina gene expression sample preparation kit. Briefly, total RNA from the three samples was used for mRNA capture with magnetic oligo(dT) beads. First and second strand cDNA were synthesized and bead-bound cDNA was subsequently digested with NlaIII. The cDNA fragments with 3' ends were then purified with magnetic beads and Illumina adapter 1 was added to their 5' ends. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts 17 bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, Illumina adapter 2 was introduced at 3' ends of tags, acquiring tags with different adapters at both ends to form a tag library. After 15 cycles of linear PCR amplification, 85 base strips were purified by PAGE gel electrophoresis. These strips were then digested, and the single-chain molecules were fixed onto the Illumina sequencing chip for sequencing.

tag: strain

tag: developmental stage

value: zoosporangia


title: ZO

description: Digital gene expression tag profiling

source_name: zoospores

value: zoospores


title: MY

description: Digital gene expression tag profiling

source_name: mycelia

value: mycelia


title: chimp sperm donor 1 bs seq reads

tag: cell type

value: Sperm

tag: individual

value: donor 1


title: USC_ChipSeq_PBMC_H3K4me1_UCDavis

source_name: PBMC

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: PBMC

tag: cell organism

value: human

tag: cell description

value: Peripheral blood mononuclear cells

tag: cell lineage

value: M

tag: treatment

value: rabbit polyclonal

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam


title: USC_ChipSeq_NT2-D1_H3K9acB_UCDavis

value: malignant pluripotent embryonal carcinoma (Ntera2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell karyotype

value: cancer

value: inner cell mass

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal

tag: antibody targetdescription

value: Histone H3 (acetyl K9) marks promoters in chromatin regions

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

value: tier 1


title: USC_ChipSeq_K562_H3K4me1_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

value: ChIP-Seq

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: mesoderm

value: F

tag: controlid

tag: replicate

tag: replicate description


title: USC_ChipSeq_NT2-D1_H3K4me1_UCDavis

value: immortalized cell line

tag: datatype description

tag: line

tag: cell organism

value: human

tag: cell description

value: malignant pluripotent embryonal carcinoma (Ntera2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell lineage

value: M

tag: treatment

value: rabbit polyclonal

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

value: Abcam


title: USC_ChipSeq_K562_H3K4me3B_UCDavis

tag: cell

tag: cell karyotype

value: cancer

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

value: Rabbit monoclonal antibody

tag: antibody targetdescription

value: Histone H3 (tri-methyl K4) marks promoters in chromatin regions

value: Cell Signaling

value: UCDavis


title: USC_ChipSeq_NT2-D1_H3K9me3_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

value: ChIP-Seq

value: inner cell mass

value: rabbit polyclonal, ChIP grade

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

tag: antibody vendorname

tag: antibody vendorid

tag: control

tag: control description

value: Input library was prepared at UC Davis.

value: tier 1


title: CY

description: Digital gene expression tag profiling

source_name: cysts

tag: strain

tag: developmental stage

value: cysts


title: USC_ChipSeq_NT2-D1_Input_UCDavis

tag: datatype description

tag: cell organism

value: human

tag: cell description

value: malignant pluripotent embryonal carcinoma (Ntera2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell lineage

value: M

tag: treatment

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid


title: USC_ChipSeq_PBMC_H3K9me3_UCDavis

tag: cell

value: PBMC

value: Peripheral blood mononuclear cells

value: mesoderm

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

tag: antibody antibodydescription

tag: antibody targetdescription

value: Abcam

tag: replicate

tag: replicate description


title: USC_ChipSeq_K562_H3K9acB_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

value: ChIP-Seq

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell karyotype

value: cancer

value: F

value: Rabbit polyclonal

value: Histone H3 (acetyl K9) marks promoters in chromatin regions

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description


title: USC_ChipSeq_U2OS_H3K9me3_UCDavis

tag: datatype description

tag: cell organism

value: human

tag: cell description

value: Osteosarcoma from the tibia of a 15 year old human female, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972. (PMID:6081590)

tag: cell lineage

tag: treatment

value: rabbit polyclonal, ChIP grade

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: Input library was prepared at UC Davis.

tag: controlid

value: tier 1


title: USC_ChipSeq_K562_Input_UCDavis

value: USC

tag: cell

value: mesoderm

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: labversion

value: remapped from hg18, Illumina 2.0, low confidence sequences excluded


title: USC_ChipSeq_U2OS_H3K36me3B_UCDavis

tag: lab

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

value: ChIP-Seq

tag: cell karyotype

value: cancer

value: F

tag: antibody antibodydescription

value: rabbit polyclonal

tag: antibody targetdescription

value: Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions

value: Cell Signaling

tag: replicate

tag: replicate description


title: GC

description: Digital gene expression tag profiling

source_name: germinating cysts

tag: strain

tag: developmental stage

value: germinating cysts


title: USC_ChipSeq_PBMC_H3K27me3B_UCDavis

tag: datatype description

value: PBMC

tag: cell organism

value: human

tag: cell description

value: Peripheral blood mononuclear cells

tag: cell lineage

value: M

tag: treatment

value: rabbit monoclonal

value: Histone H3 (tri-methyl K27) marks repressed chromatin regions

tag: antibody vendorname

tag: antibody vendorid

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid


title: USC_ChipSeq_NT2-D1_H3K36me3B_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

tag: cell

value: malignant pluripotent embryonal carcinoma (Ntera2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell karyotype

value: inner cell mass

tag: cell sex

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: tier 1


title: USC_ChipSeq_NT2-D1_H3K4me3B_UCDavis

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell organism

value: cancer

tag: antibody antibodydescription

value: Rabbit monoclonal antibody

tag: antibody targetdescription

value: Histone H3 (tri-methyl K4) marks promoters in chromatin regions

tag: replicate

tag: replicate description


title: USC_ChipSeq_U2OS_Input_UCDavis

value: human

tag: cell description

value: Osteosarcoma from the tibia of a 15 year old human female, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972. (PMID:6081590)

tag: cell lineage

value: mesoderm

value: F

tag: treatment

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control


title: IF1.5h

description: Digital gene expression tag profiling

source_name: mycelia, 1.5 h after inoculation onto susceptible soybean leaf tissues

tag: strain

tag: infection

value: P.sojae inoculation onto susceptible soybean leaf tissues

tag: infection time

tag: tissue

value: mycelia


title: Can_0_root_validation_rep1

status: Public on Aug 29 2011

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
r40_l2_can_0_root
polyA RNA

data_processing: Samples were mapped to the TAIR9 Arabidopsis reference genome sequence with the CLC Workbench program (the TAIR10 annotation was used as the annotation for mapping). RPKM values are as calculated by CLC for TAIR10 gene models (number of read alignments set to one).

organism: Arabidopsis thaliana

source_name: 10-day-old root, Can-0

growth_protocol: Plants were germinated on soil (seedling and floral bud samples) or plates (root samples) and grown for approximately 10 or 11 days under standard long day conditions (16 hours light 8 hours dark, at 20C) for seedling and root samples or until stage 12 floral bud for flower samples.

extract_protocol: Libraries were generated by adapting the Illumina small RNA protocol to use fragmented mRNA as input for library construction.

tag: accession

value: root

tag: age

value: 10 days

value: biological replicate 1


title: IF3h

description: Digital gene expression tag profiling

source_name: mycelia, 3 h after inoculation onto susceptible soybean leaf tissues

value: 3 h


title: Can_0_floral_bud_validation_rep1

description:
r35_l3_can_0_floral_bud
polyA RNA

source_name: stage 12 floral bud, Can-0

value: floral bud

value: stage 12


title: IF12h

description: Digital gene expression tag profiling

organism:
Glycine max
Phytophthora sojae

source_name: mycelia and soybean leaf, 12 h after inoculation onto susceptible soybean leaf tissues

value: mycelia and soybean leaf


title: USC_ChipSeq_HCT-116_TCF7L2_UCDavis

status: Public on Aug 30 2011

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: colorectal carcinoma (PMID:7214343)

tag: cell karyotype

value: cancer

value: endoderm

tag: cell sex

value: M

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit monoclonal

value: TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following:Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4

tag: antibody vendorname

value: Cell Signaling Technology

tag: antibody vendorid

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

tag: labversion

value: Fragmented using Bioruptor, precipitated with protein G magnetic beads,

value: tier 1

tag: softwareversion

value: PeakSeq1.0 (fdr 0.001)


title: Can_0_seedling_validation_rep1

description:
r33_1_can_0_seedling
polyA RNA

source_name: 11-day-old seedling, Can-0

tag: accession

tag: tissue

value: seedling

value: 11 days

tag: replicate

value: biological replicate 1


title: Col_0_seedling_validation_rep1

description:
r33_l2_col_0_seedling
polyA RNA

source_name: 11-day-old seedling, Col-0

tag: age


title: ws_0_seedling_br2

description:
r39_l2_ws_0_seedling_3
polyA RNA

data_processing: Technical replicates were mapped to TAIR9 gene models. Biological replicates were mapped to a mix of TAIR10 gene models and computationally predicted gene models. Data for all gene models in the annotations are given in the supplementary processed data files.

source_name: 11-day-old seedling, Ws-0

growth_protocol: Arabidopsis seeds were stratified for 5 days at 4C. Plants were germinated on soil and grown for approximately 11 days under standard long day conditions, 16 hours light 8 hours dark, at 20C.

extract_protocol: Libraries were generated with methods adapted from the Illumina mRNA sample preparation protocol (cat. no 1004894 Rev.A).

value: biological replicate 2


title: wu_0_seedling_br1

description:
r39_l1_wu_0_seedling_1
polyA RNA

source_name: 11-day-old seedling, Wu-0


title: wu_0_seedling_br2

description:
r39_l2_wu_0_seedling_2
polyA RNA


title: Col_0_floral_bud_validation_rep1

description:
r36_l2_col_0_floral_bud
polyA RNA

source_name: stage 12 floral bud, Col-0

value: floral bud

value: stage 12


title: ws_0_seedling_br1

description:
r39_l1_ws_0_seedling_1
polyA RNA


title: zu_0_seedling_br1

description:
r39_l1_zu_0_seedling_1
polyA RNA

source_name: 11-day-old seedling, Zu-0


title: wil_2_seedling_br2

description:
r38_l8_wil_2_seedling_3
polyA RNA

source_name: 11-day-old seedling, Wil-2


title: zu_0_seedling_br2

description:
r39_l1_zu_0_seedling_3
polyA RNA


title: wil_2_seedling_br1

description:
r38_l7_wil_2_seedling_1
polyA RNA


title: tsu_0_seedling_br2

description:
r38_l8_tsu_0_seedling_2
polyA RNA

source_name: 11-day-old seedling, Tsu-0


title: sf_2_seedling_br2

description:
r38_l8_sf_2_seedling_3
polyA RNA

source_name: 11-day-old seedling, Sf-2


title: sf_2_seedling_br1

description:
r38_l7_sf_2_seedling_2
polyA RNA


title: po_0_seedling_br2

description:
r38_l6_po_0_seedling_2
polyA RNA

source_name: 11-day-old seedling, Po-0


title: tsu_0_seedling_br1

description:
r38_l7_tsu_0_seedling_1
polyA RNA


title: oy_0_seedling_br2

description:
r38_l6_oy_0_seedling_3
polyA RNA

source_name: 11-day-old seedling, Oy-0


title: IF24h

description: Digital gene expression tag profiling

source_name: mycelia and soybean leaf, 24 h after inoculation onto susceptible soybean leaf tissues

tag: strain

tag: infection

value: P.sojae inoculation onto susceptible soybean leaf tissues

tag: infection time

value: mycelia and soybean leaf


title: po_0_seedling_br1

description:
r38_l5_po_0_seedling_1
polyA RNA


title: oy_0_seedling_br1

description:
r38_l5_oy_0_seedling_1
polyA RNA


title: no_0_seedling_br2

description:
r38_l6_no_0_seedling_3
polyA RNA

source_name: 11-day-old seedling, No-0


title: rsch_4_seedling_br2

description:
r38_l8_rsch_4_seedling_4
polyA RNA

source_name: 11-day-old seedling, Rsch-4


title: rsch_4_seedling_br1

description:
r38_l7_rsch_4_seedling_2
polyA RNA


title: no_0_seedling_br1

description:
r38_l5_no_0_seedling_1
polyA RNA


title: mt_0_seedling_br2

description:
r38_l6_mt_0_seedling_2
polyA RNA

source_name: 11-day-old seedling, Mt-0


title: mt_0_seedling_br1

description:
r38_l5_mt_0_seedling_1
polyA RNA


title: ler_0_seedling_br2

description:
r38_l4_ler_0_seedling_2
polyA RNA

source_name: 11-day-old seedling, Ler-0


title: USC_ChipSeq_PBMC_H3K4me3B_UCDavis

source_name: PBMC

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

value: PBMC

tag: cell organism

value: human

tag: cell description

value: Peripheral blood mononuclear cells

tag: cell lineage

value: mesoderm

value: M

tag: treatment

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit monoclonal antibody

tag: antibody targetdescription

value: Histone H3 (tri-methyl K4) marks promoters in chromatin regions

value: Cell Signaling

tag: control

tag: replicate description


title: ler_0_seedling_br1

description:
r38_l3_ler_0_seedling_1
polyA RNA

tag: accession

tag: tissue

value: seedling

tag: age

value: 11 days

tag: replicate

value: biological replicate 1


title: kn_0_seedling_br2

description:
r38_l4_kn_0_seedling_1
polyA RNA

source_name: 11-day-old seedling, Kn-0

value: biological replicate 2


title: hi_0_seedling_br2

description:
r38_l4_hi_0_seedling_2
polyA RNA

source_name: 11-day-old seedling, Hi-0


title: hi_0_seedling_br1

description:
r38_l3_hi_0_seedling_1
polyA RNA


title: IF6h

description: Digital gene expression tag profiling

source_name: mycelia and soybean leaf, 6 h after inoculation onto susceptible soybean leaf tissues

tag: strain

tag: infection

value: P.sojae inoculation onto susceptible soybean leaf tissues

tag: infection time

value: 6 h

value: mycelia and soybean leaf


title: edi_0_seedling_br2

description:
r38_l4_edi_0_seedling_2
polyA RNA

source_name: 11-day-old seedling, Edi-0


title: ct_1_seedling_br2

description:
r38_l2_ct_1_seedling_2
polyA RNA

source_name: 11-day-old seedling, Ct-1


title: edi_0_seedling_br1

description:
r38_l3_edi_0_seedling_1
polyA RNA


title: can_0_seedling_br2

description:
r38_l2_can_0_seedling_2
polyA RNA

source_name: 11-day-old seedling, Can-0


title: ct_1_seedling_br1

description:
r38_l1_ct_1_seedling_1
polyA RNA


title: col_0_seedling_br1

description:
r38_l1_col_0_seedling_1
polyA RNA

source_name: 11-day-old seedling, Col-0


title: can_0_seedling_br1

description:
r38_l1_can_0_seedling_1
polyA RNA


title: col_0_seedling_br2

description:
r38_l2_col_0_seedling_2
polyA RNA


title: bur_0_seedling_br2

description:
r38_l2_bur_0_seedling_1
polyA RNA

source_name: 11-day-old seedling, Bur-0


title: bur_0_seedling_br1

description:
r38_l1_bur_0_seedling_2
polyA RNA


title: col_0_seedling_tr4

description:
r35_l7_col_0_seedling_4
polyA RNA

value: technical replicate 4


title: col_0_seedling_tr3

description:
r35_l7_col_0_seedling_3
polyA RNA

value: technical replicate 3


title: col_0_seedling_tr1

description:
r35_l7_col_0_seedling_1
polyA RNA

value: technical replicate 1


title: col_0_seedling_tr2

description:
r35_l7_col_0_seedling_2
polyA RNA

value: technical replicate 2


title: Input DNA, Canton S

city: Vienna

first: Jonas

last: Steinmann

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA

description: Input DNA.

data_processing:
Reads were mapped to the Drosophila genome (Flybase version 5.27; dmel_r5.27) using Bowtie using the parameters -p4 -m1 -sam. Mapped reads were converted to BED format and peaks were called using pypeak (https://github.com/steinmann/pypeak). FDR was calculated from the peaks found in the input sample.

.bed file: control_peaks_pypeak.bed

organism: Drosophila melanogaster

source_name: Third instar larval brain and wing/haltere/third leg imaginal discs tissue, input

growth_protocol: Larvae were raised on standard food at 25 C.

extract_protocol: Illumina library preparation protocol for ChIP-seq (Part # 11257047 Rev. A).

value: Canton S

value: third instar larval brain and wing/haltere/third leg imaginal discs

tag: chip antibody

tag: temperature


title: Input DNA, w1118

description: Input DNA.


title: l(3)mbt ChIP, Canton S

description: ChIP against l(3)mbt.

data_processing:
Reads were mapped to the Drosophila genome (Flybase version 5.27; dmel_r5.27) using Bowtie using the parameters -p4 -m1 -sam. Mapped reads were converted to BED format and peaks were called using pypeak (https://github.com/steinmann/pypeak). FDR was calculated from the peaks found in the input sample.

.bed file: ip_peaks_pypeak.bed

source_name: Third instar larval brain and wing/haltere/third leg imaginal discs tissue,  l(3)mbt ChIP

value: guinea pig 1 anti-l(3)mbt 1244-1477aa (glycine elution)


title: l(3)mbt ChIP, w1118

description: ChIP against l(3)mbt.


title: RNA-Seq Lung Fibroblasts batch 3

status: Public on Aug 28 2011

city: Cambridge

first: Nataly

middle: Moran

last: Cabili

state: MA

address: 7  Cambridge Center

institute: Broad Institute ;  Harvard University

data_processing: All files were mapped against Hg19 using TopHat 1.1.4

source_name: Cultured human foreskin fibroblast

growth_protocol: Whole tissue samples were purchased from Ambion.

extract_protocol: RNA was extracted from in-house cultured cell lines using TRIzol (Invitrogen) following the manufacturer instructions. After extraction a DNAse treatment was applied using Turbo DNAse (Ambion) and a second RNA extraction with TRIzol was performed.  The standard mRNA-seq library preparations was done using the Illumina mRNA-Seq Sample Prep Kit (Part #RS-100-0801). Briefly, poly A+ RNA is purified from 100ng of total RNA with oligo-dT beads. Purified mRNA or RiboMinus RNA (200 ng)  is then fragmented with divalent cations under elevated temperature. First strand cDNA synthesis is performed with random hexamers and reverse transcriptase. Second strand cDNA synthesis is performed using RNAseH and DNA PolI.  Following cDNA synthesis, double stranded products are end repaired, a single A base is added, and then the Illumina PE adaptors are ligated onto the cDNA products. For this study ligation products were purified using gel electrophoresis.  The target size range for these libraries was ~350-500 bp on the gel such that the final library for sequencing would have cDNA inserts with sizes of ~160-380 bp long.  Following gel purification the adapter ligated cDNA is then amplified with 12-14 cycles of PCR.

tag: cell type

value: Cultured primary human foreskin fibroblast


title: RNA-Seq Foreskin Fibroblasts

description: inal library for sequencing would have cDNA inserts with sizes of ~160-380 bp long

source_name: Cultured human lung fibroblast

value: Cultured primary human lung fibroblast


title: RNA-Seq Lung Fibroblasts batch1, sample 2


title: RNA-Seq Testes

source_name: testes tissue

value: testes


title: USC_ChipSeq_HEK293_TCF7L2_UCDavis

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: ChIP-Seq

tag: cell

tag: cell organism

value: human

tag: cell description

value: embryonic kidney. (PMID:11967234)

tag: cell karyotype

value: cancer

value: mesoderm

tag: cell sex

value: U

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Rabbit monoclonal

value: TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following:Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4

tag: antibody vendorname

value: Cell Signaling Technology

tag: antibody vendorid

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid

value: tier 1


title: RNA-Seq Placenta

source_name: Placenta Tissue

tag: tissue

value: placenta


title: RNA-Seq HeLa

source_name: HeLa cell line

tag: cell line

value: HeLa


title: RNA-Seq Brain

source_name: brain tissue

value: brain


title: RNA-Seq Lung Fibroblasts batch1, sample 1

tag: cell type

value: Cultured primary human lung fibroblast


title: RNaseP, pT181 variant library

status: Public on Aug 26 2011

first: Cole

last: Trapnell

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: RRRY (positive SHAPE channel) and YYYR (negative SHAPE channel)

data_processing:
Custom pipeline (see methods of Lucks et al, PNAS, 2011, PMID 21642531)
The mean insert size for complex_no_PEGG library is: 118.922479 The std dev for the complex_no_PEGG is: 47.156295

organism: Bacillus subtilis

source_name: IVT

growth_protocol: All RNAs were synthesized with standard in vitro synthesis and modified with 1M7 (6.5 mM, final) with minor modifications for the analysis by deep sequencing.  See see Lucks et al, PNAS, 2011, PMID 21642531 for additional details.

tag: ivt rna

value: RNaseP, pT181 variant

tag: library strategy

value: SHAPE-Seq


title: RNA-Seq Liver

source_name: liver tissue

value: liver


title: Col_0_root_validation_rep1

description:
r40_l3_col_0_root
polyA RNA

source_name: 10-day-old root, Col-0

tag: accession

value: root

tag: age

value: 10 days

tag: replicate

value: biological replicate 1


title: RNaseP barcode library

data_processing:
Custom pipeline (see methods of Lucks et al, PNAS, 2011, PMID 21642531)
The mean insert size for barcode library is: 143.665409 The std dev for the barcode is: 46.829797

extract_protocol: see Lucks et al, PNAS, 2011, PMID 21642531

value: RNaseP


title: TDRD1IPshort

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: Small RNA sequence data (RIP-Seq)

data_processing: 3' adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome (Zv9).

organism: Danio rerio

source_name: RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract

extract_protocol: Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 Âµl Dynabeads (Invitrogen), 3 or 6 testes, and Tdrd1 antibody 1:100 in a total volume of 500 Âµl.  RNA was then size selected (18-35 nucleotides) from gel. For cDNA synthesis, adaptors were ligated to the 3' and 5' ends of the RNAof the size-selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLVRNase H- reverse transcriptase. cDNA was PCR-amplified with adapter-specific primers and used in Illumina sequencing.

tag: strain

value: TL