description:
design description: WGS analysis of UCSF-4 embryonic stem cell line (A27731) using Illumina HiSeq 2000
library name: A27731
EXPERIMENT_TYPE: Whole Genome Sequencing
EXTRACTION_PROTOCOL: Refer to document 'SLX-PET Protocol for Illumina Sample Prep' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris-E210
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.75 min
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: cell line

tag: line

value: Embryo ICM

value: Embryonic stem cell


status: Public on May 27 2016

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: Bisulfite-Seq analysis of breast fibroblast from RM071 (A27334) using Illumina HiSeq 2000
library name: A27334
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 1 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 300 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 181-676 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.57
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing: Various levels of processed data files will be made available as this project proceeds.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: female

tag: body site

value: Breast

tag: histological type

value: Fibroblast cultured cell

tag: is tumor

value: No

value: primary cell culture

tag: cell type

value: breast fibroblast


description:
design description: WGS analysis of foreskin keratinocyte from skin03 (A20918) using Illumina HiSeq 2000
library name: A20918
EXPERIMENT_TYPE: Whole Genome Sequencing
EXTRACTION_PROTOCOL: Refer to document 'SLX-PET Protocol for Illumina Sample Prep' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris-E210
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.75 min
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: library construction protocol: Refer to document 'SLX-PET Protocol for Illumina Sample Prep' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: male

value: Penis

value: Keratinocyte

value: foreskin keratinocyte


description:
design description: WGS analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC02 (A22981) using Illumina HiSeq 2000
library name: A22981
EXPERIMENT_TYPE: Whole Genome Sequencing
EXTRACTION_PROTOCOL: Refer to document 'SLX-PET Protocol for Illumina Sample Prep' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris-E210
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.75 min
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Brain

value: Ganglionic eminence neurosphere culture


description:
design description: RNA-Seq analysis of placenta (trophoblast) tissue from CTL07 (A27177) using Illumina HiSeq 2000
library name: A27177
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.8
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 250-430 bp
****************
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

molecule: total RNA

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: Placenta

value: Trophoblast

value: primary tissue

value: placenta (trophoblast) tissue


description:
design description: RNA-Seq analysis of skin (nevus) tissue from Nevus03 (A27174) using Illumina HiSeq 2000
library name: A27174
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.6
RNA_PREPARATION_INITIAL_RNA_QNTY: 1.98 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 250-430 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Skin

value: Nevus tissue

value: skin (nevus) tissue


description:
design description: Bisulfite-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL02 (A26616) using Illumina HiSeq 2000
library name: A26616
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 1 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 300 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 263-578 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.58
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Chorion smooth tissue


description:
design description: WGS analysis of placenta (basal plate and villi) tissue from CTL02 (A32367) using Illumina HiSeq 2000
library name: A32367
EXPERIMENT_TYPE: Whole Genome Sequencing
EXTRACTION_PROTOCOL: Refer to document 'SLX-PET Protocol for Illumina Sample Prep' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris-E210
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 45 min
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Basal plate tissue

value: No

value: placenta (basal plate and villi) tissue


description:
design description: RNA-Seq analysis of peripheral mononuclear cell from TC017 (A23163) using Illumina HiSeq 2000
library name: A23163
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.5
RNA_PREPARATION_INITIAL_RNA_QNTY: 2.91 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: male

value: Blood

value: Peripheral blood mononuclear cell

value: primary cell


description:
design description: WGS analysis of foreskin fibroblast from skin01 (A20921) using Illumina HiSeq 2000
library name: A20921
EXPERIMENT_TYPE: Whole Genome Sequencing
EXTRACTION_PROTOCOL: Refer to document 'SLX-PET Protocol for Illumina Sample Prep' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Covaris-E210
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 0.75 min
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Penis

value: Fibroblast

value: primary cell culture

value: foreskin fibroblast


description:
design description: Bisulfite-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL01 (A26612) using Illumina HiSeq 2000
library name: A26612
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 1 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 300 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 173-659 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 96.55
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: female

value: Placenta

value: primary tissue


description:
design description: RNA-Seq analysis of pancreas islet from ZGI 213 (A25283) using Illumina HiSeq 2000
library name: A25283
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.7
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.88 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 250-430 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Pancreas

value: Islet

value: pancreas islet


description:
design description: RNA-Seq analysis of placenta (trophoblast) tissue from CTL04 (A23161) using Illumina HiSeq 2000
library name: A23161
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.8
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.38 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Trophoblast

value: placenta (trophoblast) tissue


description:
design description: RNA-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL02 (A21764) using Illumina HiSeq 2000
library name: A21764
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.3
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.65 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Chorion smooth tissue

value: No


description:
design description: RNA-Seq analysis of placenta (villi) tissue from CTL03 (A21766) using Illumina HiSeq 2000
library name: A21766
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 5.5
RNA_PREPARATION_INITIAL_RNA_QNTY: 5.08 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Villi tissue

value: placenta (villi) tissue


description:
design description: RNA-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21765) using Illumina HiSeq 2000
library name: A21765
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.9
RNA_PREPARATION_INITIAL_RNA_QNTY: 3.9 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: male

value: Amnion tissue

value: placenta (amniotic membrane) tissue


description:
design description: RNA-Seq analysis of placenta (trophoblast) tissue from CTL05 (A23162) using Illumina HiSeq 2000
library name: A23162
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.1
RNA_PREPARATION_INITIAL_RNA_QNTY: 5.51 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************


description:
design description: RNA-Seq analysis of placenta (villi) tissue from CTL04 (A23159) using Illumina HiSeq 2000
library name: A23159
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 6.8
RNA_PREPARATION_INITIAL_RNA_QNTY: 2.89 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************


description:
design description: RNA-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL04 (A23158) using Illumina HiSeq 2000
library name: A23158
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.6
RNA_PREPARATION_INITIAL_RNA_QNTY: 2.35 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************


description:
design description: RNA-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL03 (A21767) using Illumina HiSeq 2000
library name: A21767
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 5.5
RNA_PREPARATION_INITIAL_RNA_QNTY: 5.53 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************


description:
design description: RNA-Seq analysis of placenta (basal plate and villi) tissue from CTL04 (A23160) using Illumina HiSeq 2000
library name: A23160
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.6
RNA_PREPARATION_INITIAL_RNA_QNTY: 2.34 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Basal plate tissue

value: placenta (basal plate and villi) tissue


title: ribo_tif3delta replicate 2_15 deg

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 CENTER DR Room 230, MSC 0609

institute: NICHD

description:
Experiment 2
processed data file: tif3_15_deg.csv

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Read quantitation using custom scripts
Analysis of reads using DESeq
Genome_build: sacCer2
Supplementary_files_format_and_content: processed  txt (csv) files per experiment show a matrix (with columns: yORF name, gene name, WT ribosome occupancy, mutant ribosome occupancy, WT mRNA occupancy, mutant mRNA occupancy, ribosome occupancy change, mRNA occupancy change, TE change). All numerical columns have log values with base 2

organism: Saccharomyces cerevisiae

source_name: ribo_tif3Δ_15 deg

growth_protocol: Cells were generally grown to an OD600 of ~  0.7 in synthetic complete medium and subjected to temperature shifts as indicated

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill.
Ribosome profiling (Rnase I footprinting, size selection,RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223

treatment_protocol: All cultures were treated  with cycloheximide (100 ug / ml) for 2 min prior to harvesting

tag: strain

tag: genotype/variation

value: tif3 delta mutant

tag: temperature shift to

tag: molecule subtype

value: Ribosome-protected RNA


title: ribo_tif3delta replicate 1_15 deg


title: ribo_wild-type replicate 2_15 deg

source_name: ribo_wild-type_15 deg

value: wild-type TIF3


description:
design description: Bisulfite-Seq analysis of brain (cerebellum) tissue from HuFGM02 (A27336) using Illumina HiSeq 2000
library name: A27336
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 1 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: 300 bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 166-614 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 95.68
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 5
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Brain

value: Cerebellum tissue

value: primary tissue

value: brain (cerebellum) tissue


title: mRNA_tif3delta replicate 1_15 deg

source_name: mRNA_tif3Δ_15 deg

value: mRNA


title: ribo_wild-type replicate 1_15 deg


title: mRNA_wild-type replicate 1_15 deg

source_name: mRNA_wild-type_15 deg


title: mRNA_tif3delta replicate 2_15 deg


title: mRNA_wild-type replicate 2_15 deg


title: mRNA_tif3delta replicate 1_37 deg

description:
Experiment 1
processed data file: tif3_37_deg.csv

source_name: mRNA_tif3Δ_37 deg


title: Starved_L1_daf16_B

city: Durham

first: Colin

middle: Scott

last: Maxwell

state: NC

address: 4314 FFSC

department: Biology

institute: Duke University

data_processing:
Bowtie was used to map the reads to the WS210 genome in colorspace with the options "--best -k 1 -m 2 -S"
Reads were counted using hseq-count using WS220 annotations mapped to WS210 coordinates and the the options "-s yes"
Genome_build: WS210 with WS220 annotations
Supplementary_files_format_and_content: htseq-count files

organism: Caenorhabditis elegans

source_name: Arrested L1 larvae of strain GR1307 [daf-16(mgDf50)]

growth_protocol: C. elegans strain GR1307 [daf-16mgDf50)] was used for RNA-seq. This strain was obtained from the Caenorhabditis Genetics Center in March 2009, expanded, and frozen. Nematodes were maintained on standard NGM plates with E. coli OP50 as food (Lewis 1995), but liquid culture was used to prepare RNA-seq samples. A starved 5-cm plate was used to inoculate 25 mL of liquid culture (S-complete plus 40 mg/mL E. coli HB101) (Lewis 1995). The culture was incubated for 65 h at 20°C and 180 rpm and then bleached to produce a clean preparation of embryos. Embryos were suspended in S-complete at 5 eggs/μL and incubated for 24 h at 20°C and 180 rpm so that they hatch and enter L1 arrest. After 24 h, cultures were fed with 40 mg/mL HB101 to initiate synchronous development, and they were incubated for 57 h at 20°C and 180 rpm. In these conditions, the first eggs are fertilized at ∼53 h, and when bleached at 57 h the yield is typically about 10 eggs per worm. After 57 h, the cultures were bleached, and the eggs were suspended in S-complete at 10 eggs/μL. Animals were incubated for 24 h at 20°C and 180 rpm so that they hatch and enter L1 arrest. Larvae were collected by centrifugation and washed three times in S-basal before being flash-frozen. Two biological replicates were collected.

extract_protocol:
RNA was prepared using TRIzol (Invitrogen) according to the manufacturer's protocol with minor modifications. One milliliter of TRIzol was used per sample, and homogenization was supplemented with 100 μL of acid-washed sand. Poly-adenylated mRNA was isolated from total RNA using Dynal oligo(dT) magnetic beads (Invitrogen) according to the manufacturer's protocol.
Two hundred nanograms of poly-adenylated RNA was used in a Tobacco Acid Pyrophosphatase reaction (Epicentre) according to the manufacturer's protocol in order to remove 5′ caps. The product was purified with phenol:chloroform extraction and ethanol precipitation using GlycoBlue as a coprecipitant (Ambion). This purified product was then used in the RNase III fragmentation reaction at the beginning of the Solid Total RNA-Seq Kit Whole Transcriptome protocol (Applied Biosystems). The manufacturer's instructions were followed for the remainder of the library preparation process. Fragmentation efficiency was analyzed with the BioAnalyzer (Agilent), and one-half of each sample (corresponding to ∼100 ng of RNA) was used for adapter ligation. cDNA was gel-purified to capture inserts of RNA fragment size 100–200 nt. Twelve PCR cycles were used to amplify the libraries.


title: Starved_L1_daf16_A


title: mRNA_wild-type replicate 2_37 deg

source_name: mRNA_wild-type_37 deg


title: mRNA_wild-type replicate 1_37 deg


title: ribo_tif3delta replicate 2_37 deg

source_name: ribo_tif3Δ_37 deg


title: ribo_tif3delta replicate 1_37 deg


description:
design description: RNA-Seq analysis of brain astrocyte from NHA (A27178) using Illumina HiSeq 2000
library name: A27178
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.5
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 250-430 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: NHA

value: Astrocyte cell culture

value: primary cell culture

value: brain astrocyte


title: ribo_wild-type replicate 2_37 deg

source_name: ribo_wild-type_37 deg


description:
design description: Bisulfite-Seq analysis of breast myoepithelial cell from RM045 (A18473) using Illumina HiSeq 2000
library name: A18473
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 18 min
DNA_PREPARATION_INITIAL_DNA_QNTY: 10 ug
DNA_PREPARATION_FRAGMENT_SIZE_RANGE: N/A bp
DNA_PREPARATION_ADAPTOR_SEQUENCE: Methylated Illumina PE adaptor
DNA_PREPARATION_ADAPTOR_LIGATION_PROTOCOL: Refer to document 'Bisulfite Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
DNA_PREPARATION_POST-LIGATION_FRAGMENT_SIZE_SELECTION: 100-352 bp
BISULFITE_CONVERSION_PROTOCOL: 2 rounds of Qiagen Epitect conversion
BISULFITE_CONVERSION_PERCENT: 98.96
LIBRARY_GENERATION_PCR_TEMPLATE_CONC: N/A
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Agilent PfuTurbo Cx Hotstart DNA Polymerase
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 2 minutes at 95C, 30 seconds at 98C, 15 cycles of 10 seconds at 98C, 30 seconds at 65C and 30 seconds at 72C, then 5 minutes at 72C
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: PE primer 1.0
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: PE primer 2.0
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: female

value: Breast

value: Myoepithelial cell

value: No

value: primary cell

value: breast myoepithelial cell


description:
design description: RNA-Seq analysis of placenta (villi) tissue from CTL02 (A21763) using Illumina HiSeq 2000
library name: A21763
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 13
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 6.2
RNA_PREPARATION_INITIAL_RNA_QNTY: 5.34 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 240-420 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: male

value: Placenta

value: Villi tissue

value: placenta (villi) tissue


title: ribo_wild-type replicate 1_37 deg

value: wild-type TIF3

value: Ribosome-protected RNA


title: Top1_cKO_Topot_Rep3

city: Chapel Hill

first: Mark

last: Zylka

address: 5109D Neuroscience Research Building

institute: University of North Carolina - Chapel Hill

data_processing:
RNA-seq reads were filtered using TagDust
Reads were aligned to the reference mouse genome (mm9) with TopHat using default parameters
Reads aligning to rRNA genes were removed
Transcript abundance was estimated by computing RPKM and raw counts using RefSeq gene models aggregated by gene symbol
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of raw counts for each sample and each RefSeq gene. Cntnap2 gene model was adjusted to reflect the neuronal isoform

molecule: polyA RNA

organism: Mus musculus

source_name: Cortical neurons

growth_protocol: Embryonic day E13.5-15.5 mouse cortical neuron cultures were prepared from adult C57BL6/J wild-type females as described in Huang et al (Nature, 2012).

extract_protocol:
RNA was isolated with the RNeasy plus mini kit (Cat. #74134, Qiagen).  RNA yield and quality was determined with a Nanodrop 1000 Spectrophotometer (Thermo Scientific).  Samples were further assessed for quality using either an Agilent Bioanalyzer 2100 or TapeStation 2200 to obtain a RNA integrity number (RIN).  RIN values exceeding 7 were used for sequencing
RNA samples were used to generate and barcode cDNA libraries using the TruSeq RNA Library Preparation Kit at the UNC High Throughput Sequencing Facility.

treatment_protocol: Lentivirus from the pLenti-CaMKIIα-tdTomato and pLenti-CamKIIα-tdTomato-P2A-CRE vectors were prepared by the UNC Lentiviral Core.  Lentiviral Top1 shRNA was generated as previously described [22].  Briefly, cortical neurons were transduced at DIV 3 with lentivirus at a multiplicity of infection of at least two to maximize the number of transduced cells (around 85-90% transduction efficiency).  Media containing lentivirus was removed 24 hours later and replaced with conditioned media.  The CaMKIIα promoter limited tdTomato expression to neurons and was detectable without antibody amplification 3-4 days post transduction.  Neurons were then treated at DIV 15 with vehicle (0.003% DMSO, Neurobasal medium) or 300 nM topotecan (Molcan Corporation; in 0.003% DMSO, Neurobasal medium) and harvested 3 days later.

tag: genotype

value: cortical neurons

tag: treatment

value: Topotecan


title: PD86 H4K20me3 ChIP-seq (Ab1)

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed using trim galore v0.3.0 with parameter --quality 20 and remaining default settings
Sequenced reads were mapped to hg19 whole genome using bowtie v2.1.0 under default settings
Duplicate reads removed using picard tools v1.98 mark duplicates
Peak finding performed by SICER v1.1 (normalised to histone H4) using redundancy threshold of 1, window size of 200bp, fragment size of 150bp, effective genome fraction of 0.75, gap size of 200bp and R of 0.01.
Peaks from both antibodies were intersected.
Differential peaks were called using Diffbind (v1.8.3)
Genome_build: hg19
Supplementary_files_format_and_content: Peak files (bed format) were generated using SICER, Differential region file (bed format) was generated using DESeq

source_name: IMR90 fibroblasts

growth_protocol: IMR90 cells were cultured in DMEM supplemented with 20% (v/v) FBS, 2 mM L-Glutamine, 50 U/ml Pen-Strep and incubated at 37°C in a humidified 5% CO2 and 3% O2 atmosphere. Every 3-4 days the cells were passaged to maintain 40%–90% confluence level until they stopped proliferating through replicative senescence.

extract_protocol:
Cross-linked cells were pre-extracted with (1:1) modified nuclear lysis buffer (mNLB):IP dilution buffer (IPDB) [35 mM Tris-HCl pH 8.0, 75 mM NaCl, 5.5 mM EDTA pH 8.0, 3 mM EGTA pH 8.0, 0.5% SDS, 0.5% Triton X-100] supplemented with 10 μg/ml aprotinin, 5 μg/ml leupeptin, 50 μg/ml PMSF and sonicated at a density of 2 x 107 cells per 1 ml cold (1:1) mNLB:IPDB plus inhibitors. Sonicated chromatin solutions were cleared by centrifugation, diluted with IPDB [20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS] to a final mNLB:IPDB ratio of 1:10, transferred to microcentrifuge tubes containing antibodies (from Millipore (04-079) and Cell Signaling Technology (5737)) pre-bound to Dynabeads M-280 Sheep anti-Rabbit IgG magnetic beads (Life Technologies), and incubated overnight at 4° C with rotation. The ChIP reactions were washed twice with IPDB, once with High Salt Wash Buffer [20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X- 100], once with LiCl Wash Buffer [10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid] and twice with 1X TE. Beads were aspirated to dryness, resuspended in 500 μl IP Elution Buffer [50 mM Tris-HCl pH 8.0, 300 mM NaCl, 10 mM EDTA pH 8.0, 1% SDS] and 0.5 μl 100 mg/ml RNase A and incubated at 65° C for 4-6 hours. To each tube, 6 μl 20 mg/ml proteinase K was added and the tubes were incubated at 45° C for 12 hours. ChIP DNA was purified by phenol/chloroform extraction with ethanol precipitation, resuspended with 20 μl nuclease-free dH2O and quantified using the Qubit dsDNA HS Assay Kit and a Qubit fluorometer (Life Technologies).
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®(E6240S). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by agarose gel excision and PCR-amplified using Illumina primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: Cells were cultured to approximately 95% confluence in 100 mm cell culture dishes containing 10 ml growth medium. This corresponds to approximately 4-5 million proliferating cells or 1-2 x million senescent cells per 100 mm culture dish. Cells were subjected to cross- linking in the presence of 1% formaldehyde by the addition of 271 μl of 37% formaldehyde (Sigma) to 10 ml of growth medium. Cross-linking was conducted for 10 minutes at room temperature, with gentle agitation on a rocking platform. The cross-linking reaction was quenched for 5 minutes at room temperature by the addition of 500 μl 2.5 M glycine to a final concentration of 125 mM. Cells were detached from the culture dishes using plastic cell scrapers and collected in 50 ml centrifuge tubes kept on ice. Cells were subjected to centrifugation for 5 minutes at 200 x g and 4° C. The supernatant was removed by aspiration, the cell pellets were washed with cold 1X PBS and subjected to centrifugation for an additional 5 minutes at 200 x g and 4° C. The supernatant was removed by aspiration, cell pellets were snap frozen with dry ice and ethanol and stored at -80° C.

tag: cell line

tag: chip antibody

value: anti-H4K20me3, Millipore, 04-079, rabbit mAb


title: PD86 H4K20me3 ChIP-seq (Ab2)

value: anti-H4K20me3, Cell Signaling Technology, 5737, rabbit mAb


title: PD32 H4K20me3 ChIP-seq (Ab1)


title: PD32 H4K20me3 ChIP-seq (Ab2)


title: Top1_cKO_Topot_Rep1


title: Top1_cKO_Veh_Rep2

value: Vehicle


title: Top1_cKO_Veh_Rep3


title: mRNA_tif3delta replicate 2_37 deg

value: tif3 delta mutant

value: mRNA


title: WT_Topot_Rep2

value: Wild-type


title: WT_Topot_Rep1


title: WT_Veh_Rep3


title: WT_Topot_Rep3


title: WT_Veh_Rep1


title: RedRock_Late

city: Pittsburgh

first: Travis

last: Mavrich

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.2.6
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.2
BAM format was converted to BED format using bedtools version 2.25.0
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.25.0
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: JN699005.1 (Alma)
Genome_build: KF861510.1 (EagleEye)
Genome_build: KT285706.1 (Pioneer)
Genome_build: GU339467.1 (RedRock)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycolicibacterium smegmatis MC2 155

source_name: Mycobacterium smegmatis infected with mycobacteriophage RedRock for 2 hours 30 minutes (Late)

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using Ribo-Zero (Illumina)
Libraries were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: host strain

value: Mycobacterium smegmatis str. MC2 155

tag: phage

value: Mycobacterium phage RedRock

tag: infection timepoint

value: 2 hours 30 minutes


title: RedRock_Lysogen

source_name: Mycobacteriophage RedRock lysogen

value: no exogenous phage added


title: WT_Veh_Rep2


title: Pioneer_Lysogen

source_name: Mycobacteriophage Pioneer lysogen

value: Mycobacterium phage Pioneer


title: EagleEye_Lysogen

source_name: Mycobacteriophage EagleEye lysogen

value: Mycobacterium phage Eagle


title: RedRock_Early

source_name: Mycobacterium smegmatis infected with mycobacteriophage RedRock for 30 minutes (Early)

value: 30 minutes


title: control_no3

city: Nijmegen

first: Duy

last: Nguyen

address: Heyendaalseweg 135

department: Molecular Plant Physiology

country: Netherlands

institute: Radboud University

description: processed data column: 42

data_processing:
read mapping by bowtie v. 0.12.7
Global normalization among samples was performed by the method implemented in the R-package DESeq
Reads per kilobase of contig length per million mapped reads (RPKM) values were also calculated and used to filter out noise contigs with RPKM lower than 1 in all samples
Differential expression calls, based on normalized read counts, were performed using the DESeq
false discovery rate (FDR) p values calculated according to the Benjamini & Hochberg procedure
Genome_build: Solanum dulcamara transcriptome DAgostino2013 Contigs, solgenomics.net
Supplementary_files_format_and_content: each file is a matrix of contig numbers and their raw (or normalized) read counts in each sample

organism: Solanum dulcamara

source_name: leaf_control_no insect

growth_protocol: plants were grown in standard greenhouse

extract_protocol:
Total RNA of the following tissues was isolated with the Plant RNeasy kit (Qiagen). DNase treatment done using TURBO DNA-free kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5 days water treatments + 2 days insect treatments, water treatments were maintained during insect treatments

tag: water treatment

value: control

tag: insect treatment

value: no

tag: tissue

value: leaf


title: Alma_Lysogen

source_name: Mycobacteriophage Alma lysogen

value: Mycobacterium phage Alma


title: flooding_no2

description: processed data column: 44

source_name: leaf_flooding_no insect

value: flooding


title: control_no2

description: processed data column: 41


title: flooding_no3

description: processed data column: 45


title: flooding_no1

description: processed data column: 43


title: Top1_cKO_Topot_Rep2

value: cortical neurons

value: Topotecan


title: Msmegmatis_Null

source_name: Mycobacterium smegmatis


description:
design description: ChIP-Seq input analysis of brain (germinal matrix) tissue from HuFGM02 (A02759) using Illumina Genome Analyzer IIx
library name: A02759
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 50-307 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Brain

tag: histological type

value: Germinal matrix tissue

value: No

value: primary tissue

value: brain (germinal matrix) tissue


title: S. epidermidis ET-024 in single species biofilms_replicate E2

city: Ghent

first: Ilse

last: Vandecandelaere

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: E vs.EM.xls

data_processing:
illumina base-calling
all data were analysed according to the manufacturer's instructions of the CLC Genomic Workbench 8.5.1
reads were mapped to the entire gene with 100 % similarity and no mapping to the flanking regions was allowed
RPKM values were calculated and the p value was determined using edgeR statistics
Supplementary_files_format_and_content: M vs. EM.xls and E vs. EM.xls summarized the gene expression levels in dual species biofilms compared to single species biofilms

organism: Staphylococcus epidermidis

source_name: single species biofilms

growth_protocol: Single and dual species biofilms of S. epidermidis ET-024 and S. aureus Mu50 were grown in mueller hinton broth for 24 hours at 37°C.

extract_protocol:
RiboPure RNA purification Bacteria Kit
TruSeq stranded library preparation Kit (Illumina)

tag: sample type

value: S. epidermidis ET-024


title: S. epidermidis ET-024 in single species biofilms_replicate E1

description: E vs.EM.xls


title: drought_no3

description: processed data column: 39

source_name: leaf_drought_no insect

value: drought


title: S. epidermidis ET-024 in single species biofilms_replicate E

description: E vs.EM.xls


title: Top1_cKO_Veh_Rep1

tag: strain

tag: cell type

value: Vehicle


title: drought_no1

description: processed data column: 37


title: flooding_baw3

description: processed data column: 18

value: 48-h herbivory by Spodoptera exigua (BAW)


title: drought_no2

description: processed data column: 38


title: flooding_baw1

description: processed data column: 16


title: control_baw2

description: processed data column: 14

value: control


title: flooding_baw2

description: processed data column: 17


title: control_baw3

description: processed data column: 15


title: control_baw1

description: processed data column: 13


title: drought_baw2

description: processed data column: 11


title: drought_baw3

description: processed data column: 12


title: pCRISPR-I, II

city: Berkeley

first: James

last: Nunez

address: 731 Stanley Hall

institute: University of California, Berkeley

description: pUC19 with CRISPR-I+II locus

data_processing:
3' adapters were removed using Cutadapt, discarding reads shorter than 15nt
Reads containing integrated protospacer were selected using Cutadapt, requiring at least 10 nt of protospacer sequence with no errors
Reads were mapped to plasmid fasta usinig Bowtie, allowing up to 2 mismatches and requiring unique mapping
Genome_build: pCRISPR or pUC19
Supplementary_files_format_and_content: .xls files containing protospacer sequence, plasmid strand and location of integration, and number of reads found

organism: Cloning vector pUC19

source_name: Purified plasmid DNA

extract_protocol:
Integration reactions were performed with Cas1-Cas2, protospacer, and plasmid.
Integration products were fragmented, end-repaired, adapter ligated, PCR amplified, and analyzed by Illumina sequencing.

tag: host

value: Escherichia coli BL21

tag: protospacer strand 1

value: GCCCAATTTACTACTCGTTCTGGTGTTTCTCGT

tag: protospacer strand 2

value: ACGAGAAACACCAGAACGAGTAGTAAATTGGGC

value: plasmid DNA


title: dual species biofilms of S. aureus Mu50 and S. epidermidis ET-024_replicate EM2

description: M vs. EM.xls / E vs. EM.xls

organism:
Staphylococcus aureus
Staphylococcus epidermidis

source_name: dual species biofilms

value: S. aureus Mu50 + S. epidermidis ET-024


title: pCRISPR-I, with IHF

description: pUC19 with CRISPR-I locus


title: drought_baw1

description: processed data column: 10

value: leaf


title: pCRISPR-I, no IHF

description: pUC19 with CRISPR-I locus


title: dual species biofilms of S. aureus Mu50 and S. epidermidis ET-024_replicate EM1

description:
i.e. outliner; was excluded from analysis
M vs. EM.xls / E vs. EM.xls


title: control_no1

description: processed data column: 40

value: no


title: epi90_3_0.3x

status: Public on May 26 2016

city: Seattle

first: Jay

last: Shendure

state: Wa

address: 6528 19th Avenue NE

department: Genome Sciences

institute: University of Washington

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample75

data_processing:
Sequences were trimmed, filtered and called according to the v1.0 of the FateMap pipeline publicly available here: https://github.com/shendurelab/Cas9FateMapping
Genome_build: HG19
Supplementary_files_format_and_content: called UMI file (.stats.txt): A file containing rows for the sequencing read recovered (when done without UMIs) or the UMI sequence.  Each row contains the name, whether the read was 2) kept after filtering, 3) if the read couldn't be merged, did the calls per-target site conflict?, 3) were the calls from paired reads or a merged read, 4+) the indel events over each of the targets in the read
Supplementary_files_format_and_content: annotations file: the annotations of node names in the PHYLIP MIX input file to their event identity
Supplementary_files_format_and_content: MIX data matrix: the data matrix input to the PHYLIP mix tool
Supplementary_files_format_and_content: JSON tree file: a richly annotated lineage tree stored in the JSON format, compatible with D3 tree visualization
Supplementary_files_format_and_content: MIX genotype output: the raw output file containing genotypes produced by PHYLIP MIX
Supplementary_files_format_and_content: MIX newick tree output: the newick trees produced as output from PHYLIP MIX

organism: Danio rerio

extract_protocol:
Kapa High Fidelity Polymerase was used for all barcode amplification steps. Gradient PCRs were performed to optimize annealing temperatures for amplification from gDNA. For experiments performed without UMIs, up to 250 ng of gDNA was loaded into a single 50 µl PCR reaction and amplified using primers immediately flanking the barcode (see table S4 for oligo sequences). If there was less than 250 ng from a sample, all of it was used in a single reaction. For experiments performed with UMIs, a primer with a sequencing adapter and 10 nt of fully degenerate sequence 5' to the barcode-flanking sequence was used for a single prolonged extension step, in which the temperature was ramped between annealing and extending for five cycles (without a denaturing step to prevent re-sampling of gDNA barcodes). All cell culture experiments and v6 zebrafish embryos received a single extension to incorporate UMIs, whereas v7 embryo time-course experiments and all ADR1 tissues (also v7) received 2 UMI incorporation cycles due to having low gDNA consequent to fewer cells being present in early embryo and sorted heart samples. To minimize repetitive amplification of the same barcode, no reverse primer was included in UMI-tagging reactions. DNA was then purified using AMPure beads (Agencourt), and loaded into a PCR primed from the sequencing adapter flanking each UMI and a site immediately 3' of the barcode.
For all experiments, two ensuing qPCRs were performed prior to sequencing to incorporate sequencing adapters, sample indexes, and flow cell adapters. AMPure beads were used to purify PCR products after each reaction.

tag: developmental stage


title: epi90_9_0.3x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample124


title: epi90_5_1x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample83


title: epi90_8_1x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample69


title: epi90_9_1x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample77


title: epi90_2_0.3x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample113


title: epi90_12_0.3x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample108


title: epi90_10_1x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample82


title: epi90_2_1x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample85


title: epi90_10_0.3x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample132


title: Dome_7_0.3x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample45


title: epi90_12_1x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample101


title: Dome_9_1x

description:
GESTALT_Barcode
barcode readout of 30 hours post fertilization embryo with lineage barcode V6
sample90


title: epi90_1_0.3x

description:
GESTALT_Barcode
barcode readout of 9 hours post fertilization embryo with lineage barcode V7
sample42


title: Dome_8_1x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample15


title: dual species biofilms of S. aureus Mu50 and S. epidermidis ET-024_replicate EM

description: M vs. EM.xls / E vs. EM.xls


title: Dome_5_0.3x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample63


title: Dome_3_1x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample40


title: Dome_10_0.3x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample50


title: Dome_5_1x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample121


title: Dome_6_0.3x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample71


title: 7B_Upper_GI

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample64

value: adult


title: 7B_Heart_GFP+

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample7


title: 7B_Heart_diss

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample114


title: 7B_Gills

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample68

value: Gills


title: 7B_Heart_chunk

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample94


title: 7B_Heart_GFP-

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample92


title: 7B_Intestine

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample23

value: Intestine


title: Dome_1_1x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample10


title: 7B_Eye1

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample30


title: 7B_Brain

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample76

value: Brain


title: 7B_Eye2

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample44


title: 7B_1_to_20_blood

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample66


title: 3d_6_1x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample135


title: 3d_6_0.3x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample74


title: 7B_1_to_100_blood

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample96


title: 7B_1_to_500_blood

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample115


title: 3d_5_0.3x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample125


title: 3d_3_0.3x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample48


title: 3d_4_0.3x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample51


title: 3d_4_1x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample104


title: Dome_10_1x

description:
GESTALT_Barcode
barcode readout of 4.3 hours post fertilization embryo with lineage barcode V7
sample49


title: 3d_3_1x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample35


title: 3d_1b_1x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample41


title: 3d_2_0.3x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample60


title: 3d_1b_0.3x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample8


title: 3d_2_1x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample20


title: 3d_1_1x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample61


title: 3d_1_0.3x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample46


title: 7B_Blood

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR1 with V7 lineage barcode
sample88

value: Blood


title: 30hr_5_1x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample52


title: 3d_5_1x

description:
GESTALT_Barcode
barcode readout of 72 hours post fertilization embryo with lineage barcode V7
sample134


title: 30hr_5_0.3x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample33


title: 30hr_3_0.3x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample17


title: 30hr_6_0.3x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample26


title: 30hr_3_1x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample55


title: 30hr_4_1x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample127


title: 30hr_2_1x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample105


title: 17_Upper_GI

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample58


title: 30hr_1_0.3x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample2


title: 30hr_6_1x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample24


title: 17_Heart_GFP+

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample14


title: 17_Heart_GFP-

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample73


title: 30hr_1_1x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample5


title: 30hr_2_0.3x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample130


title: 17_Heart_diss

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample120


title: 17_Intestine

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample43


title: 17_Gills

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample28


title: 17_Heart_chunk

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample6


title: 17_Eye2

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample59


title: 17_Eye1

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample97


title: 17_Brain

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample54


title: 17_Blood

description:
GESTALT_Barcode
DNA barcode sequencing of adult ADR2 with V7 lineage barcode
sample79


title: HITS-CLIP_NOVA1_rep2

city: New York

first: Yuhki

last: Saito

state: NY

address: 1230 York avenue

institute: The Rockefeller University

data_processing:
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping on mm9)
collapsing of PCR duplicates
clustering of unique reads
Genome_build: mm9
Supplementary_files_format_and_content: bed file containing genomic coordinates of NOVA2 or NOVA1 clusters and unique reads numbers in the clusters>=10 and BC>=2

source_name: cortex

extract_protocol:
Brain tissue was UV irradiated and subjected to NOVA2 and NOVA1 HITS-CLIP (detailed description in accompanying paper)
partial RNAse digestion, RNA linker ligation and PCR amplificiation. NOVA bound fragments were ligated to a degenerate 5'linker and a 3'linker

value: brain

tag: tissue compartment

value: cortex

value: embryonic day 18.5


title: 30hr_4_0.3x

description:
GESTALT_Barcode
barcode sequencing of 30 hours post fertilization embryo with lineage barcode V7
sample21


title: HITS-CLIP_NOVA1_rep1


title: HITS-CLIP_NOVA1_rep3


title: HITS-CLIP_NOVA2_rep1


title: HITS-CLIP_NOVA2_rep2


title: HITS-CLIP_NOVA2_rep3


title: RNAseq_Nova1-KO2_midhindbrain

data_processing:
alignment with Olego
inference of exon junctions (Bayesian method)
RNA abundance analysis (edgeR) and alternative splicing events analysis (Quantas)
Genome_build: mm9
Supplementary_files_format_and_content: txt file containing gene symbol, raw read number, log2 fold change (ko/wt), FDR, chr number, start and end positon, strand, dI

source_name: mid- and hind-brain

extract_protocol:
Trizol extraction
Illumina High-throughput TruSeq RNA Sample preparation: ribozero selection

tag: strain background

value: mid- and hind-brain

tag: genotype


title: RNAseq_Nova1-KO3_midhindbrain


title: RNAseq_Nova1-KO1_midhindbrain


title: RNAseq_WT6_midhindbrain

value: wild-type


title: WGBS from H1-hESC (ENCLB098BGY)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR617FKV/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing H1-hESC
experiment encode accession: ENCSR617FKV
assay title: WGBS
assembly: GRCh38
encode release date: 2015-10-13
lab: Richard Myers, HAIB
library encode accession: ENCLB098BGY

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

tag: description

value: embryonic stem cells

tag: biosample encode accession

tag: age

value: unknown

tag: dev stage

value: embryonic

value: male

tag: health state

value: healthy

tag: lab

value: Richard Myers, HAIB

tag: link

value: ENCBS111ENC at ENCODE; https://www.encodeproject.org/ENCBS111ENC/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: RNAseq_WT4_midhindbrain

tag: tissue


title: RNAseq_WT6_cortex


title: RNAseq_WT5_midhindbrain


title: WGBS from skeletal muscle myoblast (ENCLB587BLQ)

description:
https://www.encodeproject.org/experiments/ENCSR328TBS/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing HSMM
experiment encode accession: ENCSR328TBS
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB587BLQ

source_name: Homo sapiens skeletal muscle myoblast primary cell

value: skeletal muscle myoblast

value: primary cell

tag: Sex

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS665DRD at ENCODE; https://www.encodeproject.org/ENCBS665DRD/

value: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/


title: RNAseq_Nova1-KO2_cortex

value: brain

value: cortex


title: RNAseq_Nova2-KO2_cortex


title: RNAseq_WT5_cortex

value: wild-type


title: RNAseq_WT4_cortex


title: RNAseq_Nova2-KO3_cortex


title: RNAseq_Nova1-KO3_cortex


title: RNAseq_WT2_cortex

description: wild-type _cortex2


title: RNAseq_WT3_cortex

description: wild-type _cortex3


title: RNAseq_Nova2-KO1_cortex


title: RNAseq_WT1_cortex

description: wild-type _cortex1


title: RLN05

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Avenue South, Suite 276/11

institute: University of Alabama at Birmingham

data_processing:
50bp reads were demultiplexed according to 10bp barcodes using BioScope software (Applied Biosystems)
Reads were aligned using BioScope software (Applied Biosystems)
Expression data presented as reads per million total mapped reads (RPM)
Genes with < 3 RPM for all samples were omitted from further consideration
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPM values for each non-omitted gene (row, n=14725) and each sample (column, n=27)

source_name: Regulatory T Cells from Lymph Node

extract_protocol:
Regulatory T cells were sorted by FACS from single cell suspensions.  Total RNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) following manufacturers protocol.  RNA quality was assessed by 2100 BioAnalyzer (Agilent).
Total RNA was used for cDNA synthesis using Ovation RNA-Seq (NuGEN) with normalized RNA input for each sample.  Amplified cDNA was purified through MinElute reaction cleanup column (Qiagen).  cDNA quality was assessed using 2100 BioAnalyzer (Agilent).  SOLiD protocols were followed for library prepartion for 50bp sequencing.

value: Lymph Node

tag: diagnosis

value: Reactive Lymph Node

tag: cell type

value: Regulatory T Cells

tag: gender

tag: follicular lymphoma grade


title: RLN07


title: WGBS from skeletal muscle myoblast (ENCLB988SSO)

description:
https://www.encodeproject.org/experiments/ENCSR328TBS/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing HSMM
experiment encode accession: ENCSR328TBS
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB988SSO

value: skeletal muscle myoblasts

value: unknown

value: ENCBS328AAA at ENCODE; https://www.encodeproject.org/ENCBS328AAA/

value: ENCODE dbxrefs HSMM; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HSMM

value: Lonza  sample source; http://www.lonza.com/


title: RLN02


title: FL102

value: Follicular Lymphoma

value: F


title: FL101

value: M


title: RLN01


title: RNAseq_Nova1-KO1_cortex

tag: developmental stage


title: FL12


title: FL14


title: FL11


title: FL09


title: FL08


title: FL04


title: NLN10

value: Normal Lymph node


title: NLN12


title: FL03


title: NLN08


title: RLN03


title: NLN07


title: NLN06


title: NLN03


title: NLN04


title: NLN02


title: RNAseq_siCont2

city: Edinburgh

first: Julie

last: Rodor

address: Western General Hospital

department: MRC Human Genetics Unit

institute: University of Edinburgh

data_processing:
Reads mapping and transcript quantification were done using Sailfish (Rapid Alignment-free Quantification of Isoform Abundance) (Patro, Mount, & Kingsford, 2014) using the hg19 annotation of the human genome. The TPM (transcripts per million) for each gene were obtained after pooling the value of its different transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: [tpm.txt] Reports TPMs (transcripts per million) per ENSEMBL gene Id

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in medium (DMEM, 10% FCS, 1% penicillin/streptomycin) at 37 °C in an atmosphere containing 5% CO2.

extract_protocol:
RNA extractions were performed using RNeasy Mini Kit (Qiagen) with DNAse treatment on column.
The libraries have been obtained using the Truseq Transcriptome kit (polyA transcript enrichment) at the Beijing Genomics Institute (BGI).

treatment_protocol: Depletion of Acinus was achieved after two rounds of transfection using Dharmafect Reagent 1 (Dharmacon) and siRNA (CUGCAGAGCAUGAAGUAAAUU). As a control, cells were transfected with ON-TARGETplus Non-targeting siRNA (Dharmacon).

tag: sirna transfection


title: RNAseq_siCont1

value: ON-TARGETplus Non-targeting siRNA (Dharmacon)


title: RNAseq_siCont3


title: FL13


title: RNAseq_siAci3

value: siAcinus (CUGCAGAGCAUGAAGUAAAUU)


title: FL10


title: RNAseq_siAci2


title: RNAseq_siAci1


title: iCLIP_ContS2

description:
Cont_common_peaks.bedpk.txt
ContS_peaks.bedpk.txt

data_processing:
library strategy: iCLIP-seq
To identify Acinus binding sites, we used the peak calling algorithm Pyicoclip from the Pyicoteo tools (https://bitbucket.org/regulatorygenomicsupf/pyicoteo) (Althammer et al. 2011). Mapped reads were trimmed to 10 nt and reads overlapping simple and complex repeats as well as known non-coding RNAs were removed for this analysis. As we obtained a good correlation between replicates, we pooled reads from the different replicates. Peaks were called specifically on regions of protein-coding genes. For further analysis, we considered peaks with a modified false discovery rate below 0.01. This analysis was done for each individual iCLIP (after pooling replicates) and the equivalent controls. We calculated those significant regions present in two out of the three iCLIP peak sets. Subsequently, reads from all iCLIP experiments that intersected these regions were kept and Pyicoclip was used again with the pooled reads to obtain the final peak set on protein coding genes.
Genome_build: hg19
Supplementary_files_format_and_content: [bedpk.txt] Reports peaks. Column header names: 1. Chromosome, 2. Start coordinate, 3. End coordinate, 4. Profile, 5. Height, 6. Strand, 7. Summit, 8. Area,  9. p-value.

extract_protocol:
RNAs were extracted following the published protocol (Konig et al. 2011).
iCLIP experiments were carried out following a published protocol (Konig et al. 2011), with minor modifications. After cell lysis, extracts were sonicated for 5 min (30 secoff and 30 secon) then centrifuged at 10,000g for 3min. Supernatants were treated with various RNAse dilutions. Before the immunoprecipitation, each extract was pre-cleared for 1h with 10uL of Dynabeads protein A. The immunoprecipitation (IP) was carried out using Acinus (Ab-2) PC552 Calbiochem antibody coupled to Dynabeads Protein A, whereas rabbit IgG was used for the control. Dephosphorylation of the RNA 3’ ends was performed on beads using Alkaline Phosphatase, Calf Intestinal (CIP) following the supplier’s protocol. The RNA linker (5’Phosphate-UGAGAUCGGAAGAGCGGTTCAG-3’Puromycin) ligated to the 3’ end of the RNAs was described in (König et al. 2010). The obtained libraries were purified with Agencourt Ampure XP system (Beckman Coulter) and quantified using High sensitivity DNA ChIP on Agilent 2100 Bioanalyzer. The four libraries for the endogenous Acinus iCLIP (2 replicates for Acinus L and 2 replicates for Acinus S/S’) were sequenced together with the control libraries on a separate lane.

treatment_protocol: Cells were irradiated once with 400 mJ/cm2 at 254 nm.

tag: clip antibody

value: Rabbit IgG (Millipore 12-370, Lot DAM1795389)


title: FL06


title: iCLIP_AciS2

description:
Aci_common_peaks.bedpk.txt
AciS_peaks.bedpk.txt

value: anti-Acinus antibody (Calbiochem, ab-2 PC552)


title: iCLIP_ContS1


title: NLN09


title: iCLIP_AciS1


title: iCLIP_AciL1

description:
Aci_common_peaks.bedpk.txt
AciL_peaks.bedpk.txt


title: iCLIP_ContL2

description:
Cont_common_peaks.bedpk.txt
ContL_peaks.bedpk.txt


title: iCLIP_ContL1


title: iCLIP_T7_Cont2

description:
Cont_common_peaks.bedpk.txt
T7cont_peaks.bedpk.txt

extract_protocol:
RNAs were extracted following the published protocol (Konig et al. 2011).
iCLIP experiments were carried out following a published protocol (Konig et al. 2011), with minor modifications. After cell lysis, extracts were sonicated for 5 min (30 secoff and 30 secon) then centrifuged at 10,000g for 3min. Supernatants were treated with various RNAse dilutions. Before the immunoprecipitation, each extract was pre-cleared for 1h with 10uL of agarose beads. A T7 Tag antibody Agarose from Novagen was used for the precipitation. Dephosphorylation of the RNA 3’ ends was performed on beads using Alkaline Phosphatase, Calf Intestinal (CIP) following the supplier’s protocol. The RNA linker (5’Phosphate-UGAGAUCGGAAGAGCGGTTCAG-3’Puromycin) ligated to the 3’ end of the RNAs was described in (König et al. 2010). The obtained libraries were purified with Agencourt Ampure XP system (Beckman Coulter) and quantified using High sensitivity DNA ChIP on Agilent 2100 Bioanalyzer. Using different barcodes in the RT primers, the three libraries obtained for T7-Acinus S* iCLIP were sequenced on a single lane while the equivalent control was sequenced on a different lane

treatment_protocol: 70-90% confluent cells were transfected with the pCG-T7 Acinus S* vector (or the empty vector pCG) using Lipofectamine 2000 (Invitrogen).Cells were transferred to a 15cm dish for 24h and irradiated once with 400 mJ/cm2 at 254 nm.

value: T7 Tag antibody Agarose (Novagen, 69026)

tag: plasmid transfection

value: pCG


title: iCLIP_T7_Aci3

description:
Aci_common_peaks.bedpk.txt
T7Aci_peaks.bedpk.txt

value: T7-Acinus S* construct


title: iCLIP_T7_Cont1


title: iCLIP_AciL2


title: iCLIP_T7_Cont3


title: iCLIP_T7_Aci2


title: NLN01

value: Lymph Node

value: Regulatory T Cells


title: iCLIP_T7_Aci1


title: shRNA RNA-seq from HepG2 (ENCLB666HTV)

description:
https://www.encodeproject.org/experiments/ENCSR998RZI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TAF15 in HepG2 cells followed by RNA-seq. (TAF15-BGHLV12)
experiment encode accession: ENCSR998RZI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB666HTV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting TAF15

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5ffd2eca-caac-44bf-a98b-b0dae530ede6/@@download/attachment/L-TAF15-BGHLV12-82.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TAF15. (TAF15-BGHLV12-82)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS145HYP at ENCODE; https://www.encodeproject.org/ENCBS145HYP/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from HepG2 (ENCLB992WHC)

description:
https://www.encodeproject.org/experiments/ENCSR995ZGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SMNDC1 in HepG2 cells followed by RNA-seq. (SMNDC1 BGHLV14)
experiment encode accession: ENCSR995ZGJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB992WHC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SMNDC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/03f23221-9c1f-46dd-b702-6b4d9b3fdffb/@@download/attachment/L-SMNDC1_BGHLV14-49.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SMNDC1. (SMNDC1_BGHLV14-49)

tag: biosample encode accession

tag: age

tag: dev stage

value: ENCBS269UBV at ENCODE; https://www.encodeproject.org/ENCBS269UBV/


title: shRNA RNA-seq from K562 (ENCLB179JOW)

description:
https://www.encodeproject.org/experiments/ENCSR961YAG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF4A3 in K562 cells followed by RNA-seq. (EIF4A3-LV08)
experiment encode accession: ENCSR961YAG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB179JOW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF4A3

extract_protocol: extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4A3. (EIF4A3-LV08-21)

value: 53 year

value: adult

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

tag: link

value: ENCBS038TWG at ENCODE; https://www.encodeproject.org/ENCBS038TWG/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: shRNA RNA-seq from K562 (ENCLB507CNH)

description:
https://www.encodeproject.org/experiments/ENCSR961YAG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF4A3 in K562 cells followed by RNA-seq. (EIF4A3-LV08)
experiment encode accession: ENCSR961YAG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB507CNH
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/92ea2955-4f39-44d1-9e86-90e1393be8b0/@@download/attachment/L-EIF4A3-LV08-22.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4A3. (EIF4A3-LV08-22)

tag: Sex

value: ENCBS119EVP at ENCODE; https://www.encodeproject.org/ENCBS119EVP/


title: shRNA RNA-seq from HepG2 (ENCLB061ITC)

description:
https://www.encodeproject.org/experiments/ENCSR998RZI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TAF15 in HepG2 cells followed by RNA-seq. (TAF15-BGHLV12)
experiment encode accession: ENCSR998RZI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB061ITC
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b0138e9c-0328-4dd8-9eba-82a7304beef6/@@download/attachment/L-TAF15-BGHLV12-81.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TAF15. (TAF15-BGHLV12-81)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS904EKE at ENCODE; https://www.encodeproject.org/ENCBS904EKE/


title: shRNA RNA-seq from HepG2 (ENCLB911MQF)

description:
https://www.encodeproject.org/experiments/ENCSR997FOT/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SUB1 in HepG2 cells followed by RNA-seq. (SUB1 BGHLV14)
experiment encode accession: ENCSR997FOT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB911MQF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SUB1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1cfe21fc-8dc0-4345-bfcc-76bbc27f563f/@@download/attachment/L-SUB1_BGHLV14-58.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUB1. (SUB1_BGHLV14-58)

value: ENCBS101LFX at ENCODE; https://www.encodeproject.org/ENCBS101LFX/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from K562 (ENCLB329EBO)

description:
https://www.encodeproject.org/experiments/ENCSR961WVL/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX21 in K562 cells followed by RNA-seq. (DDX21-LV11)
experiment encode accession: ENCSR961WVL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB329EBO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9221cdb1-8627-4f9d-9c10-d0719a394ebc/@@download/attachment/L-DDX21-LV11-9.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX21. (DDX21-LV11-9)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS963XMS at ENCODE; https://www.encodeproject.org/ENCBS963XMS/


title: shRNA RNA-seq from HepG2 (ENCLB589EHY)

description:
https://www.encodeproject.org/experiments/ENCSR957EEG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF4A3 in HepG2 cells followed by RNA-seq. (EIF4A3-BGHLV12)
experiment encode accession: ENCSR957EEG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB589EHY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EIF4A3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1400613d-c34c-400e-a37a-90393f2665a6/@@download/attachment/L-EIF4A3-BGHLV12-22.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4A3. (EIF4A3-BGHLV12-22)

value: ENCBS475AHQ at ENCODE; https://www.encodeproject.org/ENCBS475AHQ/


title: shRNA RNA-seq from K562 (ENCLB643VFC)

description:
https://www.encodeproject.org/experiments/ENCSR961WVL/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX21 in K562 cells followed by RNA-seq. (DDX21-LV11)
experiment encode accession: ENCSR961WVL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB643VFC
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4bd6f8c5-cd1b-40c5-9eaf-f3f1a8f82196/@@download/attachment/L-DDX21-LV11-10.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX21. (DDX21-LV11-10)

value: ENCBS293BDC at ENCODE; https://www.encodeproject.org/ENCBS293BDC/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004