title: polyA RNA sequencing of STL003 Pancreas Cells; polyA-RNA-seq_STL003PA_r1a

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL003 Pancreas Cells
Library name: polyA-RNA-seq_STL003PA_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13853
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11847
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010966_UCSD.Pancreas.mRNA-Seq.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003PA_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Pancreas, Donor STL003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16740
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 226,063,263
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.45

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

ANALYSIS FILE NAME: GSM1010966_UCSD.Pancreas.mRNA-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003PA_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Pancreas, Donor STL003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16775
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Pancreas mRNA 03
BROWSER_TRACK_DESCRIPTION: UCSD Pancreas mRNA-Seq Donor STL003 Library polyA-RNA-seq_STL003PA_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 226,063,263
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.45

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

value: Pancreas

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: Dynabeads oligo(dt)25 (Invitrogen)

value: TruSeq Multiplexed Adapters (Illumina)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)


title: SOD1WT_Day130_B

status: Public on Jul 15 2013

type: SRA

city: New York

first: Sean

last: O'Keeffe

address: 701 West 168th Street

country: USA

institute: Columbia University

description:
CGATGT
Paired end RNA-Seq on the Illumina platform

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome (mm9) using Bowtie.
Gene levels were calculated by counting genomic and splice alignments for each RefSeq transcript (as defined in the known Isoforms table, http://genome.ucsc.edu) using TopHat and Cufflinks
Reads Per Kilobase of exon per Megabase of library size (RPKM) was used as a normalized expression value for each sample, and are displayed for each gene across all samples in the processed data file
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file including all sample RPKM values for each RefSeq transcript id, with gene aliases

molecule: total RNA

organism: Mus musculus

source_name: Spinal cord purified microglia

extract_protocol:
Mice were transcardially perfused with PBS to remove blood, spinal cords dissected, run over a 37%/70% percoll gradient to isolate immune cells.  CD11b magnetic beads were used to purify microglia from these leukocytes, RNA was harvested using Trizol reagent and RNeasy columns. Bioanalyzer chips were used to assay quality of RNA prior to amplifcation using the Ovation RNAseq system.  Paired-end libraries were generated by standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B6SJL SOD1G93A, SOD1WT, Non-transgenic mice were collected at day 65 (pre-symptomatic), day 100 (symptomatic), and end-stage (or day 130).  B6SOD1G93A at end-stage, B6 non-transgenic or B6 mice injected intraperitoneally with LPS (48 hours prior) were used for spinal cord dissection and microglia collection.

tag: genetic background

tag: genotype

value: SOD1 transgenic

tag: age/disease timepoint

value: Day 130

tag: sample type

value: WTSOD1 end-stage control

tag: disease state

value: WTSOD1 end-stage control amyotrophic lateral sclerosis

tag: cell type

value: microglia


title: B6_LPS_A

description:
TGACCA
Paired end RNA-Seq on the Illumina platform

value: wild type

value: Day 150

value: LPS injected 48 hr timepoint


title: polyA RNA sequencing of STL002 Ovary Cells; polyA-RNA-seq_STL002OV_r1a

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL002 Ovary Cells
Library name: polyA-RNA-seq_STL002OV_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13835
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010948_UCSD.Ovary.mRNA-Seq.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002OV_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Ovary mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Ovary, Donor STL002 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16741
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 143,467,559
PERCENT_READS_MAPPING_TO_UCSC_GENES: 86.37
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1010948_UCSD.Ovary.mRNA-Seq.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002OV_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Ovary mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Ovary, Donor STL002 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16776
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Ovary mRNA 02
BROWSER_TRACK_DESCRIPTION: UCSD Ovary mRNA-Seq Donor STL002 Library polyA-RNA-seq_STL002OV_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 143,467,559
PERCENT_READS_MAPPING_TO_UCSC_GENES: 86.37
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: NA

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

organism: Homo sapiens

extract_protocol: Library construction protocol: Four µg of total RNA was extracted from frozen cell pellets using the RNeasy Mini Kit (Qiagen, Valencia, CA). PolyA RNA was isolated from total RNA using Dynabeads oligo(dt)25 (Invitrogen). PolyA selected RNA was eluted in 2x Superscript III buffer supplemented with 10mM DTT and was fragmented by incubation at 94°C for 4 minutes. First-strand cDNA was synthesized with the following reaction composition: 0.5 µL random hexamer, 0.5 µL RNase Out, 1 µL DTT (100 mM), 0.5 µL dNTP (25 mM), 0.5 µL SuperScript III (20 µL final). The reaction was incubated at 25°C for 10 min then 50°C for 50 min.  Single-stranded cDNA was isolated by purification with RNAClean XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing second-strand was synthesized with the following reaction: 1.5 µL NEBuffer 2 (NEB), 1 µL dNTP mix (10 mM dATP, dCTP, dGTP, and dUTP), 0.2 µL RNase H, 1 µL DNA Polymerase I (E. coli) (New England Biolabs) (15 µL final). The reaction was incubated at 16°C for 2.5 hours. The dUTP-containing cDNA was isolated by purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). The dUTP-containing cDNA was then end repaired and a 3'A base was added. TruSeq adapters (Illumina, San Diego, CA) were ligated to the dUTP-containing cDNA at 16°C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated cDNA was isolated by two rounds of purification with AMPure XP beads. The dUTP-containing strands were digested at 37°C for 30 min with uracil DNA glycosylase (Enzymatics). Adapter-ligated, single-stranded DNA molecules were enriched by 10 cycles of PCR with the following reaction composition: 5 µL TruSeq PCR Primer Cocktail (Illumina), 25 µL TruSeq PCR Master Mix (Illumina) (50 µL final). The thermocycling parameters were: 98°C 30 sec, then 10-15 cycles of 98°C 10 sec, 60°C 30 sec and 72°C 30 sec, ending with one 72°C 5 min step. The reaction products were purified using AMPure XP beads.

tag: sample alias

tag: sample common name

value: Ovary

tag: disease

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: polyA RNA sequencing of STL003 Psoas Cells; polyA-RNA-seq_STL003PO_r1a

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL003 Psoas Cells
Library name: polyA-RNA-seq_STL003PO_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13855
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010968_UCSD.Psoas_Muscle.mRNA-Seq.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003PO_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Psoas Muscle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Psoas Muscle, Donor STL003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16748
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 516,519,321
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.01
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

ANALYSIS FILE NAME: GSM1010968_UCSD.Psoas_Muscle.mRNA-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003PO_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Psoas Muscle, Donor STL003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16783
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PM mRNA 03
BROWSER_TRACK_DESCRIPTION: UCSD Psoas Muscle mRNA-Seq Donor STL003 Library polyA-RNA-seq_STL003PO_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 516,519,321
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.01
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

source_name: Psoas Muscle tissue; polyA-RNA-seq_STL003PO_r1a

value: Psoas Muscle

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)


title: polyA RNA sequencing of STL003 Adrenal Cells; polyA-RNA-seq_STL003AD_r1a

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL003 Adrenal Cells
Library name: polyA-RNA-seq_STL003AD_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13837
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010950_UCSD.Adrenal_Gland.mRNA-Seq.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003AD_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adrenal Gland mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Adrenal Gland, Donor STL003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16743
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 239,751,732
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.53
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.48

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

ANALYSIS FILE NAME: GSM1010950_UCSD.Adrenal_Gland.mRNA-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003AD_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Adrenal Gland, Donor STL003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16778
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: AG mRNA 03
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland mRNA-Seq Donor STL003 Library polyA-RNA-seq_STL003AD_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 239,751,732
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.53
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.48

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

source_name: Adrenal Gland tissue; polyA-RNA-seq_STL003AD_r1a

value: Adrenal Gland

value: Caucasian

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: polyA RNA sequencing of STL003 Aorta Cells; polyA-RNA-seq_STL003AO_r1a

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL003 Aorta Cells
Library name: polyA-RNA-seq_STL003AO_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13839
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010952_UCSD.Aorta.mRNA-Seq.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003AO_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Aorta mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Aorta, Donor STL003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16730
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 220,081,725
PERCENT_READS_MAPPING_TO_UCSC_GENES: 78.2
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.4

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

ANALYSIS FILE NAME: GSM1010952_UCSD.Aorta.mRNA-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003AO_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Aorta, Donor STL003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16765
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Aorta mRNA 03
BROWSER_TRACK_DESCRIPTION: UCSD Aorta mRNA-Seq Donor STL003 Library polyA-RNA-seq_STL003AO_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 220,081,725
PERCENT_READS_MAPPING_TO_UCSC_GENES: 78.2
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.4

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

value: Aorta

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers


title: SOD1WT_Day130_A

description:
CTTGTA
Paired end RNA-Seq on the Illumina platform

value: SOD1 transgenic

value: Day 130

value: WTSOD1 end-stage control

value: WTSOD1 end-stage control amyotrophic lateral sclerosis

value: microglia


title: polyA RNA sequencing of STL001 Thymus Cells; polyA-RNA-seq_STL001TH_r1a

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL001 Thymus Cells
Library name: polyA-RNA-seq_STL001TH_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13831
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010944_UCSD.Thymus.mRNA-Seq.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001TH_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Thymus mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Thymus, Donor STL001 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16738
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 635,463,380
PERCENT_READS_MAPPING_TO_UCSC_GENES: 84.51
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1010944_UCSD.Thymus.mRNA-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001TH_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Thymus mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Thymus, Donor STL001 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16773
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Thymus mRNA 01
BROWSER_TRACK_DESCRIPTION: UCSD Thymus mRNA-Seq Donor STL001 Library polyA-RNA-seq_STL001TH_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 635,463,380
PERCENT_READS_MAPPING_TO_UCSC_GENES: 84.51
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Thymus

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: polyA RNA sequencing of STL002 Lung Cells; polyA-RNA-seq_STL002LG_r1a

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL002 Lung Cells
Library name: polyA-RNA-seq_STL002LG_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13833
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12247
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010946_UCSD.Lung.mRNA-Seq.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002LG_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Lung mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Lung, Donor STL002 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16734
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 160,836,879
PERCENT_READS_MAPPING_TO_UCSC_GENES: 79.5
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.51

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

ANALYSIS FILE NAME: GSM1010946_UCSD.Lung.mRNA-Seq.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL002LG_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Lung mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Lung, Donor STL002 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16769
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Lung mRNA 02
BROWSER_TRACK_DESCRIPTION: UCSD Lung mRNA-Seq Donor STL002 Library polyA-RNA-seq_STL002LG_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 160,836,879
PERCENT_READS_MAPPING_TO_UCSC_GENES: 79.5
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.51

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

source_name: Lung tissue; polyA-RNA-seq_STL002LG_r1a

value: Lung

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers


title: polyA RNA sequencing of STL003 Right Ventricle Cells; polyA-RNA-seq_STL003RV_r1a

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL003 Right Ventricle Cells
Library name: polyA-RNA-seq_STL003RV_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13859
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010972_UCSD.Right_Ventricle.mRNA-Seq.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003RV_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Ventricle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Right Ventricle, Donor STL003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16757
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 170,168,899
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.02
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

ANALYSIS FILE NAME: GSM1010972_UCSD.Right_Ventricle.mRNA-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003RV_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Right Ventricle, Donor STL003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16792
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: RV mRNA 03
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle mRNA-Seq Donor STL003 Library polyA-RNA-seq_STL003RV_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 170,168,899
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.02
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: 0.63

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

source_name: Right Ventricle tissue; polyA-RNA-seq_STL003RV_r1a

value: Right Ventricle

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: SOD1WT_Day100_C

description:
GCCAAT
Paired end RNA-Seq on the Illumina platform

value: SOD1 transgenic

value: Day 100

value: WTSOD1 symptomatic control

value: WTSOD1 symptomatic control amyotrophic lateral sclerosis

value: microglia


title: SOD1WT_Day100_B


title: polyA RNA sequencing of STL001 Sigmoid Colon Cells; polyA-RNA-seq_STL001SG_r1a

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL001 Sigmoid Colon Cells
Library name: polyA-RNA-seq_STL001SG_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13829
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010942_UCSD.Sigmoid_Colon.mRNA-Seq.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001SG_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Sigmoid Colon, Donor STL001 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16731
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 248,960,740
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.54
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.41

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

ANALYSIS FILE NAME: GSM1010942_UCSD.Sigmoid_Colon.mRNA-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001SG_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Sigmoid Colon, Donor STL001 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16766
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SC mRNA 01
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon mRNA-Seq Donor STL001 Library polyA-RNA-seq_STL001SG_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 248,960,740
PERCENT_READS_MAPPING_TO_UCSC_GENES: 90.54
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.41

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

source_name: Sigmoid Colon tissue; polyA-RNA-seq_STL001SG_r1a

value: Sigmoid Colon

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers


title: SOD1WT_Day100_A

value: SOD1 transgenic

value: Day 100

value: WTSOD1 symptomatic control

value: WTSOD1 symptomatic control amyotrophic lateral sclerosis

value: microglia


title: NonTG_Day130_D

value: wild type

value: Day 130

value: End-stage control

value: End-stage control amyotrophic lateral sclerosis


title: NonTG_Day130_C


title: polyA RNA sequencing of STL001 Small Bowel Cells; polyA-RNA-seq_STL001SB_r1a

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL001 Small Bowel Cells
Library name: polyA-RNA-seq_STL001SB_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13827
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010940_UCSD.Small_Intestine.mRNA-Seq.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001SB_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Small Intestine mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Small Intestine, Donor STL001 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16723
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 247,928,941
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.97
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.36

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

ANALYSIS FILE NAME: GSM1010940_UCSD.Small_Intestine.mRNA-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001SB_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Small Intestine, Donor STL001 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16758
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SI mRNA 01
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine mRNA-Seq Donor STL001 Library polyA-RNA-seq_STL001SB_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 247,928,941
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.97
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.36

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

source_name: Small Intestine tissue; polyA-RNA-seq_STL001SB_r1a

value: Small Intestine

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: NonTG_Day130_B

value: wild type

value: Day 130

value: End-stage control

value: End-stage control amyotrophic lateral sclerosis

value: microglia


title: polyA RNA sequencing of STL001 Left Ventricle Cells; polyA-RNA-seq_STL001LV_r1a

description:
note: SRA Runs SRR651692, SRR651693 and SRR651694 were moved from to SRX190130 (GSM1010958) to SRX190110 (GSM1010938) on May 22, 2015.

sample_term_id: UBERON_0002084
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL001 Left Ventricle Cells
Library name: polyA-RNA-seq_STL001LV_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13825
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11835
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010938_UCSD.Left_Ventricle.mRNA-Seq.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001LV_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Left Ventricle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Left Ventricle, Donor STL001 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16744
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 142,887,393
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.91
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.66

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

ANALYSIS FILE NAME: GSM1010938_UCSD.Left_Ventricle.mRNA-Seq.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL001LV_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Left Ventricle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Left Ventricle, Donor STL001 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16779
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: LV mRNA 01
BROWSER_TRACK_DESCRIPTION: UCSD Left Ventricle mRNA-Seq Donor STL001 Library polyA-RNA-seq_STL001LV_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 142,887,393
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.91
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.66

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

source_name: Left Ventricle tissue; polyA-RNA-seq_STL001LV_r1a

value: Left Ventricle

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers


title: B6_LPS_B

value: wild type

value: Day 150

value: LPS injected 48 hr timepoint

value: microglia


title: NonTG_Day100_C

value: Day 100

value: Symptomatic control

value: Symptomatic control amyotrophic lateral sclerosis


title: NonTG_Day100_B


title: NonTG_Day100_A


title: FAP negative MEFs biological replicate 1

city: Cambridge

first: Andrew

last: Deonarine

address: Hills Road

country: United Kingdom

institute: Laboratory of Molecular Biology

description: FACS sorted FAP- embryonic cells grown for 3 passages and resorted to confirm FAP-

data_processing:
RNA-seq data was then mapped to the iGenomes mm9 reference genome using Bowtie2 and Tophat2 was used to map junction reads (the switches used to run Tophat2 were"--GTF mm9 --b2-very-sensitive --b2-D 500 --b2-R 500 --solexa1.3-quals").
To quantify transcriptome expression levels, Cufflinks2 was used to produced bias-adjusted FPKM values (using the switches "--GTF mm9--multi-read-correct --frag-bias-correct"), while RPKM values were calculated from count data produced by Htseq-count (using the switches "--quiet --stranded=no -a 30"). Fragments were also estimated from FPKM values.
Using counts, fragments, FPKM (bias-adjusted), and RPKM, correlations, clustering, PCA, and differential expression analysis (usingDESeq and edgeR) were then calculated for the Panst, VA, Skelm, and FAPN replicates against reference T-helper cell types (naive, Th1, Th2, and nTreg).
Genome_build: iGenomes mm9 reference genome

source_name: FAP negative MEFs

extract_protocol: Purelink (Invitrogen) RNA prep, amplification by MessageAmp (Ambion). After purification, the double strand cDNA was subjected to library preparation using the the Illumina mRNA sample preparation kit (Illumina, San Diego, CA) directly to the 3' adenylation step and according to manufacturer's protocol.

tag: tissue

value: FAP negative MEFs

value: FACS sorted FAP- cells


title: FAP negative MEFs biological replicate 2


title: Pancreatic stellate cells biological replicate 2

description: FACS sorted FAP+ cells from dissociated pancreas

source_name: Pancreatic stellate cells

value: Pancreatic stellate cells

value: FACS sorted FAP+ cells


title: Pancreatic stellate cells biological replicate 1


title: Skeletal Muscle biological replicate 2

description: FACS sorted FAP+ cells from dissociated skeletal muscle

source_name: Skeletal muscle

value: Skeletal muscle


title: NonTG_Day65_B

description:
CGATGT
Paired end RNA-Seq on the Illumina platform

value: Day 65

value: Pre-symptomatic control

value: Pre-symptomatic control amyotrophic lateral sclerosis


title: NonTG_Day65_C

description:
TGACCA
Paired end RNA-Seq on the Illumina platform


title: Skeletal Muscle biological replicate 1


title: Visceral Adipose biological replicate 2

description: FACS sorted FAP+ cells from dissociated visceral adipose

source_name: Visceral adipose tissue

value: Visceral adipose tissue


title: Visceral Adipose biological replicate 1


title: NonTG_Day65_A


title: SOD1G93A_Endstage_I

value: End-stage

value: End-stage amyotrophic lateral sclerosis


title: SOD1G93A_Endstage_H


title: SOD1G93A_Endstage_D

description: Paired end RNA-Seq on the Illumina platform


title: SOD1G93A_Endstage_E


title: polyA RNA sequencing of STL003 Esophagus Cells; polyA-RNA-seq_STL003EG_r1a

description:
note: SRA Run SRR651690 was withdrawn on May 22, 2015.

sample_term_id: UBERON_0001043
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of STL003 Esophagus Cells
Library name: polyA-RNA-seq_STL003EG_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13843
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11826
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1010956_UCSD.Esophagus.mRNA-Seq.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003EG_r1a.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Esophagus mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Esophagus, Donor STL003 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16736
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 342,728,446
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.29
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.5

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

ANALYSIS FILE NAME: GSM1010956_UCSD.Esophagus.mRNA-Seq.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_STL003EG_r1a.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Esophagus mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Esophagus, Donor STL003 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16771
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Esophagus mRNA 03
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus mRNA-Seq Donor STL003 Library polyA-RNA-seq_STL003EG_r1a EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 342,728,446
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.29
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.5

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

value: Esophagus

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian

value: mRNA-Seq

value: Qiagen RNeasy mini kit, performed as per manufacturer's instructions

value: 4 µg

value: Dynabeads oligo(dt)25 (Invitrogen)

value: PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min

value: SuperScript III (Invitrogen)

value: Purification with RNAClean XP beads (Agencourt)

value: DNA Polymerase I (E. coli) (New England Biolabs)

value: dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP

value: Purification with AMPure XP beads (Agencourt)

value: TruSeq Multiplexed Adapters (Illumina)

value: 16°C for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.

value: TruSeq PCR Master Mix (Illumina)

value: 98°C 30 sec; 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec; 72°C 10 min

value: TruSeq PCR Primer Cocktail (Illumina)

value: Dynabeads oligo(dt)25 protocol

value: Random hexamers

value: First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: SOD1G93A_Endstage_F

value: End-stage

value: End-stage amyotrophic lateral sclerosis

value: microglia


title: SOD1G93A_Endstage_B


title: SOD1G93A_Endstage_C


title: NonTG_Day130_A

value: wild type

value: Day 130

value: End-stage control

value: End-stage control amyotrophic lateral sclerosis


title: SOD1G93A_Endstage_A


title: SOD1G93A_Day100_D

value: Day 100

value: Symptomatic

value: Symptomatic amyotrophic lateral sclerosis


title: SOD1G93A_Day100_G


title: SOD1G93A_Day100_F


title: SOD1G93A_Day100_E


title: SOD1G93A_Day100_B


title: SOD1G93A_Day100_C


title: SOD1G93A_Day65_D

value: Day 65

value: Pre-symptomatic

value: Pre-symptomatic amyotrophic lateral sclerosis


title: SOD1G93A_Day65_E


title: SOD1G93A_Day65_B


title: SOD1G93A_Day65_C


title: SOD1G93A_Endstage_G


title: CLAMP ChIP SL2 cells control RNAi replicate 2 Input

city: Providence

first: Erica

last: Larschan

address: 185 Meeting St.

institute: Brown University

library_source: genomic

data_processing:
Alignment to Drosophila Melanogaster genome, dm3 assembly, with bowtie software, allowing at most 1 mismatch and discarding reads that do not align uniquely (parameters: -v 1 -m 1 )
Aligned reads from sample replicates were pooled
To produce wig files read counts from both input and ChIP samples were calculated within 20bp bins across the genome.  A pseudocount of one was added to both input and ChIP counts to prevent undefined ratios.  Counts were further normalized by the total number of reads in the sample.  Enrichment within each bin was then calculated as the log(2) ratio of sample-size normalized ChIP read counts to sample-size normalized input read counts.
Genome_build: dm3
Supplementary_files_format_and_content: Scores in wig files represent input-normalized CLAMP enrichment, calculated from pooled replicates in control S2 cells, control KC cells, and S2 cells treated with MSL2 RNAi.
Supplementary_files_format_and_content: RPKM values were calculated from each RNA-Seq sample by first computing the total number reads that overlap the coding sequence of each gene.  These counts were then normalized to RPKM by normalizing to coding sequence length and by total sample reads.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: CLAMP ChIP SL2 cells control RNAi

extract_protocol: Standard Illumina ChIP-seq (Tru-seq) protocol

treatment_protocol: RNAi treatment for 6 days at 25 C

tag: cell line


title: CLAMP ChIP SL2 cells control RNAi replicate 1


title: SOD1G93A_Day65_A


title: CLAMP ChIP SL2 cells control RNAi replicate 1 Input


title: mRNA-seq MSL2 RNAi SL2

source_name: mRNA-seq MSL2 RNAi SL2

extract_protocol: Standard Illumina mRNA-seq (Tru-seq) protocol


title: mRNA-seq CLAMP RNAi SL2

source_name: mRNA-seq CLAMP RNAi SL2


title: CLAMP ChIP SL2 cells MSL2 RNAi replicate 2

source_name: CLAMP ChIP SL2 cells MSL2 RNAi


title: CLAMP ChIP SL2 cells control RNAi replicate 2


title: CLAMP ChIP SL2 cells MSL2 RNAi replicate 1


title: CLAMP ChIP SL2 cells MSL2 RNAi replicate 1 Input


title: SD-nitrogen polyA RNA, light fraction, gPAR-CLIP, Replicate 2

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

description:
Sample 10 (THB4)
Processed data file: nitrogen_polyA_light_gPAR-CLIP_cluster.bed

data_processing:
Base calling was performed according to Illumina's protocols.
The raw reads were stripped of the 3' adaptor sequence using FASTX. Reads that did not contain the adaptor sequence or contained an ambiguous nucleotide were discarded. The remaining gPAR-CLIP reads were then sorted into libraries according to their 6-nt barcodes using FASTX. Finally, the barcode sequences in the reads were clipped, and reads that were poly(A/T) or shorter than 18 nucleotides in length were removed. Reads from duplicated experiments were combined for subsequent data analysis.
The processed reads from the previous step were mapped to the yeast genome (SGD version R64-1-1 for S288C strain) using Bowtie v0.12.7. We allowed at most two mismatches for one read because of the U-to-C conversions induced in PAR-CLIP. Reads from the processed libraries, other than heavy-total-RNA libraries, were mapped to the genome, allowing at most ten matching locations (parameters: -v 2 -m 10 --best --strata). Because of the multiple rDNA repeats in the yeast genome, reads from the heavy-total-RNA libraries were aligned to the rDNA consensus region (chrXII, from 451,575 to 460,711), allowing just one matching location (parameters: -v 2 -m 1 --best --strata).
RBP binding sites were then defined from mapped reads in the yeast genome using PARalyzer, which is designed specifically for PAR-CLIP data. PARalyzer relies on the U-to-C transitions introduced by the PAR-CLIP technology and the read density at the cross-link sites. It can generate high-resolution RNA–protein interaction sites with a strong signal-to-noise ratio. First, PARalyzer grouped the overlapped reads for further analysis. A group had to contain at least ten reads with conversions at two or more locations. For all positions, if there were at least five reads at the position, kernel density estimates were calculated according to read counts both with and without T-to-C conversions.
Clusters were defined as regions whose conversion (U to C) density was greater than the non-conversion density. A nucleotide with a stronger signal value (U to C) than a background value (U to U) was defined to be bound by RBPs. For each nucleotide in the clusters, a binding affinity score was calculated. A nucleotide is considered to be bound by RBPs if its score is larger than 0.5. The maximum score in a cluster was defined to be the RBP binding affinity of the cluster in our further analyses.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Binding sites generated using the PARalyzer algorithm for each gPAR-CLIP library are presented in BED format.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Whole cell

growth_protocol: Strains were grown at 30°C with rigorous shaking in synthetic defined (SD) media supplemented with 200 µM 4-thiouracil to OD600 = 0.7-0.8.

extract_protocol:
Crosslinked cells were resuspended in polysome lysis buffer (20 mM HEPES pH 7.5, 140 mM KCl, 1.5 mM MgCl2, 1% Triton X-100, 1X Complete Mini Protease Inhibitor EDTA-free (Roche 1 836 170), 0.2 U/µL SUPERase·In (Invitrogen AM2696)), mixed with ½ volume of acid-washed glass beads, and lysed by vortexing four times at 4°C, 1 min each with 1 min incubation on ice in between. Cell debris was removed by centrifugation for 5 min at 1,300Xg at 4°C. Supernatant was cleared by 20,000Xg spin for 10 min at 4°C. 15-50% (w/v) sucrose density gradients were prepared in Beckman polycarbonate centrifugation tubes (11 X 34 mm) by sequentially layering and freezing 0.24 mL of 50%, 41.25%, 32.5%, 23.75% and 15% sucrose dissolved in polysome gradient buffer (20 mM HEPES pH 7.5, 140 mM KCl, 5 mM MgCl2). Gradients were thawed overnight at 4°C before use. 100 µL of clarified lysate was loaded on top of a gradient, centrifuged for 1 hr at 54,000 rpm at 4°C using a TLS-55 rotor in an Optima MAX-E ultracentrifuge (Beckman Coulter). The top 600 µL of the gradient was recovered and supplemented with 2 µL of SUPERase·In (20 U/µL). 60 µL of freshly prepared 10mM EZ-Link NHS-SS-Biotin (Pierce 21441) dissolved in dimethylformamide was added to the recovered lysate and incubated on a Nutator for 2 hr at 4°C. 50 µL of 5 M NaCl was added to increase the total salt concentration to 0.5 M. Biotinylated lysate was mixed with 1 mg of oligo(dT)25 magnetic beads (NEB S1419S), then incubated on a Nutator for 30 min at 4°C. Beads were washed 4 times with ice-cold hybridization buffer (10 mM HEPES pH 7.5, 0.5 M NaCl, 1 mM EDTA). RNAs were eluted by incubating beads with 500 µL of elution buffer (10 mM HEPES pH 7.5, 1 mM EDTA) and heating at 65°C for 3 min. Eluted sample was transferred to a new tube and mixed with 55 µL of 10XPBS.
PolyA-selected samples were mixed with 1 mg of streptavidin M280 Dynabeads (Invitrogen 112-05D) and incubated on a Nutator for 30 min at 4°C. Beads were washed 3 times with 1XPBS, then incubated with 20 µL of 50 U/µL RNase T1 (Fermentas EN0541, 1:20 dilution in 1XPBS) at 22°C for 15 min on an Eppendorf Thermomixer (15 sec shaking at 1,000 rpm followed by a 2 min rest interval), followed by 5 min incubation on ice. Beads were washed twice with wash buffer (1XPBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), twice with high-salt wash buffer (5XPBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40), and twice with 1XPNK buffer (50 mM Tris pH 7.4,10 mM MgCl2, 0.5% NP-40). Beads were incubated with 20 µL of CIP mix (50 mM Tris pH 7.9, 100 mM NaCl, 10 mM MgCl2, 0.5 U/µL CIP (NEB M0290S)) at 37°C for 15 min, with 15 sec shaking at 1,000 rpm followed by a 2 min rest interval on a Thermomixer. After CIP treatment, beads were washed twice with 1XPNK+EGTA buffer (50 mM Tris pH 7.4, 20 mM EGTA, 0.5% NP-40) and twice with 1XPNK buffer. Beads were incubated with 20 µL of ligation mix (50 mM Tris pH 7.4, 10 mM MgCl2, 0.5 mM DTT, 2 µM Pre-adenylated 3’ DNA linker, 25% PEG-8000, 10 U/µL T4 RNA ligase 2, truncated K227Q (NEB M0351S)) at 16°C overnight (≥16 hr), with 15 sec shaking at 1,000 rpm followed by a 2 min interval on a Thermomixer. After linker ligation, beads were washed 3 times with 1XPNK+EGTA buffer. Beads were mixed with 12 µL of 1XPNK+EGTA buffer, 3 µL of freshly made 1M DTT and 15 µL of 4X NuPAGE LDS sample buffer (Invitrogen NP0007), and incubated at 70°C for 10 min. Beads were removed, and the supernatant was loaded onto NuPAGE 4-12% Bis-Tris gel (Invitrogen NP0335BOX) and run at 150 V for 35 min. Gel was transferred to Protran BA 85 nitrocellulose membrane (pore size 0.45 µm, Whatman 10402594) using Novex wet transfer at 30 V for 1 hr. A broad band from 31 kDa up to the top of the gel was excised, cut into small pieces, and transfered into a microfuge tube. Excised membranes were incubated with 500 µL of 4 mg/mL Proteinase K prepared in 1X PK buffer (100 mM Tris pH 7.5, 50 mM NaCl, 10 mM EDTA) for 20 min at 37°C on a Thermomixer. 500 µL of 7M urea prepared in 1X PK buffer were added to the tube followed by another 20 min incubation at 37°C. Proteinase K digestion reaction was mixed with 1 mL of Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma-Aldrich P2069) by vortexing and spun for 5 min at 20,000Xg. Liquid phase was transferred to a new tube, mixed with 125 µL of 3 M NaOAc, 2.5 mL of 100% ethanol and 1 µL of 15 mg/mL glycoblue (Invitrogen AM9516), and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature followed by 2 washes with cold 75% ethanol. RNA pellets were air-dried briefly, resuspended in 10 µL of PNK mix (70 mM Tris pH 7.6, 10 mM MgCl2, 5 mM DTT, 1 mM ATP, 1 U/µL T4 polynucleotide kinase (NEB M0201S), 1 U/µL SUPERase·In), and incubated at 37°C for 30 min. The reaction was combined with 90 µL of H2O and 100 µL of Phenol:Chloroform:Isoamyl Alcohol 25:24:1, mixed well, and spun for 5 min at 20,000Xg. The liquid phase was mixed with 12.5 µL of 3 M NaOAc, 250 µL of 100% ethanol, 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by 2 washes with cold 75% ethanol. RNA pellets were resuspended in 10 µL of ligation mix (50 mM Tris pH 7.5, 10 mM MgCl2, 10 mM DTT, 1mM ATP, 0.1 mg/mL BSA, 2 µM 5’ RNA linker, 1 U/µL T4 RNA ligase (Fermentas EL0021), 1 U/µL SUPERase•In, 10% DMSO) and incubated at 15°C for 2 hr. Ligation reaction was terminated by adding 10 µL of 2X formamide gel loading buffer (Invitrogen AM8546G), heated for 2 min at 70°C, and then quickly chilled on ice. Samples were loaded onto a 6% TBE UREA gel (Invitrogen EC6865BOX) and run at 150 V for 45 min. After staining with 1X Sybr Gold Stain (Invitrogen S-11494), a gel piece corresponding to 70-90 nt RNA (80-100 nt ssDNA) was excised, crushed, and soaked in 400 µL of 0.3 M NaOAc overnight at room temperature. After removing gel pieces, the solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. RNAs were collected by centrifugation for 20 min at 20,000Xg at room temperature, followed by two washes with cold 75% ethanol. After brief drying, RNAs were resuspended in 15 µL of H2O. 10 μL of ligated RNA was combined with 2 μL of 5 µM RT primer, heated at 65°C for 5 min, and then quickly chilled on ice, followed by the addition of 1 µL of 10 mM dNTP, 1 μL of 0.1 M DTT, 4 μL of 5X First strand buffer, 1 μL of SUPERase•In (20 U/µL) and 1 µL of SuperScript III Reverse transcriptase (Invitrogen 18080-093, 200 U/µL). RT reaction was kept at 50°C for 45 min, 55°C for 15 min and 90°C for 5 min. A test PCR was performed with 2.5 µL of RT product in 50 µL PCR mix: 1X AccuPrime PCR buffer I, 0.5 µM P5 long primer, 0.5 µM P7 primer, 0.2 µL AccuPirme Taq High Fidelity (Invitrogen 12346-086, 5 U/µL). PCR was carried out with an initial 3 min denaturation at 98°C, followed by 14-22 cycles of 80 sec denaturation at 98°C, 90 sec annealing and extension at 65°C, and termination with a final 5 min extension at 65°C. 15 µL PCR product was collected after 14, 18, and 22 cycles and analyzed on a 10% TBE gel (Invitrogen EC6275BOX) at 150 V for 1 hr to determine the optimal amplification cycles (the lowest cycle number required to generate 96-116 bp amplicons detected by Sybr Gold staining). A 50 µL PCR reaction was carried out with the determined cycle number. Amplicons were purified using DNA clean and concentrator-5 (Zymo D4013), run on 10% TBE gels at 150 V for 1 hr and stained with Sybr Gold. A gel piece corresponding to 96-116 bp DNA was excised, crushed, and soaked overnight in 400 µL 0.3 M NaOAc at room temperature. After removing gel pieces, the solution was combined with 1 mL of 100% EtOH and 1 µL of 15 mg/mL glycoblue and precipitated for 2 hr at -80°C. DNAs were collected by centrifugation for 20 min at 20,000Xg at ro

treatment_protocol: Glucose and nitrogen starvation was performed by pelleting cells, discarding media, rinsing once with H2O, and re-suspending cells in SD without glucose or nitrogen. Cells were returned to 30°C with rigorous shaking for 2 hr. For gPAR-CLIP and PAR-CLIP procedure, 50 mL of mid-log phase cultures (OD600 of 0.7-0.8) were pelleted for 5 min at 3,000Xg at room temperature, resuspended in 2 mL of 1XHBSS (Invitrogen 14025), transferred to 60 mm cell culture dish (BD Biosciences 353002), placed on ice, and irradiated with 365nm UV at 150 mJ/cm2 4 times using a UVP CL-1000L UV crosslinker. Cells were then pelleted for 2 min at 5,000Xg at 4°C. After removing 1X HBSS, the cells were frozen in liquid nitrogen.

tag: strain

value: WT BY4742 (MATa his3-delta-1 leu2-delta-0 lys2-delta-0 ura3-delta-0)

tag: growth conditions

value: SD-nitrogen

tag: fraction in sucrose gradient

value: Light

tag: barcode

value: TGACCA


title: CLAMP ChIP Kc cells control RNAi replicate 2

source_name: CLAMP ChIP Kc cells control RNAi

value: Kc


title: SD-glucose, polyA RNA, light fraction, gPAR-CLIP, Replicate 2

description:
Sample 8 (THB2)
Processed data file: glucose_polyA_light_gPAR-CLIP_cluster.bed

value: SD-glucose

value: CGATGT


title: SD, polyA RNA, light fraction, gPAR-CLIP, Replicate 2

description:
Sample 6 (THA2)
Processed data file: polyA_light_gPAR-CLIP_cluster.bed

value: SD


title: SD-glucose, polyA RNA, light fraction, gPAR-CLIP, Replicate 1

description:
Sample 7 (THB1)
Processed data file: glucose_polyA_light_gPAR-CLIP_cluster.bed

value: ATCACG


title: SOD1G93A_Day100_A

source_name: Spinal cord purified microglia

value: microglia


title: CLAMP ChIP Kc cells control RNAi replicate 1


title: SD, total RNA, heavy fraction, gPAR-CLIP, Replicate 2

description:
Sample 4 (THA8)
Processed data file: total_heavy_gPAR-CLIP_cluster.bed

value: Heavy

value: ACTTGA


title: CLAMP ChIP Kc cells control RNAi replicate 2 Input


title: CLAMP ChIP Kc cells control RNAi replicate 1 Input


title: SD-nitrogen polyA RNA, light fraction, gPAR-CLIP, Replicate 1

description:
Sample 9 (THB3)
Processed data file: nitrogen_polyA_light_gPAR-CLIP_cluster.bed

value: TTAGGC


title: SD, total RNA, heavy fraction, gPAR-CLIP, Replicate 1

description:
Sample 3 (THA7)
Processed data file: total_heavy_gPAR-CLIP_cluster.bed

value: CAGATC


title: mRNA-seq Control RNAi SL2

source_name: mRNA-seq Control RNAi SL2


title: SD, total RNA, light fraction, gPAR-CLIP, Replicate 2

description:
Sample 2 (THA4)
Processed data file: total_light_gPAR-CLIP_cluster.bed


title: SD, polyA RNA, light fraction, gPAR-CLIP, Replicate 1

description:
Sample 5 (THA1)
Processed data file: polyA_light_gPAR-CLIP_cluster.bed


title: H111 wt aeobic

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

description: Burkholderia_cenocepacia_RNA_aerob_A_minus_TEX

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer.
Sequencing reads were mapped to the Bc H111 genome (CAFQ00000000.1) using CLC Genomics Workbench v4.9 (CLCbio) allowing up to 2 mismatches per read.
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010).
Genome_build: CAFQ00000000.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM and mean values for each sample.

organism: Burkholderia cenocepacia H111

source_name: Bc H111 planktonic cells, aerobic conditions

growth_protocol: Burkholderia cenocepacia H111 cells were grown in complex medium LB under aerobic or micro-oxic conditions.

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al. 2007) and DNA was removed. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.
The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The following adapter sequences flank the cDNA inserts: TrueSeq_Sense_primer 5' ́-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'; TrueSeq_Antisense_NNNNNN_primer Barcode 5'-CAAGCAGAAGACGGCATACGAGAT-NNNNNN-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC(dT25)-3'.

tag: strain/background

tag: genotype/variation

value: wild-type

tag: growth condition

value: aerobic

value: planktonic cells, OD600 equal 0.8

tag: medium

value: complex medium LB


title: TH-S

city: Beijing

first: Nina

last: Yang

state: Beijing

address: 12 Zhongguancun Nandajie, Haidian District

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whitefly transcriptome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads per kilobase of exon model per million mapped reads (RPKM) were calculated using a protocol from Mortazavi et al.,2008 . In short,  The RPKM measure of read density reflects  the molar concentration of a transcript in the starting sample by normalizing for RNA length and for the total read number in the measurement. This facilitates transparent comparison of transcript levels both within and between samples.
Genome_build: whitefly transciptome (see transcript_IDs.fa file)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample. Transcript IDs and sequences can be found in the transcript_IDs.fa file on the Series record.

organism: Bemisia tabaci

source_name: thiamethoxam-susceptible

growth_protocol: The B-biotype B. tabaci susceptible strain (TH-S) and resistant strain to thiamethoxam (TH-R) were maintained on cabbage under the same conditions. The TH-S strain was cultured without exposure to any chemical insecticides. While the TH-R strain exhibited >70-fold resistance to thiamethoxam compared to the TH-S.

extract_protocol:
Total RNA was isolated from TH-S and TH-2000 whitefly samples with Trizol reagent. Briefly, mRNA was purified from each sample with Dynal oligo (dT) beads, respectively, Then fragmented the mRNA by using the RNA fragmentation kit, first and second strand cDNA was synthesized using random hexamer primers, The double-stranded cDNA fragments were further processed by an end repair using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase (NEB) followed by a single <A> base addition using Klenow 3’ to 5’ exo-polymerase, and then ligated with Illumina ’ s adaptor.Finally, the library products were then subjected to sequencing analysis on the flow cell via Illumina HiSeq™ 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TH-S

value: total insect

tag: development stage

value: adult


title: SD, total RNA, light fraction, gPAR-CLIP, Replicate 1

description:
Sample 1 (THA3)
Processed data file: total_light_gPAR-CLIP_cluster.bed

value: WT BY4742 (MATa his3-delta-1 leu2-delta-0 lys2-delta-0 ura3-delta-0)

value: Light


title: CLAMP ChIP SL2 cells MSL2 RNAi replicate 2 Input


title: duf:CD2- rep. 6

status: Public on Jul 13 2013

city: Boston

first: Luis

middle: Alberto

last: Barrera

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

data_processing:
Base calls were performed with Illumina CASAVA 1.8
Matches to the common primer sequence were removed from read ends when present
Reads were mapped to the Drosophila genome using segemehl 0.0.9.4 with parameters -M 100 -E 5 -D 2 -A 80
The number of reads mapping to each genomic region in the library was computed, along with various summary statistics (see processed files).
Genome_build: dm3
Supplementary_files_format_and_content: Processed files are tab-delimited text files. The contents of each column are described in the header line. The first three columns give the chromosome and start and end positions of the genomic region. The "weight" column contains the sum of "StartHeight" and "EndHeight". "Count" contains the number of reads that mapped to that region. "StartHeight" and "EndHeight" contain the number of reads whose 5' ends mapped exactly to the start and end of the region, respectively. "Name" is the internal name given to the region in the library. "CenteredPositionsCovered" counts the number of positions within the region that had reads mapping to them; reads from different strands and with different lengths are counted separately, even if the read start maps to the same position.

growth_protocol: D. melanogaster embryos of informative genotypes (from transgenic pool males crossed to cell-type-specific CD2 transgenic females) were collected for 2-2.5 hours at 25 degrees, aged 9-10 hours at 18 degrees, then dechorionated in 50% bleach, rinsed, and dissociated into single cell suspensions by Dounce homogenization (loose pestle, 0.0035-0.005 inch clearance) in Schneider medium.

extract_protocol:
Crude genomic DNA was prepared by suspending cells in Gloor & Engel's extraction buffer (25 mM NaCl, 10 mM Tris pH 7-8, 1 mM EDTA, 200 micrograms/mL proteinase K) and incubating 30 minutes at 37 degrees, then 10 minutes at 95 degrees to inactivate proteinase K, then stored at -20 degrees. Stored extracts were pooled by sample type, split five ways, and used as template for nested PCR of specific transgenic inserts. PCR products were gel-purified and pooled by sample type.
5 micrograms of each PCR pool was fragmented by Covaris sonication and prepared for Illumina sequencing using standard protocols (end repair with the EpiCentre Biotechnologies End-IT kit, A-tailing with New England Biolabs Klenow exo-, and adapter ligation with New England Biolabs Quick T4 DNA ligase), with the Illumina Multiplexing Sample Preparation Oligonucleotide kit, and 10 cycles of enrichment PCR after adapter ligation.

treatment_protocol: Cells were stained with Alexa647-conjugated anti-rat CD2 + DAPI in Schneider medium + 8% FBS and sorted by FACS into CD2-expressing and non-expressing populations (as input control) or GFP-expressing subsets of the same larger populations.

value: Embryo

tag: cell population

tag: cell number


title: duf:CD2 input control rep. 5

source_name: duf:CD2- input


title: duf:CD2 input control rep. 4


title: duf:CD2- rep. 3


title: duf:CD2-/GFP+ rep. 6


title: duf:CD2-/GFP+ rep. 1


title: TH-2000

source_name: thiamethoxam-resistant


title: duf:CD2 input control rep. 2


title: duf:CD2 input control rep. 3


title: duf:CD2-/GFP+ rep. 5


title: duf:CD2-/GFP+ rep. 4


title: duf:CD2+/GFP+ pooled


title: duf:CD2-/GFP+ rep. 2


title: duf:CD2 input control rep. 1


title: duf:CD2- rep. 4


title: H111 wt micro-oxic

description: Burkholderia_cenocepacia_RNA_microaerob_M_minus_TEX

source_name: Bc H111 planktonic cells, micro-oxic conditions

value: micro-oxic

tag: cell type

value: planktonic cells, OD600 equal 0.4


title: twi-CD2+/GFP+ rep. 3


title: mef2-CD2- input (comparison/variance) control rep. 5

source_name: mef2-CD2- input


title: mef2-CD2-/GFP+ rep. 2


title: twi-CD2-/GFP+ rep. 3


title: twi-CD2+/GFP+ rep. 2


title: twi-CD2-/GFP+ rep. 2


title: twi-CD2-/GFP+ rep. 1


title: twi-CD2+/GFP+ rep. 1


title: duf:CD2- rep. 5


title: twi-CD2- input rep. 3

source_name: twi-CD2- input


title: twi-CD2+ input rep. 3

source_name: twi-CD2+ input


title: mef2-CD2-/GFP+ rep. 1


title: duf:CD2- rep. 2


title: mef2-CD2- input (comparison/variance) control rep. 2


title: twi-CD2+ input rep. 2


title: duf:CD2- rep. 1


title: duf:CD2-/GFP+ rep. 3


title: mef2-CD2- input (comparison/variance) control rep. 1


title: mef2-CD2- input (comparison/variance) control rep. 4


title: mef2-CD2- input rep. 2


title: twi-CD2- input rep. 2


title: twi-CD2- input rep. 1


title: twi-CD2+ input rep. 1


title: HF_HS_d7_m3

status: Public on Jul 12 2013

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University

data_processing:
Library strategy: COPRO-Seq
Demultiplexing: sequences were demultiplexed by 4 nt barcode, requiring an exact match (sequences without a barcode match were excluded from the analysis)
Trimming: after demultiplexing, all sequences were trimmed to 25 bases to eliminate low-quality bases at the ends of each read
Mapping: sequences were aligned to the reference genomes of the 12 bacteria included in the study using Illumina's ELAND aligner (as provided in GAPipeline-1.4.0). Only perfect, non-redundant matches were carried forward in the analysis.
Normalization: raw counts were normalized based on the informative genome size (IGS) of each organism included in the analysis, as described by McNulty et al (PMID: 22030749).
Summarization: the proportional representation of each organism in the analysis was determined by dividing its normalized counts within a sample by the total normalized counts for all organisms within that sample.
Genome_build: AAVM00000000;  AE015928.1; AAVN00000000; ACCL00000000; NC_000913.2;  NZ_AAXF00000000.2; NC_012781.1; assembly for C. symbiosum can be found at http://genome.wustl.edu/pub/organism/Microbes/Human_Gut_Microbiome; for D. piger: PRJNA30377
Supplementary_files_format_and_content: Tab-delimited text file. The file header (in angle brackets, <>) specifies the sample from which data were derived. Subsequent rows specify the organism/reference genome, raw counts, normalized counts, and normalized relative proportion for each taxon included in the alignment. Additional details are available in the accompanying 'README.txt' file.

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656
Desulfovibrio piger GOR1

source_name: Defined bacterial assemblage from the feces of a gnotobiotic mouse

growth_protocol: Bacteria from frozen culture stocks were introduced as an artificial community (AC) into 7-8 week-old male gnotobiotic NMRI mice.  Cells were therefore maintained over the course of the experiment within mice until sampling occurred.

extract_protocol:
DNA was extracted from fecal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749).
Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence.  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I, II or IIx following the manufacturer's protocols.

treatment_protocol: Immediately after collection, samples were subjected to flash-freezing in liquid nitrogen and storage at -80 C until total community DNA extractions could be performed.

tag: experiment

tag: group/diet

value: HF/HS

tag: collection site

value: Feces

tag: days after colonization


title: mef2-CD2- input rep. 3

tag: tissue


title: mef2-CD2-/GFP+ rep. 3


title: LF_HPP_d7_m4

value: LF/HPP


title: mef2-CD2- input (comparison/variance) control rep. 3


title: LF_HPP_d7_m2


title: mef2-CD2+/GFP+ pooled


title: LF_HPP_d7_m5


title: mef2-CD2- input rep. 1


title: LF_HPP_d7_m1


title: LF_HPP_d7_m3


title: HF_HS_d7_m1


title: HF_HS_d7_m2


title: Dp4_d14_CS_S20


title: Dp2_d14_CS_S18


title: Dp11_d14_CS_S11


title: Dp3_d14_CS_S19


title: Dp15_d14_CS_S15


title: Dp14_d14_CS_S14


title: Dp13_d14_CS_S13


title: Dp20_d14_CS_S20


title: HF_HS_d7_m4


title: Dp16_d14_CS_S16


title: Dp12_d14_CS_S12


title: LF_HPP_d14_m2


title: HF_HS_d14_m3


title: Dp19_d14_CS_S19


title: Dp1_d14_CS_S17


title: E12_FP010912_Dp_m8


title: M2_090711


title: M10_083111

value: No added Cys, 0.12% SO4


title: M7_083111

value: No SO4, 0.1% ThioSO4


title: LF_HPP_d14_m3


title: LF_HPP_d14_m1


title: Dp18_d14_CS_S18


title: Dp17_d14_CS_S17


title: M1_082411

value: No SO4


title: M9_091411

value: No SO4, 3% Chond. SO4


title: M11_082411


title: M11_081711

value: HF/HS (control diet; 0.12% SO4)


title: M13_081711


title: M6_082411


title: M8_091411


title: M7_081711


title: M3_082411


title: M5_082411


title: M3_090711


title: M9_083111


title: HF_HS_d14_m1


title: M3_081711


title: M9_082411


title: M9_090711


title: M12_083111


title: M10_091411


title: M2_082411


title: M13_091411


title: M11_091411


title: HF_HS_d14_m2


title: M2_081711


title: M7_090711


title: M6_091411


title: M5_091411


title: M12_090711


title: M13_082411


title: M11_090711


title: M10_081711


title: M7_082411


title: M4_083111


title: M8_090711


title: M8_083111


title: M2_083111


title: M8_082411


title: M2_091411


title: M1_081711


title: M4_091411


title: M3_083111


title: M1_091411


title: M12_081711


title: M5_081711


title: M4_090711


title: M5_083111


title: M6_090711


title: M10_082411


title: M5_090711


title: M4_081711


title: M12_082411


title: Dp5_d14_CS_S21


title: M12_091411


title: M1_090711


title: M11_083111


title: M7_091411


title: M13_090711


title: M6_083111


title: M13_083111


title: M1_083111


title: RSQ8 Embryo 12-14 hr svb Input Control

first: Rebecca

middle: Fran

last: Spokony

state: NY

address: 17 Lexington Avenue

department: Natural Sciences

institute: Baruch College

description: Input

data_processing:
BWA to make BAM files from FASTQ files
samtools to filter BAM files
SPP to make WIG files
MAC2 to call peaks
IDR to call peaks
Genome_build: Drosophila melanogaster Build 5 2006
Supplementary_files_format_and_content: BED and WIG

source_name: 12-14 hour old embryos svb::GFP

growth_protocol: Adults were expanded and maintained at 25 degrees C.  Adults were put into cages with apple juice plates covered in yeast and allowed to prelay for 1 hour.  Prelay plates were changed and adults were allowed to lay for 2 hours.  Plates were removed and then aged for 12 hours at 25 degrees C.

extract_protocol:
Chromatin extract protocol was as described in    Nègre N, Brown CD, Ma L, Bristow CA et al. A cis-regulatory map of the Drosophila genome. Nature 2011 Mar 24;471(7339):527-31. PMID: 21430782
Nextera libraries were made as described in    Nègre N, Brown CD, Ma L, Bristow CA et al. A cis-regulatory map of the Drosophila genome. Nature 2011 Mar 24;471(7339):527-31. PMID: 21430782

tag: genotype

tag: age

value: 12-14 hour embryo

value: embryo

tag: chip antibody

value: input


title: RSQ8 Embryo 12-14 hr svb Replicate2

description: ChIP-seq

value: anti-GFP


title: RSQ8 Embryo 12-14 hr svb Replicate1

description: ChIP-seq


title: Dp7

description: mice colonized with 8 human gut bacterial species plus Desulfovibrio piger

data_processing:
Splitting barcodes - Sequence runs were split into their respective experiments using the 4-bp barcode at the beginning of each sequencing read.
Mapping reads - After trimming reads to 42nt and dividing sequence runs by barcode, we mapped the reads to the mouse genome using the TopHat and  Bowtie algorithm
Counts were normalized to upper quartile and significance between groups was assessed using CyberT
Genome_build: genome mm37.63 (from ENSEMBL).

source_name: Proximal colon from gnotobiotic mice colonized with defined bacterial assemblage

extract_protocol:
Proximal colon samples were homogenized in trizol and purified using the Qiagen Rneasy kit including the in column DNAse treatment. mRNA was furter purified using Dynabeads mRNA purification kit (Invitrogen) following manufacters protocol
cDNA libraries were prepared for sequencing using a modified version of Illumina's sample preparation protocol

treatment_protocol: proximal colon samples obtained from mice were immediately frozen at -80C and maintained at this temperature prior to processing.

value: 7-8 weeks old

tag: strain

value: NMRI

tag: diet

value: High fat/ High sugar supplemented with 3% chondroitin sulfate

tag: colonization


title: NoDp4

description: mice colonized with 8 human gut bacterial species


title: Dp5

value: mice colonized with 8 human gut bacterial species plus Desulfovibrio piger


title: M9_081711


title: NoDp2

value: mice colonized with 8 human gut bacterial species