description:
design description: ChIP-Seq input analysis of foreskin keratinocyte from skin01 (A05019) using Illumina Genome Analyzer IIx
library name: A05019
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 135-499 bp
****************
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: GSM817242_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A05019-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.12539
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,266,774
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0875
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2823
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9121
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5554
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817242_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A05019-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.12562
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: PFK Input 01 19
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin01 Library A05019 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,266,774
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0875
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2823
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9121
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5554
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: male

value: Penis

value: Keratinocyte

value: No

value: primary cell culture

value: foreskin keratinocyte


status: Public on Apr 17 2012

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: H3K36me3 ChIP-Seq analysis of foreskin keratinocyte from skin01 (A05018) using Illumina Genome Analyzer IIx
library name: A05018
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 80-480 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-058-050
CHIP_ANTIBODY_LOT: A241-0011
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM817225_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K36me3.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A05018-1-A02883-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.12527
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,824,875
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4106
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.4195
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9571
IROC_PERCENTILE: 9
POISSON_SCORE: 0.5933
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.24

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

ANALYSIS FILE NAME: GSM817225_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K36me3.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A05018-1-A02883-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.12550
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: PFK H3K36me3 01 18
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin01 Library A05018 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,824,875
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4106
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.4195
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9571
IROC_PERCENTILE: 9
POISSON_SCORE: 0.5933
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.24

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

molecule: genomic DNA

organism: Homo sapiens

tag: Sex

tag: body site

tag: histological type

tag: is tumor

tag: cell type


title: V9M_H3K4me3_ChIPSeq

status: Public on Apr 16 2012

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

description:
V9M
processed data file: all_mFOLD7_MACS_peaks_H3K4me3.txt
genome build: hg18

data_processing: MACS peak calls: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)[.txt processed files are available as Series Supplementary files]; paired end data files were treated as single end experiments.

source_name: Colon cancer_H3K4me3_ChIPSeq

growth_protocol: Primary colon cancer cell lines were grown in 15 cm dishes to 70% confluency prior to harvest for ChIP-seq and RNA extraction. Normal colon crypts were isolated from surgical specimens of colon excised past the normal margin of tumors. Specimens were verified by microscopy to be free of any cancer cells.  Samples were washed in cold PBS, placed in cold DMEM+10%FBS, and then transported from the operating room to the laboratory within 8 hours of surgery.  Extraction of colonic crypts was performed by EDTA fractionation.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 17 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Colon Cancer

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot #


title: rmr2-1 (mutant)

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
rrn2-1/rmr2-1
Small RNA-Seq.

library_source: transcriptomic

data_processing:
Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances. To account for differences in library depth, the library abundance for each signature was normalized to 10 million [units of transcripts per 10 million (TP10M)]. The data were matched to the maize genome, annotation version 4a.53 AGPv1.
Processed data files: Distinct small RNAs with their raw abundance after removing the adapter sequences.
Genome_build: 4a.53 AGPv1

molecule: total RNA

organism: Zea mays

source_name: developing cobs (4 cm in length), rmr2-1 (mutant)

growth_protocol: Temperature was 65-85°F (depending on outside conditions), humidity was not monitored, and the light conditions depended on sunlight levels from 6 AM to 10 PM.

extract_protocol: Total RNA was extracted from developing cobs (4 cm in length) of both rmr2-1 homozygotes (n=2) and Rmr2/rmr2-1 (n=2) siblings. Cobs were collected prior to flowering and processed after the rmr2 genotype was determined by diagnostic anther colors. The RNA was extracted using TRIzol reagent (Invitrogen). The sRNA library preparation protocol was based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). The libraries were sequenced on an Illumina GAII at the Delaware Biotechnology Institute (Newark, DE).

tag: inbred line

value: mostly K55

tag: pl alleles

value: Pl'/Pl'

tag: modifiers

tag: genotype

tag: variation

value: rmr2-1/rmr2-1 (mutant)

tag: tissue

value: developing cobs


title: Rmr2/rmr2-1 (non-mutant)

description:
Rmr2/rmr2-1
Small RNA-Seq.

source_name: developing cobs (4 cm in length), Rmr2/rmr2-1 (non-mutant)

value: Rmr2/rmr2-1 (non-mutant)


title: Crypt2_H3K27ac_ChIPSeq

description:
Crypt2
processed data file: all_mFOLD7_MACS_peaks_H3K27ac.txt
genome build: hg18

source_name: Normal Colon Crypt_H3K27ac_ChIPSeq

value: Normal Colon Crypt

value: Abcam


title: Crypt3_H3K27ac_ChIPSeq

description:
Crypt3
processed data file: all_mFOLD7_MACS_peaks_H3K27ac.txt
genome build: hg18


title: ChIP-Seq analysis of WCE in human cingulate gyrus cells; DNA_Lib 621

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 621
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8680
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9452
****************
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: GSM772990_BI.Brain_Cingulate_Gyrus.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 621-DNA_Lib 621-DNA_Lib 621.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Cingulate Gyrus, Donor 149, 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.12313
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,797,024
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0061
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0341
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772990_BI.Brain_Cingulate_Gyrus.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 621-DNA_Lib 621-DNA_Lib 621.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Cingulate Gyrus, Donor 149, 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.12360
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BCG Input 49 21
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 621 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,797,024
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0061
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0341
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 621

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Cingulate Gyrus

value: Post-Mortem

value: no AD evident at demise

tag: molecule

value: genomic DNA

tag: disease

value: Cingulate Gyrus

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: V503_H3K4me3_ChIPSeq

description:
V503
processed data file: all_mFOLD7_MACS_peaks_H3K4me3.txt
genome build: hg18

value: Colon Cancer

value: Active Motif


title: V503_H3K27ac_ChIPSeq

description:
V503
processed data file: all_mFOLD7_MACS_peaks_H3K27ac.txt
genome build: hg18

source_name: Colon cancer_H3K27ac_ChIPSeq

value: Abcam


title: Leaves

city: Campinas

first: Renato

last: Vicentini

state: SP

address: Cidade Universitaria "Zeferino Vaz"

department: Centro de Biologia Molecular e Engenharia Genetica - CBMEG

country: Brazil

institute: Universidade Estadual de Campinas - UNICAMP

description: small RNA populations in the sugarcane leaves that shows match against sugarcane LTR-RTs

data_processing: Raw sequences were retrieved in a FASTQ formatted file and the adapter sequences were removed using Perl Scripts. After trimming of adapter sequences, the inserts were sorted into separate files according to their lengths. We used the program MAQ to map 20-25 ntsRNA reads against sugarcane LTR-RT reference sequences.

organism: Saccharum officinarum

source_name: Leaves

extract_protocol: Ten micrograms of total RNA, prepared using TRizol reagent (Invitrogen) according to the manufacturer’s instructions, were used to generate sRNA library following Illumina’s modified protocol. The sRNA fraction of 19–28 nt was purified by size fractionation on a 15% TBE–Urea polyacrylamide gel. A 5`-adenylated single-stranded adapter was first ligated to the 3’-end of the RNA using T4 RNA ligase without ATP, followed by a second single-stranded adapter ligation at the 5’-end of the RNA using T4 RNA ligase in the presence of ATP. The resulting products were fractioned on a 10% TBE–Urea polyacrylamide gel and then used for cDNA synthesis and PCR amplification.

value: Leaves of one-month old

tag: cultivar


title: ChIP-Seq analysis of WCE in human inferior temporal lobe cells; DNA_Lib 622

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 622
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8681
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9458
****************
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: GSM772991_BI.Brain_Inferior_Temporal_Lobe.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 622-DNA_Lib 622-DNA_Lib 622.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Inferior Temporal Lobe, Donor 149, 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.12307
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,742,098
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0327
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772991_BI.Brain_Inferior_Temporal_Lobe.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 622-DNA_Lib 622-DNA_Lib 622.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Inferior Temporal Lobe, Donor 149, 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.12354
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: BITL Input 49 22
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 622 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,742,098
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0048
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0327
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 622

value: Brain, Inferior Temporal Lobe

value: Post-Mortem

value: no AD evident at demise

value: Inferior Temporal Lobe


title: V9M_H3K27ac_ChIPSeq

description:
V9M
processed data file: all_mFOLD7_MACS_peaks_H3K27ac.txt
genome build: hg18


title: V429_DNase I ChIPSeq

description:
V429
processed data file: all_mFOLD7_peaks_DNase.txt
genome build: hg18

source_name: Colon cancer_DNase I ChIPSeq


title: V429_H3K27ac_ChIPSeq

description:
V429
processed data file: all_mFOLD7_MACS_peaks_H3K27ac.txt
genome build: hg18


title: IgG_Human_Peripheral_Blood_Lymphocytes

city: Copenhagen

first: Sheroy

last: Minocherhomji

state: Copenhagen N

address: Blegdamsvej 3B, Building 18.1

department: Nordea Centre for Healthy Aging, Faculty Of Health Sciences Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: IP against IgG using a polyclonal IgG antibody (Cat # kch-819-015 Diagenode or 2729S: Cell Signalling Tech

data_processing:
Unique sequenced reads from all high-throughput experiments were re-aligned using Bowtie (Langmead et al., 2009) to an altered hg18 assembly that included sequence for all three chr20 gaps (termed hg18+chr20 gaps genome assembly) newly identified in this study. 709bp starting from the 5' end of gap 2 was not included in the re-alignment assembly (hg18+chr20 gaps) file so as to not change the genome base positions (chromosome offsets) on either side of the gap 2 during alignment. Importantly no significant reads were shown to align to this region in any high-throughput experiment. The required numbers of NNNs were maintained in gaps 1 and 3 as they were estimated to be 20kb and 110kb respectively in the hg18 human-genome assembly. MBD-Seq, MRE-Seq and ChIP-Seq reads were analyzed using Cisgenome software as published elsewhere using an FDR or <0.01 (Ji et al., 2008). ChIP-Seq data was analyzed using IgG as a negative control.
Alignment: Sequence reads were obtained and mapped to an edited human genome assembly having the sequence for human chromsome 20 gap regions (termed hg18+chr20 gaps) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned. ChIP-Seq, MBD-Seq and MRE-Seq analysis was performed using Chromosome 20 gaps were sequenced here using touchdown PCR conditions, overlapping PCR primers and Sanger sequencing. These sequences have been deposited at GenBank with accessions: JN854134, JN854135 and JN854136. Reads were aligned using Bowtie and visuallised using the UCSC genome browser at UCSC.
Genome Build:
IgG_Human_Peripheral_Blood_Lymphocytes.wig: hg18+chr20 gaps

source_name: Human Peripheral Blood Lymphocytes

extract_protocol:
Chromatin IP (ChIP-Seq): ChIP was performed using sonicated chromatin obtained from EBV transformed PBLs of a translocation carrier (Hertz et al., 2004), antibodies for H3K27me3 (Active Motif, Cat. #39155), IgG (Cell Signaling Technology Cat #2729S) and performed as previously published (Pasini et al., 2010) or using the ChIP-IT express kit (Cat # 53008, Active Motif) followed by high-throughput Illumina sequencing according to manufacturers instructions.  The average insert size (fragment length not including adapters) of the libraries was 300bp.
High-throughput Illumina Sequencing of gDNA libraries:  Library preparation of gDNA obtained from MBD-Seq, MRE-Seq and ChIP-Seq experiments were sequenced using single read or paired-end adapters and run on a Genome Analyzer II according to manufacturer’s instructions (Illumina) and as indicated.

value: Cebrellum

tag: protocol

value: ChIP (polyclonal IgG antibody, Cat # kch-819-015 Diagenode or 2729S:Cell Signalling Tech)


title: V432_DNase I ChIPSeq

description:
V432
processed data file: all_mFOLD7_peaks_DNase.txt
genome build: hg18

tag: cell type


title: C101_input DNA

source_name: Normal Colon Crypt_input DNA

value: Normal Colon Crypt


title: C104_input DNA


title: C91_input DNA


title: V9M_input DNA

source_name: Colon cancer_input DNA


title: V703_input DNA


title: V9P_input DNA


title: V503_input DNA


title: V457_input DNA


title: V429_input DNA


title: C104_H3K4me1_ChIPSeq

description:
C104
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18

source_name: Normal Colon Crypt_H3K4me1_ChIPSeq

tag: chip antibody


title: V481_input DNA


title: V400_input DNA


title: V400_H3K27ac_ChIPSeq

description:
V400
processed data file: all_mFOLD7_MACS_peaks_H3K27ac.txt
genome build: hg18

tag: chip antibody vendor


title: V432_input DNA


title: C101_H3K4me1_ChIPSeq

description:
C101
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18

tag: chip antibody cat. #


title: V8_H3K4me1_ChIPSeq

description:
V8
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18

source_name: Colon cancer_H3K4me1_ChIPSeq

tag: chip antibody lot #


title: V9P_H3K4me1_ChIPSeq

description:
V9P
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: V9M_H3K4me1_ChIPSeq

description:
V9M
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: V503_H3K4me1_ChIPSeq

description:
V503
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: Crypt1_H3K27ac_ChIPSeq

description:
Crypt1
processed data file: all_mFOLD7_MACS_peaks_H3K27ac.txt
genome build: hg18


title: C91_H3K4me1_ChIPSeq

description:
C91
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: V432_H3K4me1_ChIPSeq

description:
V432
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: V457_H3K4me1_ChIPSeq

description:
V457
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: V481_H3K4me1_ChIPSeq

description:
V481
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: V703_H3K4me1_ChIPSeq

description:
V703
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: V429_H3K4me1_ChIPSeq

description:
V429
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt
genome build: hg18


title: V400_H3K4me1_ChIPSeq

description:
V400
processed data files: all_mFOLD7_MACS_peaks_H3K4me1.txt, all_samples_control_enhancers_and_VELs.txt, common_VELs.txt
genome build: hg18


title: RPE1_PABPN1kd2_3seq

status: Public on Apr 15 2012

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description:
3'-Seq in RPE-1 cells transfected with PABPN1 - si#2
hg18

data_processing: Reads were aligned to the hg18 using bowtie. Wig files summarize read coverage at each genomic ccordinate (hg18)

molecule: polyA RNA

source_name: RPE-1 cells

growth_protocol: U2OS osteosarcoma cells and RPE-1 (hTERT-immortalized retinal pigment epithelial) cells were either transfected with two different scrambled control siRNAs (siC1 and siC2), pcDNA5 vector (vecC1 and vecC2) or two different siRNAs against PABPN1. 72 hours after transfection the cells were harvested and further processed for construction of the 3’Seq libraries

extract_protocol: Total RNA was extracted from either U2OS or RPE-1 cells.  mRNA was isolated, heat fragmented and the fragmented mRNA was then converted to single-stranded cDNA using SuperScript III reverse transcriptase and P7-t25-vn oligo-dT primer. This was followed by second-strand cDNA synthesis and end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. After purification, a P5-splinkerette was ligated and the splikerette-ligated cDNA was size-selected for approximately 220 bp long cDNA fragments using the E-Gel iBase Power System from Invitrogen. The final 3'Seq libraries were then generated by PCR amplification of the linker-ligated cDNA with P5 and P7 primers. After a last purification step the 3'Seq libraries were sequenced on the Illumina Genome Analyzer.

tag: cell line

value: RPE-1 cells

tag: transfection

value: PABPN1 - si#2


title: V8_input DNA


title: RPE1_siC2_3seq

description:
3'-Seq in control transfected RPE-1 cells (siC#2)
hg18

value: hTERT-immortalized retinal pigment epithelial

value: scrambled siRNA


title: RPE1_siC1_3seq

description:
3'-Seq in control transfected RPE-1 cells (siC#1)
hg18


title: U2OS_PABPN1kd1_3seq

description:
3'-Seq in U2OS cells transfected with PABPN1 - si#1
hg18

source_name: U2OS cells

value: osteosarcoma cell line

value: U2OS cells

value: PABPN1 - si#1


title: U2OS_vecC2_3seq

description:
3'-Seq in U2OS cells transfected with control vector #12
hg18


title: U2OS_vecC1_3seq

description:
3'-Seq in U2OS cells transfected with control vector #1
hg18


title: U2OS_siC2_3seq

description:
3'-Seq in control transfected U2OS cells (siC#2)
hg18


title: C3.20wks

description: 3'-Seq in control mouse #3; age of 20 weeks

data_processing: Reads were aligned to the mouse genome (mm9) using bowtie.

organism: Mus musculus

extract_protocol: Total RNA was extracted from muscle tissue of either 20 weeks or 12 months old mice (either control mice or OPMD mice).  mRNA was isolated, heat fragmented and the fragmented mRNA was then converted to single-stranded cDNA using SuperScript III reverse transcriptase and P7-t25-vn oligo-dT primer. This was followed by second-strand cDNA synthesis and end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. After purification, a P5-splinkerette was ligated and the splikerette-ligated cDNA was size-selected for approximately 220 bp long cDNA fragments using the E-Gel iBase Power System from Invitrogen. The final 3'Seq libraries were then generated by PCR amplification of the linker-ligated cDNA with P5 and P7 primers. After a last purification step the 3'Seq libraries were sequenced on the HiSeq systems. The 3 trePABPN1.A17 20-weeks old mice samples were indexed, pooled and sequenced together in one lane.  Same is true for the 3 control 20-weeks old samples.

tag: strain

value: FvB

value: muscle

tag: age

value: 20 weeks


title: trePABPN1.A17.1.20wks

description: 3'-Seq in OPMD mouse model #1; age of 20 weeks


title: C2.20wks

description: 3'-Seq in control mouse #2; age of 20 weeks


title: trePABPN1.A17.3.20wks

description: 3'-Seq in OPMD mouse model #3; age of 20 weeks


title: trePABPN1.A17.1.12mth

description: 3'-Seq in OPMD mouse model #1; age of 12 months

value: 12 months


title: C1.20wks

description: 3'-Seq in control mouse #1; age of 20 weeks


title: trePABPN1.A17.2.12mth

description: 3'-Seq in OPMD mouse model #2; age of 12 months


title: C2.12mth

description: 3'-Seq in control mouse #2; age of 12 months


title: C1.12mth

description: 3'-Seq in control mouse #1; age of 12 months


title: control IP

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
ChIP-seq reads were aligned to the March 2006 build (hg18) of the human genome using Genomatix Mining Station. All reads mapping with zero, one, or two mismatches were retained for further analysis.
The H1.4K34ac replicates showed very good correlation both globally (Pearson correlation: 0.94, determined using RefSeq TSS as reference coordinates for seqMINER), as well as on single locus level by manual inspection in genome browser (see Supplemental Fig. S4A), therefore they were combined for downstream analysis.
Sites enriched for H1.4K34ac were identified with MACS using combined H1.4K34ac reads as the tag file, and the control_IP reads as the control file. The parameters used to run MACS were as follows: tag size, 36; band width, 300; model fold, 10; pvalue, 1e-05; and levels, 2000, 5000, 10000.
Only 1% of the identified binding regions were bigger than 5000bp, therefore they were regarded as outliers and excluded from further analysis. This procedure produced 3072 H1.4K34ac binding regions in the human genome, of average size 910 bp. Random peaks were generated using MACS with identical parameters, using mock reads as the tag file.
Genome_build: hg18

growth_protocol: MCF-7 cells were cultivated at 37°C and 95% humidity with 5% CO2 in Dulbecco's Modified Eagle's Medium (DMEM), high glucose (4,5 g/l) with 10% fetal calf serum (FCS, Perbio) and 1% L-Glutamine (200 mM).

extract_protocol: MCF-7 cells were fixed with formaldehyde, lysates were clarified from sonicated nuclei and H1.4K34ac-DNA complexes were isolated with antibody. Libraries were prepared according to the Illumina ChIP-seq protocol.

tag: source

value: human breast adenocarcinoma

value: no antibody control


title: H1.4K34ac ChIP-Seq

value: H1.4K34ac rabbit polyclonal made in-house


title: FLDN2b_RNA-seq_sample3

status: Public on Apr 14 2012

city: Pasadena

first: Jingli

middle: A

last: Zhang

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

description: Poly(A) selected mRNA

data_processing: Sequence reads from each cDNA library (38bp, single-read)  were trimmed to 32bp long, and mapped onto NCBI37/mm9 using Bowtie (bowtie-0.12.1, http://bowtie-bio.sourceforge.net/index.shtml) with two or fewer mismatches. Uniquely mapped reads were used for further analysis. The obtained data were processed by the ERANGE v. 3.3 (available at http://woldlab.caltech.edu/wiki/Software) to generate alignment file (bigbed file).

growth_protocol: Lin- c-Kit+ CD27+ multi-lineage fetal liver precursors were sorted from lineage-depleted fetal liver cells and co-cultured with OP9-DL1 stromal cells in Minimum Essential Medium Alpha (Invitrogen), supplemented with 20% fetal bovine serum (Hyclone) and 5 ng/mL Flt3-L and 5 ng/mL IL-7. After 4.5 d of culture, half of the cells were harvested and sorted for DN1 (FLDN1, c-KithiCD45+CD44+CD25-Lin-) and DN2a (FLDN2a, c-KithiCD45+CD44+CD25+Lin- ). After 8.5d of culture, the rest of cells were harvested and sorted for FLDN2a and DN2b (FLDN2b, c-Kitint CD45+CD44intCD25+Lin-). The FLDN2a samples used for analysis were each pools of day 4.5 and day 8.5 DN2a cells in approximately equal ratio. Thymic DN3 (ThyDN3) cells were sorted from lineage-depleted thymocytes as c-Kit-CD44-CD25+Lin-. ThyDP cells were collected from TCRa-/- thymi by magnetic bead depletion of red blood cells, B cells, macrophage, dendritic cells, NK cells and DN1-3 thymocytes.  Independent biological replicates were isolated from separate experiments.

extract_protocol: Total RNA was subjected to two rounds of selection using Oligo-dT coupled magnetic beads (Dynabeads) according to the manufacturerâs protocol. mRNA was then fragmented to an average length of 200 bp by magnesium-catalyzed hydrolysis and converted into cDNA by random priming. Purified cDNA fragments were end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3' 'A' base for ligation of Illumina's adapters  which have a single 3'  overhanging 'T' base. After (paired-end) adapter ligation DNA was purified and size selected for ~300bp by gel electrophoresis and extraction. The purified DNA was treated with Beckman/Coulter Genomics SPRI beads (Agencourt AMPure XP catalog # A63880)  to remove low MW fragments (<100 bp) from the target size population that was selected on the agarose gel. The recovered DNA was enriched by PCR amplification for 15 cycles. PCR product was treated again with SPRI beads to remove extra primer. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: genetic background

value: wildtype

value: Fetal liver precursor derived DN2b


title: ThyDP_RNA-seq_sample1

description: Poly(A) selected mRNA

source_name: ThyDP

value: TCRa -/-

value: Adult thymic DP (pre-positive selection)


title: ThyDN3_RNA-seq_sample1

description: Poly(A) selected mRNA

value: Adult thymic DN3


title: ThyDP_RNA-seq_sample2

description: Poly(A) selected mRNA


title: U2OS_PABPN1kd2_3seq

description:
3'-Seq in U2OS cells transfected with PABPN1 - si#2
hg18

value: PABPN1 - si#2


title: FLDN2b_RNA-seq_sample2

description: Poly(A) selected mRNA


title: FLDN2a_RNA-seq_sample2

description: Poly(A) selected mRNA

value: Fetal liver precursor derived DN2a


title: FLDN2a_RNA-seq_sample1

description: Poly(A) selected mRNA


title: U2OS_siC1_3seq

description:
3'-Seq in control transfected U2OS cells (siC#1)
hg18

value: osteosarcoma cell line

value: scrambled siRNA


title: ThyDP_Input_sample1

description:
Input
ThyDP_Input_sample1

data_processing: DNA sequence reads from each ChIP-seq library (single-read) were trimmed to 32bp long, and mapped onto NCBI37/mm9 using Bowtie (bowtie-0.12.1, http://bowtie-bio.sourceforge.net/index.shtml) with two or fewer mismatches. Data from multiple lanes of the same biological sample were combined. Uniquely mapped reads were used for further analysis. The obtained data were processed by the ERANGE v. 3.3 (available at http://woldlab.caltech.edu/wiki/Software) to generate alignment file (bigbed file).

extract_protocol: ChIP DNA were purified and end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3â 'A' base for ligation of Illumina's adapters which have a single 3'  overhanging  'T' base. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles, and the product was selected for 200~300 bp (insert plus adaptor and PCR primer sequences) by gel electrophoresis and extraction (QIAex II, Qiagen). The purified DNA was subjected for a second round of PCR amplification for 10 cycles. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.


title: FLDN1_RNA-seq_sample1

description: Poly(A) selected mRNA

value: Fetal liver precursor derived DN1


title: trePABPN1.A17.2.20wks

description: 3'-Seq in OPMD mouse model #2; age of 20 weeks

value: FvB

tag: tissue


title: ThyDN3_Input_sample1

description:
Input
ThyDN3_Input_sample1.1
ThyDN3_Input_sample1.2


title: FLDN2b_Input_sample1

description:
Input
FLDN2b_Input_sample1


title: FLDN1_Input_sample1

description:
Input
FLDN1_Input_sample1


title: ThyDP_GATA3_sample1

description:
Chromatin IP against GATA3
ThyDP_GATA3_sample1

value: GATA3 (Santa cruz sc-268)


title: FLDN2a_Input_sample1

description:
Input
FLDN2a_Input_sample1


title: FLDN2b_GATA3_sample1

description:
Chromatin IP against GATA3
FLDN2b_GATA3_sample1


title: FLDN1_GATA3_sample1

description:
Chromatin IP against GATA3
FLDN1_GATA3_sample1


title: ThyDP_PU.1_sample1

description:
Chromatin IP against PU.1
ThyDP_PU.1_sample1

value: PU.1 (Santa cruz sc-352)


title: FLDN2a_PU.1_sample1

description:
Chromatin IP against PU.1
FLDN2a_PU.1_sample1


title: FLDN2b_PU.1_sample1

description:
Chromatin IP against PU.1
FLDN2b_PU.1_sample1


title: ThyDP_H3K27me3_sample2

description:
Chromatin IP against H3K27me3
ThyDP_H3K27me3_sample2

value: H3K27me3 (Millipore 07-449)


title: FLDN2b_RNA-seq_sample1

description: Poly(A) selected mRNA


title: FLDN1_PU.1_sample1

description:
Chromatin IP against PU.1
FLDN1_PU.1_sample1


title: ThyDN3_RNA-seq_sample2

description: Poly(A) selected mRNA


title: ThyDN3_H3K27me3_sample2

description:
Chromatin IP against H3K27me3
ThyDN3_H3K27me3_sample2.1
ThyDN3_H3K27me3_sample2.2


title: ThyDN3_H3K27me3_sample1

description:
Chromatin IP against H3K27me3
ThyDN3_H3K27me3_sample1.1
ThyDN3_H3K27me3_sample1.2
ThyDN3_H3K27me3_sample1.3


title: FLDN2b_H3K27me3_sample2

description:
Chromatin IP against H3K27me3
FLDN2b_H3K27me3_sample2.1
FLDN2b_H3K27me3_sample2.2


title: FLDN2b_H3K27me3_sample1

description:
Chromatin IP against H3K27me3
FLDN2b_H3K27me3_sample1.1
FLDN2b_H3K27me3_sample1.2
FLDN2b_H3K27me3_sample1.3


title: FLDN1_H3K27me3_sample1

description:
Chromatin IP against H3K27me3
FLDN1_H3K27me3_sample1.1
FLDN1_H3K27me3_sample1.2
FLDN1_H3K27me3_sample1.3


title: ThyDP_H3K4me2_sample1

description:
Chromatin IP against H3K4me2
ThyDP_H3K4me2_sample1.1
ThyDP_H3K4me2_sample1.2

value: H3K4me2 (Millipore 07-030)


title: ThyDP_H3K4me2_sample2

description:
Chromatin IP against H3K4me2
ThyDP_H3K4me2_sample2


title: FLDN1_H3K27me3_sample2

description:
Chromatin IP against H3K27me3
FLDN1_H3K27me3_sample2.1
FLDN1_H3K27me3_sample2.2


title: ThyDN3_H3K4me2_sample1

description:
Chromatin IP against H3K4me2
ThyDN3_H3K4me2_sample1.1
ThyDN3_H3K4me2_sample1.2


title: FLDN2a_H3K27me3_sample1

description:
Chromatin IP against H3K27me3
FLDN2a_H3K27me3_sample1


title: ThyDN3_H3K4me2_sample2

description:
Chromatin IP against H3K4me2
ThyDN3_H3K4me2_sample2


title: FLDN2b_H3K4me2_sample1

description:
Chromatin IP against H3K4me2
FLDN2b_H3K4me2_sample1.1
FLDN2b_H3K4me2_sample1.2


title: FLDN2a_H3K4me2_sample1

description:
Chromatin IP against H3K4me2
FLDN2a_H3K4me2_sample1


title: FLDN2b_H3K4me2_sample2

description:
Chromatin IP against H3K4me2
FLDN2b_H3K4me2_sample2.1
FLDN2b_H3K4me2_sample2.2


title: FLDN1_H3K4me2_sample1

description:
Chromatin IP against H3K4me2
FLDN1_H3K4me2_sample1.1
FLDN1_H3K4me2_sample1.2


title: ThyDP_H3Ac_sample2

description:
Chromatin IP against H3K(9,14)Ac
ThyDP_H3Ac_sample2


title: FLDN1_RNA-seq_sample2

description: Poly(A) selected mRNA


title: ThyDN3_H3Ac_sample2

description:
Chromatin IP against H3K(9,14)Ac
ThyDN3_H3Ac_sample2


title: ThyDP_H3K27me3_sample1

description:
Chromatin IP against H3K27me3
ThyDP_H3K27me3_sample1.1
ThyDP_H3K27me3_sample1.2


title: FLDN2a_H3Ac_sample1

description:
Chromatin IP against H3K(9,14)Ac
FLDN2a_H3Ac_sample1


title: FLDN1_H3Ac_sample2

description:
Chromatin IP against H3K(9,14)Ac
FLDN1_H3Ac_sample2


title: FLDN2b_H3Ac_sample1

description:
Chromatin IP against H3K(9,14)Ac
FLDN2b_H3Ac_sample1.1
FLDN2b_H3Ac_sample1.2


title: ThyDN3_H3Ac_sample1

description:
Chromatin IP against H3K(9,14)Ac
ThyDN3_H3Ac_sample1.1
ThyDN3_H3Ac_sample1.2


title: ThyDP_H3Ac_sample1

description:
Chromatin IP against H3K(9,14)Ac
ThyDP_H3Ac_sample1.1
ThyDP_H3Ac_sample1.2
ThyDP_H3Ac_sample1.3
ThyDP_H3Ac_sample1.4


title: FLDN2b_H3Ac_sample2

description:
Chromatin IP against H3K(9,14)Ac
FLDN2b_H3Ac_sample2.1
FLDN2b_H3Ac_sample2.2


title: polyA RNA sequencing of H1 Derived Neuronal Progenitor Cell; polyA-RNA-seq_h1-npc_r1a

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 Derived Neuronal Progenitor Cell
Library name: polyA-RNA-seq_h1-npc_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12092
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12090
****************
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: GSM915326_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-npc_r1a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-npc_r1a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library polyA-RNA-seq_h1-npc_r1a 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.13721
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 317,791,488
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.6

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

ANALYSIS FILE NAME: GSM915326_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-npc_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-npc_r1a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Library polyA-RNA-seq_h1-npc_r1a 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.13731
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 8
BROWSER_TRACK_NAME: HDNP mRNA 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r1a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 317,791,488
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.6

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

source_name: H1 Derived Neuronal Progenitor Cultured Cell Line, biological replicate 1 (r1); polyA-RNA-seq_h1-npc_r1a

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: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

tag: passage

tag: medium

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

tag: Sex

value: Male

tag: batch

value: Replicate 1

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: 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: FLDN1_H3Ac_sample1

description:
Chromatin IP against H3K(9,14)Ac
FLDN1_H3Ac_sample1.1
FLDN1_H3Ac_sample1.2

value: wildtype

tag: cell type

value: Fetal liver precursor derived DN1

tag: chip antibody


title: polyA RNA sequencing of H1 derived mesenchymal cells; polyA-RNA-seq_h1-msc_r2a

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 derived mesenchymal cells
Library name: polyA-RNA-seq_h1-msc_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12089
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12087
****************
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: GSM915323_UCSD.H1_Derived_Mesenchymal_Stem_Cells.mRNA-Seq.polyA-RNA-seq_h1-msc_r2a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-msc_r2a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 Derived Mesenchymal Stem Cells, Library polyA-RNA-seq_h1-msc_r2a 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.13723
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 308,832,544
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 86.72
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM915323_UCSD.H1_Derived_Mesenchymal_Stem_Cells.mRNA-Seq.polyA-RNA-seq_h1-msc_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-msc_r2a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 Derived Mesenchymal Stem Cells, Library polyA-RNA-seq_h1-msc_r2a 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.13733
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 8
BROWSER_TRACK_NAME: HDMSC mRNA 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r2a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 308,832,544
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 86.72
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: H1-Mesenchymal Stem Cell Line, biological replicate 2 (r2); polyA-RNA-seq_h1-msc_r2a

value: H1 Derived Mesenchymal Stem Cells

tag: disease

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Male

value: Replicate 2

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


title: polyA RNA sequencing of H1 derived mesenchymal cells; polyA-RNA-seq_h1-msc_r1a

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 derived mesenchymal cells
Library name: polyA-RNA-seq_h1-msc_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12088
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12086
****************
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: GSM915322_UCSD.H1_Derived_Mesenchymal_Stem_Cells.mRNA-Seq.polyA-RNA-seq_h1-msc_r1a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-msc_r1a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 Derived Mesenchymal Stem Cells, Library polyA-RNA-seq_h1-msc_r1a 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.13729
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 305,599,108
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 86.66
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM915322_UCSD.H1_Derived_Mesenchymal_Stem_Cells.mRNA-Seq.polyA-RNA-seq_h1-msc_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-msc_r1a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 Derived Mesenchymal Stem Cells, Library polyA-RNA-seq_h1-msc_r1a 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.13739
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 8
BROWSER_TRACK_NAME: HDMSC mRNA 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r1a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 305,599,108
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 86.66
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

source_name: H1-Mesenchymal Stem Cell Line, biological replicate 1 (r1); polyA-RNA-seq_h1-msc_r1a

value: H1 Derived Mesenchymal Stem Cells

value: Replicate 1

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

value: Purification with AMPure XP beads (Agencourt)

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)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: polyA RNA sequencing of H1 Derived Neuronal Progenitor Cell; polyA-RNA-seq_h1-npc_r2a

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 Derived Neuronal Progenitor Cell
Library name: polyA-RNA-seq_h1-npc_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12093
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12091
****************
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: GSM915327_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-npc_r2a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-npc_r2a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library polyA-RNA-seq_h1-npc_r2a 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.13726
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 324,033,956
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.05
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.6

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

ANALYSIS FILE NAME: GSM915327_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-npc_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-npc_r2a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Library polyA-RNA-seq_h1-npc_r2a 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.13736
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 8
BROWSER_TRACK_NAME: HDNP mRNA 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r2a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 324,033,956
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.05
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.6

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

source_name: H1 Derived Neuronal Progenitor Cultured Cell Line, biological replicate 2 (r2); polyA-RNA-seq_h1-npc_r2a

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Male

value: Replicate 2

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


title: polyA RNA sequencing of H1 BMP4 Derived Trophoblast cells; polyA-RNA-seq_h1-bmp4_r2a

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 BMP4 Derived Trophoblast cells
Library name: polyA-RNA-seq_h1-bmp4_r2a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12103
****************
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: GSM915321_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-bmp4_r2a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-bmp4_r2a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library polyA-RNA-seq_h1-bmp4_r2a 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.13728
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 303,942,008
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.27
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.61

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

ANALYSIS FILE NAME: GSM915321_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-bmp4_r2a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-bmp4_r2a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 BMP4 Derived Trophoblast Cultured Cells, Library polyA-RNA-seq_h1-bmp4_r2a 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.13738
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 8
BROWSER_TRACK_NAME: HBDT mRNA 2a
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r2a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 303,942,008
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.27
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.61

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

source_name: H1 BMP4 Derived Trophoblast Cultured Cell Line, biological replicate 2 (r2); polyA-RNA-seq_h1-bmp4_r2a

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

value: Purification with AMPure XP beads (Agencourt)

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)

value: cDNA

value: 5 ng/µL

value: 5' CAAGCAGAAGACGGCATACGAGAT 3'


title: dncV_pdncV_1q

status: Public on Apr 13 2012

city: Boston

first: Bryan

last: Davies

address: 200 Longwood Avenue

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: processed data file: dncV_RNAseq_pro_data_1.txt

data_processing:
Helicos data was filtered using Helisphere; Illumina data was processed and used in fastq format
Alignments were performed using CLC genomic benchwork
ChIP peaks were called using CLC genomic benchwork
RNA-seq analysis was done using CLC genomic benchwork
Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: all files are in tab-delimited text. ChIP-seq data show locations of peaks in each sample. RNA-seq data show expression, normalization and statistical analysis of data

organism: Vibrio cholerae O1 str. C6706

extract_protocol: samples were processed according to Helicos and Illumina muanufacture protocols

tag: strain background

tag: biotype

value: El Tor

tag: genotype/variation

value: dncV (VC0179) deletant expressing DncV from pBAD18-Cm


title: tarB_pToxT_3q

description: processed data file: tarB_RNAseq_pro_data_1.txt

value: tarB deletant expressing ToxT from pBAD18-Cm

tag: strain


title: tarB_pToxT_1q


title: dncV_pBAD_1q

value: dncV (VC0179) deletant  carrying empty plasmid pBAD18-Cm


title: dncV_pdncV_2q


title: dncV_pBAD_3q


title: WT_pToxT_3q

value: wild type Vibrio cholerae El Tor strain C6706 expressing ToxT from pBAD18-Cm


title: WT_pToxT_2q


title: tarB_pToxT_2q


title: polyA RNA sequencing of H1 BMP4 Derived Trophoblast cells; polyA-RNA-seq_h1-bmp4_r1a

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: polyA RNA sequencing of H1 BMP4 Derived Trophoblast cells
Library name: polyA-RNA-seq_h1-bmp4_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12104
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12102
****************
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: GSM915320_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-bmp4_r1a.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-bmp4_r1a.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library polyA-RNA-seq_h1-bmp4_r1a 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.13725
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 264,082,692
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.61

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

ANALYSIS FILE NAME: GSM915320_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.mRNA-Seq.polyA-RNA-seq_h1-bmp4_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: polyA-RNA-seq_h1-bmp4_r1a.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from H1 BMP4 Derived Trophoblast Cultured Cells, Library polyA-RNA-seq_h1-bmp4_r1a 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.13735
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 8
BROWSER_TRACK_NAME: HBDT mRNA 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r1a EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 264,082,692
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.61

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

source_name: H1 BMP4 Derived Trophoblast Cultured Cell Line, biological replicate 1 (r1); polyA-RNA-seq_h1-bmp4_r1a

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated by treatment with fibronectin and human collagen

value: H1 cells were cultured on plates coated with fibronectin and human collagen

value: 50% StemLine II serum-free HSC expansion medium (HSFEM; Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.

value: Male

value: Replicate 1

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)


title: dToxT_pToxT_1q

description: processed data file: ToxT_RNAseq_pro_data_1.txt

value: El Tor

value: ToxT deletant expressing ToxT from pBAD18-Cm


title: FLDN1_H3K4me2_sample2

description:
Chromatin IP against H3K4me2
FLDN1_H3K4me2_sample2

tag: genetic background

value: wildtype

value: Fetal liver precursor derived DN1

value: H3K4me2 (Millipore 07-030)


title: dToxT_pBAD_3q

value: ToxT deletant carrying empty plasmid pBAD18-Cm


title: dToxT_pBAD_2q


title: ToxT_ChIP_controlq

description: processed data file: ToxT_ChIPseq_pro_data_1.txt


title: dToxT_pBAD_1q


title: ToxT_ChIP_4q

value: Monoclonal Anti-V5 antibody produced in mouse

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat #

tag: chip antibody lot #


title: dToxT_pToxT_2q


title: ToxT_ChIP_3q


title: ToxT_ChIP_2q


title: Caltech_ChipSeq_C2C12_CTCF_Control_32bp

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: Caltech-m

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

tag: antibody

value: CTCF

tag: antibody description

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: control

tag: control description

value: This data represents a control being compared to experiments using read length of 32 bp

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: labexpid

tag: labversion

value: Myoblast

tag: replicate

tag: strain description

value: Strain C3H, Very related to C57BL/6


title: dncV_pBAD_2q

tag: strain background

tag: biotype

value: El Tor

tag: genotype/variation

value: dncV (VC0179) deletant  carrying empty plasmid pBAD18-Cm

tag: strain


title: Caltech_ChipSeq_C2C12_E2F4_Control_50bp_EqS_2.0pct_60hr

tag: lab

value: Caltech-m

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

tag: antibody description

value: rabbit polyclonal. Antibody Target:E2F4

tag: antibody targetdescription

value: mapping at the C-terminus of E2F4 of human origin

tag: antibody vendorname

value: Santa Cruz Biotech

value: This data represents a control being compared to experiments using read length of 50 bp

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

value: Myocyte

tag: labversion description


title: Caltech_ChipSeq_C2C12_MyoD_(sc-32758)_Control_32bp

value: Chromatin IP Sequencing

value: mouse

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

value: mouse monoclonal antibody raised against recombinant MyoD of mouse origin with an epitope mapping to amino acids 180-189. Antibody Target:MyoD

value: This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq)

tag: antibody vendorid

tag: control

tag: control description

value: This data represents a control being compared to experiments using read length of 32 bp

tag: treatment

tag: treatment description

tag: age

tag: age description

tag: controlid

tag: labexpid

tag: labversion

tag: replicate

tag: strain description


title: dncV_pdncV_3q

tag: strain background

tag: biotype

value: El Tor

tag: genotype/variation

value: dncV (VC0179) deletant expressing DncV from pBAD18-Cm

tag: strain


title: Caltech_ChipSeq_C2C12_MyoD_(sc-32758)_Control_32bp_EqS_2.0pct_60hr

tag: lab

value: Caltech-m

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

tag: antibody description

tag: antibody targetdescription

tag: antibody vendorname

value: immortalized

value: Immortal cells

tag: labversion description

value: Strain C3H, Very related to C57BL/6


title: dToxT_pToxT_3q

tag: strain background

value: ToxT deletant expressing ToxT from pBAD18-Cm


title: WT_pToxT_1q

tag: biotype

value: wild type Vibrio cholerae El Tor strain C6706 expressing ToxT from pBAD18-Cm


title: Caltech_ChipSeq_C2C12_FOSL1_(sc-605)_Control_36bp

value: ChipSeq

value: Rabbit polyclonal antibody raised against the N-terminus of FOSL1 of rat origin. Antibody Target:FOSL1

value: The Fos gene family consists of 4 members:FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq)

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: control description

value: This data represents a control being compared to experiments using read length of 36 bp

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: age

tag: age description

tag: controlid

tag: labexpid

tag: labversion

value: Myoblast

tag: replicate

tag: strain description


title: Caltech_ChipSeq_C2C12_MyoD_(sc-32758)_Control_32bp_EqS_2.0pct_24hr

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

tag: antibody

tag: antibody description

value: mouse monoclonal antibody raised against recombinant MyoD of mouse origin with an epitope mapping to amino acids 180-189. Antibody Target:MyoD

tag: antibody targetdescription

value: This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq)

value: This data represents a control being compared to experiments using read length of 32 bp

value: 24 h with 2.0% Equine Serum and Insulin (Wold)

value: Myocyte

tag: strain


title: Caltech_ChipSeq_C2C12_Input_Control_36bp_EqS_2.0pct_60hr

value: Caltech-m

value: Wold - Califonia Institute of Technology

value: Input

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

tag: control

tag: control description

tag: treatment

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: labversion description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_CEBPB_Control_50bp

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: CEBPB

value: Rabbit polyclonal IgG. Antibody Target:CEBPB

value: epitope mapping at the C-terminus of C/EBP-beta of rat origin

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: This data represents a control being compared to experiments using read length of 50 bp

value: No special treatment or protocol applies

tag: labexpid

tag: labversion

value: Myoblast

tag: replicate

tag: strain description


title: Caltech_ChipSeq_C2C12_NRSF_Control_32bp_EqS_2.0pct_60hr

value: Caltech-m

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

tag: antibody

value: NRSF

tag: antibody description

value: Mouse monoclonal. Antibody Target:NRSF

tag: antibody targetdescription

value: Neuron-restrictive silencer transcription factor

value: David Anderson, Caltech

value: (Made by Protein Expression Center:pec@caltech.edu)

tag: control

tag: control description

value: This data represents a control being compared to experiments using read length of 32 bp

value: Myocyte

tag: strain


title: Caltech_ChipSeq_C2C12_Input_Control_50bp_EqS_2.0pct_60hr

tag: lab

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Input

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

tag: treatment

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: labversion description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_CEBPB_Control_50bp_EqS_2.0pct_60hr

value: Caltech-m

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

value: CEBPB

value: Rabbit polyclonal IgG. Antibody Target:CEBPB

value: epitope mapping at the C-terminus of C/EBP-beta of rat origin

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: This data represents a control being compared to experiments using read length of 50 bp

tag: labexpid

tag: labversion

tag: replicate

tag: strain description


title: Caltech_ChipSeq_C2C12_Max_Control_50bp

tag: lab

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

value: ChipSeq

tag: datatype description

tag: antibody

value: Max

tag: antibody description

value: Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target:Max

tag: antibody targetdescription

value: The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq).

tag: control

tag: control description

value: No special treatment or protocol applies

value: Myoblast

tag: strain


title: Caltech_ChipSeq_C2C12_Pol2_Control_32bp_EqS_2.0pct_60hr

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: This data represents a control being compared to experiments using read length of 32 bp

tag: treatment

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

value: Myocyte

tag: labversion description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_Max_Control_50bp_EqS_2.0pct_60hr

tag: lab

value: Caltech-m

tag: lab description

value: Wold - Califonia Institute of Technology

tag: datatype

tag: datatype description

value: mouse

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: This data represents a control being compared to experiments using read length of 50 bp

tag: labexpid

tag: labversion

tag: replicate

tag: strain description


title: ToxT_ChIP_1q

tag: strain background

tag: biotype

value: El Tor

tag: genotype/variation

value: ToxT deletant expressing ToxT from pBAD18-Cm

tag: chip antibody

value: Monoclonal Anti-V5 antibody produced in mouse

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat #

tag: chip antibody lot #

tag: strain


title: Caltech_ChipSeq_C2C12_TCF3_(SC-349)_Control_32bp_EqS_2.0pct_5d

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

tag: antibody description

value: E2A.E12(V-18) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of E2A.E12 of human origin. Recommended for detection of E12 and E47 of m, r and h origin by WB, IP, IF, IHC(P), ELISA and indirect FCM using PE (sc-3739)- or FITC (sc-2012)-conjugated goat anti-rabbit IgG. Antibody Target:TCF3

tag: antibody targetdescription

value: Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs:5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer.

tag: control

tag: control description

value: This data represents a control being compared to experiments using read length of 32 bp

tag: treatment

tag: treatment description

value: 5 d with 2.0% Equine Serum and Insulin (Wold)

tag: age

tag: age description

tag: controlid

tag: labversion description


title: Caltech_ChipSeq_C2C12_Input_Control_32bp_EqS_2.0pct_60hr

tag: lab

value: Caltech-m

tag: datatype

tag: datatype description

value: Input

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

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

value: immortalized

value: Immortal cells

tag: labexpid

tag: labversion

value: Myocyte

tag: replicate

tag: strain

tag: strain description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_Input_Control_50bp

tag: lab description

value: Wold - Califonia Institute of Technology

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

tag: antibody

tag: antibody description

value: This data represents a control being compared to experiments using read length of 50 bp

value: No special treatment or protocol applies

value: Myoblast


title: Caltech_ChipSeq_C2C12_Myogenin_(sc-12732)_Control_32bp

value: ChipSeq

value: Chromatin IP Sequencing

value: mouse monoclonal antibody; epitope mapping within amino acids 138-158 of myogenin of rat origin. Antibody Target:Myogenin

tag: antibody targetdescription

value: Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq)

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: control

tag: control description

value: This data represents a control being compared to experiments using read length of 32 bp

tag: treatment

tag: treatment description

tag: age

tag: age description

tag: controlid


title: Caltech_ChipSeq_C2C12_Input_Control_32bp_EqS_2.0pct_24hr

tag: lab

value: Caltech-m

tag: lab description

tag: datatype

tag: datatype description

value: Input

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

value: 24 h with 2.0% Equine Serum and Insulin (Wold)

value: immortalized

tag: labexpid

tag: labversion

tag: labversion description

tag: replicate

tag: strain

tag: strain description


title: Caltech_ChipSeq_C2C12_Pol2(phosphoS2)_Control_32bp_EqS_2.0pct_60hr

value: Wold - Califonia Institute of Technology

tag: cell

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

tag: antibody

tag: antibody description

value: Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target:POL2S2

tag: antibody targetdescription

value: RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

value: Immortal cells

value: Myocyte

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_SRF_Control_32bp_EqS_2.0pct_24hr

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

value: SRF

value: Rabbit polyclonal. Antibody Target:SRF

value: Serum response transcription factor

tag: control description

tag: treatment

tag: treatment description

tag: age

tag: age description

tag: controlid