|
| Status |
Public on Jan 07, 2010 |
| Title |
RNA-Seq analysis of H1 embryonic stem cell line (HS1272) |
| Sample type |
SRA |
| |
|
| Source name |
HS1272-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC20-RNA
biomaterial_type: cell line
line: H1
Sex: male
body site: Embryo ICM
histological type: Embryonic stem cell
is tumor: No
|
| Extracted molecule |
total RNA |
| Extraction protocol |
library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
design description: RNA-Seq analysis of H1 embryonic stem cell line (HS1272) using Illumina Genome Analyzer IIx
library name: HS1272
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.9
RNA_PREPARATION_INITIAL_RNA_QNTY: 20000 ng
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 270-500 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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run105124Lane7.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.7
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1892
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106055Lane2.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.1
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1893
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106056Lane3.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.2
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1894
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106057Lane4.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.3
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1895
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106058Lane5.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.4
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1896
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106059Lane6.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.5
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1897
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106060Lane7.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.6
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1898
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-seq.wig
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the H1 cell line 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.1890
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.bed
ANALYSIS ALIAS: HS1272-1_612FTAAXX-HS1272-1_42VR1AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the H1 Cell Line, Library H1EScd1 batch2 vial2 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.4273
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 2
QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.50
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25
**********************************************************************
ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.wig
ANALYSIS ALIAS: HS1272-1_612FTAAXX-HS1272-1_42VR1AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the H1 Cell Line, Library H1EScd1 batch2 vial2 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.4268
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 2
BROWSER_TRACK_NAME: H1 mRNA l2
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line mRNA-Seq Library H1EScd1 batch2 vial2 EA Release 2
QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.50
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25
**********************************************************************
|
| |
|
| Submission date |
Dec 11, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSF-UBC CENTER |
| Organization name |
UCSF-UBC
|
| Street address |
UCSF-UBC
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
| Relations |
| Reanalyzed by |
GSE99453 |
| Named Annotation |
GSM484408_UCSF-UBC.H1.mRNA-seq.wig.gz |
| Named Annotation |
GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.wig.gz |
| SRA |
SRX014392 |
| BioSample |
SAMN03416738 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.bed.gz |
2.9 Gb |
(ftp)(http) |
BED |
| GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.wig.gz |
36.3 Mb |
(ftp)(http) |
WIG |
| GSM484408_UCSF-UBC.H1.mRNA-seq.Run105124Lane7.bam |
2.0 Gb |
(ftp)(http) |
BAM |
| GSM484408_UCSF-UBC.H1.mRNA-seq.Run106055Lane2.bam |
2.9 Gb |
(ftp)(http) |
BAM |
| GSM484408_UCSF-UBC.H1.mRNA-seq.Run106056Lane3.bam |
2.9 Gb |
(ftp)(http) |
BAM |
| GSM484408_UCSF-UBC.H1.mRNA-seq.Run106057Lane4.bam |
3.0 Gb |
(ftp)(http) |
BAM |
| GSM484408_UCSF-UBC.H1.mRNA-seq.Run106058Lane5.bam |
2.9 Gb |
(ftp)(http) |
BAM |
| GSM484408_UCSF-UBC.H1.mRNA-seq.Run106059Lane6.bam |
2.9 Gb |
(ftp)(http) |
BAM |
| GSM484408_UCSF-UBC.H1.mRNA-seq.Run106060Lane7.bam |
2.9 Gb |
(ftp)(http) |
BAM |
| GSM484408_UCSF-UBC.H1.mRNA-seq.wig.gz |
26.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
