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Status |
Public on Sep 05, 2012 |
Title |
RNA-Seq analysis of cDNA_Lib 4 derived from human liver cells; cDNA_Lib 4 |
Sample type |
SRA |
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Source name |
normal liver,resected from patient with metastatic carcinoid; cDNA_Lib 4
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Organism |
Homo sapiens |
Characteristics |
sample alias: BioSam 321 REMC 27 sample common name: Adult Liver collection_method: Surgery donor_health_status: patient with metastatic carcinoid disease: patient with metastatic carcinoid tissue_type: Adult Liver donor_ethnicity: Caucasian donor_sex: Female biomaterial_type: Primary Tissue tissue_depot: Liver donor_id: Donor 177 REMC 27 biomaterial_provider: MGH donor_age: 45.0 Years rna_preparation_5'_rna_adapter_ligation_protocol: NA rna_preparation_3'_rna adapter_ligation_protocol: NA rna_preparation_5'_rna_adapter_sequence: NA library_generation_pcr_f_primer_sequence: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence: NA mrna_preparation_initial_mrna_qnty: 200ng library_generation_pcr_product_isolation_protocol: 1.8X SPRI cleanup (no size selection) rna_preparation_5'_dephosphorylation: NA extraction_protocol_mrna_enrichment: Dynabeads mRNA purification kit (Invitrogen) library_generation_pcr_thermocycling_program: 95C 2mins, 10 cycles of: 98C for 30 sec, 55C for 30 sec, 72C for 1 min, then 72C for 10 min, hold 4C rna_preparation_reverse_transcription_primer_sequence: NNNNNN extraction_protocol: Qiagen AllPrep DNA/RNA/Protein Mini Kit library_generation_pcr_template: Adapter ligated cDNA made by reverse transcription of RNA library_generation_pcr_polymerase_type: PFU Ultra II library_generation_pcr_number_cycles: 10 library_generation_pcr_primer_conc: 0.83 uM library_generation_pcr_r_primer_sequence: CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation: 98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min. rna_preparation_5'_phosphorylation: NA experiment_type: mRNA-Seq rna_preparation_reverse_transcription_protocol: We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h. mrna_preparation_fragment_size_range: 400bp
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Extracted molecule |
total RNA |
Extraction protocol |
Library construction protocol: Strand specific cDNA libraries were constructed for Illumina sequencing using the dUTP method essentially as described in S. Zhong et al, Cold Spring Harbor Protoc 8, 940 - 949 (2011).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
sample_term_id: UBERON_0002107 assay_term_id: OBI_0001271 nucleic_acid_term_id: SO_0000871 Design description: mRNA-Seq for REMC on Illumina Library name: cDNA_Lib 4 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.12079 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.12085 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM916093_BI.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: cDNA_Lib 4.hg19.level.1.release.8 ANALYSIS TITLE: Mapping of Adult Liver mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Adult Liver, Donor Donor 177 REMC 27 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.13717 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: 122,094,489 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22 PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.29 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 36 MAXIMUM_REPLICATE_CORRELATION: NA
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ANALYSIS FILE NAME: GSM916093_BI.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: cDNA_Lib 4.hg19.level.2.release.8 ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Adult Liver, Donor Donor 177 REMC 27 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.13720 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: AL mRNA 77 BROWSER_TRACK_DESCRIPTION: BI Adult Liver mRNA-Seq Donor 177 REMC 27 Library cDNA_Lib 4 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 122,094,489 NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22 PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.29 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 36 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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Submission date |
Apr 16, 2012 |
Last update date |
May 30, 2017 |
Contact name |
BROAD INSTITUTE |
E-mail(s) |
rharris1@bcm.tmc.edu
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Organization name |
Broad Institute
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Street address |
-
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE17312 |
BI Human Reference Epigenome Mapping Project |
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Relations |
Reanalyzed by |
GSE99453 |
BioSample |
SAMN00857858 |
Named Annotation |
GSM916093_BI.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM916093_BI.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.bed.gz |
1.1 Gb |
(ftp)(http) |
BED |
GSM916093_BI.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.wig.gz |
12.3 Mb |
(ftp)(http) |
WIG |
Processed data provided as supplementary file |
Raw data not provided for this record |
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