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Status |
Public on Jun 22, 2013 |
Title |
RNA-Seq analysis of cDNA_Lib 14 derived from human CD56+ ectoderm cells; cDNA_Lib 14 |
Sample type |
SRA |
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Source name |
CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; cDNA_Lib 14
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Organism |
Homo sapiens |
Characteristics |
sample alias: BioSam 1248 sample common name: hESC Derived CD56+ Ectoderm Cultured Cells lineage: ectoderm medium: CD56 ectoderm - Days 0-5: DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um) disease: presumed normal passage: 23 line: CD56+ ectoderm differentiation_method: adherence batch: BioSAli 1891 biomaterial_type: Cell Line differentiation_stage: intermediate Sex: Male biomaterial_provider: Harvard rna_preparation_5'_rna_adapter_ligation_protocol: 3' cDNA ligation rna_preparation_3'_rna adapter_ligation_protocol: Our protocol using T4 RNA ligase from NEB rna_preparation_5'_rna_adapter_sequence: 5ILL-21 library_generation_pcr_f_primer_sequence: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1 rna_preparation_3'_rna_adapter_sequence: C3trunc mrna_preparation_initial_mrna_qnty: around 10ng library_generation_pcr_product_isolation_protocol: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI rna_preparation_5'_dephosphorylation: yes extraction_protocol_mrna_enrichment: OligodT - Dynabeads mRNA purification kit (Invitrogen) library_generation_pcr_thermocycling_program: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C rna_preparation_reverse_transcription_primer_sequence: AR2 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: Phusion High Fidelity library_generation_pcr_number_cycles: 8 library_generation_pcr_primer_conc: 12 pmoles of each/50 ul of reaction library_generation_pcr_r_primer_sequence: 2P_Universal extraction_protocol_fragmentation: 70C for 4 min in Ambion Fragmentation Buffer rna_preparation_5'_phosphorylation: NO experiment_type: mRNA-Seq rna_preparation_reverse_transcription_protocol: We synthesized first-strand cDNA using affinity-script reverse transcriptase mrna_preparation_fragment_size_range: 50-300 nt
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Extracted molecule |
total RNA |
Extraction protocol |
Library construction protocol: Direct RNA-seq method based on RNA 3' linker ligation, unpublished
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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: CL_0000221 assay_term_id: OBI_0001271 nucleic_acid_term_id: SO_0000871 Design description: mRNA-Seq for REMC on Illumina Library name: cDNA_Lib 14 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15786 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15411 **************** 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: GSM1112844_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_14.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: cDNA_Lib 14.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library cDNA_Lib 14 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.16658 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: mRNA-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: Pash SOFTWARE_VERSION: 3.0 MAXIMUM_ALIGNMENT_LENGTH: Read length MISMATCHES_ALLOWED: 10% of read length ALIGNMENTS_ALLOWED: 1 TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration. TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None ALIGNMENT_POSTPROCESSING: None RELEASE_NUMBER: Human Epigenome Atlas 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 141,559,504 PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.24 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 23 MAXIMUM_REPLICATE_CORRELATION: 0.68
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ANALYSIS FILE NAME: GSM1112844_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_14.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: cDNA_Lib 14.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells mRNA-Seq Data ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library cDNA_Lib 14 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.16667 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: mRNA-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 0bp GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 9 BROWSER_TRACK_NAME: hDCEcto mRNA 14 BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells mRNA-Seq Library cDNA_Lib 14 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 141,559,504 PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.24 PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 23 MAXIMUM_REPLICATE_CORRELATION: 0.68
**********************************************************************
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Submission date |
Apr 02, 2013 |
Last update date |
May 15, 2019 |
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 |
SRA |
SRX259089 |
BioSample |
SAMN01997272 |
Named Annotation |
GSM1112844_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_14.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM1112844_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_14.bed.gz |
1.3 Gb |
(ftp)(http) |
BED |
GSM1112844_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_14.wig.gz |
16.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data not provided for this record |
Raw data are available in SRA |
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