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| Status |
Public on Jun 22, 2013 |
| Title |
RNA-Seq analysis of cDNA_Lib 13 derived from human CD56+ ectoderm cells; cDNA_Lib 13 |
| 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 13
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: BioSam 1247
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 1890
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 13
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15788
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15412
****************
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: GSM1112846_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_13.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 13.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 13 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.16657
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: 87,695,601
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.68
**********************************************************************
ANALYSIS FILE NAME: GSM1112846_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_13.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 13.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 13 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.16666
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 13
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells mRNA-Seq Library cDNA_Lib 13 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 87,695,601
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.98
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 18
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 |
-
|
| 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 |
SRX259091 |
| BioSample |
SAMN01997273 |
| Named Annotation |
GSM1112846_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_13.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1112846_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_13.bed.gz |
798.7 Mb |
(ftp)(http) |
BED |
| GSM1112846_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_13.wig.gz |
11.7 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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