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Sample GSM1112844 Query DataSets for GSM1112844
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
 
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
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
Extracted molecule total RNA
Extraction protocol Library construction protocol: Direct RNA-seq method based on RNA 3' linker ligation, unpublished
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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
****************
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

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

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

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

 
Submission date Apr 02, 2013
Last update date May 15, 2019
Contact name BROAD INSTITUTE
E-mail(s) rharris1@bcm.tmc.edu
Organization name Broad Institute
Street address -
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (1)
GSE17312 BI Human Reference Epigenome Mapping Project
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 SelectorHelp
Processed data provided as supplementary file
Raw data not provided for this record
Raw data are available in SRA

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