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Sample GSM1112818 Query DataSets for GSM1112818
Status Public on Jan 15, 2014
Title RNA-Seq analysis of cDNA_Lib 8 derived from human CD56+ ectoderm cells; cDNA_Lib 8
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 8
Organism Homo sapiens
Characteristics sample alias: BioSam 803
sample common name: hESC Derived CD56+ Ectoderm Cultured Cells
lineage: ectoderm
medium: Days 0-5: DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)
disease: presumed normal
passage: 21
line: CD56+ ectoderm
differentiation_method: adherence
batch: BioSAli 1011
biomaterial_type: Cell Line
differentiation_stage: NA
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 8
EDACC Genboree Experiment Page:
EDACC Genboree Sample Page:
For data usage terms and conditions, please refer to:
Data processing Various levels of processed data files will be made available as this project proceeds.
Submission date Apr 02, 2013
Last update date May 15, 2019
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
SRA SRX259063
BioSample SAMN01997269

Supplementary data files not provided
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Raw data not provided for this record
Raw data are available in SRA

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