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| Status |
Public on Jan 15, 2014 |
| Title |
RNA-Seq analysis of cDNA_Lib 5 derived from human CD56+ ectoderm cells; cDNA_Lib 5 |
| 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 5
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: BioSam 802
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 1010
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
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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 |
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 5
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15041
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15046
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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 |
Various levels of processed data files will be made available as this project proceeds.
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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 |
| SRA |
SRX259060 |
| BioSample |
SAMN01997270 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data not provided for this record |
| Raw data are available in SRA |
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