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| Status |
Public on Apr 20, 2016 |
| Title |
CAGE_EPP |
| Sample type |
SRA |
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| Source name |
Erythroid progenitors/precursors (EPP)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+-derived human erythroid progenitors/precursors
tissue: Human umbilical cord blood
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| Growth protocol |
Committed erythroid and myeloid progenitors/precursors (EPP and MPP) were isolated as pools of CD34lowCD36high and CD34-CD13+ populations, after induction for five days in culture in the presence of SCF, IL3 and either Epo or G-CSF, respectively
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from multipotent and lineage-committed progenitors using RNeasy Plus Mini kit (QIAGEN).
CAGE library preparation was performed by DNAFORM Inc. at RIKEN Omics Science Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
CAGE promoters
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| Data processing |
DNAFORM at RIKEN GeNAS performed CAGE data analysis. Briefly, tags were extracted and mapped to human genome version hg19 (NCBI build 37), with a minimum match length of 21 bases and a maximum of one error; tags mapping the human ribosomal DNA sequence were eliminated. For CAGE tags mapping to multiple genome locations, a weighting strategy, based on the number of CAGE tags within a 200bp neighbourhood around each candidate mapping location, was applied. Equal weights were used if no unique tags were found within the 200 bp region for all candidate mapping locations (Faulkner et al. 2008).
We defined level‐1 promoters ("transcription start sites") by summing the weighted number of CAGE tags at each genome position. Then we clustered level-1 promoters into level-2 promoters ("promoters") if they were within 20 bp of each other on the same chromosomal strand. We calculated the expression level for each level-1 and level-2 promoter by dividing the number of CAGE tags of each promoter in each experimental condition by the total number of mapped CAGE tags in that condition, and multiplying by 1,000,000 (tags-per-million, TPM). The expression of each level-2 promoter of at least 10 TPM in at least one experimental condition was imposed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM (tags-per-million) values of CAGE promoters for each Sample
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| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
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| Phone |
+39-049-827-6108
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| Organization name |
University of Padova
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| Department |
Molecular Medicine
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| Street address |
via U. Bassi 59/b
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| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
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| Platform ID |
GPL10999 |
| Series (2) |
| GSE70674 |
Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [RNA-seq (CAGE)] |
| GSE70677 |
Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation |
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| Relations |
| BioSample |
SAMN03267299 |
| SRA |
SRX814688 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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