|
| Status |
Public on Apr 20, 2016 |
| Title |
ChIP-seq_EPP_input |
| Sample type |
SRA |
| |
|
| Source name |
Erythroid progenitors/precursors (EPP)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+-derived human erythroid progenitors/precursors
tissue: Human umbilical cord blood
antibody: none (nuclear extracts sonicated but non-immunoprecipitated)
|
| 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
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was prepared after cross-linking for 10’ at RT with 1% formaldehyde-containing medium, using truChIP™ High Cell Chromatin Shearing Kit with SDS Shearing Buffer (Covaris). Nuclear extracts were sonicated to obtain DNA fragments averaging 200 bp in length and immunoprecipitated the equivalent of 107 cells overnight with 10 μg of rabbit antibodies against H3K4me1, H3K4me3 and H3K27ac, as previously described (Cattoglio et al., 2010b; Cui et al., 2009).
Libraries were prepared according to Illumina's instructions accompanying the standard protocol of Illumina ChIP-seq DNA sample preparation kit (IP-102-1001, Illumina Inc.).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Input DNA
|
| Data processing |
Reads from each sample were mapped in three consecutive steps taking into account from 0 to a maximum of 2 mismatches. After each mapping step the unmapped reads were filtered out and remapped by increasing of one. The results of each mapping step were then pooled together into a single bam file.
We performed ChIP-seq peak calling using SICER default parameters (Zang et al. 2009) and using each INPUT data to model the background noise.
Genome_build: hg19
Supplementary_files_format_and_content: peak bed file
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
|
| Phone |
+39-049-827-6108
|
| Organization name |
University of Padova
|
| Department |
Molecular Medicine
|
| Street address |
via U. Bassi 59/b
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE70675 |
Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [ChIP-Seq] |
| GSE70677 |
Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation |
|
| Relations |
| BioSample |
SAMN03266527 |
| SRA |
SRX813529 |
