|
| Status |
Public on Feb 17, 2012 |
| Title |
zebrafish adult red cells Total Input |
| Sample type |
SRA |
| |
|
| Source name |
adult red blood cells
|
| Organism |
Danio rerio |
| Characteristics |
chip antibody: None
cell type: adult red blood cells
|
| Growth protocol |
primar red cells isolated from adult zebrafish
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
red blood cells from 10 adults
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all WICMT samples, reads were aligned to their indicated build using Eland.
For all WICMT samples, aligned sequences were processed with MACS (Zhang et al., 2008) software to produce a single difference signal: control = WCE, treatment = gata1 ChIP, and with command line input parameters: gsize = 15000000000; bandwidth = 50; and p-value = 1e-09.
For all HMSBPF samples, reads were aligned to their indicated build using SOAP2
For all HMSBPF samples, aligned sequences were processed with MACS (Zhang et al., 2008) software to produce a single difference signal: control = WCE, treatment = H3K4me3, and with command line input parameters: gsize = 15000000000; bandwidth = 50; and p-value = 1e-09.
|
| |
|
| Submission date |
Feb 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Anthony Dominc DiBiase |
| E-mail(s) |
adibiase@enders.tch.harvard.edu
|
| Organization name |
Children's Hospital Boston
|
| Department |
Hem/Onc
|
| Lab |
Zon Lab
|
| Street address |
KFRB, 1 Blackfan St, Suite 8216
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9319 |
| Series (2) |
|
| Relations |
| SRA |
SRX120317 |
| BioSample |
SAMN00790962 |
