|
| Status |
Public on Dec 25, 2013 |
| Title |
DP_H3K27me3_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
DPdouble positive thymocytes derived from in vitro expanded bone marrow cells transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse
|
| Organism |
Mus musculus |
| Characteristics |
cell type: double positive thymocytes derived from in vitro expanded bone marrow cells transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse
strain: B6
chip antibody: anti H3K27me3 antibody (Cell Signaling #9733)
chip antibody catalog #: #9733
chip antibody manufacturer: Cell Signaling
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to Illumina's instructions accompanying the Agilent_DNA _Kit _100. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were generated and sequenced on the Genome Analyzer following the Illumina manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Sequence reads were mapped using Botwie version 0.12.7 with up to 2 mismatches and up to 100 best alignment positions were reported (bowtie options –v 2 –a --best --strata –m 100).
In case a read had more hits n to an individual sequence from any of these data bases, the weight 1/n was used instead. These weights were used in all the subsequent analyses. DNA fragment length was estimated from cross correlation. profile of read density on both chromosomal strands.
Mapped reads were shifted towards their 3’ end by the half of the fragment length
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated with a custom Perl script
|
| |
|
| Submission date |
Jun 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
maria alessandra vigano |
| E-mail(s) |
alessandra.vigano@unibas.ch
|
| Organization name |
university of basel
|
| Department |
department of biomedicine
|
| Street address |
mattenstrasse,28
|
| City |
basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE47995 |
An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. |
|
| Relations |
| BioSample |
SAMN02204656 |
| SRA |
SRX306599 |
