|
| Status |
Public on Nov 01, 2011 |
| Title |
Sox3 ChIP-Seq in neural progenitor cells, biol repl 2 |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES-derived neural progenitor cells
differentiation specificity: 4 days in differentiation conditions with retinoic acid
chip antibody: Sox3 (T. Edlund)
|
| Treatment protocol |
Formaldehyde 1% crosslink 9min at 37°C. Cells were mechanically dissociated from the surface before lysis.
|
| Growth protocol |
Mouse ES-cells were differentiated with B27 and N2 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) with 0.5uM retinoic acid (all-trans, Sigma) at day 0 and day 2. C2C12 cells were cultured with serum unless for 3h during lipofectamine transfection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit (1003473).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against Sox3
|
| Data processing |
Reads were aligned by Bowtie, with options -n 2 -m 1, against genome build mm9.
|
| |
|
| Submission date |
Oct 18, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Rickard Sandberg |
| E-mail(s) |
Rickard.Sandberg@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Cell and Molecular Biology
|
| Street address |
Berzelius vag 35
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE33024 |
Sequentially acting Sox transcription factors in neural lineage development |
| GSE33059 |
Sequentially acting Sox transcription factors in neural lineage development [ChIP-seq] |
|
| Relations |
| SRA |
SRX101685 |
| BioSample |
SAMN00739988 |
