|
| Status |
Public on Mar 07, 2019 |
| Title |
Sox2 ChIP_Spheres |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells (Spheres)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed C57BL/6 x DBA
cell type: Hippocamus-derived neural progenitor cells
chip antibody: Sox2 (Santa cruz sc-17320)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and Sox2-DNA complexes were isolated by immunoprecipitation
Libraries were prepared from 10ng of immunoprecipitated or inut DNA according to Illumina's instructions accompanying the ChIp-seq Sample Kit.. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols to generate 50bp single read data.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.5
We used MACS (Zhang et al. 2008) version 2.0.9 to define Sox2 bound regions (peaks). As this tool is very sensitive to the unbalanced number of reads in the real and the input set, we decided to reduce the larger dataset to match the number of mapped reads in the smaller dataset by randomly sampling reads, as described previously (Mateo et al 2015).
Genome_build: mm9
Supplementary_files_format_and_content: *bed.txt: enriched ChIP-Seq peaks
|
| |
|
| Submission date |
Nov 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico Zambelli |
| Organization name |
University of Milan
|
| Department |
Department of Biosciences
|
| Street address |
Via Giovanni Celoria 26
|
| City |
Milano |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE90559 |
Sox2 is required for global chromatin interactions in brain-derived neural stem cells [ChIP-seq] |
| GSE90561 |
Sox2 is required for functional chromatin connectivity in brain-derived neural stem cells. |
|
| Relations |
| BioSample |
SAMN06060051 |
| SRA |
SRX2378798 |
