|
| Status |
Public on Nov 01, 2013 |
| Title |
Brg1_ChIP_Seq |
| Sample type |
SRA |
| |
|
| Source name |
mouse primary epidermal keratinocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: newborn
tissue: skin
cell type: mouse primary epidermal keratinocytes
chip antibody: anti-Brg1 (H-88)
chip antibody vendor: Santa Cruz Biotechnologies
chip antibody cat. #: SC-10768
chip antibody lot #: F1312
|
| Growth protocol |
Skin from the newborn mice has been treated with 1% Trypsin in PBS buffer at 4 C overnight, dermis was separated from epidermis and the single cell suspension was prepared from the epidermis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell were fixed with 1% formaldehyde in PBS, the nuclei were isolated, chromatin was sonicated and immuno-precipitated using anti-Brg1 anti-bodies (Santa Cruz Biotechnologies). The DNA has been isolated from the immuno-precipitated and input chromatin
Indexed ChIP-seq libraries were generated using NEBNext reagents (New England Biolabs) and
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 1
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 1.1.2
Data were filtered using the following specifications…
peaks were called using Sicer version 0.0.1 with the following setting:FDR 0.01
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using Sicer
|
| |
|
| Submission date |
Sep 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Y Fessing |
| Organization name |
University of Bradford
|
| Street address |
Richmond Road
|
| City |
Bradford |
| ZIP/Postal code |
BD7 1DP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE50921 |
ChIP-seq analysis of genome wide Brg1 binding in mouse primary keratinocytes |
|
| Relations |
| BioSample |
SAMN02357082 |
| SRA |
SRX352043 |
