|
| Status |
Public on Sep 16, 2012 |
| Title |
M1-1 H3K9me3 #1926 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: In house anti-H3K9me3 #1926
genotype: wt
cell type: Embryonic Fibroblasts
|
| Treatment protocol |
For Pax9 kd, 5 shRNAs were obtained from the Sigma Mission RNAi library, packaged into lentiviral particles and transduced into wt and Pax3-deficient iMEFs. Transduced cells were selected with puromycin and kd efficiency was corroborated by qRT-PCR.
|
| Growth protocol |
Cell were growth in normal MEFs medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed on formaldehyde fixed cells, lysates were incubated with the corresponding antibodies, histones-DNA complexes were immunoprecipitated with dynabeads and DNA was purified using columns. Libraries were prepared following the standard illumina Pair-end protocol. Libraries were sequenced on the GAIIx, 2x36 bases following the standard protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 1
|
| Data processing |
Illumina Casava 1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.3 with the following parameters: -v 2 -X 1000 --tryhard -m 1 --best --strata
For each wt (M1-1) versus ko (M1-3, M1-3/9) combination the two corresponding BAM files were compared based on the number of reads as follows: The reads were elongated to a fragment size of 300 nucleotides. The number of reads in each BAM file was normalized based on the SES method proposed by Diaz et al. (2012), "Normalization, bias correction, and peak calling for ChIP-seq", Statistical applications in genetics and molecular biology, 11(3). The genome was partitioned into bins of size 25bp and then the number of reads found in each BAM file was counted for those bins. The log2 of the ratio (wt vs. ko) of those counts was written to a bigWiggle file.
Genome_build: mm9
Supplementary_files_format_and_content: bigWiggle files containing log2 ratios
|
| |
|
| Submission date |
Aug 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Manke |
| Organization name |
Max-Planck-Institute for Immunobiology and Epigenetics
|
| Department |
Bioinformatics and Deep-Sequencing Unit
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg im Breisgau |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE40086 |
A transcription factor based mechanism for mouse heterochromatin formation |
|
| Relations |
| SRA |
SRX176317 |
| BioSample |
SAMN01113017 |
