|
| Status |
Public on Nov 09, 2022 |
| Title |
H3K27me3_wt_13-17hr_rep1_#6 |
| Sample type |
SRA |
| |
|
| Source name |
13-17hr old embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: 13-17hr old embryos
genotype: wt
antibodies: H3K27me3 (Cell Signaling (#9733))
reference sample_for_normalization_with_exogenous_chromatin: H3K27me3_wt_21-24hr_rep3_#6
normalization factor: 0.183852720224172
|
| Growth protocol |
Drosophila embryos and larvae were grown on standard medium at 25˚C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated fixed nuclei (for embryos) and from sonicated fixed hand-dissected imaginal disc tissues (for 3rd instar larvae). Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:5 ratio of dm / dp chromatin before the addition of the antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of H3K36me2 enriched-regions and H3K27me3 enriched-regions.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Nov 09, 2022 |
| Contact name |
Jürg Müller |
| Organization name |
Max Planck Institute of Biochemistry
|
| Street address |
Am Klopferspitz
|
| City |
Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE210233 |
PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking (ChIP-Seq) |
| GSE210236 |
PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking |
|
| Relations |
| BioSample |
SAMN30081852 |
| SRA |
SRX16752348 |
