|
| Status |
Public on Nov 28, 2020 |
| Title |
input_wt_larvae_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
H3K36 wild-type 3rd instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 3rd instar larvae
antibody: none
genotype: wildtype
|
| Growth protocol |
Drosophila embryos 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 CNS and imaginal disc tissues (for 3rd instar larvae). Histone-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:1 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)
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 in 21-24 hr wt embryos and in wt 3rd instar larvae.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the H3K36me2 and H3K27me3 ChIP-seq datasets from H3K36A and H3K36R mutants to the corresponding wild-type H3K36me2 and H3K27me3 ChIP-seq datasets respectively.
Genome_build: dm6
Supplementary_files_format_and_content: Bedgraph files (for visualizing ChIP-seq datasets) contain the normalized number of reads per million reads per 200 bp bins covering the 7 chromosomal arms of the Drosophila genome.
|
| |
|
| Submission date |
Aug 19, 2020 |
| Last update date |
Nov 29, 2020 |
| 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 (1) |
| GSE148254 |
Inhibition of PRC2 activity by H3K36 methylation |
|
| Relations |
| BioSample |
SAMN15859604 |
| SRA |
SRX8973507 |
