|
| Status |
Public on Mar 30, 2017 |
| Title |
Input_for_H3K27_in_can_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Input_for_H3K27_in_can
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: can
gender: male
age: 3 days old
tissue: adult testes
chip antibody: none
|
| Growth protocol |
The flies were kept at 23°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To perform H3K27me3 ChIP-seq, we used the True MicroChIP & MicroPlex Library Preparation™ Package (Diagenode), according to manufacturer’s recommendations. 400 adult testes of comr or can homozygotes were used as a starting material for two biological replicates. Abcam anti-H3K27me3 antibodies (#6002) were used for chromatin immunoprecipitation. Chromatin was sheared using BioRuptor instrument (Diagenode).
DNA from precipitated material and input were used for library preparation using MicroPlex Library Preparation protocol. The libraries were sequenced on the Illumina MiSeq system.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Input sample for the Replicate2 of can-mutants ChIP-Seq
can_H3K27me3_1kb_QN.txt.gz
|
| Data processing |
The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with the following parameters: -m all -mmp 0.1 -act 20 -a single. Paired reads were combined.
For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample.
Log2 of the ChIP to input ratio was used as a measure of local H3K27me3 enrichment. To build the whole genome profile, the data were processed using a 1kb sliding window, step 100 bp. Occupancy profiles were quantile normalized.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: .txt files report occupancy profiles
|
| |
|
| Submission date |
Mar 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Petr Laktionov |
| E-mail(s) |
laktionov@mcb.nsc.ru
|
| Organization name |
Institute of molecular and cellular biology SD RAS
|
| Lab |
Genomics lab
|
| Street address |
Lavrenitev ave 8/2
|
| City |
Novosibirsk |
| ZIP/Postal code |
630090 |
| Country |
Russia |
| |
|
| Platform ID |
GPL16479 |
| Series (2) |
| GSE97127 |
Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [ChIP-Seq] |
| GSE97182 |
Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis |
|
| Relations |
| BioSample |
SAMN06647767 |
| SRA |
SRX2677155 |
