|
| Status |
Public on May 24, 2024 |
| Title |
ChIPseq_DMC1_KEInput_sticklebackLiverPool_Freshwater |
| Sample type |
SRA |
| |
|
| Source name |
LiverPool
|
| Organism |
Gasterosteus aculeatus |
| Characteristics |
tissue: LiverPool
strain: wild-derived freshwater strain
|
| Growth protocol |
Wild-derived strains of marine and freshwater sticklebacks from the River Tyne, East Lothian, Scotland under a seasonally varying day length (3 months of 16 hours light, 8 hours dark, followed by 3 months of winter 8 hours dark, 16 hours light). Juvenile sticklebacks were reared from fertilisation under 3 months of summer light cycle followed by 3 months of winter light cycle. Testes and livers were collected during the last three weeks of the 3-month low light period, snap-frozen in liquid nitrogen, and stored in -80’C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue lysate was prepared from frozen tissue following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65.
The ChIP pulldown of DMC1-bound single stranded DNA was performed with "kinetic enrichment" following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65 and was followed sequentially by a ChIP pull down H3K4me3 on the same tissue lysate.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
ChIPseq reads were trimmed to 40 bp using Trimmomatic (Bolger et al 2014 Bioinformatics 30:2114-20).
For DMC1 ChIP a specialized bioinformatic pipeline described in Khil et al (2012) Genome Research 22:957-65 was used to process paired-end sequencing data and extract 'Type 1' sequencing reads obtained from pulldown of DMC1-bound single stranded DNA. This generated bedfiles used as input for MACS2 peak calling (described below). This was not performed for H3K4me3 ChIPseq.
MACS2 (v2.1.1) was used to call peaks from DMC1 'Type 1' reads relative to DMC1 kinetic enrichment ChIP Input controls. (v2.1.1) with the following parameters: -q 0.1 --nomodel --slocal 5000 --llocal 10000 --extsize 800 -f BED --SPMR -g 463000000 -B. For H3K4me3 ChIP reads, macs2 peak calling was performed using default parameters.
ChIPseq normalized treatment coverage plots (DMC1 or H3K4me3 ChIP) and control (kinetic enrichment control, or H3K4me3 ChIPseq input control) coverage plots were generated using MACS2. narrowPeak files were generated using MACS2
Assembly: Broad/gasAcu1
Supplementary files format and content: bed (representing 'Type 1' DMC1-bound single stranded DNA reads used as input for MACS2; only for DMC1 ChIPseq), bedGraph (from MACS2 ChIPseq treatment and input controls), peak files (except for ChIP input samples)
|
| |
|
| Submission date |
Jan 30, 2024 |
| Last update date |
May 24, 2024 |
| Contact name |
Felicity C Jones |
| E-mail(s) |
fcjones@tuebingen.mpg.de
|
| Organization name |
Friedrich Miescher Laboratory of the Max Planck Society
|
| Lab |
Felicity Jones
|
| Street address |
Max-Planck-Ring 9
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL34145 |
| Series (2) |
| GSE254557 |
Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish [ChIP-Seq] |
| GSE254561 |
Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish |
|
| Relations |
| BioSample |
SAMN39670829 |
| SRA |
SRX23447690 |
