Kvist 2020, ChIP-seq for H3K4me3 and H3k27me3 in Daphnia pulex females and males.

Description

This series contains ChIP-seq data for H3K4me3 and H3k27me3 in Daphnia pulex females and males, strain H3K4me3 and H3k27me3, genotype EB45.

Source

Samples

From D. pulex (Sep 2019 PA42 4.1/dpu2).

ChIP-seq data:

Filename Description Feature GEO-ID
1 H3K27me3_F_EB45.1.sga Female|H3K27me3||rep1 H3K27me3 GSM3533039
2 H3K27me3_F_EB45.2.sga Female|H3K27me3||rep2 H3K27me3 GSM3533040
3 H3K27me3_F_EB45.3.sga Female|H3K27me3||rep3 H3K27me3 GSM3533041
4 H3K27me3_M_EB45.1.sga Male|H3K27me3||rep1 H3K27me3 GSM3533042
5 H3K27me3_M_EB45.2.sga Male|H3K27me3||rep2 H3K27me3 GSM3533043
6 H3K27me3_M_EB45.3.sga Male|H3K27me3||rep3 H3K27me3 GSM3533044
7 H3K4me3_F_EB45.1.sga Female|H3K4me3||rep1 H3K4me3 GSM3533045
8 H3K4me3_F_EB45.2.sga Female|H3K4me3||rep2 H3K4me3 GSM3533046
9 H3K4me3_F_EB45.3.sga Female|H3K4me3||rep3 H3K4me3 GSM3533047
10 H3K4me3_M_EB45.1.sga Male|H3K4me3||rep1 H3K4me3 GSM3533048
11 H3K4me3_M_EB45.2.sga Male|H3K4me3||rep2 H3K4me3 GSM3533049
12 H3K4me3_M_EB45.3.sga Male|H3K4me3||rep3 H3K4me3 GSM3533050
13 Input_F_EB45.0.sga Female|Input Input GSM3533051
14 Input_M_EB45.0.sga Male|Input Input GSM3533052
15 H3K27me3_F_EB45_merged.sga Female|H3K27me3||merged H3K27me3 GSM3533039, GSM3533040, GSM3533041
16 H3K27me3_M_EB45_merged.sga Male|H3K27me3||merged H3K27me3 GSM3533042, GSM3533043, GSM3533044
17 H3K4me3_F_EB45_merged.sga Female|H3K4me3||merged H3K4me3 GSM3533045, GSM3533046, GSM3533047
18 H3K4me3_M_EB45_merged.sga Male|H3K4me3||merged H3K4me3 GSM3533048, GSM3533049, GSM3533050

Merged samples:

This series contains both merged and individual replicates samples.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.10.8) and mapped to the genome using Bowtie v1.2.2. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 from bedtools. BED to SGA conversion was carried out using bed2sga v1.5.4 from ChIP-Seq.

References

Last update: 17 Apr 2021