Albritton 2017, The genetic mechanisms that allow dosage compensation of the X chromosomes.

Description

This serie contain chromatin maps for components of the dosage compensation complex (DCC): DPY-21, DPY-30, SDC-2 and SDC-3; and histone H3 and H3K4me3 in wild type (N2) and several mutants (for a complete lest read section 'Sample nomenclature')

Source

Samples

From C. elegans (Oct 2010 WBcel215/ce10).

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM2339594.sga N2|SDC-2|mixed embryo|rep1 SDC2 GSM2339594
2 GSM2339595.sga N2|SDC-2|mixed embryo|rep2 SDC2 GSM2339595
3 GSM2339596.sga N2|SDC-2|mixed embryo|rep3 SDC2 GSM2339596
4 GSM2339597.sga N2|SDC-2|mixed embryo|rep4 SDC2 GSM2339597
5 GSM2339598.sga N2|SDC-2|mixed embryo|rep5 SDC2 GSM2339598
6 GSM2339599.sga N2|SDC-3|mixed embryo|rep1 SDC3 GSM2339599
7 GSM2339600.sga N2|SDC-3|mixed embryo|rep2 SDC3 GSM2339600
8 GSM2339601.sga N2|SDC-3|mixed embryo|rep3 SDC3 GSM2339601
9 GSM2339602.sga N2|SDC-3|mixed embryo|rep4 SDC3 GSM2339602
10 GSM2339603.sga N2|SDC-3|mixed embryo|rep5 SDC3 GSM2339603
11 GSM2339604.sga N2|DPY-30|mixed embryo|rep1 DPY30 GSM2339604
12 GSM2339605.sga N2|DPY-30|mixed embryo|rep2 DPY30 GSM2339605
13 GSM2339606.sga N2|DPY-30|mixed embryo|rep3 DPY30 GSM2339606
14 GSM2339607.sga N2|DPY-30|mixed embryo|rep4 DPY30 GSM2339607
15 GSM2339608.sga N2|DPY-30|mixed embryo|rep5 DPY30 GSM2339608
16 GSM2339609.sga N2|DPY-27|mixed embryo|rep1 DPY27 GSM2339609
17 GSM2339610.sga N2|DPY-27|mixed embryo|rep2 DPY27 GSM2339610
18 GSM2339611.sga N2|DPY-27|mixed embryo|rep3 DPY27 GSM2339611
19 GSM2339612.sga N2|DPY-27|mixed embryo|rep4 DPY27 GSM2339612
20 GSM2339613.sga N2|H3K4me3|mixed embryo|rep1 H3K4me3 GSM2339613
21 GSM2339614.sga N2|H3K4me3|mixed embryo|rep2 H3K4me3 GSM2339614
22 GSM2339615.sga N2|H3K4me3|mixed embryo|rep3 H3K4me3 GSM2339615
23 GSM2339616.sga N2|H3|mixed embryo|rep1 H3 GSM2339616
24 GSM2339617.sga N2|H3|mixed embryo|rep2 H3 GSM2339617
25 GSM2339618.sga TY1072|H3|mixed embryo|rep1 H3 GSM2339618
26 GSM2339619.sga TY1072|H3|mixed embryo|rep2 H3 GSM2339619
27 GSM2339620.sga TY2205|SDC-2|mixed embryo|rep1 SDC2 GSM2339620
28 GSM2339621.sga TY2205|SDC-2|mixed embryo|rep2 SDC2 GSM2339621
29 GSM2339622.sga TY1072|SDC-2|mixed embryo|rep1 SDC2 GSM2339622
30 GSM2339623.sga TY1072|SDC-2|mixed embryo|rep2 SDC2 GSM2339623
31 GSM2339624.sga TY1072|SDC-2|mixed embryo|rep3 SDC2 GSM2339624
32 GSM2339625.sga ERC38|DPY-27|mixed embryo|rep1 DPY27 GSM2339625
33 GSM2339626.sga ERC38|DPY-27|mixed embryo|rep2 DPY27 GSM2339626
34 GSM2339627.sga ERC38|DPY-27|mixed embryo|rep3 DPY27 GSM2339627
35 GSM2339628.sga ERC38|SDC-3|mixed embryo|rep1 SDC3 GSM2339628
36 GSM2339629.sga ERC38|SDC-3|mixed embryo|rep2 SDC3 GSM2339629
37 GSM2339630.sga ERC38|SDC-3|mixed embryo|rep3 SDC3 GSM2339630
38 GSM2339631.sga ERC38|SDC-3|mixed embryo|rep4 SDC3 GSM2339631
39 GSM2339632.sga ERC54|DPY-27|mixed embryo|rep1 DPY27 GSM2339632
40 GSM2339633.sga ERC54|DPY-27|mixed embryo|rep2 DPY27 GSM2339633
41 GSM2339634.sga ERC64|DPY-27|mixed embryo|rep1 DPY27 GSM2339634
42 GSM2339635.sga ERC64|DPY-27|mixed embryo|rep2 DPY27 GSM2339635
43 GSM2339636.sga ERC64|DPY-27|mixed embryo|rep3 DPY27 GSM2339636
44 GSM2339637.sga ERC51|DPY-27|mixed embryo|rep1 DPY27 GSM2339637
45 GSM2339638.sga ERC51|DPY-27|mixed embryo|rep2 DPY27 GSM2339638
46 GSM2339639.sga ERC51|DPY-27|mixed embryo|rep3 DPY27 GSM2339639
47 GSM2339640.sga N2-EE4|INPUT|mixed embryo| input GSM2339640
48 GSM2339641.sga N2-LW53|INPUT|mixed embryo| input GSM2339641
49 GSM2339642.sga N2-LW78|INPUT|mixed embryo| input GSM2339642
50 GSM2339643.sga TY1072-SE243|INPUT|mixed embryo| input GSM2339643
51 GSM2339644.sga TY1072-LW43|INPUT|mixed embryo| input GSM2339644
52 GSM2339645.sga TY2205-SE35|INPUT|mixed embryo| input GSM2339645
53 GSM2339646.sga TY2205-SE344|INPUT|mixed embryo| input GSM2339646
54 GSM2339647.sga TY1072-LW44|INPUT|mixed embryo| input GSM2339647
55 GSM2339648.sga ERC38-SE365|INPUT|mixed embryo| input GSM2339648
56 GSM2339649.sga ERC38-SE389|INPUT|mixed embryo| input GSM2339649
57 GSM2339650.sga ERC38-SE391|INPUT|mixed embryo| input GSM2339650
58 GSM2339651.sga ERC54-SEA167|INPUT|mixed embryo| input GSM2339651
59 GSM2339652.sga ERC54-SEA166|INPUT|mixed embryo| input GSM2339652
60 GSM2339653.sga ERC64-SEA214|INPUT|mixed embryo| input GSM2339653
61 GSM2339654.sga ERC51-SEA164|INPUT|mixed embryo| input GSM2339654
62 GSM2339655.sga ERC51-SEA196|INPUT|mixed embryo| input GSM2339655
63 GSM2339656.sga ERC51-SEA197|INPUT|mixed embryo| input GSM2339656
64 GSM2339657.sga N2-EE6|INPUT|mixed embryo| input GSM2339657
65 GSM2339658.sga N2-EE13|INPUT|mixed embryo| input GSM2339658
66 GSM2339659.sga N2-SE210|INPUT|mixed embryo| input GSM2339659
67 GSM2339660.sga N2-SE176|INPUT|mixed embryo| input GSM2339660
68 GSM2339661.sga N2-EE9|INPUT|mixed embryo| input GSM2339661
69 GSM2339662.sga N2-EE14|INPUT|mixed embryo| input GSM2339662
70 GSM2339663.sga N2-CJ43|INPUT|mixed embryo| input GSM2339663
71 GSM2339664.sga N2-CJ19|INPUT|mixed embryo| input GSM2339664
72 GSM2339665.sga N2-EE8|INPUT|mixed embryo| input GSM2339665

Notes on samples nomenclature:

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

References

Last update: 17 Oct 2017