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

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')

• Raw data was downloaded from: Provide the website and link to raw data
• Input file format: SRA, TXT, BED, ...
• Download date: 17-10-2017

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:

• Wild-type (N2)
• ERC06 (knuSi254[SNP400bprex-1, unc-119(+)] II; unc-119(ed3) III)
• ERC08 (knuIs6[pSE-02(400bprex-1SNP), unc-119(+))] I; unc-119(ed3) III)
• ERC09 (knuIs7[pSE-02(400bprex-1SNP), unc-119(+))] III; unc-119(ed3) III)
• ERC38 (ers30[delX:17544437-17544484, delX:17545624-17545624])
• ERC51 (ersIs17[SNP400bp_rex1, X:14373144])
• ERC54 (ers20[delX:4394846-4396180]; knuIs6[pSE-02 (400bprex-1SNP), unc-119(+))] I; unc-119(ed3) III)
• ERC64 (ers28[delX:806628-806813]; knuIs6[pSE-02(400bprex-1SNP), unc-119(+))] I; unc-119(ed3) III)
• ERC61 (ersSi25[wt400bp_rex8, cb-unc-119(+)] II; unc-119(ed3) III)
• ERC62 (ersIs26[X:11093923-11094322[rex-8], II: 8449965); knuSi254[SNP400bprex-1, unc-119(+)] II; unc-119(ed3) III)
• ERC63 (ersIs27[X:11093923-11094322[rex-8], II:8371600, II:8449968); knuSi254[SNP400bprex-1, unc-119(+)] II; unc-119(ed3) III)
• ERC66 (ersIs30[V:14040305-14040785[chrV_clusteredmotifs], X:14373144])
• TY2205 (her-1(e1520) sdc-3(y126) V; xol-1(y9) X)
• TY1072 (her-1(e1520) V; sdc-2 (y74) X), MT14911 (set-4 (n4600) II)

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).

• Albritton SE, Kranz AL, Winterkorn LH, Street LA, Ercan S
  Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. Elife. 2017 May 30;6. pii: e23645. doi: 10.7554/eLife.23645. 28562241
• GEO series GSE87741: Cooperation between a hierarchical set of recruitment sites specifically targets the C. elegans dosage compensation complex to the X chromosomes.