Steiner 2014, Map of centromeric histone (cenH3) in wild type and mutant embryos.

Maps of centromeric H3 nucleosome (cenH3) in wild type (WT) and mutant (knl-2) embryos. A detail description of samples nomenclature can be found further down this page. Samples are MNase treated.

• Raw data was downloaded from: GEO
• Input file format: BED
• Download date: 3-4-2017

From C. elegans (May 2008 WS190/ce6).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1089265_WT_CenH3_1min_20110706_5.sga	WT|CenH3|1min	CenH3	GSM1089265
2	GSM1089266_WT_CenH3_2min_rep1_20110706_6.sga	WT|CenH3|2min|rep1	CenH3	GSM1089266
3	GSM1089267_WT_CenH3_2min_rep2_20111011_3.sga	WT|CenH3|2min|rep2	CenH3	GSM1089267
4	GSM1089268_WT_CenH3_5min_20110706_7.sga	WT|CenH3|5min	CenH3	GSM1089268
5	GSM1089264_WT_CenH3_10min_20110706_8.sga	WT|CenH3|10min	CenH3	GSM1089264
6	GSM1089269_WT_HCP4_FCL_20120817_3_4.sga	WT|HCP-4|FCL	HCP4	GSM1089269
7	GSM1089271_WT_input_1min_20110706_1.sga	WT|input|1min	input	GSM1089271
8	GSM1089272_WT_input_2min_rep1_20110706_2.sga	WT|input|2min|rep1	input	GSM1089272
9	GSM1089273_WT_input_2min_rep2_20111011_1.sga	WT|input|2min|rep2	input	GSM1089273
10	GSM1089274_WT_input_5min_20110706_3.sga	WT|input|5min	input	GSM1089274
11	GSM1089270_WT_input_10min_20110706_4.sga	WT|input|10min	input	GSM1089270
12	GSM1089275_WT_input_FCL_20120817_3_12.sga	WT|input|FCL|rep1	input	GSM1089275
13	GSM1320329_WT_input_FCL_rep2.sga	WT|input|FCL|rep2	input	GSM1320329
14	GSM1089277_WT_pellet_2min_20111011_2.sga	WT|pellet|2min	pellet	GSM1089277
15	GSM1089276_WT_pellet_10min_20110914_7.sga	WT|pellet|10min	pellet	GSM1089276
16	GSM1089278_knl2_CenH3_20120223_3.sga	knl2|CenH3	CenH3	GSM1089278
17	GSM1089279_knl2_input_20120223_2.sga	knl2|input	input	GSM1089279
18	GSM1089280_knl2_pellet_20120223_8.sga	knl2|pellet	pellet	GSM1089280
19	GSM1320328_WT_HLH1_FCL.sga	WT|HLH-1|FCL	HLH1	GSM1320328

Notes on samples nomenclature:

• 1min, 2min, 5min, 10min: duration of MNase treatment
• WT: wild type embryo
• knl2: mutant embryos for the gene knl-2(RNAi) that is part of the kinetochore and is responsible for the incorporation of cenH3 into chromatin
• input: digested chromatin not subjected to ChIP purification for cenH3
• pellet: chromatin fraction that is insoluble under native conditions after MNase digestion and is strongly enriched for kinetochore complexes
• FCL: chromatin was crosslinked in 1% formaldehyde for 10 min
• HCP-4: inner kinetochore protein CENP-C
• HLH-1: a muscle-specific transcription factor

Provided BED files, mapped on ce10, were lifted over to ce6 using liftOver (from UCSC Genome Browser Utilities). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

• Steiner FA, Henikoff S
  Holocentromeres are dispersed point centromeres localized at transcription factor hotspots. Elife. 2014 Jan 1;3:e02025. doi: 10.7554/eLife.02025. 24714495
• GEO series GSE44412: Holocentromeres are dispersed point centromeres localized at transcription factor hotspots