Goldberg 2010, Factors controlling histone variant H3.3 localization.

Genome-wide survey of H3.3 localization and of its deposition mechanisms. H3.3 histone variant is encoded by two genes : H3.3A and H3.3B. H3.3B was edited using zing finger nucleases in several ways : i) to add an HA tag to the protein, ii) to turn H3.3 into H3.2 (one of the two H3 canonical variant) and to add an HA tag and iii) to turn H3.3 into H3.1 (one of the two H3 canonical variants) with an H3.3 specific serin residue at position 31 (H3.1S31). H3.1S31, H3.2 and H3.3 occupancy was measured by ChIP-seq targetting the HA tag. under native condition and using crosslinking in three cell lines : in mouse embryonic stem cells (ES), in mouse neuronal progenitors (NCP) and in hybrid ES cells. Additionally, H3K4me1, H3K4me3, H3K27me3, H3K36me3 and RNAPII phosphorylated on serine 5 of its Cterm domain (RNAPII-S5P) occupancies were also measured.

• Raw data was downloaded from: GSE16893
• Input file format: SRA
• Download date: 6-12-2011

From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM423355.sga	ES|c H3.3-HA|H3.3HA	H3.3_HA	GSM423355
2	GSM423356.sga	ES|c H3K36me3|H3.3HA	H3K36me3	GSM423356
3	GSM423357.sga	ES|c H3K4me1|H3.3HA	H3K4me1	GSM423357
4	GSM423358.sga	ES|c RNAPII-Ser5P|H3.3HA	RNAPII_Ser5p	GSM423358
5	GSM423359.sga	ES|c H3.2-HA|H3.2HA	H3.2_HA	GSM423359
6	GSM423360.sga	ES|c H3K36me3|H3.2HA	H3K36me3	GSM423360
7	GSM423361.sga	NCP|c H3.3-HA|H3.3HA	H3.3_HA	GSM423361
8	GSM423362.sga	NCP|c H3K36me3|H3.3HA	H3K36me3	GSM423362
9	GSM423363.sga	NCP|c H3K4me1|H3.3HA	H3K4me1	GSM423363
10	GSM423364.sga	NCP|c RNAPII-Ser5P|H3.3HA	RNAPII_Ser5p	GSM423364
11	GSM423365.sga	NCP|c H3.2-H|H3.2HAA	H3.2_HA	GSM423365
12	GSM423366.sga	NCP|c H3K36me3|H3.2HA	H3K36me3	GSM423366
13	GSM487538.sga	ES-hyb|c input|H3.3HA	input	GSM487538
14	GSM487539.sga	ES-hyb|c H3.3-HA|H3.3HA	H3.3_HA	GSM487539
15	GSM487540.sga	ES-hyb|c H3K36me3|H3.3HA	H3K36me3	GSM487540
16	GSM487541.sga	ES-hyb|c input|H3.1S31HA	input	GSM487541
17	GSM487542.sga	ES-hyb|c H3.1S31-HA|H3.1S31HA	H3.1S31_HA	GSM487542
18	GSM487543.sga	ES-hyb|c H3K36me3|H3.1S31HA	H3K36me3	GSM487543
19	GSM487544.sga	ES|n H3.3-HA|H3.3HA	H3.3_HA	GSM487544
20	GSM487545.sga	ES|n H3K4me3|H3.3HA	H3K4me3	GSM487545
21	GSM487546.sga	ES|n input|H3.3HA	input	GSM487546
22	GSM487547.sga	ES|n H3.2-HA|H3.2HA	H3.2_HA	GSM487547
23	GSM487548.sga	ES|n H3K4me3|H3.2HA	H3K4me3	GSM487548
24	GSM487549.sga	ES|n H3K27me3|H3.2HA	H3K27me3	GSM487549
25	GSM487550.sga	ES|n input|H3.2HA	input	GSM487550
26	GSM487551.sga	ES|n H3.3-EYFP|H3.3EYFP	H3.3_EYFP	GSM487551
27	GSM487552.sga	ES|n input|H3.3EYFP	input	GSM487552
28	GSM487553.sga	ES|n H3K4me1|H3.3EYFP	H3K4me1	GSM487553
29	GSM487554.sga	ES|n H3K36me3|H3.3EYFP	H3K36me3	GSM487554
30	GSM487555.sga	ES|n H3.3-EYF|H3.3EYFP Hira.nullP	H3.3_EYFP	GSM487555
31	GSM487556.sga	ES|n H3K4me1|H3.3EYFP Hira.null	H3K4me1	GSM487556
32	GSM487557.sga	ES|n H3K36me3|H3.3EYFP Hira.null	H3K36me3	GSM487557
33	GSM487558.sga	ES|n input|H3.3EYFP Hira.null	input	GSM487558
34	GSM487559.sga	ES|n H3.3-EYFP|H3.3EYFP Atrx.flox	H3.3_EYFP	GSM487559
35	GSM487560.sga	ES|n input|H3.3EYFP Atrx.flox	input	GSM487560
36	GSM487561.sga	ES|n H3.3-EYFP|H3.3EYFP Atrx.null	H3.3_EYFP	GSM487561
37	GSM487562.sga	ES|n input|H3.3EYFP Atrx.null	input	GSM487562
38	GSM487563.sga	ES|c HA|wildtype	HA	GSM487563

Notes on samples nomenclature:

H3.1 and H3.2 are the two H3 canonical variants and are often referred to as H3.
The sample description field contains 3 information separated by a '|' character : i) the cell line from which the data were generated, ii) the ChIP-seq condition ('c' for crosslink, 'n' for native) and the ChIP-seq target and iii) the cellular context.
In the cellular context information, 'H3.3HA' means that gene H3.3B was edited to contain an extra HA tag, 'H3.2HA' that the gene was edited to turn H3.3 sequence into an H3.2 sequence followed by an HA tag, 'H3.1S31HA' that the gene was edited to be turned into an H3.1 sequence with a serine at position 31 (H3.3 specific residue) followed by an HA tag, 'Hira.null' that HirA was totally missing in the cells and 'Atrx.flox' and 'Atrx.null' that Atrx was subjected to a target truncation using the Cre-recombinase system.

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the mm9 mouse 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. 1.5.2).

• Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, Wen D, Chapgier A, DeKelver RC, Miller JC, Lee YL, Boydston EA, Holmes MC, Gregory PD, Greally JM, Rafii S, Yang C, Scambler PJ, Garrick D, Gibbons RJ, Higgs DR, Cristea IM, Urnov FD, Zheng D, Allis CD
  Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell. 2010 Mar 5;140(5):678-91. doi: 10.1016/j.cell.2010.01.003. 20211137
• GEO series GSE16893: Distinct factors control histone variant H3.3 localization at specific genomic regions