Histone Modifications in H3K9 (ChIP-Seq)

Histone Modifications in H3K9 (ChIP-seq) (Lieb project, Ahringer, Strome, and Dernburg subgroups)

Details

Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 acetylated on lysine 9, histone H3 methylated on lysine 9, histone H3 trimethylated on lysine 9, or histone H3 dimethylated on lysine 9. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call binding peaks with the MACS algorithm to generate the track showing sequence features.

General Description

The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.

Protocols

  1. Growth and isolation: Worm L3 growth and harvest:JL:PK1, worm_embryo_growth_and_harvest_vSS5, worm_embryo_growth_and_harvest_vSS4, Worm_adult_growth_and_harvest_germCW1, Worm_L3_Formaldehyde_Extract Preparation_vPK2, worm_embryo_extraction_vSS2, Worm_adult_purified_germline_extract_v1
  2. Sample preparation: Worm chromatin immunoprecipitation:JL:IL2, worm_chromatin_immunoprecipitation_vSS4, Worm_chromatin_immunoprecipitation_vCW2, Illumina Library Preparation ChIPseq:JL:JA1, Homebrew_Solexa_SE_prep, Illumina TruSeq Library Preparation:JL:JA1:JL:1, Truseq_Library_Prep_vACD1, Illumina_DNA_Sequencing:JL:1
  3. Other Protocols: ChIP-seq_alignment-BWA:JL:1

Experimental Reagents

  1. Antibodies: H3K9Acetyl, H3K9me1, H3K9me3, H3K9acS10ph, H3K9me3, H3K9me2, H3K9me2, H3K9me3
  1. External Links: GSM1195389, GSM1195390, GSM1195387, GSM1195388, GSM1206390, GSM1206391, GSM1206388, GSM1206389, GSM1217257, GSM1217258, GSM1217255, GSM1217256, GSM1195421, GSM1195422, GSM1195419, GSM1195420, GSM1206342, GSM1206343, GSM1206340, GSM1206341, GSM1206330, GSM1206331, GSM1206328, GSM1206329, GSM1206358, GSM1206359, GSM1206356, GSM1206357, GSM1217527, GSM1217528, GSM1217525, GSM1217526, GSM1195409, GSM1195410, GSM1195407, GSM1195408


Release Date: 2013-05-31 Submission 3578
Release Date: 2013-06-13 Submission 5171
Release Date: 2013-06-12 Submission 5154
Release Date: 2013-05-24 Submission 5988
Release Date: 2013-06-12 Submission 5155
Release Date: 2013-06-12 Submission 5149
Release Date: 2013-06-12 Submission 5161
Release Date: 2013-06-17 Submission 6325
Release Date: 2013-06-13 Submission 5153