Transcription Factors ChIP-Seq Early Embryo

seq-SDQ3927_MRG1_N2_Eemb (Lieb project, Strome subgroup)


seq-SDQ3927_MRG1_N2_Eemb (Lieb project, Strome subgroup)

Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes mrg-1. 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 RNA polymerase II isoforms,
dosage-compensation proteins, centromere components, homolog-pairing
facilitators, recombination markers, and nuclear-envelope constituents.
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.


  1. Growth and isolation: worm_embryo_extraction_vSS6, worm_embryo_growth_and_harvest_vSS5, worm_embryo_extraction_vSS5, worm_embryo_growth_and_harvest_vSS4, worm_embryo_extraction_vSS2, worm_embryo_growth_and_harvest_vSS8
  2. Sample preparation: worm_ChIP-seq_Library_prep_vSS2, worm_chromatin_immunoprecipitation_vSS4, worm_chromatin_immunoprecipitation_vSS4, Worm chromatin immunoprecipitation:JL:IL2, Illumina TruSeq Library Preparation:JL:JA1:JL:1, worm_ChIP-seq_Library_prep_vSS4, Illumina_DNA_Sequencing:JL:1, Homebrew_Solexa_SE_prep
  3. Other Protocols: ChIP-Seq_MACS_Peak-calling_over_reps:JL:1, Histone_Replicates_QC, ChIP-Seq_MACS_Peak-calling:JL:1, ChIP-seq_alignment-BWA:JL:1, BEADS_Normalization

Experimental Reagents


Sample Details

  1. External Links: GEO:TMPID:6341_chip_rep1, GEO:TMPID:5031_input_rep2, GEO:TMPID:5031_input_rep1, GEO:TMPID:6329_chip_rep2, GEO:TMPID:6341_input_rep1, GEO:TMPID:6344_chip_rep2, GEO:TMPID:6329_chip_rep1, GEO:TMPID:5031_chip_rep2, GEO:TMPID:5031_chip_rep1, GEO:TMPID:6329_input_rep2, GEO:TMPID:6344_chip_rep1, GEO:TMPID:6341_chip_rep2, GEO:TMPID:6341_input_rep2, GEO:TMPID:6329_input_rep1

Release Date: 2013-06-06 Submission 6341