Transcription Factors ChIP-Seq Mixed embryo

seq-SDQ2966_MIS12_N2_Mxemb (Lieb project, Desai subgroup)

Details

seq-SDQ2966_MIS12_N2_Mxemb (Lieb project, Desai subgroup)

Synchronized C. elegans mixed stage 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 mis-12. 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.

Protocols

  1. Growth and isolation: embryo_extraction_protocol_v3, worm_embryo_extraction_v5, Worm_embryo_growth_and_harvest:JL:5, Worm_embryo_extraction:JL:2, Worm_ChIP_Extract_Preparation_SE_v3, Worm embryo extraction-JL-RG2, modENCODE N2 embryos culture protocol_v5, Worm embryo growth and harvest RNAi:JL:1, Worm embryo growth and harvest-JL-RG2
  2. Sample preparation: Worm Chromatin Immunoprecipitation-JL-RG2, Solexa-Library-Prep:JL:KI1, True_Seq_Illumina_Prep_ SEA_v2, Worm_chromatin_immunoprecipitation:JL:KI3, Chromatin_Immunoprecipitation_SE_v1, Illumina_DNA_Sequencing:JL:1, Solexa_Library_Prep_vKI3, True_Seq_Illumina_Prep_ SEA_v2, Homebrew_Solexa_SE_prep, worm_chromatin_immunoprecipitation_v5, Illumina_DNA_Sequencing:JL:1
  3. Other Protocols: ChIP-Seq_MACS_Peak-calling_over_reps:JL:1, ChIP-Seq_MACS_Peak-calling:JL:1, ChIP-Seq_MACS_Peak-calling:JL:1, ChIP-seq_alignment-BWA:JL:1, ChIP-Seq_MACS_Peak-calling_over_reps:JL:1, ChIP-seq_alignment-BWA:JL:1, ChIP-seq_alignment-BWA:JL:1

Experimental Reagents

    Antibodies:

Sample Details

    Animals/Lines:
  1. External Links: GEO:TMPID:6285_chip_rep1, GEO:TMPID:6291_input_rep2, GEO:TMPID:6218_input_rep1, GEO:TMPID:6230_input_rep1, GEO:TMPID:6235_input_rep1, GEO:TMPID:6021_chip_rep1, GEO:TMPID:6297_chip_rep2, GEO:TMPID:6257_input_rep2, GEO:TMPID:6227_input_rep1, GEO:TMPID:6283_chip_rep1, GEO:TMPID:6267_chip_rep2, GSM706160, GEO:TMPID:6219_chip_rep2, GEO:TMPID:6234_chip_rep2, GEO:TMPID:6023_input_rep1, GEO:TMPID:6281_chip_rep2, GEO:TMPID:6281_input_rep1, GEO:TMPID:6234_input_rep1, GEO:TMPID:6283_chip_rep2, GEO:TMPID:6291_chip_rep1, GEO:TMPID:6281_input_rep2, GEO:TMPID:6218_chip_rep1, GEO:TMPID:6281_chip_rep1, GEO:TMPID:6269_chip_rep2, GEO:TMPID:6237_chip_rep2, GEO:TMPID:6023_chip_rep2, GEO:TMPID:6219_chip_rep1, GEO:TMPID:6208_input_rep2, GEO:TMPID:6297_chip_rep1, GEO:TMPID:6230_chip_rep2, GEO:TMPID:6257_chip_rep1, GEO:TMPID:6232_chip_rep1, GEO:TMPID:6021_input_rep2, GEO:TMPID:6208_chip_rep1, GEO:TMPID:6267_chip_rep1, GEO:TMPID:6230_input_rep2, GEO:TMPID:6269_chip_rep1, GEO:TMPID:6257_input_rep1, GEO:TMPID:6232_input_rep1, GEO:TMPID:6237_chip_rep1, GEO:TMPID:6267_input_rep2, GEO:TMPID:6265_input_rep2, GEO:TMPID:6269_input_rep1, GEO:TMPID:6297_input_rep2, GEO:TMPID:6257_chip_rep2, GEO:TMPID:6251_chip_rep1, GEO:TMPID:6218_input_rep2, GEO:TMPID:6021_input_rep1, GEO:TMPID:6208_input_rep1, GEO:TMPID:6235_input_rep2, GEO:TMPID:6297_input_rep1, GEO:TMPID:6291_chip_rep2, GEO:TMPID:6234_input_rep2, GEO:TMPID:6227_input_rep2, GEO:TMPID:6283_input_rep2, GEO:TMPID:6023_input_rep2, GEO:TMPID:6265_chip_rep2, GEO:TMPID:6230_chip_rep1, GEO:TMPID:6234_chip_rep1, GEO:TMPID:6227_chip_rep2, GEO:TMPID:6232_chip_rep2, GEO:TMPID:6208_chip_rep2, GEO:TMPID:6237_input_rep2, GEO:TMPID:6021_chip_rep2, GEO:TMPID:6291_input_rep1, GEO:TMPID:6269_input_rep2, GEO:TMPID:6265_chip_rep1, GEO:TMPID:6237_input_rep1, GEO:TMPID:6283_input_rep1, GEO:TMPID:6218_chip_rep2, GEO:TMPID:6285_input_rep2, GEO:TMPID:6232_input_rep2, GEO:TMPID:6251_input_rep1, GEO:TMPID:6265_input_rep1, GEO:TMPID:6235_chip_rep1, GEO:TMPID:6285_input_rep1, GEO:TMPID:6227_chip_rep1, GEO:TMPID:6235_chip_rep2, GEO:TMPID:6267_input_rep1, GEO:TMPID:6251_input_rep2, GEO:TMPID:6285_chip_rep2, GEO:TMPID:6023_chip_rep1, GEO:TMPID:6251_chip_rep2


Release Date: 2013-05-27 Submission 6021