{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["DCC modENCODE"],"study_type":["ChIP-seq"],"organism":["Caenorhabditis elegans"],"species":["Caenorhabditis elegans"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-50258"],"description":["modENCODE_submission_3931 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: 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. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Strain N2; Antibody SDQ2370-LIN53 (target is LIN-53)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Worm_embryo_growth_and_harvest_vSS7. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were incubated for 3.5 hours in M9 then frozen in liquid nitrogen.","Library Construction - Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later,washed pellets are resuspended in FA buffer and subjected to sonication in a DiagenodeBioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extractsare then spun down and the soluble fraction is stored for quality tests and future ChIP. Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ?l of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 ?L elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit. For a detailed protocol see http://www.modencode.org/. Short description for UNC NimbleGen Database:Both ChIP and input DNA samples have their ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3?-dA overhangs are then added with Klenow Fragment (3? to 5?exo minus), and Illumina adapters are subsequently ligated to the ends. Next, PCRamplification is performed using Illumina 1.1 and 2.1 primers, for a total of 18 cycles. AmplifiedDNA libraries are size-selected on a 2% agarose gel so that fragments sized between 250-350bp are obtained; gel extraction is carried out at room temperature."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"pubmed_authors":["Andreas Rechtsteiner","Susan Strome","Thea Egelhofer","DCC modENCODE"],"additional_accession":[]},"is_claimable":false,"name":"seq-SDQ2370_LIN53_N2_LTemb","description":"modENCODE_submission_3931 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: 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. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Late Embryos; Genotype: wild type; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryos; temp (temperature) 20 degree celsius; Strain N2; Antibody SDQ2370-LIN53 (target is LIN-53)","dates":{"release":"2013-08-28T00:00:00Z","modification":"2023-09-20T12:20:34.238Z","creation":"2021-09-28T11:26:23Z"},"accession":"E-GEOD-50258","cross_references":{"GEO":["GSE50258"],"EFO":["EFO_0002692"]}}