Illumina HiSeq 2000 sequencing; ChIPSeq profiling of LIR3 binding sites in C.elegans
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Unclassified
Cell type
Unclassified
NA
NA
Attributes by original data submitter
Sample
ENA first public
2017-03-16
ENA last update
2015-12-23
ENA-CHECKLIST
ERC000011
External Id
SAMEA3719419
INSDC center alias
European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, UMC Groningen, The Netherlands
INSDC center name
European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, UMC Groningen, The Netherlands
INSDC first public
2017-03-16T17:01:55Z
INSDC last update
2015-12-23T16:08:36Z
INSDC status
public
Submitter Id
E-MTAB-4174:LIR3_Rep2
broker name
ArrayExpress
sample name
E-MTAB-4174:LIR3_Rep2
Sequenced DNA Library
library_name
LIR3_Rep2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Worm staging was achieved by bleaching and L1 starvation. Arrested L1 animals were plated on peptone-enriched NGM plates seeded with OP50 bacteria and grown for 48 hours for L4 collection at 20C. Samples were crosslinked with 2% formaldehyde for 30 minutes at room temperature and then quenched with 1 M Tris pH 7.5. The pelleted worms were subsequently flash frozen in liquid nitrogen and stored at -80C. Samples were sonicated using a microtip to obtain mostly 200 to 800 bp DNA fragments. For each sample, 2.2 or 4.4 mg of cell extract was immunoprecipitated using a goat anti-GFP, GoatV (gift from Kevin White). The enriched DNA fragments and input control (genomic DNA from the same sample) for two biological replicates were used for library preparation and sequencing as previously described (Kasper et al., 2014). Briefly, samples were libraried and multiplexed using the Ovation Ultralow DR Multiplex Systems 1-8 and 9-16 (NuGEN Technologies Inc., San Carlos, CA) following the manufacturers protocol except Qiagen MinElute PCR purification kits were used to isolate the DNA. Library size selection in the 200-800 bp range was achieved using the SPRIselect reagent kit (Beckman Coulter, Inc., Brea, CA