|
| Status |
Public on Mar 01, 2016 |
| Title |
DAF-16 chip_daf-16(-);daf-2(-) |
| Sample type |
SRA |
| |
|
| Source name |
mix stage culture
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: Mix Culture
temperature: 20 °C
genotype: daf-16(mgDf50);daf-2 (e1370)
|
| Growth protocol |
Wild-type (N2), daf-2 (e1370), daf-16(mgDf50);daf-2(e1370) and daf-16(mgDf50)mutant worm strains were obtained from Caenorhabditis Genetics Centre (Minneapolis, MN, USA). Mixed culture of worms were grown on 15-20 OP50 E coli. seeded 150 X 15 mm NGM (Nematode Growth Media) petri-plates maintained at 20 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms were harvested from plates with 1 X PBS buffer and washed four times. The compact worm slurry (250 µl) was resuspended in 4 ml cross-linking buffer (1% formaldehyde in 1 X PBS) followed by homogenization with 7 ml glass Dounce homogenizer.
A total of 5 ng of DNA was used as a starting material for library preparation according to the Illumina, Inc. ( San Diego, CA, USA) protocol, "Preparing Samples for ChIP Sequencing of DNA".
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Demultiplexing and conversion of BCL file format reads to FASTQ file format was done with Illumina CASAVA v1.8.2 software package
Quality filtered reads were aligned to the C. elegans annotated reference genome (W230) using Bowtie v.0.12.7 with parameters: -q -m 1 --best --strata
Peak calling was done with uniquely aligned reads containing no more than one mismatch using peak calling algorithm MACS v1.4.2 with parameters: --mfold=5,30 --bw=175 -w
Genome_build: C. elegans annotated reference genome (W230)
Supplementary_files_format_and_content: peak and summit file
|
| |
|
| Submission date |
Apr 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Arnab Mukhopadhyay |
| E-mail(s) |
arnab@nii.ac.in
|
| Phone |
919871229286
|
| Organization name |
National Institute of Immunology
|
| Lab |
Molecular Aging Lab
|
| Street address |
Aruna asaf ali marg
|
| City |
Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL13776 |
| Series (1) |
| GSE63865 |
Endogenous DAF-16 genome-wide recruitment under low Insulin signaling condition in Caenorhabditis elegans |
|
| Relations |
| BioSample |
SAMN03487568 |
| SRA |
SRX997749 |
