|
| Status |
Public on Apr 15, 2023 |
| Title |
C. elegans, HIF-1a, IP, Bio rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole organism
strain: ZG434
genotype: egl-9(sa307);iaIS28[Phif-1::hif-1a::Myc::HA];hif-1(ia04)
chip antibody: ChIP grade anti-HA antibody (Abcam, cat. no. ab9110)
|
| Growth protocol |
Worms were grown on NGM plates seeded with OP50 at 21°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms were harvested and cross-linked in 2% formaldehyde at 21°C for 30 minutes. Nuclear lysates were sonicated using a Branson sonifer microtip to fragment the chromatin to 200-800 bp. Immunoprecipitated protein-DNA complexes were captured on protein A-Sepharose beads (Sigma) and eluted in elution buffer (1% SDS and 100 mM NaHCO3) at 65°C for 30 minutes. Following RNase treatment and cross-link reversal, the ChIP DNA was purified with the Qiagen MinElute Kit for sequencing in parallel with the corresponding input DNA.
The ChIP-seq library preparation and sequencing were performed by the Iowa State University DNA facility. In brief, NEXTflex™ ChIP-Seq Barcodes kit (Illumina compatible) (BIOO Scientific Corp., cat. no. 514123) was used to prepare multiplexed single-end genomic DNA libraries. The gel slices corresponding to the 200-300 bp maker were cut and purified. The purified DNA was amplified and sequenced in a single flow cell on the IlluminaHiSeq 2000 platform. The length of single-end reads was 50 bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The fastq files were provided by the Iowa State University DNA facility. The quality scores of the fastq reads for the input and ChIP DNA samples from both biological replicates were checked and they were all above 30, indicating high quality sequencing data.
Reads were mapped to C. elegans reference genome ce11 using bowtie 2 with the default settings.
Reads with mapping quality (MAPQ) score less than 10 and reads mapped to the mitochondrial genome were excluded for peak calling.
Reads were assigned to bins, the size of which was set at 200 bp. Bin-level read counts were analyzed by R package MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data) to call peaks (https://www.bioconductor.org/packages/release/bioc/manuals/mosaics/man/mosaics.pdf). The false discovery rate (FDR) was set at 0.05. Neighboring peaks were merged. The wiggle files were also generated with this package.
Assembly: ce11
Supplementary files format and content: wig, narrowPeak
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
Apr 16, 2023 |
| Contact name |
Jo Anne Powell-Coffman |
| E-mail(s) |
japc@iastate.edu
|
| Phone |
515-294-3906
|
| Organization name |
Iowa State University
|
| Department |
Department of Genetics, Development and Cell Biology
|
| Street address |
2213 Pammel Dr.
|
| City |
Ames |
| State/province |
Iowa |
| ZIP/Postal code |
50011-1101 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE228846 |
Identifying the direct targets for transcription factor HIF-1a in Caenorhabditis elegans by ChIP-seq. |
|
| Relations |
| BioSample |
SAMN34059714 |
| SRA |
SRX19856962 |
