|
| Status |
Public on May 31, 2019 |
| Title |
4082 3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: isp-1(qm150);ctb-1(qm189);Is[pvha-6::klf-1-yfp]
developmental stage: First day of adulthood
tissue: Whole body
antibody: GFP-TRAP (Chromotek; Cat. #gtma-20; Lot. 81025001MA)
|
| Treatment protocol |
Worms were plated as eggs on plates seeded with HT115 bacterial strain, carrying L4440 plasmid.
|
| Growth protocol |
Worms were synchronized by treating with alkaline hypochlorite solution.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were sonicated and cleared by centrifugation. Protein-DNA complexes were pulled-down using GFP-TRAP (Chromotek).
Libraries were prepared by using the Illumina TruSeq DNA Nano Kit with some modifications. The preparation was started with the end repair step of the protocol. Up to 100ng ChIP/Input DNA was used as starting material. After end repair and A-tailing dual indexing adapters were ligated. The products were then purified and amplified (12 PCR cycles for the Input Samples and 15 cycles for the ChIP Samples) to create the final libraries. After validation (Agilent 4200 TapeStation) each single library was quantified by using the Roche KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The libraries were then pooled equimolar. Finally the pool was sequenced on one Illumina HiSeq4000 lane 1x51bp (51+8+8).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The ChIP-Seq workflow takes advantage of BWA for genomic alignment of the reads. Reads was mapped to the caenorhabditis_elegans (Ensembl database version 93).
Quality check of sequencing data were performed with FastQC version0.10.1.
For peak calling used MACS2 version 2.0.10.
QuickNGS pipeline identifies all genes which are 2000 bp up- or downstream from the MACS2 peaks.
The peak sequences are analyzed for enrichment of transcription factor binding motifs using MEME-ChIP Version 4.10.0.
Genome_build: Ensembl 93
Supplementary_files_format_and_content: The results comprise lists of significant peaks and reports for motif enrichment.
|
| |
|
| Submission date |
Apr 18, 2019 |
| Last update date |
Jun 01, 2019 |
| Contact name |
Aleksandra Trifunovic |
| E-mail(s) |
aleksandra.trifunovic@uk-koeln.de
|
| Organization name |
Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases
|
| Lab |
AG Trifunovic
|
| Street address |
Joseph-Stelzmann-Str. 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE130035 |
C. elegans KLF-1 promoter binding sites |
|
| Relations |
| BioSample |
SAMN11463165 |
| SRA |
SRX5709770 |
