|
| Status |
Public on Jul 04, 2016 |
| Title |
ChIPSeq_327_H3K27me3_0 |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Fusarium fujikuroi |
| Characteristics |
tissue: mycelium
glutamine: 6 mM
antibody: H3K27me3
|
| Growth protocol |
Strains were grown in liquid synthetic ICI medium in low nitrogen conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated mycelial tissue and histone-DNA complexes were isolated with antibody [anti-Histone H3K27me3 antibody (pAb) Active Motif (Catalog No. AM39155)]
DNA obtained by ChIP was end-repaired and ligated to adapters as described in Pomraning KR, Smith KM, Bredeweg EL, Connolly LR, Phatale PA, et al. (2012) Library preparation and data analysis packages for rapid genome sequencing. Methods Mol Biol 944: 1-22.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls were made with RTA1.8_CASAVA1.7
ChIPSeq reads were trimmed of adapter sequence and mapped to v2 of the Fusarium fujikuroi genome with BWA software using default options
samtools were used to convert BWA output to sorted bam files, and BEDTools bamToBed was used to convert alignment files to bed format
EpiChIP_V0.9.7-e3.jar was used to calculate normalized locus chromatin state (NLCS) values for each gene. Window size was each gene without upstream or downstream sequence.
Genome_build: Genome_build: Fusarium fujikuroi v2
Supplementary_files_format_and_content: bed files holding coverage values for the whole genome (chromosomes)
|
| |
|
| Submission date |
Apr 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulrich Guldener |
| E-mail(s) |
u.gueldener@tum.de
|
| Organization name |
Technische Universität München
|
| Department |
Chair of genome-oriented bioinformatics
|
| Street address |
Maximus-von-Imhof-Forum 3
|
| City |
Freising |
| State/province |
Bavaria |
| ZIP/Postal code |
D-85354 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17016 |
| Series (2) |
| GSE80478 |
Knock-down of the methyltransferase Kmt6 reliefs H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi [ChIP-seq] |
| GSE80479 |
Knock-down of the methyltransferase Kmt6 reliefs H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi |
|
| Relations |
| BioSample |
SAMN04875444 |
| SRA |
SRX1715981 |
