|
| Status |
Public on Feb 27, 2014 |
| Title |
H3K4me3_ChIP-seq; Sample 23_HTS636 |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Fusarium graminearum |
| Characteristics |
strain number: FMF248
genotype: DELkmt6::neoR
nitrogen level: low
antibody: abcam ab 8580
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA obtained by ChIP was end-repaired and ligated to adapters as described elsewhere {Pomraning, 2012 #12099}. Fragments (300 to 500 bp long) were gel-purified and amplified by 21-24 cycles of PCR with Phusion polymerase (Finnzymes Oy, NEB) and Illumina PCR primers {Pomraning, 2012 #12099}.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were made with RTA1.8_CASAVA1.7
ChIPSeq reads were trimmed of adapter sequence and mapped to the F. graminearum genome with BWA software using default options
RNASeq reads were trimmed of adapter sequence and mapped to the F. graminearum genome with Tophat software with options (-a 5 -m 1 -i 30 -I 2000)
samtools were used to convert BWA or Tophat output to sorted bam files
cufflinks v2.1.1 was used (--max-bundle-length 20000 -I 2000 --min-intron-length 30) to calculate FPKM values for Broad assembly 3 transcripts from sorted bam files of RNA-seq reads
Genome_build: Broad chromosome assembly 3
Supplementary_files_format_and_content: ChIP-seq processed files are tab delimited EpiChIP output containing gene name, NLCS value
Supplementary_files_format_and_content: RNA-seq processed files are tab delimited cufflinks output containing gene name, FPKM value
|
| |
|
| Submission date |
Sep 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristina M Smith |
| E-mail(s) |
smitkris@science.oregonstate.edu
|
| Organization name |
Oregon State University
|
| Department |
Biochemisty and Biophysics
|
| Lab |
Freitag
|
| Street address |
ALS2011
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL17573 |
| Series (1) |
| GSE50689 |
The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters |
|
| Relations |
| BioSample |
SAMN02361135 |
| SRA |
SRX357565 |
