|
| Status |
Public on Sep 01, 2015 |
| Title |
ccg1-xlr1-gfp-4X-63 |
| Sample type |
SRA |
| |
|
| Source name |
whole tissue
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: Neurospora crassa OR74A (FGSC2489)
genotype: his-3::p_ccg1::xlr1-GFP, deltaxlr1::HygR
chip antibody: GFP
|
| Treatment protocol |
The filamentous fungus was washed and transferred to fewsh Vogel's Media with Avicel, Xylan, or Sucrose as the carbon source
|
| Growth protocol |
Neurospora crassa was grown on Vogel's Mininal Media for 16 hrs with Sucrose as the carbon source
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were ground in liquid nitrogen and DNA sheared by sonication, the chromatin was immunoprecipitated by antibody to epitope-tagged transcription factors
Libraries were prepared according to Illumina's instructions for the Genomic DNA Prep Kit, adapters were diluted 1:20, and PCR amplification was carried out to 24 cycles.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
chromatin immuno precipitated DNA
2015_04_14_SD2_MACS_output_&_Nearby_genes.xlsx
|
| Data processing |
reads were aligned with Bowtie2
MACS
genes surrounding the identified peaks were annotated
Genome_build: aligned to Neurospora crassa genome version 12 mitochondria version 10
Supplementary_files_format_and_content: tab delimited spreadsheet of the MACS output with the nearest genes surrounding the peak annotated
|
| |
|
| Submission date |
May 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Craig |
| E-mail(s) |
jimcraig134@gmail.com
|
| Organization name |
UC Berkeley
|
| Department |
Plant & Microbial Biology
|
| Lab |
N. Louise Glass
|
| Street address |
341A Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL16164 |
| Series (2) |
| GSE68516 |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 (ChIP-Seq) |
| GSE68517 |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 |
|
| Relations |
| BioSample |
SAMN03581160 |
| SRA |
SRX1017025 |
