|
Status |
Public on Sep 01, 2015 |
Title |
ccg1-xlr1-gfp-4A-67 |
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 |
SAMN03581158 |
SRA |
SRX1017023 |