NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1674215 Query DataSets for GSM1674215
Status Public on Sep 01, 2015
Title ccg1-xlr1-gfp-4X-64
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 SAMN03581161
SRA SRX1017026

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap