|
| Status |
Public on May 14, 2020 |
| Title |
dnsdC_16h_calcium_1 |
| Sample type |
SRA |
| |
|
| Source name |
cultured colonies
|
| Organism |
Aspergillus fumigatus |
| Characteristics |
strain: ΔnsdC [ΔnsdC::pyrG, akuB (KU80)Δ, MAT1-1]
tag: untagged
chip antibody: anti-RNA polymerase II subunit antibodies (clone 3E8, Millipore)
|
| Treatment protocol |
After 16 h of growth, calcium samples were treated for 10 minutes with 200mM of calcium chloride, crosslinked (formaldehyde 1% for 20 min, then glycine 1M for 10min), washed with cold water for 2 times and collected; control samples were crosslinked, washed and collected after 16h of growth.
|
| Growth protocol |
CEA17 and ∆nsdC strains conidia (1.10^7) were grown into liquid AMM for 16 h at 37oC under shaking conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The micelia were lysed in 800 μl of FA lysis buffer for 3 min (6 times) using a Bullet Blender and sonicated using the Qsonica Q800R at 100% amplitude with 10 seconds ON and 15 seconds OFF cycles for a total sonication time of 30 minutes.
Library preparation was carried out using NEBNext® Ultra II Library Prep kit (Illumina, cat. no. E7645L) according to manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Chromatin
ΔnsdC treated with calcium
|
| Data processing |
Raw data was aligned to A. fumigatus reference genome using Bowtie2 v2.3.5 tool. Initial 8bp of reads were clipped during mapping step using argument "bowtie2 --trim5 8 --local "
Normalized the reads depth to 1 million mapped reads using "macs2 bdgopt " command from MACS2 v2.1.1
Converted bedGraph files to bigWig files using UCSC Kent Utils v369 tool "bedGraphToBigWig"
Normalized PolII signal (FPKM) was calculated for all the genes using inhouse Perl script
Genome_build: Aspergillus fumigatus Af293 reference genome from AspGD. Version s03-m05-r06
Supplementary_files_format_and_content: bigwig files were generated using UCSC Kent Utils v369; Scores represent normalized read depth to 1 million reads
|
| |
|
| Submission date |
Apr 13, 2020 |
| Last update date |
May 14, 2020 |
| Contact name |
Gustavo Henrique Goldman |
| E-mail(s) |
ggoldman@usp.br
|
| Organization name |
Sao Paulo University
|
| Street address |
Avenida do Cafe
|
| City |
Ribeirao Preto |
| State/province |
Sao Paulo |
| ZIP/Postal code |
14040900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL23160 |
| Series (1) |
| GSE148557 |
Characterization of Aspergillus fumigatus NsdC transcription factor (RNA polII ChIP-seq) |
|
| Relations |
| BioSample |
SAMN14591329 |
| SRA |
SRX8110334 |
