|
| Status |
Public on Jun 25, 2024 |
| Title |
ChIPseq of Atf1-FLAG, 0h, FLAG-IP, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
S. pombe cell culture
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
tissue: S. pombe cell culture
strain: SPB4877
genotype: h- leu1-32 ura4-D18 ade6-704 atf1-6xGly-3xFlag::kanMX
treatment: --
|
| Treatment protocol |
2h growth at low density (OD=0.01) either with NSF or MeOH as control.
|
| Growth protocol |
S. pombe cell cultures were grown in standard YES medium (OD = 1, exponential phase) at 30 degrees celsius. At time point 0, cells were diluted to OD = 0.01 and shifted to EMM(187mM NH4Cl) with MeOH or NSF at 30 degrees celsius.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde and lysed by beat-beating. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol and the IP was performed for 2h at 4°C. ChIPs were decrosslinked overnight at 65°C and cleaned up using AMPure XP beads. For a detailed protocol, see Kuzdere et al, 2022.
ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities) were used and read coverage was normalized to 1 million genome mapping reads (RPM).
Assembly: Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized read counts (to 1 mio genome mapping reads per library) for visualization in UCSC or IGV genome browser.
|
| |
|
| Submission date |
Dec 13, 2023 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Fabio Mohn |
| E-mail(s) |
fabio.mohn@fmi.ch
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Lab |
Buehler Lab
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL28961 |
| Series (2) |
| GSE250092 |
Nitrogen signaling factor changes gene expression and binding of transcription factors [ChIP-seq] |
| GSE250095 |
Nitrogen signaling factor changes gene expression and binding of transcription factors |
|
| Relations |
| BioSample |
SAMN38810524 |
| SRA |
SRX22878351 |
