|
| Status |
Public on Dec 01, 2023 |
| Title |
H26_1_glc_IP |
| Sample type |
SRA |
| |
|
| Source name |
DS70 ∆pyrE2
|
| Organism |
Haloferax volcanii DS2 |
| Characteristics |
strain: H26
cell type: {delta}pyrE2 cell culture
genotype: DS70 {delta}pyrE2
treatment: HvCA + uracil + 0.1% glucose (w/v)
chip antibody: Abcam #ab9110
|
| Growth protocol |
Strains H26 and AK239 were struck from freezer stocks onto YPC18+uracil plates and incubated at 42C until single colonies formed. Independent colonies were used to start 2 cultures of H26 and 4 cultures AKS239 in 5 mL YPC18+uracil. Precultures were grown at 42C with 250 rpm shaking until average optical density at 600nm reached ~1. Cells were transferred to fresh 100 mL HvCa with or without 0.1% glucose and harvested at exponential phase (OD600 ~ 0.3-0.5).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were processed as described in Wilbanks et al. (2012) using anti-HA polyclonal antibody (Abcam #ab9110) to immunoprecipitate cross-linked fragments.
Libraries were constructed by the Center for Genomic and Computational Biology at Duke University (Durham, NC) using KAPA Hyper Prep kit and Illumina TruSeq adapters, and the 50 bp, single-ended libraries were sequenced on an Illumina HiSeq 4000
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
∆pyrE2 cell culture
Parental, no-tag control. Replicate 1. Immuno-precipitated sample. Media supplemented with 0.1% glucose (w/v)
|
| Data processing |
Adapter sequences were removed with Trim_galore! 0.4.3, cutadapt 2.3, and and sample quality assessed with FastQC 0.11.7 using default parameters.
Reads were aligned to the Haloferax volcanii DS2 reference genome (GCA_000025685.1, accessed 2023-09-11) with Bowtie2 2.3.5.1 in single-end mode.
Aligned sequence files were converted to binary format, sorted, and indexed using samtools 1.9.
Aligned and sorted BAM files were imported in to R coding environment and fragment length was optimized for each IP and input (WCE) sample using ChIPQC 1.30.
Peaks were called using Mosaics 2.32 in R 4.1.2 using the estimated fragment lengths from ChIPQC and FDR < 0.01.
For per base coverage plots, BAM files were extended in the 3' direction to 150 bps with samtools 1.10 and converted to BEDGRAPH format using bedtools 2.30.0 as described in Grünberger et al. 2020.
Assembly: GCA_000025685.1
Supplementary files format and content: BED files with mosaics called peaks (except for input (WCE) samples)
Supplementary files format and content: bedgraph files with per base read coverage, generated from extended .bam files.
|
| |
|
| Submission date |
Nov 24, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Amy Schmid |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University
|
| Street address |
3242 French Family Science Center
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL33952 |
| Series (2) |
| GSE248565 |
Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii [CHIP-seq] |
| GSE248566 |
Transciptome profile of TrmB and TbsP, Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii |
|
| Relations |
| BioSample |
SAMN38413283 |
| SRA |
SRX22635999 |
