|
| Status |
Public on May 30, 2023 |
| Title |
HCA_trmB_0glu_C_IP |
| Sample type |
SRA |
| |
|
| Source name |
delta-pyrF trmB::HA cell culture
|
| Organism |
Haloarcula hispanica ATCC 33960 |
| Characteristics |
strain: AKS155
genotype: delta-pyrF trmB::HA
cell type: delta-pyrF trmB::HA cell culture
treatment: Hh-CA + uracil
chip antibody: Abcam #ab9110
|
| Growth protocol |
Strains DF60 and AKS155 were struck from freezer stocks onto YPC23+uracil plates and incubated at 37 C for 8 days. Independent colonies were used to start 2 cultures of DF60 and 4 cultures AKS155 in 10 mL YPC23+uracil. Precultures were grown for 29 hours at 37C with 250 rpm shaking (average optical density at 600nm = 2) then collected at 6000 rpm for 2 min and washed twice with Hh-CA+uracil. AKS155 pellets were resuspended in either Hh-CA+uracil or Hh-CA+uracil + 0.1% glucose and grown to mid-log phase (average OD = 0.35) at 37C with shaking.
|
| 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 |
TrmB:HA translational fusion. Replicate C. HhCA media. Immuno-precipitated sample.
|
| 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 Haloarcula hispanica ATCC33960 reference genome (GCF_000223905.1, accessed 2018-11-13) with Bowtie2 2.3.4.3 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: GCF_000223905.1
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
|
| |
|
| Submission date |
Mar 09, 2023 |
| Last update date |
May 31, 2023 |
| Contact name |
Amy Schmid |
| E-mail(s) |
amy.schmid@duke.edu
|
| Organization name |
Duke University
|
| Street address |
3242 French Family Science Center
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL33237 |
| Series (2) |
| GSE227032 |
Genome-wide binding of TrmB in Haloarcula hispanica |
| GSE227034 |
TrmB in Haloarcula hispanica |
|
| Relations |
| BioSample |
SAMN33705015 |
| SRA |
SRX19624265 |
