|
| Status |
Public on Jan 29, 2024 |
| Title |
H3 profile, normalization for whole worm HCF-1 binding profile in set-26(tm2467) mutant, L4440, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
somatic and germline cells
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
cell type: somatic and germline cells
strain: IU719
genotype: rwIs33[hcf-1::gfp::3xflag] set-26(tm2467)
diet: L4440 (E.V.)
antibody: H3 (abcam #ab1791)
|
| Growth protocol |
Worms were grown for ~48h at 25C until they reached the young adult/day 1 adult stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms were exposed to an SDS-DTT buffer to weaken their cuticle, then dounced in CUT&RUN wash buffer and the resulting worm/cell mixture was used for standard CUT&RUN protocol (See Emerson & Lee, 2022, Current Protocols, DOI: 10.1002/cpz1.445)
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina with 14 PCR cycles for amplification, as previously described (See Emerson & Lee, 2022, Current Protocols, DOI: 10.1002/cpz1.445)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
set-26mutant_HCF-1.vs.H3_L4440_MergedReps.bigwig
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak
set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt
set-26HCF-1GFP_L4440_H3antibody_rep1
|
| Data processing |
Adaptor sequences were trimmed and low quality reads were filtered out from sequencing files using Trim Galore! (v0.6.5) with the settings –paired –q 20 –fastqc.
Trimmed paired-end sequencing files were then aligned to the ce11/WBcel235 C. elegans reference genome using bowtie2 (v2.4.3) with the options –very-sensitive-local –no-unal –no-mixed –no-discordant –phred33 -p 4 -I 10 -X 700.
The individual bam files corresponding to two biological replicates were merged using the ‘samtools merge’ command in SAMTools.
Indexed bam files combined from both replicates were used for narrow peak calling with MACS2 (v2.1.4) using the settings -f BAM - g ce –call-summits –keep-dup all -q 0.01 -m 5 50 –nomodel. Peaks were called against a control track, representing a bam file with combined replicates of CUT&RUN experiments targeting either the tagged factor of interest in untagged control worms or H3 CUT&RUN in the same genotype run in parallel for normalization.
To generate bigwig files for visualization, combined bam files from both biological replicates were put through the ‘bamCompare’ command in deepTools (v3.3) with the settings –binSize 20 –operation log2 –scaleFactors Method None –normalizeUsing CPM –numberOfProcessors 8 –outFileFormat bigwig –smoothLength 60 –extendReads –centerReads, and with –bamfile2 representing a bam file with combined replicates of CUT&RUN experiments targeting either the tagged factor of interest in untagged control worms or H3 for normalization.
Assembly: WBcel235/ce11
Supplementary files format and content: bigWig and narrowPeakfiles (normalized to either antibody or H3 control files)
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Jan 30, 2023 |
| Last update date |
Jan 29, 2024 |
| Contact name |
Siu Sylvia Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
Cornell University
|
| Street address |
520 Campus road
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (2) |
| GSE224076 |
The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans [CUT&RUN] |
| GSE224078 |
The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans |
|
| Relations |
| BioSample |
SAMN32962170 |
| SRA |
SRX19217770 |
