|
| Status |
Public on Feb 13, 2023 |
| Title |
EV-cn-1 |
| Sample type |
SRA |
| |
|
| Source name |
nuclei
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole body
treatment: control RNAi
temperature: 15C
strain: N2
chip antibody: H3K4me3 Cell signalling
|
| Treatment protocol |
C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50. Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 15C. The adults were then subjected to heat shock at 37C for hours and collected for CUT&Tag library prep
|
| Growth protocol |
C. elegans (N2) were cultured using standard laboratory conditions on E. coli OP50. Adults were bleached onto RNAi plates and allowed to develop to the L4 to young adult at 15C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Young adult C. elegans were lysed in nuclear purification buffer using tissue homogenizer and histone-DNA-antibody complexes were isolated using activated pA-Tn5
CUT&Tag libraries were prepared for sequencing using established protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Paired end reads from each sample were aligned to the C. elegans genome (ce11 with ws245 annotations) using Bowtie2 (Langmead et al., 2009)with the parameters -N 1 and -X 2000.
Duplicate reads were removed using Picard (http://broadinstitute.github.io/picard/) and the reads with low quality scores (MAPQ < 10) were removed.
HOMER software suite was used to process the remaining mapped reads (Heinz et al., 2010). The “makeUCSCfile” command was used for generating genome browser tracks, the “findPeaks” command was used for calling H3K4me3 peaks and the “annotatePeaks” command was used for making aggregation plots.
Differential peak calling was accomplished using ChipPeakAnno (Zhu et al., 2010). TSS plots were generated using HOMER (Heinz et al., 2010)
Assembly: ce11 with ws254 notations
Supplementary files format and content: peak text files
Library strategy: CUT&Tag
|
| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Feb 13, 2023 |
| Contact name |
Amy K Walker |
| E-mail(s) |
[email protected]
|
| Organization name |
UMass Chan Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Amy Walker
|
| Street address |
Suite 137, Biotech 2, 373 Plantation St
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (2) |
| GSE223594 |
S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress [CUT&Tag] |
| GSE223597 |
S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress |
|
| Relations |
| BioSample |
SAMN32886848 |
| SRA |
SRX19148121 |
