 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 29, 2021 |
| Title |
fca_liver_h3k27ac_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
liver-left_lateral_lobe
|
| Organism |
Felis catus |
| Characteristics |
tissue: liver, left lateral lobe
chip antibody: H3K27ac (Diagenode; C15410196)
treatment: untreated
totalreads: 37761229
qcmetric_nrf: 0.873028
qcmetric_pbc1: 0.87278
qcmetric_pbc2: 7.832267
qcmetric_nsc: 1.031124
qcmetric_rsc: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue samples were collected from adult male domestic shorthair cats (2 biological replicates). Tissues included: heart, liver, kidney, small intestine, testes, lung, and thyroid. No lesions were identified grossly in the collected tissues. Tissues were flash frozen within 30 minutes of euthanasia and stored at -80 C. All steps leading up to and including chromatin immunoprecipitation (ChIP) and ChIP qPCR were performed using the iDeal ChIP-seq Kit for Histones (Diagenode) per manufacturer guidelines. This included DNA sonication to 100-300 bp using a Bioruptor Pico (Diagenode) at 7 cycles of 30 seconds on and 30 seconds off.
Library preparation for sequencing was performed with the NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext® Multiplex Oligos for Illumina (New England Biolabs) according to manufacturer guidelines. Sequencing was performed on a NovaSeq 6000 platform (Illumina) with a single-end 100 bp format.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data was processed according to the ENCODE3 pipeline v1 specifications (https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit#), following the guidelines for histone modifications. Briefly, reads were mapped to a highly contiguous, single-haplotype domestic cat reference genome assembly (GCA_018350175.1) using Bowtie2 v.2.4.2. Domestic cat Y chromosome sequences (GenBank accession KP081775.1 plus sequences from Y chromosome ampliconic regions) were added during mapping to act as bait for male cat Y reads. Relaxed peaks were generated with MACS2 v.2.2.5 for narrow marks(-g 1.61e9 -p 1e-2 --nomodel --keep-dup all -B --SPMR) and epic2 v.0.0.51 for the broad mark(--effective-genome-fraction 0.66) for each biological replicate, pooled replicates, and pooled pseudoreplicates (pseudoreplicates consist of half the reads of a true replicate sampled without replacement). Peaks from the pooled replicate set were retained in the final replicated peak set if they overlapped by at least half their length in bases with peaks from both biological replicates. Additionally, peaks that overlapped both pooled pseudoreplicates were also included in the final replicated peak set. Final peak files are not filtered for blacklisted regions as a blacklist has not yet been developed for Felis catus.
Genome_build: GCA_018350175.1 (tentatively felCat10)
Supplementary_files_format_and_content: narrowPeak; broadPeak; bigWig; peak files from individual replicates contain relaxed peak calls while the final replicated peak files contain the optimal peak sets for each tissue.
|
| |
|
| Submission date |
Aug 27, 2021 |
| Last update date |
Aug 31, 2021 |
| Contact name |
William J Murphy |
| Organization name |
Texas A&M University
|
| Department |
Veterinary Integrative Biosciences
|
| Street address |
4458 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL28702 |
| Series (1) |
| GSE182952 |
Genome-wide mapping of regulatory regions in seven domestic cat tissues [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN21025004 |
| SRA |
SRX11955097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5543633_liver-h3k27ac.Rep2.narrowPeak.gz |
1.2 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM5543633_liver-h3k27ac.Rep2_foldChangeOverInput.signal.bw |
566.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
