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Sample GSM5543650

Query DataSets for GSM5543650

Status

Public on Aug 29, 2021

Title

fca_liver_input_rep2

Sample type

SRA

Source name

liver-left_lateral_lobe

Organism

Felis catus

Characteristics

tissue: liver, left lateral lobe
chip antibody: Input
treatment: untreated
totalreads: 47936507
qcmetric_nrf: 0.857835
qcmetric_pbc1: 0.857583
qcmetric_pbc2: 7.000868
qcmetric_nsc: .
qcmetric_rsc: .

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 30, 2021

Contact name

William J Murphy

Organization name

Texas A&M University

Department

Veterinary Integrative Biosciences

Street address

4458 TAMU