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Sample GSM7843855 Query DataSets for GSM7843855
Status Public on Jan 01, 2024
Title unT-183-03, methylseq
Sample type SRA
 
Source name Polyp-Tissue
Organism Acropora palmata
Characteristics cell line: Polyp-Tissue
genotype: 1
treatment: Underside_Treatment
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) was extracted from 32 A. palmata fragments (n= 8 per group condition; 16 fragments per genet). We used the DNeasy Blood and Tissue Kit (Qiagen, Switzerland), as per the manufacturer’s protocol. gDNA concentration was quantified at 0.5-1.5 μg (Qubit® dsDNA BR Assay Kit on a Qubit® 2.0. Fluorometer) and sent for Whole Genome Bisulfite Sequencing (WGBS) at Admera Health (New Jersey, USA).
Sequencing libraries were prepared with an average sequencing library insert size of 450 bp and according to TruSeq® DNA Methylation Kit protocol, Sample Preparation Guide (Illumina Inc., USA). Briefly, standard reaction mix consisting of 130 µl of the CT Conversion Reagent and 20 µl of each DNA sample were used for bisulfite conversion (EZ DNA Methylation-Gold™ Kit) in a thermal cycler (Eppendorf® Mastercycler® Pro S). After the incubation period, bisulfite converted DNA was purified following the protocol of EZ DNA Methylation-Gold™ Kit. The bisulfite converted sequencing library was enriched following the TruSeq® DNA Methylation Kit protocol. Libraries were validated and quantified with qPCR. Sequencing was performed in Illumina Hi-Seq platform with pair-end reads of 2x150 and a mean depth coverage of 30x (Illumina Inc., USA). The estimated number of passed filter reads per sample was 110-120 million paired-end reads (55-60M reads in each direction).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 4000
 
Description Sample 23
Data processing Methylation analysis was performed using Bismark 020.0 (Krueger and Andrews, 2011). Briefly, FASTQ files were quality-filtered, and adapter sequences trimmed using Trim Galore 0.5.0 (Krueger, 2018). A bisulfite-converted reference genome file was generated using Bismark-Bowtie2 algorithm, and the epigenome library sequenced data was aligned to the Acropora palmata genome
Methylation information was then extracted from the output SAM files and resulting genome tracks were used for the visualization and reporting of downstream differential methylation calculations. Methylated and unmethylated read counts for all cytosines across the genome in the CG, CHG, and CHH context were obtained from census files.
Assembly: Acropora palmata genome, assembled and annotated by Sheila Kitchen 2023, in prep. Associated fasta is uploaded as well as the associated annotation file
Supplementary files format and content: tab-delimited text files include bismark report
 
Submission date Oct 16, 2023
Last update date Jan 01, 2024
Contact name KELLY Johanna GOMEZ-CAMPO
E-mail(s) kellygomezcampo@gmail.com, kjg27@psu.edu
Organization name PSU
Department Biology
Lab Baums
Street address 212 Mueller Laboratory
City University Park
State/province Pennsylvania
ZIP/Postal code 16802
Country USA
 
Platform ID GPL33847
Series (2)
GSE245492 Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals [Methyl-seq]
GSE245494 Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals
Relations
BioSample SAMN37849487
SRA SRX22106877

Supplementary file Size Download File type/resource
GSM7843855_23_R1_val_1_bismark_bt2_PE_report.txt.gz 931 b (ftp)(http) TXT
GSM7843855_23_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.gz 556.1 Mb (ftp)(http) TXT
GSM7843855_23_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz 496.7 Mb (ftp)(http) COV
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