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Status |
Public on Jan 01, 2024 |
Title |
unC-185-03, methylseq |
Sample type |
SRA |
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Source name |
Polyp-Tissue
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Organism |
Acropora palmata |
Characteristics |
cell line: Polyp-Tissue genotype: 2 treatment: Underside_Control
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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).
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 4000 |
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Description |
Sample 9
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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
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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
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Organization name |
PSU
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Department |
Biology
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Lab |
Baums
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Street address |
212 Mueller Laboratory
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City |
University Park |
State/province |
Pennsylvania |
ZIP/Postal code |
16802 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN37849501 |
SRA |
SRX22106856 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7843841_9_R1_val_1_bismark_bt2_PE_report.txt.gz |
931 b |
(ftp)(http) |
TXT |
GSM7843841_9_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.gz |
554.2 Mb |
(ftp)(http) |
TXT |
GSM7843841_9_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz |
496.2 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
Raw data are available in SRA |
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