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SRX17956170: Bisulfite-seq_25R2ZEB_2_Roots_ 50Zeb_ 3 weeks recovery in vitro_ JAN2019_ rep2
1 ILLUMINA (Illumina HiSeq 4000) run: 46.1M spots, 13.8G bases, 4.4Gb downloads

Design: Genome-wide DNA Methylation (Bisulphite-seq) (Novogene): DNA quantification and qualification: Genomic DNA degradation and contamination was monitored on agarose gels. DNA concentration was measured using Qubit DNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). Library preparation and quantification: A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-400 bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturers instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research). And the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was checkedBoinoaAngaliyleznetr 2100 system. Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturers instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated. Image analysis and base calling were performed with the standard Illumina pipeline, and finally 150 bp paired-end reads were generated.
Submitted by: Institute of Plant Genetics, Polish Academy of Sciences
Study: PurpleWalls - Unraveling genome expression (de) regulation to modulate wood formation in Salix purpurea: an integrative approach
PRJNA889596 • SRP402646 • All experiments • All runs
show Abstracthide Abstract
The use of bioenergetic plantations of sources of renewable energy is one of the main directives of the energetic policy in Europe. Being part of the natural composition of Polish vegetation, willow has been recommended as bioenergy crop for Poland.PurpleWalls will address new and relevant insight genetic and molecular mechanisms controlling phenotype determination, and phenotypic adaptation to growing conditions in Salix purpurea as model for other Salicaceae and perennial species used for bioenergy.PurpleWalls is a 36 month project, funded by NCN (Poland) UMO-2015/18/NZ2/00694.Starting date: 12th May 2016
Sample: 25R2ZEB_2
SAMN31364909 • SRS15473250 • All experiments • All runs
Organism: Salix purpurea
Library:
Name: BIS_25R2ZEB_3
Instrument: Illumina HiSeq 4000
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: size fractionation
Layout: PAIRED
Runs: 1 run, 46.1M spots, 13.8G bases, 4.4Gb
Run# of Spots# of BasesSizePublished
SRR2197270046,073,62013.8G4.4Gb2023-11-01

ID:
24899159

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