|
| Status |
Public on Dec 07, 2022 |
| Title |
atxr5/atxr6 rep2 (DNA seq) |
| Sample type |
SRA |
| |
|
| Source name |
16C nuclei
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
tissue: leaves
age: 4 weeks
genotype: atxr5/atxr6 mutant
|
| Growth protocol |
Arabidopsis plants were grown under cool‐white fluorescent lights (~100 μmol m−2 s−1) in long‐day conditions (16 h light/8 h dark).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from sorted 16C nuclei using the ArcturusTM PicoPureTM DNA Extraction Kit (ThermoFisher Scientific, Waltham, MA). Samples were incubated at 65C overnight and at 95C for 10 minutes. The DNA samples were then purified using a genomic DNA Clean and Concentrator kit (Zymo Research, Irvine, CA).
Sequencing libraries were generated at the Yale Center for Genome Analysis (YCGA) using the xGen Prism DNA library prep kit for NGS (Integrated DNA Technologies, Coralville, IA).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
sorted 16C nuclei
|
| Data processing |
Library strategy: DNA-seq
DNA-seq:Paired-end reads were filtered and trimmed using fastp. Reads with quality inferior to 20 were removed from the data sets. Sequencing datasets were aligned against the A. thaliana genome (TAIR10) using bowtie2 with default parameters. Duplicate reads were removed using Picard toolkit (MarkDuplicates with REMOVE_DUPLICATES=true). The mapped reads were then filtered based on mapping quality using samtools (-q 30). For generating the chromosomal representations, the program featureCounts (version 1.6.4,) was used to count the paired-end fragments present in each 200kb regions of the A. thaliana genome. The log2 ratio was centered on the average ratio of any two compared libraries on the first 5 Mbp of chromosome 1 for normalization.
RNA-seq: Paired-end reads were filtered and trimmed using fastp. Reads with quality inferior to 20 were removed from the data sets. Biological replicates were analyzed for consistency with deepTools2. Data sets were aligned against the Arabidopis genome (TAIR10) using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Transposable elements (TE) were defined according Panda et al 2016. FeatureCounts (version 1.6.4)was used to count the paired-end fragments overlapping with TEs. TPM (transcripts per million) values were calculated for TEs. They were considered to be upregulated in mutant lines if they showed 2-fold up-regulation as compared to Col in both biological replicates and had a value of TPM >= 5.
Genome_build: RNA-seq: TAIR10; DNA-seq: TAIR10
Supplementary_files_format_and_content: bedgraph: 200kb windows, normalized against the wild type (see DNA seq processing)
Supplementary_files_format_and_content: bigwig: RPKM of RNA seq over the genome using deeptools.
|
| |
|
| Submission date |
Sep 24, 2021 |
| Last update date |
Dec 07, 2022 |
| Contact name |
Yannick Jacob |
| E-mail(s) |
yannick.jacob@yale.edu
|
| Phone |
203-432-8908
|
| Organization name |
Yale university
|
| Department |
Department of Molecular, Cellular & Developmental Biology
|
| Lab |
Jacob Lab
|
| Street address |
YSB 416 260 Whitney Avenue
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE184738 |
TONSOKU reads the histone H3.1 variant to mediate DNA repair during replication |
|
| Relations |
| SRA |
SRX12334455 |
| BioSample |
SAMN21601156 |
