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| Status |
Public on Aug 07, 2012 |
| Title |
atxr56_seedling_RNAseq_setC |
| Sample type |
SRA |
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| Source name |
atxr56_seedling_RNAseq
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: atxr56
tissue: 10 day seedlings
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
DNA-seq libraries: One gram of mature rosette leaves were collected from 3-4-week-old plants, chopped in 0.5 ml of filtered Galbraith buffer, and stained with propidium iodide. A BD FACS Aria II in the UCLA Jonsson Comprehensive Cancer Center (JCCC) Flow Cytometry Core Facility was used to sort the nuclei. For sequencing, 7,000-9,000 8C nuclei of each sample were collected, and purified DNA with Picopure purification kit (Arcturus) following manufacturer instructions. Libraries were generated and sequenced following manufacturer instructions (Illumina).
RNA-seq libraries: RNA-seq experiments were performed in two biological replicates for each genotype. 0.1g of tissue was ground in Trizol (Invitrogen). Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina).
Bisufite-Seq libraries: 0.5-1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated and sequenced as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 16
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| Data processing |
DNA-Seq reads were were first trimmed to 36mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Reads mapping to identical coordinates were collapsed into one read.
Genome_build: TAIR8
Supplementary_files_format_and_content: DNA-seq data: Column 1 is chromosome. Column 2 is strand read mapped to (+/-). Column 3 is the genomic coordinate.
mRNA-Seq reads were first trimmed to 50mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.
Genome_build: TAIR8
Supplementary_files_format_and_content: Each RNA-seq processed file gives 20- or 25-basepair resolution signal normalized as mapped reads per genomic kilobasepair per million mapped reads. Column 1 is chromosome. Column 2 is the genomic coordinate. Column 3 is the normalized counts.
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR8 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR8
Supplementary_files_format_and_content: BS-seq data: Column 1 is chromosome (1..5). Column 2 is the coordinate of the genomic cytosine. Column 2 is genomic strand (+/-) of the cytosine. Column 3 is context (CG, CHG, or CHH) of the genomic cytosine. Column 4 is the empirical observed fraction of 5'-methylation, calculated as (# read C) / (# read C + # read T).
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| Submission date |
May 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hume Stroud |
| Organization name |
UT Southwestern
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE38286 |
DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis. |
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| Relations |
| SRA |
SRX150073 |
| BioSample |
SAMN00998789 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM938345_atxr56_seedling_RNAseq_setC_processed.txt.gz |
17.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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