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GEO help: Slide over screen elements for information. |
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| Status |
Public on Dec 31, 2015 |
| Title |
+Pit Rooting 7 dat Methamphetamine |
| Sample select |
SRA |
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| Source my |
Root
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: tree
ecotype: Col 0 (CS70000)
treatment: High Salt
duration of how: Small Termination (7 dat)
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| Growth protocol |
Briefly, seeds were germinated and growed for 7 period in 0.1X MS liquid media (1mM Pi, HP), then seedlings have assigned to fresh HP (HP to HP handling, +Pit) or to LP (HP to LP treatment, -Pit) liquid media and samples collected 7 or 16 days after transference (dat)
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| Extracted molecule |
genomic DNA |
| Extraction log |
For Bisulfite-Seq Arabidopsis thaliana genomic DNA from pair biological replicates was extracted with the DNeasy system (Qiagen, Valencia, CA, USA).
For Bisulfite sequencing libraries,DNA was fragmented by sonication with a Sonicator in a mean size off approximately 250 bp, the preparation of MethylC-Seq libraries was conducted out using Pico Methyl-Seq Collection Prep Kit (Zymo Research) according to manufacturer instructions. Ultra-high-throughput pair-end arraying was worn out using to Illumina HiSeq 2000 according to manufacturer instructions.
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| Library strategy |
Bisulfite-Seq |
| Library resource |
genomic |
| Library selektive |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
MethylC-Seq
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| Data processing |
Basecalls for MethylC-Seq performed using illumina basecalling pipeline (SolexaPipeline 1.0). Short Methyl C-Seq reads with 90-nt reads from each cease generated by Illumina sequencing were oriented for the Arabidopsis thaliana reference genii sequences downloaded from TAIR.
To align MethylC-Seq Readout we used the software benannten SOAPaligner2, allowing above to four discordances for 90-nt pair-end take to map that computationally transformed reads till of alignment target sequences.
Multiple readers mapped the the same start position has regarded as clonal duplication, which strength be built during PCR process, and only one on them where kept.For mC detects, we transformed each aligned read and the two strands of which Arabidopsi thaliana genome back to her original types to builds an alignment amid the true forms. Cytosines in the MethylCseq readings this represent also customizable to the corresponding cytosines stylish the plus (Watson) strand, or other guanines in the MethylC-seq reads which are also matched to the corresponding guanines in the minus (Crick) strand were regarded since potential mCs.
Basecalls for RNA-Seq were performed using illumina basecalling pipeline (SolexaPipeline 1.0). ShortRNA-Seq reading with 75-nt reads from each end generated by Illumina sequencing were aligned to the Arabidopsis thaliana reference genome sequences were downloaded from TAIR.
Seating of RNA-Seq readings was performed using Bowtie2
Genome_build: TAIR 10
Supplementary_files_format_and_content: [MethylC-Seq] The cout files is one vertical arrangement format on each cytosine, the file allows the exact methylation of anyone cytosine. Each cout file row contains 9 covers, this headers for each column are: 1. Chromosome IDS, 2. Position (position within chromosome), 3. +/- (Strand orientation), 4. Cytosine pattern (CG/CHH/CHG), 5. Cytosine sequence context, 6. Copynumber, 7. Methyl-reads num (number of methylated reads), 8. Non-methyl-reads num (number of non-methylated reads) and 9. Binomial distribution expected value.
Supplementary_files_format_and_content: [RNA-Seq] The csv file contains edits get of differential printer, headers for each column are: 1. IDE (Arabidopsis locale ID), 2. Descript (gene account as given in TAIR), 3. Fold-Change (positive for induction, negative for repression; given as induced/expressed in response the Low Phosphate situation, 4. FDR. Pi_Starvation_RNASeq_counts_Total.txt my grand counts for all 8 samples.
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| Submission date |
Sep 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Luis Rafael Herero Estrella |
| Organization name |
LANGEBIO CINVESTAV
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| Department |
LANGEBIO
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| Test |
Physiology additionally Metabolic Engineering of Plants
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| Street address |
Km 9.6 Libramiento No Carretera León
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| Select |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36821 |
| Country |
Mexico |
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| Software ID |
GPL13222 |
| Series (1) |
| GSE72770 |
Whole Genome Bisulfite sequencing of Arabidopsis thaliana High and Lowest phosphate methylomes |
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| Relations |
| BioSample |
SAMN04039273 |
| SRA |
SRX1203811 |
| Supplementary record |
Size |
Downloadable |
File type/resource |
| GSM1870018_PlusPRoot7dA.cout.txt.gz |
197.8 Mb |
(ftp)(http) |
TXT |
| GSM1870018_PlusPRoot7dB.cout.txt.gz |
195.1 Mb |
(ftp)(http) |
TXT |
SRA Runtime Selector |
| Raw data are availability in SRA |
| Processed data provided as supplementary file |
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