|
| Status |
Public on Jun 15, 2022 |
| Title |
Pp_00min_ABA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
P. patens protonema
|
| Organism |
Physcomitrium patens |
| Characteristics |
differentiation stage: 00 minutes ABA
|
| Treatment protocol |
10 -day old P. patens protonema tissue was sonicated and then transferred to 250 mL liquid PpNH4 media. After 3 days of growth on a plate shaker at ~100 rpm, ABA was added to the liquid culture for a final concentration of 10 mM and the same volume of methanol was added to the control samples. Samples were placed back on the shaking incubator for 30 or 60 minutes before being collected and flash frozen with liquid nitrogen.
|
| Growth protocol |
Physcomitrella patens was grown on PpNH4 media plates for 7-10 days and then propagated following instructions provided by the Benzanilla lab. Specifically, samples are homogenized until no big clumps remain visible. Each new plate is layered with a sterile cellophane and 0.5 mL of the tissue mixture is placed on the cellophane. The plate is then gently swirled to evenly distribute the tissue and sealed with micropore plate. Then the plates are placed in Percival chambers at 25C with 16 hours/8 hours light/dark cycles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol Reagent per the manufacturer's protocol
TruSeq Stranded mRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapters were trimmed with cutadapt -f fastq -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG-e 0.06 -O 6 -m 14
Reads were mapped with tophat --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --no-coverage-search -p 4 -o
HTSeq was used to create read counts from the aligned BAM files
Genome_build: P.pates_318
Supplementary_files_format_and_content: Read counts are presented in tab-delimited format (*mRNA_read_counts.txt) with transcript ID in the first column and the number of reads in the second column; variance stabilize transformed values are calculated by DESeq2 and found in allDays_VSTvalues.txt
|
| |
|
| Submission date |
Apr 09, 2020 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Mengge Shan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennylsvania
|
| Department |
Biology
|
| Lab |
Brian Gregory
|
| Street address |
433 South University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17793 |
| Series (1) |
| GSE148422 |
Global analysis reveals large scale dynamics of protein-RNA interaction and RNA secondary structure characteristics of Physcomitrella patens ABA response (mRNA) |
|
| Relations |
| BioSample |
SAMN14569705 |
| SRA |
SRX8092710 |
