 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 21, 2022 |
| Title |
CUT_T24_2 |
| Sample type |
SRA |
| |
|
| Source name |
CUT_T24_2
|
| Organism |
Physcomitrium patens |
| Characteristics |
genotype: wild type (Gransden strain)
developmental stage: gametophore
tissue: stem
|
| Treatment protocol |
decap T24h-decap t24h,biotic stress-decap t24h-decap t24h
|
| Growth protocol |
Moss colonies were initiated from 1 mm2 spot cultures and cultivated in sterile Magenta GA-7 tissue culture vessels (Bioworld, Dublin, OH, USA) on BCDAT medium (250 mg/L MgSO4.7H2O, 250 mg/L KH2PO4 (pH 6.5), 1010 mg/L KNO3, 12.5 mg/L, FeSO4.7H2O, 0.001% Trace Element Solution (0.614 mg/L H3BO3, 0.055 mg/L AlK(SO4)2.12H2O, 0.055 mg/L CuSO4.5H2O, 0.028 mg/L KBr, 0.028 mg/L LiCl, 0.389 mg/L MnCl2.4H2O, 0.055 mg/L CoCl2.6H2O, 0.055 mg/L ZnSO4.7H2O, 0.028 mg/L KI and 0.028 mg/L SnCl2.2H2O), 0.92 g/L di-ammonium tartrate (C4H12N2O6) and 8 g/L agar with CaCl2 added to a 1 mM concentration after autoclaving, at 23°C under a 16h light/8h dark cycle, at 50-150 umol.m-2.s-1 in MLR-352 growth cabinets (PHCbi, Etten-Leur, The Netherlands). For each biological replicate and condition, RNA were pooled from 5-10 gametophores collected from 4 week-old colonies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CUT_T24_2(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Genome_build: transcriptome of 32926 genes Physcomitrella patens
transcriptome mapping and counts of reads by gene locus are done with bowtie2; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,gene_length,counts_SEreads,counts_PEreads
|
| |
|
| Submission date |
Nov 15, 2021 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Véronique BRUNAUD |
| E-mail(s) |
veronique.brunaud@inrae.fr
|
| Organization name |
INRA - CNRS - UPSUD
|
| Lab |
IPS2
|
| Street address |
rue Noetzlin
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL30955 |
| Series (1) |
| GSE188843 |
Genes affected by auxin and decapitation in moss gametophores |
|
| Relations |
| BioSample |
SAMN23167203 |
| SRA |
SRX13140780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5690882_samcount_CUT_T24_2.txt.gz |
260.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
