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| Status |
Public on Jun 21, 2022 |
| Title |
CUT_TO_3 |
| Sample type |
SRA |
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| Source name |
CUT_TO_3
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| Organism |
Physcomitrium patens |
| Characteristics |
genotype: wild type (Gransden strain)
developmental stage: gametophore
tissue: stem
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| Treatment protocol |
decap T0h-decap t0h-decap t0h-decap t0h
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
CUT_TO_3(4ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Nov 15, 2021 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Véronique BRUNAUD |
| E-mail(s) |
[email protected]
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| Organization name |
INRAE - CNRS - UPSUD
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| Lab |
IPS2
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| Street address |
rue Noetzlin
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| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
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| Platform ID |
GPL30955 |
| Series (1) |
| GSE188843 |
Genes affected by auxin and decapitation in moss gametophores |
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| Relations |
| BioSample |
SAMN23167193 |
| SRA |
SRX13140790 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5690892_samcount_CUT_TO_3.txt.gz |
262.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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