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| Status |
Public on Apr 29, 2022 |
| Title |
wt_Col0_rep3 |
| Sample type |
SRA |
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| Source name |
root meristems
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| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 5 day old
extraction: manually dissected under stereomicroscope
tissue: root meristems
genotype: Col0
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| Treatment protocol |
meristems were manually dissected under the stereomicroscope, prserved with RNAlater and processed using the RNA Qiagen extraction kit
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| Growth protocol |
Seedlings were grown on plates containing 1/2 x MS Media (0.5 x MS Salts, 1% Difco agar, 1% sucrose) at 23ºC for 5 days in long day conditions
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the RNA extraction kit from Qiagen and RNA integrity and concentration were checked using TapeStation and Qubit 2.0 fluorometer (Life Technologies) respectively. After quality control in Novogene company, the best 3 replicates for mutant and wild type were used for library construction and sequencing following the Novogene pipeline.
mRNA is enriched by using oligo dT, fragmented randomly followed by cDNA synthesis using random hexamers and reverse transcriptase. Second strand is synthesized by nick-translation. Library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
map to a reference genome using TopHat2
HTSeq software was used to analyze the gene expression level using the union mode. FPKM value of 0.1 or 1 is set as the threshold to determine whether a gene is expressed or not
The differential gene exprsesion analysis consists on readcount normalization, model-dependent mean value stimation and FDR value estimation based on multiple hypotheses testing. DESeq was used for thtese steps
Genome_build: TAIR10 genome with Araport 11 gene annotation
Supplementary_files_format_and_content: CSV file with counts estimated by HTSeq. These can be imported into R, for example, using the `read.csv()` function and used in the DESeq2 differential expression analysis.
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| Submission date |
Aug 24, 2021 |
| Last update date |
Apr 29, 2022 |
| Contact name |
Yrjö Helariutta |
| E-mail(s) |
[email protected]
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| Organization name |
University of Cambridge
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| Department |
Sainsbury Laboratory
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| Street address |
47 Bateman Street,
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1LR |
| Country |
United Kingdom |
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| Platform ID |
GPL23157 |
| Series (2) |
| GSE182672 |
An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq] |
| GSE182673 |
An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy |
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| Relations |
| BioSample |
SAMN20960039 |
| SRA |
SRX11895997 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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