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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 01, 2016 |
| Title |
H20_4H_1 |
| Sample type |
SRA |
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| Source name |
Control replicate 1
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| Organism |
Medicago truncatula |
| Characteristics |
tissue: Root Hairs
age: 5 days
genotype: wild type A17
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| Treatment protocol |
Nod Factors 4h and 20h
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| Growth protocol |
in vitro culture: Media Fahraeus
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| Extracted molecule |
total RNA |
| Extraction protocol |
100 Root Hairs (Qiagen_RNeasy.pdf)
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA (TruSeq_RNA_SamplePrep_v2_Guide_15026495_C.pdf); RNA- Seq in Paired-end, sizing 260 (polyA selection)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
HiSeq2000 multiplex
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| Data processing |
Mapping with Bowtie2 version 2.0 with option –local against transcripts
count by gene: count only consistent paired-end reads
Genome_build: Medicago Transcripts, one transcript by gene : 50899 genes
Supplementary_files_format_and_content: Gene ID, Length of Gene, nb single reads, nb PE reads
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| Submission date |
Apr 15, 2015 |
| Last update date |
May 15, 2019 |
| 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 |
GPL17491 |
| Series (1) |
| GSE67921 |
Transcriptomic response to Nod Factor treatments on Medicago |
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| Relations |
| BioSample |
SAMN03486443 |
| SRA |
SRX996334 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1658543_samcount_H20_4H_1.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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