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Sample GSM3496050

Query DataSets for GSM3496050

Status

Public on Dec 14, 2018

Title

Rhizophore2

Sample type

SRA

Source name

Rhizophore2

Organism

Selaginella moellendorffii

Characteristics

tissue: Rhizophore

Treatment protocol

No treatment. For growth characterizations, a root was defined as a 10-20 day-old ventral angle meristem outgrowth that was 5-10cm in length, as measured from the distal-most tip to the main shoot axis, and displayed a well-developed root cap and root hairs. A rhizophore was defined as a 4-7 day-old ventral angle meristem outgrowth 2.5-3.5cm in length that lacked all of the following features: a root cap, root hairs, green pigmentation, and mature or presumptive microphylls.

Growth protocol

Y-shaped cuttings of mature stems that included existing points of angle meristem outgrowths were applied to soil for general propagation. Explants were kept in high humidity (80%) and in a 16h ambient light/8h dark cycle.

Extracted molecule

total RNA

Extraction protocol

For each sample, 40 excised tissues were pooled in 20µL of RLT Buffer (Qiagen RNeasy Micro Kit), flash frozen, and ground using methods described previously (Sena et al., 2009). RNA yields and quality were assessed by a Bioanalyzer 2100 (RNA Picochip).
Illumina libraries for two biological repeats of each tissue were generated using the Nugen Ovation Amp V2 DR kit, with modifications made for multiplexing.
Pooled libraries were sequenced using Illumina HiSeq 2500 to generate 50bp single-end reads.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

A rhizophore was defined as a 4-7 day-old ventral angle meristem outgrowth 2.5-3.5cm in length that lacked all of the following features: a root cap, root hairs, green pigmentation, and mature or presumptive microphylls.
processed data file: Table_S2.xlsx
processed data file: Table_S3.xlsx

Data processing

Reads were aligned to the Selaginella moellendorffii v1.0 genome (including the full genome, i.e. both haplotypes) using bowtie2 (bowtie2 --local).
Gene models were obtained from Phytozome and 2,719 new ORFs were included from a list of 4,763 additional gene models from a recent transcriptomic characterization in Selagenella (Zhu et al., 2017), which were filtered for duplicates and gene fragments.
Gene read counts were obtained using ngsutils (bamutil count -library unstranded -multiple partial).
EdgeR was used to normalize the libraries using the trimmed mean method.
Genome_build: Selaginella moellendorffii v1.0
Supplementary_files_format_and_content: Table_S2.xlsx: Excel spreadsheet of raw counts.
Supplementary_files_format_and_content: Table_S2.xlsx: Excel spreadsheet of normalized counts.

Submission date

Nov 29, 2018

Last update date

Dec 14, 2018

Contact name

Kenneth David Birnbaum

E-mail(s)

ken.birnbaum@nyu.edu

Phone

212-998-8257

Organization name

New York University