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Sample GSM1290037

Query DataSets for GSM1290037

Status

Public on Jan 23, 2014

Title

C. elegans L1 larvae (sample A, replicate 2)

Sample type

SRA

Source name

poly(A)-extracted mRNA library

Organism

Caenorhabditis elegans

Characteristics

strain: N2
temperature: 20C
developmental stage: L1 larvae

Growth protocol

Gravid adult worms were treated with bleach to isolate embryos Part of the embryos were used for RNA extraction and further analysis, while the remaining embryos were incubated in M9 buffer without food at room temperature for 12h to hatch and arrest at the L1 stage. The starved, synchronized L1 larvae were set out in S-medium (S-Basal supplemented with 3 mM MgCl2, 3 mM CaCl, 10 mM potassium citrate, supplemented with a mix of antibiotics and antimycotics. Worms were fed with the E. coli strain AT713 and cultivated at 20°C. Staging was determined by examining a subset of animals under an inverted microscope at intervals for size determination and vulval development. Animals were collected at the L1, L2, L3, early L4, late L4 and young adult (pre-gravid) stages and washed several times in M9 buffer. Exact times for growth after addition of food to starved L1s for wildtype C. elegans N2 were as follows: L1 larvae were grown for 7h, L2 for 20h, L3 for 29h, early L4 for 41h, late L4 for 52h and young Adults for 57 h. For wild type C. briggsae AF16 the harvesting time points were: 6h for L1, 20h for L2, 28h for L3, 41h for early L4, 53h for late L4 and young adult after 63h. This timeline was repeated once to obtain biological replicate samples, the initial samples are referred to as biological replicate samples A, the samples from the second time course as biological replicate samples B.

Extracted molecule

total RNA

Extraction protocol

All samples were cleaned from bacteria and debris by either several M9 buffer washing steps or sucrose gradient centrifugation, pelleted by centrifugation at 3000 rpm, 3 min, 4°C and stored in TRIzol Reagent, 1 ml per 100 µL worm pellet, at -80°C for RNA and protein isolation.
Poly(A)+ RNA libraries were prepared from total RNA.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

Data processing

Sequencing reads for each sample and stage were seperately mapped to the transcriptome using bwa (version 0.5.7) with default parameters.
Reads were aggregated across all isoforms of a given gene.
Aggregated reads were converted to reads per million mapped reads per kilobase of transcript length (RPKM).
Genome_build: WS190
Supplementary_files_format_and_content: data_rpkm.txt: Tab separated data file listing all genes (rows) and expression data in RPKM for all samples and stages. Column name indicates species (cel: C. elegan; cbr: C. briggsae), stage and sample name, separated by an underscore.

Submission date

Dec 16, 2013

Last update date

May 15, 2019

Contact name

Dominic Grün

E-mail(s)

[email protected]

Phone

+491791073352

Organization name

Max Planck Institute of Immunobiology and Epigenetics