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| Status |
Public on Apr 11, 2019 |
| Title |
mrg-1_rep2 |
| Sample type |
SRA |
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| Source name |
XA6227
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| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L1 larvae
strain: XA6227
genotype: mrg-1 -/-
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| Growth protocol |
worms were expanded by hand picking to select worms carrying the balancer for mrg-1 mutants. 2000-4000 (depending on the replica) non rollers of F1 gravid adults, homozygous for mrg-1 mutation, were hand-picked and hypochlorite treated to collect embryos. For control N2, an equivalent number of gravid adults were washed off from plates and hypochlorite treated. Eggs were let hatch in M9 for 18 hrs and then refed for 2 hrs and 30 min
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| Extracted molecule |
total RNA |
| Extraction protocol |
L1s were lysed in XB buffer from ARCTURUS® PicoPure® RNA Isolation Kit (Thermo Fisher), incubated 30 min at 42°C and snap-frozen in liquid nitrogen. After freeze cracking of the samples by 6 subsequent transfers from liquid nitrogen to 42°C, samples were let vigorously shake 10 min at RT and 10 min at 42°C. Next, RNA was extracted following the manufacturer’s instructions, including an on column DNAse digestion
NGS libraries were prepared from 2 ng of input RNA, using the Total RNA-Seq NuGen Ovation v2 kit in combination with the Illumina TruSeq DNA Nano kit, according to manufacturer’s guides
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The RNA-seq data were mapped to the c.elegans genome (ce10) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons belonging to a particular gene (WormBase, WS220). The command used to create the count table was qCount(proj,exons) which does not consider the strand of the reads (unstranded protocol). To compensate for differences in the read depths of the various libraries, each library was normalized to a total of 24.8M reads which represents the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce10
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| Submission date |
Jun 19, 2018 |
| Last update date |
Apr 11, 2019 |
| Contact name |
Dimos Gaidatzis |
| E-mail(s) |
[email protected]
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| Organization name |
Friedrich Miescher Institute
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL18245 |
| Series (2) |
| GSE115998 |
Gene expression changes in mrg-1 mutant L1 larvae compared to wild type. |
| GSE116037 |
Active chromatin marks, H3K36me and MRG-1, drive spatial sequestration of heterochromatin |
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| Relations |
| BioSample |
SAMN09454572 |
| SRA |
SRX4237746 |
| 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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