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| Status |
Public on Sep 12, 2019 |
| Title |
WT_B |
| Sample type |
SRA |
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| Source name |
C. elegans fluorescent BAG cells
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: FQ424
genotype: wzIs113[Pgcy-9::GFP]
developmental stage: embryonic
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| Growth protocol |
Embryonic cell cultures were prepared as previously described (Christensen et al., 2002, Zhang et al., 2002) from wild-type and pmk-3(wz31) mutant animals expressing the BAG-specific and pmk-3 independent marker wzIs113[Pgcy-9::GFP].In brief, embryos were isolated from synchronized populations of hypochlorite treated hermaphrodites, and dissociated into single cells by chitinase treatment. Cells were resuspended in L-15 medium supplemented with 10% FBS (Sigma) and antibiotics, and passed through a 5 um syringe filter (Millipore). Cells were plated onto poly-D-lysine coated single-well chambered cover glasses (Lab-Tek II) and incubated overnight at 25degC.
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| Extracted molecule |
total RNA |
| Extraction protocol |
GFP-labeled BAG neurons were isolated approximately 24 hours after dissociation using Fluorescence Activated Cell Sorting (FACS); sorted cells were confirmed to be >90% GFP positive by direct inspection on a fluorescent microscope. Non-fluorescent, ‘non-BAG’, cells were also collected. Dead cells were marked with propidium-iodide and excluded from sorted cells. Sorting was performed on a FACSAria Ilu SORP cell sorter using a 70 um nozzle. Cells were sorted directly into RNA Extraction Buffer (10,000 cells/100 uL buffer), and RNA was purified using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher). RNA integrity and concentration were evaluated using an Agilent Bioanalyzer. RNA samples had an RNA Integrity score of at least 8, indicating that all samples were of high quality.
cDNA libraries were prepared from RNA (1-2 ng) using the Ovation RNA-Seq System V2 (NuGEN), multiplexed, and sequenced as 100 base pair paired end reads using the HiSeq 2500 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
wild type BAG cells replicate 2
WT-B
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| Data processing |
fastq files were aligned to the Caenorhabditis elegans genome and transcriptome (Wormbase WS243) using the STAR software package (Dobin et al., 2013).
Gene expression quantification was performed on the resulting BAM files using HTSeq (Anders et al., 2014)
Differential expression analysis was done using the DeSeq2 software package (Love et al., 2014) in R.
Tiled-data files (TDF) were generated from the genomic alignments (BAM files) using Integrative Genomics Viewer (Thorvaldsdottir et al., 2013) and used to generate read coverage histograms.
Genome_build: version 243 of the Caenorhabditis elegans reference genome from Wormbase, WS243
Supplementary_files_format_and_content: comma-separated file of the normalized read counts in the different cell populations sequenced; TDF files for the different cell-populations sequenced.
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| Submission date |
Sep 11, 2019 |
| Last update date |
Sep 12, 2019 |
| Contact name |
Lauren Bayer Horowitz |
| E-mail(s) |
lauren.bayerhorowitz@nyumc.org
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| Phone |
2122630830
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| Organization name |
NYU School of Medicine
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| Department |
Cell Biology
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| Lab |
Ringstad
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| Street address |
540 1st Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE137267 |
Repression of an activity-dependent autocrine insulin signal is required for sensory neuron development in C. elegans |
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| Relations |
| BioSample |
SAMN12727742 |
| SRA |
SRX6830816 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4074165_WT-B.dd.bam.tdf |
12.3 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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