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| Status |
Public on Apr 29, 2024 |
| Title |
SEA06_emb_RNA_rep2 |
| Sample type |
SRA |
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| Source name |
whole worms
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worms
cell type: embryo
genotype: SEA06 (EM08 - rex-1 deletion ; 3X Backcross)
treatment: rex-1 depletion
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| Treatment protocol |
Auxin treatment: synchronized L2/L3s were washed three times with M9 and split into two aliquots. Half of the worms were transferred to NGM plates containing 1mM of indole-3-acetic-acid (Fisher 87-51-4) prepared as in (Zhang et al., 2015). The other half were placed in normal NGM plates (no-auxin control) for the indicated time. Worms were then washed one time with M9 and processed accordingly to future application. For ChIP and Hi-C, L2/L3 worms were incubated in 2% formaldehyde for 30 minutes, followed by quenching with glycine, one wash with M9 and two washes with PBS, PMSF and protease inhibitors. For RNA-seq, worms were stored in Trizol.
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| Growth protocol |
Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Total RNA was purified following Trizol manufacturer’s instructions after freeze-cracking samples five times. RNA was cleaned up using Qiagen RNeasy MinElute Cleanup kit. mRNAs were purified using Sera-Mag Oligo (dT) beads (Thermo Scientific) from 10 µg of total RNA. cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212, cDNA synthesis was performed in the presence of dUTP in order to prepare stranded mRNA-seq libraries.
RNA-seq: cDNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalls were performed using CASAVA version 1.8.
RNA-seq:We aligned reads to the WS220 genome version using HISAT2 version 2.2.1 (Kim et al., 2019) using the parameter --rna-strandness R. Count data was calculated using HTSeq version 0.13.5 (Anders et al., 2015). The raw counts were normalized FPKM using cufflinks version 2.2.1 (Roberts et al., 2011), and then FPKM was converted to TPM. The raw counts were used for the R package DESeq2 version 1.30.0 (Love et al., 2014).
Assembly: WS220
Supplementary files format and content: RNA-seq: normalized counts (TPM and FPKM) for individual replicates. Log2fold change values generated using DEseq2
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| Submission date |
Apr 26, 2024 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Sevinc Ercan |
| E-mail(s) |
se71@nyu.edu
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| Phone |
2129929518
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| Organization name |
New York University
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| Department |
Biology
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| Lab |
Ercan
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| Street address |
31 Washington Place
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| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platform ID |
GPL19757 |
| Series (1) |
| GSE265989 |
mRNA-seq analysis of rex-1 deletion in C. elegans |
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| Relations |
| BioSample |
SAMN41096942 |
| SRA |
SRX24381194 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8239087_SEA06_emb_RNA_rep2.fastq.gz_genes.fpkm_TPM.tab.gz |
456.9 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
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