|
| Status |
Public on Jul 25, 2024 |
| Title |
biol rep 2 YA Hermaphrodite him-5(e1490) strain of Caenorhabditis elegans exposed to OP50 for 6 hours |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole animal
genotype: him-5(e1490)
treatment: exposed to OP50 for 6 hours
|
| Treatment protocol |
YA animals were sex separated inot hermaphrodites and males and were exposed to OP50/PA14 for 6 hours.
|
| Growth protocol |
animals were grown at lab temperature (22C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Worms pellet were collected in 500 µL of Trizol and flash frozen in liquid nitrogen and stored at -80oC until further processing. Total RNA was prepared from the frozen worm pellets following the instructions for the TRIzol LS (Invitrogen) protocol. After the isopropanol precipitation step, the RNA was re-suspended in the extraction buffer of the RNA isolation kit (PicoPure, Arcturus), and further isolation was carried out in accordance with the manufacturer's instructions.
RNA libraries for RNA seq were prepared using a bulk version of the MARS-Seq procedure was employed. Briefly, reverse transcription was used to barcode and pool 18 ng of input RNA from each sample. The pooled samples underwent second strand synthesis after Agencourt Ampure XP beads cleanup (Beckman Coulter), and they were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and then converted into final library by tagging the samples with Illumina sequences during ligation, RT, and PCR
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
OP50F2
|
| Data processing |
Raw next-generation sequencing (NGS) data in the FASTQ format were analyzed using user-friendly transcriptome analysis pipeline (UTAP).
Briefly, reads were trimmed using “cutadapt” and mapped to the C. elegans reference genome WBcel235 using STAR v2.4.2a.
UMI counting was done using HTSeq-count after marking duplicates in union mode. Differential gene expression analysis and normalization of the counts was performed using DESeq2 using the rld (log2 normalized) gene expression values on OP50-PA14 exposed basis within sexes.
Assembly: C. elegans reference genome WBcel235
Supplementary files format and content: Tab-delimited file include raw counts for each sample
Supplementary files format and content: Tab-delimited file include processed counts for each sample
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| |
|
| Submission date |
Jul 25, 2024 |
| Last update date |
Jul 25, 2024 |
| Contact name |
Rizwanul Haque |
| E-mail(s) |
rizwanul.haque@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Brain Sciences
|
| Lab |
Meital Oren-Suissa lab
|
| Street address |
Herzl St 234, Rehovot
|
| City |
Rehovot |
| State/province |
Israel |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE273091 |
Modulation by NPYR underlies experience-dependent, sexually dimorphic learning |
|
| Relations |
| BioSample |
SAMN42814175 |
| SRA |
SRX25468157 |
