|
| Status |
Public on May 24, 2022 |
| Title |
lin-52 WT rep3 |
| Sample type |
SRA |
| |
|
| Source name |
late embryo
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/genotype: lin-52(bn139[lin-52::GFP::3xFLAG])
developmental stage: late embryo
tissue: whole body
|
| Growth protocol |
Synchronized lin-52(WT) or lin-52(3A) L1s were grown in standard S-basal media liquid culture for 72 hours at 20°C and fed HB101 bacteria. Adult worms were treated with standard bleaching solution to collect embryos, and embryos were incubated at 20°C for up to 3.5 hours then frozen in TRIzol reagent (ThermoFisher) using liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted after three freeze/thaw cycles following TRIzol manufacturer instructions and purified by isopropanol precipitation.
A total of 1 µg of RNA was used for RNA-seq library preparation. Poly(A) transcripts were enriched using the NEBNext Poly(A) mRNA Magentic Isolation Module and prepped for sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Samples were multiplexed using the NEBNext Multiplex Oligos for Illumina Dual Index Primers Set. Libraries were sequenced on an Illumina HiSeq X system by Novogene Corporation Inc. (Davis, CA) to acquire 150-bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequence reads were trimmed using fastp.
Transcriptome was mapped to version WBcel235 using STAR.
Reads counts per transcript were obtained using HTSeq.
Differentially expressed genes were assessed using DESeq2.
Assembly: WBcel235
Supplementary files format and content: *_htseq.txt: Tab-delimited text files include reads counts for genes in each replicate as determined by htseq-count.
|
| |
|
| Submission date |
Mar 23, 2022 |
| Last update date |
May 24, 2022 |
| Contact name |
Paul Donald Goetsch |
| E-mail(s) |
[email protected]
|
| Phone |
906487179
|
| Organization name |
Michigan Technological University
|
| Department |
Biological Sciences
|
| Street address |
1400 Townsend Drive
|
| City |
Houghton |
| State/province |
MI |
| ZIP/Postal code |
49931 |
| Country |
USA |
| |
|
| Platform ID |
GPL25147 |
| Series (1) |
| GSE199287 |
DREAM Interrupted: Severing LIN-35-MuvB association in Caenorhabditis elegans impairs DREAM function but not its chromatin localization |
|
| Relations |
| BioSample |
SAMN26900436 |
| SRA |
SRX14591244 |
