|
| Status |
Public on Nov 02, 2023 |
| Title |
Xenopus laevis egg extract, input, time 0, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
egg extract
|
| Organism |
Xenopus laevis |
| Characteristics |
cell type: egg extract
treatment: input
time: time 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol-based RNA extraction followed by isopropanol precipitation and RNA Clean & Concentrator kit (Zymo)
The RiboCop rRNA depletion Kit was used to deplete ribosomal RNA, followed by the PrepX RNA-Seq protocol (stranded - firststrand) to prepare the libraries according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
input_rep2
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to X. laevis v10.1 using STAR
Count normalization and differential expression analysis was performed with DESeq2
Assembly: X. laevis v10.1
Supplementary files format and content: rawCounts_allsamples.txt tab-delimited text file with raw counts for each sample
Supplementary files format and content: DESeq2.counts_normalized.txt tab-delimited text file with normalised DESeq2 counts for each sample
|
| |
|
| Submission date |
May 16, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Martin H Wühr |
| Phone |
609-258-7653
|
| Organization name |
Princeton Univeristy
|
| Department |
Lewis-Sigler Institute for Integrative Genomics
|
| Lab |
Wühr lab
|
| Street address |
246 Carl Icahn Laboratory
|
| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08544 |
| Country |
USA |
| |
|
| Platform ID |
GPL28901 |
| Series (1) |
| GSE232651 |
Eukaryotic cytoplasm is widely structured via mesoscale condensates |
|
| Relations |
| BioSample |
SAMN35120066 |
| SRA |
SRX20378634 |
