|
| Status |
Public on Jun 26, 2024 |
| Title |
XL_St11_5_NPB_WT_RNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
animal pole explant
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: animal pole explant
cell line: Stage 11.5
cell type: neural plate border
genotype: wild type
treatment: Wnt8a +Chordin mRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from animal pole explants using trizol and LiCl was used to precipitate RNA.
Ultra™ II Directional RNA Library Prep Kit for Illumina was used to generate libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
NPB_11_5_counts.txt
NPB_11_5_TPMs.txt
|
| Data processing |
fastq files were trimmed using fastp. Rsem/botwie2 was used to generate TPMs ( --estimate-rspd \ --append-names\ --output-genome-bam\ --forward-prob 0)
Read counts were genrated using STAR (--outSAMstrandField intronMotif --outSAMtype BAM \ SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.03 \ --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3) and Htseq (-r pos -f bam -s reverse -m union)
DeSeq was used to determine differential expression from read counts (design = ~ Replicate + Treatment; lowly expressed genes (TPM <3) were filtered out)
Assembly: Xenopus Laevis 9.2
Supplementary files format and content: DESeq output in txt format
Supplementary files format and content: TPM data with each column being a different replicate in txt format
|
| |
|
| Submission date |
Jan 04, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Carole LaBonne |
| Organization name |
Northwestern University
|
| Department |
Molecular Biosciences
|
| Street address |
2220 Campus Drive
|
| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60208 |
| Country |
USA |
| |
|
| Platform ID |
GPL21248 |
| Series (2) |
| GSE252573 |
SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [RNA-seq] |
| GSE252617 |
SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression |
|
| Relations |
| BioSample |
SAMN39263035 |
| SRA |
SRX23103269 |
