|
| Status |
Public on Aug 28, 2023 |
| Title |
Nanog control, replicate 1, bulk RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
midbrain
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: midbrain
age: HH7/HH8-
cell type: neural crest
genotype: WT
treatment: control MO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library preparation was performed by Genewiz/Azenta following the protocol for ultra-low input samples. The libraries were then pooled and sequenced on a HiSeq 2500 sequencer (Illumina) on 150x150 paired end mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Nanog.C.1
|
| Data processing |
Basecalls performed using Illumina’s RTA 2.0.12
Sequenced reads were mapped to GRCg6a chicken genome using STAR v2.7.2a in single-pass mode
Gene counts were generated with STAR v2.7.2a built-in counting option --quantMode GeneCounts against a custom GRCg6a genome annotation GTF which included select ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRC6a.98
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.
|
| |
|
| Submission date |
May 12, 2023 |
| Last update date |
Aug 28, 2023 |
| Contact name |
Laura Kerosuo-Pahlberg |
| E-mail(s) |
laura.kerosuopahlberg@nih.gov
|
| Organization name |
NIDCR
|
| Street address |
30 Convent Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE232432 |
Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation |
|
| Relations |
| BioSample |
SAMN35061243 |
| SRA |
SRX20308394 |
