|
| Status |
Public on Aug 24, 2023 |
| Title |
HH27, rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
HH27 distal wing bud
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: HH27 distal wing bud
cell type: Mesenchyme
genotype: WT
treatment: None
|
| Treatment protocol |
For tissue grafting 150 um strip of distal mesoderm was dissected from HH20 wing buds of GFP transgenic chicken. The epithelim was removed and the mesoderm cut into cubes.
The HH20 mesoderm was then placed in slits between the AER and the underlying mesoderm in the mid-distal region of WT HH24 wing buds and allowed to develop for 24 hours before collection.
|
| Growth protocol |
Eggs were incubated at 37C until the desired stage according to Hamburger Hamilton (HH).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples using Trizol-chloroform extractions.
TrueSeq Stranded Total RNA and Ribo-Zero.
Enzymatic fragmentation by Illumina Elute, Fragment, Prime mix.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw sequencing reads were cleaned by removing reads containing adapter, reads containing poly-N and low quality reads.
Reads were mapped to the reference genome using Hisat2 v2.0.2 with default parameters.
Salmon output was used to quantify the data (number of reads).
Count data for the samples were normalised using trimmed mean of m-value normalisation and transformed with Voom, resulting in log2-counts per million with associated precision weights.
A statistical analysis using an adjusted p-value of <0.05 and fold-chage >2 identified differentially expressed genes.
Gene clusters were identified from the set of differential expressed genes cIValud R package.
Assembly: UCSC Gallus_gallus galGal4
Supplementary files format and content: samplequant.csv are tab-separated files that include name, length, effective length, Transcripts per million (TPM) and estimated number of reads mapping to each transcript (NumReads) of each sample per gene.
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
Aug 24, 2023 |
| Contact name |
Sofia Sedas Perez |
| E-mail(s) |
s.sedas-perez@sheffield.ac.uk
|
| Organization name |
The University of Sheffield
|
| Street address |
Western Bank
|
| City |
Sheffield |
| ZIP/Postal code |
S10 2TN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16133 |
| Series (1) |
| GSE232959 |
RNA sequencing of chicken limb distal mesenchyme to compare gene expression over time and in heterochronic grafted cells. |
|
| Relations |
| BioSample |
SAMN35220705 |
| SRA |
SRX20452843 |
