|
| Status |
Public on Feb 28, 2020 |
| Title |
pigeon_scale_HL_HH21_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
limb bud
|
| Organism |
Columba livia |
| Characteristics |
developmental stage: HH21
limb type: HL
phenotype: scale
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pairs of forelimb (FL) and hindlimb (HL) buds were dissected from scaled, grouse and muff pigeon embryos or chicken embryos at HH21 (embryonic day E3.5), HH25 (E4.5), and HH29 (E6) and stored in RNAlater (ThermoFisher Scientific) at -80°C. Total RNA was extracted from FL and HL bud samples using the RNeasy Mini Kit with RNase-Free DNAse Set and a TissueLyser LT (Qiagen).
RNA-sequencing libraries were prepared and sequenced by the High-Throughput Genomics and Bioinformatic Analysis Shared Resource at the University of Utah. RNA sample quality was assessed using the RNA ScreenTape Assay (Agilent) and a sequencing library was prepared using the TruSeq Stranded mRNA Sample Prep Kit with oligo(dT) selection (Illumina). 125-cycle paired-end sequencing was performed on an Illumina HiSeq 2500 instrument (12 libraries/lane).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing read quality was assessed with FastQC.
Illumina adapters were trimmed with STAR.
Reads were aligned to the pigeon Cliv_2.1 reference assembly or chicken Gallus_gallus-5.0 genome assembly with STAR using the 2-pass mode.
Mapped reads were assigned to genes using FeatureCounts.
Principal component and differential expression analyses were performed with the R package DESeq2.
Genome_build: Cliv_2.1
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: Tab-delimited text (.txt) files include read count files (FeatureCounts output) for each sample.
Supplementary_files_format_and_content: Comma-separated value (.csv) files include differential expression results (DESeq2 output) for each phenotypic comparison at each developmental stage.
|
| |
|
| Submission date |
Mar 04, 2019 |
| Last update date |
Feb 28, 2020 |
| Contact name |
Elena Boer |
| E-mail(s) |
boer@biology.utah.edu
|
| Phone |
8015816812
|
| Organization name |
University of Utah
|
| Department |
School of Biological Sciences
|
| Lab |
Shapiro Lab
|
| Street address |
257 S 1400 E
|
| City |
SLC |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL22642 |
| Series (1) |
| GSE127775 |
Shifts in pigeon limb identity reveal conserved genetic networks |
|
| Relations |
| BioSample |
SAMN11049953 |
