|
| Status |
Public on Nov 27, 2018 |
| Title |
HH20_HL_WT_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Hindlimb
|
| Organism |
Gallus gallus |
| Characteristics |
breed: White Leghorn
age: HH20
tissues: Whole hindlimb bud
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Micro-dissected limb tissues either from mouse or chick were used for RNA extraction by using the RNeasy Micro Kit (QIAGEN) according to manufacturer instruction.
A total of 100 ng of pure total RNA was amplified following standard Illumina procedure for polyA-selected RNA. Libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on either Illumina HiSeq 2500 or NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
chick HH20 WT whole hindlimb RNA-seq
|
| Data processing |
Demultiplexed RNA-seq reads were mapped onto mm10 genome or galGal5, respectively. Regarding chick distal hindlimb at HH30, the two fastq files derived from phalanges and metatarsals were concatenated and used for analysis.
The RNA-seq data were aligned against respective genomes using Tophat2 (Version 2.0.9)(Kim et al. 2013) and the unique mapped reads were extracted. The number of uniquely mapped reads was calculated using FLAGSTAT (Samtools, Version 0.1.18) (Li et al. 2009) and this value was used for the subsequent normalization of each coverage data to be the million reads number.
All analysis was done by our Galaxy server (the Bioteam Appliance Galaxy Edition; https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: bedgraph of the forward or reverse strand unique read coverage, divided by the number of millions of mapped reads in each sample.
|
| |
|
| Submission date |
Jun 11, 2018 |
| Last update date |
Nov 28, 2018 |
| Contact name |
Nayuta Yakushiji-Kaminatsui |
| E-mail(s) |
nayuta.yakushiji@riken.jp
|
| Phone |
+81 45 503 9690
|
| Organization name |
RIKEN Center for Integrative Medical Sciences
|
| Lab |
Laboratory for Developmental Genetics
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE115559 |
Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [RNA-Seq] |
| GSE115563 |
Similarities and differences in the regulation of HoxD genes during chick and mouse limb development. |
|
| Relations |
| BioSample |
SAMN09390052 |
| SRA |
SRX4191461 |
