|
| Status |
Public on Jun 30, 2019 |
| Title |
Alligator early stage forelimb D2 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
forelimb digit2
|
| Organism |
Alligator mississippiensis |
| Characteristics |
developmental stage: st. 18
tissue: forelimb digit2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
RNA libraries for alligator and mouse were prepared for sequencing using standard illumina protocols. Anolis RNA libraries were prepared using Clontech's Ultra Low V4 kit (Catalog # 634890).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Am_FL_E_D2_Rep1
processed data file:
am_HTSeq_upload.txt
|
| Data processing |
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: alligator (allMis0.2), Anolis (AnoCar2.0), and mouse (GRCm38)
Supplementary_files_format_and_content: tab-delimited txt files include read counts for each sample. Gene IDs for Anolis and Mouse are from Ensembl while alligator gene IDs are available at: http://crocgenome.hpc.msstate.edu
|
| |
|
| Submission date |
Dec 20, 2017 |
| Last update date |
Jun 30, 2019 |
| Contact name |
Cong Liang |
| E-mail(s) |
cong.liang@yale.edu
|
| Organization name |
Yale University
|
| Street address |
300 Heffernan Dr.
|
| City |
West Haven |
| ZIP/Postal code |
06516 |
| Country |
USA |
| |
|
| Platform ID |
GPL24412 |
| Series (1) |
| GSE108337 |
Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings |
|
| Relations |
| BioSample |
SAMN08213295 |
| SRA |
SRX3489457 |
