|
| Status |
Public on Jul 02, 2018 |
| Title |
2012-07-26_Bud |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryos
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: Bud
strain: TL/AB
|
| Treatment protocol |
Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen
|
| Growth protocol |
~100 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol. Genomic DNA was removed by DNase treatment. Two rounds of PolyA+-RNA purification were performed for each sample.
Strand-specific libraries for 76-bp paired-end sequencing were prepared according to a modified UTP-method (Parkhomchuk et al. 2009), as detailed by Levin et al. (2010).
Libraries were sequenced on the Illumina HiSeq 2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Strand-specific libraries for 76-bp paired-end sequencing
|
| Data processing |
Aligned using Tophat2, with supplied transcript junctions from Ensembl 72
Timecourse quantified with Cufflinks on Ensembl 72 transcripts
Genome_build: danRer7/Zv9
Supplementary_files_format_and_content: genes.fpkm_tracking from cufflinks for gene expression quantification at loci level (FPKM)
|
| |
|
| Submission date |
Jul 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Guo-Liang Chew |
| E-mail(s) |
chew@fas.harvard.edu
|
| Organization name |
Harvard University
|
| Department |
Dept of Molecular and Cellular Biology
|
| Lab |
Schier
|
| Street address |
16 Divinity Ave BL 1019
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE70549 |
RNA-Seq matched to ribosome profiling over a zebrafish developmental timecourse |
|
| Relations |
| BioSample |
SAMN03840624 |
| SRA |
SRX1081754 |
