|
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 |