|
| Status |
Public on Aug 01, 2018 |
| Title |
run182.SB-Saline_L006 |
| Sample type |
SRA |
| |
|
| Source name |
cranial headfolds_saline
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Special black
developmental stage: Hamburger-Hamilton stage 8-9
tissue: cranial headfolds
|
| Biomaterial provider |
Fertile chicken eggs (Gallus gallus) from the commercial layer line Special Black were obtained from Sunnyside Egg Farm (Beaver Dam, WI).
|
| Treatment protocol |
0.43 mmol USP grade ethanol or isotonic saline
|
| Growth protocol |
Embryos were incubated (3-4 somites, 27 hr incubation)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a RNAqueous-4PCR Kit (Ambion/Applied Biosystems, Carlsbad, CA)
cDNA libraries were constructed using the Illumina RNA Sequencing Sample Preparation kit. mRNA was purified from approximately 8 µg total purified RNA with poly-T oligo-attached magnetic beads. Double-stranded cDNA was synthesized using SuperScript II (Invitrogen, Carlsbad, CA) with random hexamer priming, purified with QIAquick PCR purification columns (Qiagen, Valencia, CA), ligated to Illumina adapters, and size-selected using electrophoresis to approximately 300bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
neural fold-stage embryos
ALL_RUN-182-183.SB_ETOH_SALINE_EXONS-DEXSeq_unstranded-B.counts.txt
Saline_NoIndex_L006
|
| Data processing |
Illumina’s Genome Analyzer Pipeline Software v1.8 was used to transform the primary imaging output into fastq files containing sequences of nucleic acids associated with quality scores
Bowtie2 was used for alignment to the reference genome
featureCounts tool under subread package was used for exon level counts (parameters used: -f, -B, -s 0)
DEXSeq was used for generation of normalized abundances and statistics
Genome_build: Gallus gallus 5.0
Supplementary_files_format_and_content: The processed data file is in CSV or txt format with raw counts (ALL_RUN*txt) or all normalized read counts for each sample included, log2 fold changes, BH-output from DEXSeq (DAVID*csv).
|
| |
|
| Submission date |
Jun 05, 2018 |
| Last update date |
Aug 01, 2018 |
| Contact name |
Abrar E Al-Shaer |
| E-mail(s) |
abrar@email.unc.edu
|
| Organization name |
University of North Carolina Chapel Hill
|
| Department |
Nutrition
|
| Lab |
Saame Raza Shaikh
|
| Street address |
135 Dauer Dr
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL13797 |
| Series (1) |
| GSE115383 |
Exon Level Machine Learning Analyses Elucidate Novel Candidate miRNA Targets in an Avian Model of Fetal Alcohol Spectrum Disorder |
|
| Relations |
| BioSample |
SAMN09372346 |
| SRA |
SRX4170590 |
