 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 25, 2015 |
| Title |
Adrenal_20wkB |
| Sample type |
SRA |
| |
|
| Source name |
Adrenal
|
| Organism |
Homo sapiens |
| Characteristics |
age in weeks: 20.6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fetal tissue samples <100 mg in size were placed into DNase- and RNase-free 1.5 ml microfuge tubes containing 1 ml of RNAlater RNA Stabilization Reagent (Qiagen) within 1 hour of the pregnancy termination procedure. After storage at room temperature for a period of 24-72 h, excess RNAlater was removed from the microfuge tubes and the samples were placed in the -80oC freezer for storage until RNA isolation was performed. The tissues were lysed in mirVana (Life Technologies) lysis buffer, using a Mini-Beadbeater-16 (Biospec), with agitation for 1 min in the presence of 1 mm zirconia beads. Samples were then centrifuged at maximum speed in a tabletop microcentrifuge for 1 min and the lysed solution was transferred to a fresh microfuge tube. The remainder of the extraction was per the manufacturer's protocol for the mirVana kit (Life Technologies).
Following RNA isolation (mirVana miRNA Isolation Kit, Life Technologies, Inc.), the RNA was quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent). 200 ng to 1000 ng was used as input for the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, first both cytoplasmic and mitochondrial rRNA was removed by selectively hybridizing biotinylated probes to target sequences and using magnetic beads to capture the bound products. Following rRNA removal, the RNA was fragmented and copied into first strand cDNA using random primers and reverse transcriptase. Next, second strand cDNA synthesis was completed using DNA Polymerase I and RNase H. The cDNA was then ligated to Illumina supplied adapters and enriched with PCR to create the final cDNA libraries. The libraries were then pooled and sequenced on a HiSeq 2000 (Illumina, Inc.) instrument as per manufacturer’s instructions. Sequencing was performed up to 2 X 101 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw fastq files were processed using TrimGalore version 0.3.7 and cutAdapt version 1.5 to remove adapter sequences and trim poor-quality bases. All default values were used, with the exceptions that the length parameter was set to exclude reads where either mate had a trimmed length of less than 50
Circular and linear junction reads were called using custom scripts available with publication
Genome_build: hg19
Supplementary_files_format_and_content: txt files were generated by custom scripts available with publication; in denovo report files, pvalue represents the p-value from the naïve method (high p-value indicates high confidence in this splice); in other report files, pvalue represents the posterior probability from the GLM method (high posterior probability indicates high confidence)
|
| |
|
| Submission date |
Dec 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Linda Szabo |
| Organization name |
Stanford University
|
| Department |
Biochemistry
|
| Lab |
Salzman Lab
|
| Street address |
Beckman Center, B400 279 W. Campus Dr. MC: 5307
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE64283 |
Tissue-specific circular RNA induction during human fetal development |
|
| Relations |
| BioSample |
SAMN03267762 |
| SRA |
SRX815495 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1567915_Fetal_Adrenal_408_CGATGT_L008_R1_circJuncProbs.txt.gz |
78.3 Kb |
(ftp)(http) |
TXT |
| GSM1567915_Fetal_Adrenal_408_CGATGT_L008_R1_linearJuncProbs.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
| GSM1567915_unaligned_Fetal_Adrenal_408_CGATGT_L008_R1_denovo_report.txt.gz |
8.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
