|
| Status |
Public on Jun 26, 2013 |
| Title |
Vector 1 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
4T1 vector transduced
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Control
strain: BALB/cfC3H
cell line: 4T1
|
| Growth protocol |
Vector control and Wnt5a expressing 4T1 cells were grown to 70% confluency under conditions recommended by ATCC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
CASAVA version 1.8.0 was used to convert the *.bcl files to *.fastq files.
TopHat version 2.0.0 was used to align the *.fastq files to the UCSC mm9 reference genome using the default settings and parameter -r 150.
Cufflinks version 1.3.0 was used with default settings to calculate transcript abundances from the TopHat alignment files (*.bam) and also calculate differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited *.txt file of the isoform transcript list containing columns for nearest reference ID, gene name, locus, status and FPKM value which were derived from the Cufflinks suite of tools, Cuffdiff.
|
| |
|
| Submission date |
Oct 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Rosa Serra |
| E-mail(s) |
rserra@uab.edu
|
| Phone |
205-934-0842
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Cell Biology
|
| Lab |
Serra
|
| Street address |
1918 University Blvd. 660 MCLM
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294-0005 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE41792 |
Differential expression in Wn5a and vector transduced 4T1 cells. [RNA-Seq] |
| GSE41793 |
Differential expression in Wn5a and vector transduced 4T1 cells. |
|
| Relations |
| SRA |
SRX200683 |
| BioSample |
SAMN01779644 |
