|
| Status |
Public on May 10, 2016 |
| Title |
KP22-empty_1 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
KP22-empty
|
| Organism |
Mus musculus |
| Characteristics |
cell line: KP22
cell type: tumor-derived cell line
genotype/variation: Trp53-/-;Rb1-/-
nfib expression level (background): Nfib low
genotype/variation: expressing empty vector
|
| Growth protocol |
All murine and human SCLC cell lines used in this study grow as floating spheres and were cultured in RPMI with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNAeasy mini kit
Illumina TruSeq v2 kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cell line containing expression vector with no gene
processed data file: refseqmm10.exons_unique_start_end.st.merge.bed, cell_mod.refseqmm10.exons_unique_start_end.st.merge.counts, gene_expression_cqnnorm_deseq.csv
|
| Data processing |
Reads were aligned to the genome using TopHat
Exons were found from RefSeq genes, and exons with the same start and end locations were merged.
The number of reads overlapping each merged exon was found using bedtools multicov (-q30). This count was summed for exons all mapping to a particular gene.
Counts were normalized for length and GC bias using cqnnorm (Hansen et al. 2012). The sum of all reads within exons was used for the size factors. The length of all exons per gene was summed to get the length covariate, and the GC covariate was the average GC content within exons annotated per gene.
Differential expressiond was found using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: refseqmm10.exons_unique_start_end.st.merge.bed gives start and end of merged exons per gene (mm10)
Supplementary_files_format_and_content: cell_mod.refseqmm10.exons_unique_start_end.st.merge.counts gives the number of reads intersecting each of the exons given by the bed file above.
Supplementary_files_format_and_content: *deseq_results.csv gives the output from deseq2. Columns appended by '.5' (or '1') assess signficance of abs value of log2fold change being greater than 0.5 (or 1)
|
| |
|
| Submission date |
May 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
William Greenleaf |
| E-mail(s) |
wjg@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
279 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE81257 |
Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility [RNA-seq] |
| GSE81258 |
Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility |
|
| Relations |
| BioSample |
SAMN04965916 |
| SRA |
SRX1753587 |
