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Sample GSM2147643 Query DataSets for GSM2147643
Status Public on May 10, 2016
Title 16T-sh2_1 [RNA-seq]
Sample type SRA
 
Source name 16T-sh2
Organism Mus musculus
Characteristics cell line: 16T
cell type: tumor-derived cell line
genotype/variation: Trp53-/-;Rb1-/-
nfib expression level (background): Nfib high
genotype/variation: expressing shNfib
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 expressing shRNA to Nfib
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 SAMN04965909
SRA SRX1753581

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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