|
| Status |
Public on Jul 05, 2022 |
| Title |
141329_WT |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Immortalized pancreatic fibroblasts
strain: Mixed
genotype: WT
|
| Growth protocol |
Fibroblasts were grown to confluence in three independent 6-well tissue culture wells per experimental group in DMEM (Invitrogen, Gibco) + 10% Calf Serum + 1% Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in Qiagen Buffer RLT and RNA was isolated using a Qiagen RNeasy plus Mini Kit (Catalog # 74134). Samples were treated with DNase I (Qiagen 79254) to remove any contaminating DNA. 9 micrograms of RNA was then submitted to generate RNA libraries.
RNA libraries were prepared for sequencing using Poly-A NEB ultra 2 kit from 250ng input and 13 cycles PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced on a NovaSeq 150-PairedEnd s4 flowcell, RecipeVersion 1.6.0, RtaVersion 3.4.4.
STAR 2.7.2b was used to align reads with the following parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax .04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
featureCounts from the Bioconductor Rsubread package was used to count features from gencode.vM23.annotation.gtf.
Linear models calculated using standard limma pipeline and the voom technique.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: RawCounts_matrix.txt: Tab-delimited text file with 3 columns of annotation followed by 6 columns of counts, 1 for each sample.
Supplementary_files_format_and_content: Voom_LogCPM.txt: Tab-delimited text file with 3 columns of annotation followed by 6 columns of logcpm values from limma's voom, 1 for each sample.
|
| |
|
| Submission date |
Oct 12, 2021 |
| Last update date |
Jul 05, 2022 |
| Contact name |
Michael Kemper Scales |
| Organization name |
University of Michigan
|
| Department |
Cell and Developmental Biology
|
| Street address |
109 Zina Pitcher Place
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE185748 |
Combinatorial Gli activity directs immune infiltration and tumor growth in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN22228192 |
| SRA |
SRX12579838 |
