|
| Status |
Public on May 18, 2024 |
| Title |
Transformed_4 |
| Sample type |
SRA |
| |
|
| Source name |
Ba/F3 transformed with U2AF35(S34F)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C3H
cell line: Ba/F3
cell type: Immortalized pro-B cells
genotype/variation: transformed with U2AF35(S34F)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 4 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 HiSeq 2000 |
| |
|
| Description |
SP4_GCCAAT_L007
|
| Data processing |
RNA-seq reads were aligned to the Mus musculus reference genome mm10/GRCm38.p5 (Ensembl GRCm38.89) using STAR (version 2.5.3a) with the following explicit option settings: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10000 --alignMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical
The resulting BAM files were sorted by read names and processed by using MMR (Kahles et al., 2016) to assign multi-mapper reads to their most likely genomic locations.
The BAM files output by MMR were input to featureCounts (version 1.5.3) to generated a gene-level count summary table with the following explicit option settings –d 35 –t exon –M and the GTF file for the reference genome mm10/GCRm38.89 as the genome annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table in a matrix format: column 1 is the GeneID; the others are raw count per gene generated by featureCounts.
|
| |
|
| Submission date |
May 29, 2018 |
| Last update date |
May 18, 2024 |
| Contact name |
Jennifer Benanti |
| E-mail(s) |
Jennifer.Benanti@umassmed.edu
|
| Phone |
5088561773
|
| Organization name |
UMass Medical School
|
| Department |
Molecular, Cell & Cancer Biology
|
| Street address |
364 Plantation St. LRB525
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE115060 |
Identification of functional genetic variants in transformed Ba/F3 cells expressing U2AF35(S34F) |
|
| Relations |
| BioSample |
SAMN09279130 |
| SRA |
SRX4138345 |
