|
Status |
Public on May 18, 2024 |
Title |
Parental_1 |
Sample type |
SRA |
|
|
Source name |
parental Ba/F3
|
Organism |
Mus musculus |
Characteristics |
strain background: C3H cell line: Ba/F3 cell type: Immortalized pro-B cells genotype/variation: Parental (U2AF35-WT)
|
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 |
SP2_TGACCA_L006
|
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.
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|
|
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 |
SAMN09279133 |
SRA |
SRX4138342 |