|
| Status |
Public on Sep 16, 2020 |
| Title |
ES WT |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cell (ESC)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic stem cell (ESC)
strain: C57BL/6
genotype: wild type
|
| Growth protocol |
ESCs were routinely cultured in ES medium. EB cells were cultured in ES medium without LIF and then cultured in N2B27 medium supplemented with 10ng/ml bFGF for additional 5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were directly lysed using Trizol (ThermoFisher Scientific), treated with DNase (QIAGEN) and purified using RNeasy Minielute Cleanup Kit (QIAGEN). Ribosomal RNA was removed from each RNA extraction using NEBNext rRNA depletion kit (NEB).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
496-3
|
| Data processing |
Basecalls performed using Illumina's bcl2fastq version 2.18.0.12
FASTQ files were aligned with STAR version 2.5.2b with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Cufflinks version 2.2.1 was used on the STAR BAM files with parameters --library-type fr-firststrand -G -L
rMATS version 3.2.5 was used on the STAR BAM files with parameters -b1 -b2 -gtf -t paired -len 74 -novelSS1
Genome_build: GRCm38 p4 Release M11
Supplementary_files_format_and_content: Tab-delimited Excel file containing FPKM values for each sample
|
| |
|
| Submission date |
May 20, 2019 |
| Last update date |
Sep 16, 2020 |
| Contact name |
Pran K Datta |
| E-mail(s) |
prandatta@uabmc.edu
|
| Phone |
2059756039
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Medicine
|
| Lab |
WTI 530
|
| Street address |
1824 6th Ave South, WTI 520C
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE131471 |
Next generation sequencing facilitates quantitative analysis of STRAP-dependent alternative splicing events |
| GSE131474 |
STRAP-dependent alternative splicing events; STRAP-RNA interactions in mouse early embryo and lineage-committed cells. |
|
| Relations |
| BioSample |
SAMN11784072 |
| SRA |
SRX5865861 |
