|
| Status |
Public on Jul 23, 2021 |
| Title |
MEL_4day_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MEL cells
|
| Organism |
Mus musculus |
| Characteristics |
time: 4 days
|
| Growth protocol |
MEL cells were grown under standard conditions in minimal essential medium (MEM) and supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1x antibiotic antimycotic (Invitrogen). MEL cells in suspension culture at the log phase of growth at a density of 2 x 105/ml were supplemented with 2% DMSO (Sigma) to induce differentiation, and cells were collected at various time points for further analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol Reagent per the manufacturer's protocol
TruSeq Stranded mRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapters were trimmed with cutadapt -f fastq -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG -e 0.06 -O 6 -m 14 -
Reads were mapped with tophat --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --no-coverage-search -p 4 -o
HTSeq was used to create read counts from the aligned BAM files
Genome_build: mm10
Supplementary_files_format_and_content: Read counts are presented in tab-delimited format (*mRNA_read_counts.txt) with transcript ID in the first column and the number of reads in the second column; variance stabilize transformed values are calculated by DESeq2 and found in allDays_VSTvalues.txt
|
| |
|
| Submission date |
Apr 09, 2020 |
| Last update date |
Jul 24, 2021 |
| Contact name |
Mengge Shan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennylsvania
|
| Department |
Biology
|
| Lab |
Brian Gregory
|
| Street address |
433 South University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE148421 |
Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes Identifies Dynamic Changes During Mammalian Erythropoiesis (mRNA) |
|
| Relations |
| BioSample |
SAMN14569708 |
| SRA |
SRX8092707 |
