|
| Status |
Public on Jul 26, 2022 |
| Title |
E14 mESCs expressing high exogenous levels of Zmynd8 replicate#3 [WRH3c] |
| Sample type |
SRA |
| |
|
| Source name |
E14 mESCs expressing high exogenous levels of Zmynd8
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: E14 Mouse Embryonic Stem Cells (mESCs)
genotype/variation: expressing high exogenous levels of Zmynd8
|
| Treatment protocol |
mESCs were plated in 6-well plates. 24 hours later, ESCs were treated with 5ug/ml of Doxycycline to induce exogenous expression of Zmynd8. 24 hours later, RNA was harvested with Trizol and subsequently treated with TurboDNAse
|
| Growth protocol |
E14 mESCs were maintained in Hyclone KO DMEM supplemented with 15% FBS, 2mM glutamine, 100uM Non-Essential Amino Acids, .1mM 2-mercaptoethanol, and 1000U/ml LIF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. NEB Next® Ultra™ RNA Library Prep Kit was used with 2 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 NovaSeq 6000 |
| |
|
| Description |
WRH3c
|
| Data processing |
Apply FASTP( v0.19.4) to the fastq files of the pair-end reads to perform adapter trimming and bad reads filtering by default parameters
Apply STAR(STAR_2.5.3a) to align the processed FASTQ files on GRCm38 ensembl reference genome and annotation to get SAM files with parameters(intronMotif --sjdbGTFfile --quantMode TranscriptomeSAM)
The SAM files are further converted to BAM files. We did not remove duplicates from the BAM files
Apply featureCounts(v1.6.2) to obtain the counts for each gene by parameters (-T 13 -s 0 -p -g 'gene_id')
BigWig files are generated by bamCoverage(Version 3.1.3) using RPGC method with --binSize 10 --effectiveGenomeSize 2652783500(mm10 GRCm38)
Genome_build: mm10
Supplementary_files_format_and_content: raw count txt file(count.txt)
|
| |
|
| Submission date |
Jul 26, 2019 |
| Last update date |
Jul 26, 2022 |
| Contact name |
Aimin Yan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Massachusetts Medical School
|
| Street address |
55 N Lake Ave
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01655 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE134981 |
Next Generation Sequencing (NGS) Facilitates Quantitative Analysis of Wildtype and Zmynd8-Overexpressing Transcriptomes in E14 Mouse Embryonic Stem Cells (mESCs) |
|
| Relations |
| BioSample |
SAMN12384796 |
| SRA |
SRX6603785 |
