|
| Status |
Public on Jan 31, 2024 |
| Title |
TMRM_RNAseq_Low_1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by the RNeasy mini kit (QIAGEN).
Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760L), NEBNext rRNA Depletion Dit (Human/Mouse/Rat) (NEB, #E6310X), NEBNext Multiplex Oligos for Illumina (NEB, #E6440L) and ERCC RNA Spike-In control Mix (Thermo Fisher Scientific, #4456740).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Low mitochondrial membrane potential (Δ
|
| Data processing |
The cutadapt (https://cutadapt.readthedocs.org/en/stable/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) tools wrapped in Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) were used to trim low quality bases (Q<20) and adapter for raw sequences.
RNA-seq data were mapped to the mm10 (GRCm38) genome of mouse and ERCC reference using Tophat2 (2.1.1)
Duplicated reads for pair-end data were then removed by SAMtools (v1.9)
Annotation of mRNA (GRCm38 v99) was downloaded from Ensembl database. LncRNA annotation was downloaded from NONCODE database and repeat annotation was downloaded from Homer (v4.10). All three annotations were merged into one for gene annotation. Fragment (or template) count for each feature was performed by using featureCounts with parameters “-g 'gene_id' -p -M -O --fraction -C -F GTF -T 64 -s 0”
Fragment counts were transformed to fragments per kilobase of transcript per million (FPKM) by using edgeR
Assembly: mm10 (GRCm38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 10, 2022 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Wentao Yang |
| E-mail(s) |
wentaoy@usc.edu
|
| Organization name |
university of southern california
|
| Street address |
1441 Eastlake Ave
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE210914 |
Quiescence Enables Unrestricted Cell Fate in Naive Embryonic Stem Cells |
| GSE210915 |
Quiescence Enables Unrestricted Cell Fate in Naive Embryonic Stem Cells |
|
| Relations |
| BioSample |
SAMN30237358 |
| SRA |
SRX17020166 |
