|
| Status |
Public on Sep 07, 2024 |
| Title |
RSeT media Rep1, ASO-Ctr |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: ASO-Ctr
cell line: H9
cell type: Human embryonic stem cells
|
| Treatment protocol |
Cells were transfected with 25 nM ASOs using 4ul Lipofectamine Stem Transfection Reagent (Thermo Fisher Scientific) per 6-well, following manual instruction. 0.7 uM Trans-ISRIB (Sigma # 5095840001) and 5 uM Emricasan (Sigma # SML2227) together with 10 uM ROCK inhibitor Y-27632 (Stemgent) were added to improve transfection efficiency and cell survival ability (Chen et al. 2021), and removed 24 hour later. Transfected cells were collected directly without sorting for downstream analysis 48 hours post transfection.
|
| Growth protocol |
H9 hES cells were cultured in RSeT media (STEM CELL) following manual instruction. Upon transfection performed, cells were cultured in RSeT supplemented with 10 nM DZNep and 5nM TSA until 48 hours later cells are collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the RNeasy mini kit (QIAGEN), according to the manufacturer’s instructions.
80-130ng equal volume RNA each sample was used to prepare sequencing library. The cDNA library was prepared with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB # E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB # E7760L), following the manual instruction. Library cDNA were equally pooled at 10 nM for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RSeT+DT_H9,hL1KD-raw_counts,rmDup.txt
RSeT+DT_H9,hL1KD-log2Nom_counts,cutoff=0.2_BatchCo.txt
RSeT+DT_H9,ASO_sO-L1intORF,DEG_cutoff=0.2.txt
|
| Data processing |
RNA-seq reads were quality-checked and trimmed using Trim Galore! v0.4.0
The the trimmed reads were aligned to the hg19 with TopHat2 v2.0.13, which generated bam. files
FeatureCounts function from the subread package (v1.5.0) was applied to count reads of each gene to generate the raw counts table.
Assembly: hg19
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Juan Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
LTRI
|
| Street address |
25 Orde Street, Room 6-1001 MRS
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 3H7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE232931 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-Seq_RSeT+DT_H9_L1KD] |
| GSE232939 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs |
|
| Relations |
| BioSample |
SAMN35217975 |
| SRA |
SRX20440674 |
