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| Status |
Public on Sep 07, 2024 |
| Title |
Naive_HESC_RSeT_1 |
| Sample type |
SRA |
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| Source name |
H9
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: Human embryonic stem cells
treatment: Naive_HESC_RSeT
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| Treatment protocol |
N/A
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| Growth protocol |
H9 hES cells were cultured in mTESR media (STEM CELL) and RSeT media (STEM CELL) following manual instruction for mainting primed and RSeT naive condition, respectively. For RSeT+DT hESCs, cells were cultured in RSeT supplemented with 10 nM DZNep and 5nM TSA until 48 hours later cells are collected.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted from 500K cells fixed in Trizol using the miRNeasy kit (QIAGEN, cat#217084), following the manufacturer instruction. RNA integrity was assessed with the Agilent 2100 Bioanalyzer System (Agilent Technologies).
RNA library preparations were carried out on 500 ng of RNA (RIN > 7) using the Illumina TruSeq Stranded Total RNA Sample preparation kit (Illumina, cat#20020596), according to manufacturer's protocol. The libraries were size-selected using Ampure XP Beads (Beckman Coulter, cat# A63880) and quantified using the KAPA Library Quantification kit - Universal (KAPA Biosystems, cat# KK4828).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Adaptor sequences and low-quality score bases (Phred score < 33) were trimmed using Trimmomatic v.0.39.
The resulting reads were aligned to the GRCh38 genome assembly using STAR v.2.7.8a with Ensembl annotation (v104).
Raw counts of repetitive elements were obtained using the FeatureCounts function from the Subread package (v2.14.2).
Assembly: hg38
Supplementary files format and content: txt
Supplementary files format and content: csv
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| Submission date |
Aug 20, 2024 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Juan Zhang |
| E-mail(s) |
[email protected]
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| Organization name |
LTRI
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| Street address |
25 Orde Street, Room 6-1001 MRS
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 3H7 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE232939 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs |
| GSE275237 |
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-seq_primed,RSeT,RSeT+DT_hESCs] |
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| Relations |
| BioSample |
SAMN43269249 |
| SRA |
SRX25770777 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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