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| Status |
Public on Dec 13, 2023 |
| Title |
Female naïve hESCs (H9) with XIST KO (C18) R9 |
| Sample type |
SRA |
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| Source name |
H9
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: naive hESCs
library strategy: RNA-seq
genotype: XIST KO
origin: This study
culture condition: Hypoxia
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| Treatment protocol |
Cells were washed with 1xPBS and dissociated with accutase for 5 minutes at 37C. Afterwards cells were resuspended in MEF media and span down at 1000 rpm for 5 minutes. Cell pallet was washed once with PBS+0.04% BSA and after 5 minute spin cell pallet was resuspended in Trizol reagent (Life Technologies #15596018) for RNA isolation
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| Growth protocol |
All cells except HNES lines were cultured in 5iLAF naïve ESC medium (1:1 mixture of DMEM/F12 and Neurobasal supplemented with N2, B27, penicillin/streptomycin, nonessential amino acids, GlutaMAX, 0.5% KSR, 0.1mM β-mercaptoethanol, 50ug/ml bovine serum albumin, 20ng/ml rhLIF, 20ng/ml Activin A, 8ng/ml FGF2, 1uM MEK inhibitor PD0325901 0.5uM B-Raf inhibitor SB590885, 1uM GSK3-β inhibitor IM-12, 1uM Src inhibitor WH-4-023, and 10uM ROCK inhibitor Y-27632) and were cultured either in 5% CO2, 5% O2 (Hypoxia) at 37C or in 5% CO2 and atmospheric oxygen level (Normoxia) at 37C. HNES1 and HNES3 were cultured in naive ESC medium consisting of (1:1 mixture of DMEM/F12 and Neurobasal supplemented with N2, B27, penicillin/streptomycin, nonessential amino acids, GlutaMAX, 0.5% KSR, 0.1mM β-mercaptoethanol, 50ug/ml bovine serum albumin, 20ng/ml rhLIF, 2uM XAV939, 2uM Go6983, 1uM MEK inhibitor PD0325901, and 10uM ROCK inhibitor Y-27632) and were cultured in 5% CO2, 5% O2 at 37C)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using Qiagen RNAeasy kit (#74104) according to manufacturer’s instructions
Libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina 20020594) according to manufacturer’s instructions. Library quality was assessed by TapeStation (Agilent) and subsequently quantified using the Qubit dsDNA High-Sensitivity Kit (Life Technologies)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
5iLAF-cultured, derived from primed hESCs at passage 47, p19 in 5iLAF, replicate 1
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| Data processing |
Trim: RNA sequencing reads were trimmed using trim_galore (v0.4.1) with default parameters
Align: HISAT2 (v2.2.0) with default parameters was used to align RNA reads
Filter: Samtools (v1.9) was used to remove reads with mapping quality less than 30
Counts: HTSeq (v.0.6.1p1) with the following parameters “--format=bam --order=pos --stranded=reverse--minaqual=0 --type=exon --mode=union –idattr=gene_name" was used to calculate read counts overlapping with genes
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Aug 22, 2023 |
| Last update date |
Dec 13, 2023 |
| Contact name |
Kathrin Plath |
| Organization name |
UCLA
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| Street address |
BOX 951737, 36-133 CHS
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1737 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE241438 |
XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [RNA-seq] |
| GSE241444 |
XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells |
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| Relations |
| BioSample |
SAMN37115403 |
| SRA |
SRX21456157 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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