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| Status |
Public on Feb 15, 2019 |
| Title |
RNA-hESC-Ctl replicate 3 |
| Sample type |
SRA |
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| Source name |
Cell Line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Embryonic Stem cell
cell line: H9
genotype/variation: wildtype
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| Treatment protocol |
Neuronal maturation assay was performed using STEMdiff™ neuron differentiation kit (STEMCELL Technologies, #08500) and STEMdiff™ neuron maturation kit (STEMCELL Technologies, #08510). ES cells were seeded onto AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs). On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation started from day 11 to day 16. On day 17, cells were treated with Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium till days 22–24. RNA samples were collected on days 10, 11, and 22 for deep-sequencing analysis. Cells were also seeded onto multi-chamber slides for immunofluorescence (IF) analysis.
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| Growth protocol |
H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies, #85850) at 37°C and 5% CO2. To induce neural lineage, cells were plated in PSC neural induction medium (Life Technologies) at 15–25% confluency, with medium changed every other day. On day 7, cells were harvested or expanded for further analyses.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified with the GeneJET RNA purification kit (ThermoFisher Scientific, K0732). The cDNA was reverse transcribed from 300 ng of RNA, using SuperScript IV reverse transcriptase (ThermoFisher Scientific, #18090050) with random hexamers. RT reactions were performed in triplicate to minimize variability.
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (v24) (Harrow et al., 2012).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: raw reads count by HTSEQ
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| Submission date |
Dec 14, 2017 |
| Last update date |
Feb 17, 2019 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
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| Organization name |
St Jude Children's Research Hosipital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE108115 |
UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [RNA-seq] |
| GSE108116 |
UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells |
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| Relations |
| BioSample |
SAMN08178693 |
| SRA |
SRX3472358 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2890253_counts.RNA-hESC-Ctl-Rep3.txt.gz |
125.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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