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| Status |
Public on Oct 22, 2023 |
| Title |
NPC RNA-Seq rep1 |
| Sample type |
SRA |
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| Source name |
kucg-2 hiPSC
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| Organism |
Homo sapiens |
| Characteristics |
cell line: kucg-2 hiPSC
cell type: Human neural progenitor
treatment: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in LiDS/LET buffer (5% LiDS in 20 mM Tris, 100 mM LiCl, 2 mM EDTA, 5 mM DTT, pH7.4, 100 μg/ml Proteinase K). Lysates were incubated at 60°C for 10 minutes, pushed 10 times through a 1-ml syringe with a 26G needle, and mixed by vortexing. Two volumes of cold acid phenol (pH 4.3), 1/10 volume 1-Bromo-3-chloropropane and 50 µg glycogen were added. Samples were mixed vigorously by vortexing, followed by centrifuging at 10,000 g, 4°C. The aqueous phase was transferred to a new tube and the phenol/BCP extraction was repeated. RNA was by the addition of 3 volumes of 100% ethanol and incubation at -20°C for 30 min. Pellets were washed with 80% ethanol, air-dried, and resuspended in RNase-free water.
250 ng of the same total RNA used for mim-tRNAseq library preparation were used for mRNA-Seq library construction with the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, #R3000). Libraries were sequenced on a NextSeq 500 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
3’ adapters were trimmed using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Reads were aligned to the GRCh38 human genome using STAR v2.6.1c with the following parameters: --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode TranscriptomeSAM GeneCounts. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv; transcripts-per-million (TPM) counts per transcript in MANE annotation
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| Submission date |
Mar 22, 2023 |
| Last update date |
Oct 22, 2023 |
| Contact name |
Danny Nedialkova |
| E-mail(s) |
[email protected]
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| Organization name |
Max Planck Institute for Biochemistry
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| Lab |
Mechanisms of Protein Biogenesis
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| Street address |
Am Klopferspitz 18
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| City |
Planegg |
| State/province |
Bayern |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE227925 |
Transfer RNA pools in human cells are controlled by selective gene expression [RNA-seq] |
| GSE227928 |
Selective gene expression maintains human tRNA anticodon pools during differentiation |
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| Relations |
| BioSample |
SAMN33860768 |
| SRA |
SRX19748143 |
| 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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