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| Status |
Public on Mar 11, 2024 |
| Title |
ESC, long read, light polyribosome (2-4 ribosomes), rep2 |
| Sample type |
SRA |
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| Source name |
H9
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: embryonic stem cell (ESC)
treatment: control
fraction: light polyribosome (2-4 ribosomes)
riborna depletion: poly A+
pcr: 15
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| Extracted molecule |
total RNA |
| Extraction protocol |
R2C2
BIOO qRNA seq v2 Library Preparation Kit -- strand-specific, read1 is antiSense to input RNA
Frac-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| Description |
ESC_Light_2
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| Data processing |
Long read FASTQs: Bonito v0.0.1 (basecalling) and Mandalorion v4.0.0 (high confidence consensus sequence definition and transcriptome assembly)
Long read data analysis: SQANTI3 v5.1.1 (transcriptome QC and filtering) and IsoAnnot Lite v.2.7.3 (transcriptome annotation)
Short read data analysis: STAR v2.7.8a (mapping to the genome and to the transcriptome), Salmon v1.9.0 (alignment to the transcriptome) and tappAS v1.0.7 (differential and functional analyses)
Supplementary files format and content: Supplementary_tables.xlsx, contains: short read and long read library/mapping stats, transcriptome feature annotations and raw counts, differential isoform usage analysis results, alternative splicing analysis results and motif analysis results.
Supplementary files format and content: LR_transcriptome.gtf: de novo transcriptome from the long read libraries, made and filtered with Mandalorion and SQANTI3.
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| Submission date |
Oct 04, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Julie Zikherman |
| E-mail(s) |
[email protected]
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| Organization name |
University of California, San Francisco
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| Department |
Department of Molecular, Cell and Developmental Biology
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| Lab |
Sanford Lab
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| Street address |
513 Parnassus Ave
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE244655 |
Long read subcellular fractionation and sequencing reveals the translational fate of full length mRNA isoforms during neuronal differentiation |
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| Relations |
| BioSample |
SAMN37686539 |
| SRA |
SRX21992009 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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