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Status |
Public on Mar 11, 2024 |
Title |
ESC, long read, heavy polyribosome (5+ 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: heavy polyribosome (5+ 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_Heavy_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 |
SAMN37686541 |
SRA |
SRX21992007 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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