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Sample GSM7823429 Query DataSets for GSM7823429
Status Public on Mar 11, 2024
Title ESC, long read, heavy polyribosome (5+ ribosomes), rep2
Sample type SRA
 
Source name H9
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
Extracted molecule total RNA
Extraction protocol R2C2
BIOO qRNA seq v2 Library Preparation Kit -- strand-specific, read1 is antiSense to input RNA
Frac-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model PromethION
 
Description ESC_Heavy_2
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.
 
Submission date Oct 04, 2023
Last update date Mar 11, 2024
Contact name Julie Zikherman
E-mail(s) [email protected]
Organization name University of California, San Francisco
Department Department of Molecular, Cell and Developmental Biology
Lab Sanford Lab
Street address 513 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL26167
Series (1)
GSE244655 Long read subcellular fractionation and sequencing reveals the translational fate of full length mRNA isoforms during neuronal differentiation
Relations
BioSample SAMN37686541
SRA SRX21992007

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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