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Sample GSM7823424

Query DataSets for GSM7823424

Status

Public on Mar 11, 2024

Title

ESC, long read, cytosol, rep1

Sample type

SRA

Source name

Organism

Homo sapiens

Characteristics

cell line: H9
cell type: embryonic stem cell (ESC)
treatment: control
fraction: cytosol
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_Cyto_1

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