GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM6783635

Query DataSets for GSM6783635

Status

Public on Dec 04, 2022

Title

long read RNA-seq from HepG2 (ENCLB663CCA)

Sample type

SRA

Source name

Homo sapiens HepG2 cell line

Organism

Homo sapiens

Characteristics

line: HepG2
biomaterial_type: cell line
description: HepG2
biosample encode accession: ENCBS402MPB (SAMN31998116)
organism: Homo sapiens
Sex: male
health state: hepatocellular carcinoma
dev stage: child
age: 15 year
donor_id: ENCDO000AAC
lab: Ali Mortazavi, UCI
source: ATCC
link: ENCBS402MPB at ENCODE; https://www.encodeproject.org/ENCBS402MPB/
link: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

Extracted molecule

total RNA

Extraction protocol

general protocol: https://www.encodeproject.org/documents/b88f13ac-80e5-4216-bf6b-1dc1624d37b0/@@download/attachment/Direct-RNA_Wet-Lab_DCC%20v1.0.pdf, general protocol: https://www.encodeproject.org/documents/cc4b4215-9e3b-4229-ad26-af31ed502f5c/@@download/attachment/Direct-RNA_Computational-Analysis%20v1.0.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

MinION

Description

https://www.encodeproject.org/experiments/ENCSR724HQB/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT dRNA of HepG2
experiment encode accession: ENCSR724HQB
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-03-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB663CCA
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Dec 03, 2022

Last update date

Dec 06, 2022

Contact name

ENCODE DCC

E-mail(s)

encode-help@lists.stanford.edu

Organization name

ENCODE DCC

Street address

300 Pasteur Dr

City

Stanford

State/province

ZIP/Postal code

94305-5120

Country

USA

Platform ID

GPL24106

Series (1)

GSE220018

long read RNA-seq from HepG2 (ENCSR724HQB)

Relations

BioSample

SAMN31998116

SRA

SRX18486489

Supplementary file	Size	Download	File type/resource
GSM6783635_ENCFF382WAU_transcriptome_annotations_GRCh38.gtf.gz	57.9 Mb	(ftp)(http)	GTF
GSM6783635_ENCFF859LEL_transcript_quantifications_GRCh38.tsv.gz	2.4 Mb	(ftp)(http)	TSV
GSM6783635_ENCLB663CCA_README.txt.gz	548 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file