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Sample GSM6782683

Query DataSets for GSM6782683

Status

Public on Dec 04, 2022

Title

long read RNA-seq from endodermal cell (ENCLB446WHN)

Sample type

SRA

Source name

Homo sapiens male embryo endodermal in vitro differentiated cells

Organism

Homo sapiens

Characteristics

cell_type: endodermal cell
biomaterial_type: in vitro differentiated cells
description: LRGASP_H1_endo-1
biosample encode accession: ENCBS464AKI (SAMN22785838)
Sex: male
dev stage: embryonic
age: not collected
donor_id: ENCDO000AAW
lab: Barbara Wold, Caltech
source: René Maehr
health state: healthy
link: ENCBS464AKI at ENCODE; https://www.encodeproject.org/ENCBS464AKI/
link: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

Extracted molecule

total RNA

Extraction protocol

general protocol: https://www.encodeproject.org/documents/81af563b-5134-4f78-9bc4-41cb42cc6a48/@@download/attachment/ENCODE%20Long%20Read%20RNA-Seq%20Analysis%20Pipeline%20v3%20%28Human%29.pdf, general protocol: https://www.encodeproject.org/documents/3baa46d2-cb88-4608-8877-70596d200489/@@download/attachment/ENCODE_longread_wetlab_protocolv3.pdf, general protocol: https://www.encodeproject.org/documents/e909542d-44c0-4bee-9aac-4d41a0b768db/@@download/attachment/ENCODE_Protocol_Spikeins_capping_v1.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Sequel II

Description

https://www.encodeproject.org/experiments/ENCSR127HKN/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP H1 definitive endoderm
experiment encode accession: ENCSR127HKN
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-10-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB446WHN
spikeins used: Ambion mix 1 spike-ins, Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Dec 02, 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

GPL28352

Series (1)

GSE219487

long read RNA-seq from endodermal cell (ENCSR127HKN)

Relations

BioSample

SAMN22785838

SRA

SRX18485543

Supplementary file	Size	Download	File type/resource
GSM6782683_ENCFF640HEE_transcript_quantifications_GRCh38.tsv.gz	3.3 Mb	(ftp)(http)	TSV
GSM6782683_ENCFF643RMM_transcriptome_annotations_GRCh38.gtf.gz	66.8 Mb	(ftp)(http)	GTF
GSM6782683_ENCLB446WHN_README.txt.gz	542 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file