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Sample GSM6782561

Query DataSets for GSM6782561

Status

Public on Dec 04, 2022

Title

long read RNA-seq from astrocyte (ENCLB486CFV)

Sample type

SRA

Source name

Homo sapiens male adult (53 years) astrocyte in vitro differentiated cells

Organism

Homo sapiens

Characteristics

cell_type: astrocyte
biomaterial_type: in vitro differentiated cells
description: PGP1 derived astrocytes
biosample encode accession: ENCBS100HNS (SAMN19596564)
Sex: male
dev stage: adult
age: 53 year
donor_id: ENCDO336AAA
lab: Bradley Bernstein, Broad
source: George Church
link: ENCBS100HNS at ENCODE; https://www.encodeproject.org/ENCBS100HNS/
link: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

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

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Sequel II

Description

https://www.encodeproject.org/experiments/ENCSR071IHY/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_207, ENC4_208 - PGP1 derived astrocytes
experiment encode accession: ENCSR071IHY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB486CFV
spikeins used: 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., Ambion mix 1 spike-ins

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)

GSE219423

long read RNA-seq from astrocyte (ENCSR071IHY)

Relations

BioSample

SAMN19596564

SRA

SRX18485421

Supplementary file	Size	Download	File type/resource
GSM6782561_ENCFF103YEV_transcriptome_annotations_GRCh38.gtf.gz	45.2 Mb	(ftp)(http)	GTF
GSM6782561_ENCFF674WSE_transcript_quantifications_GRCh38.tsv.gz	1.4 Mb	(ftp)(http)	TSV
GSM6782561_ENCLB486CFV_README.txt.gz	537 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file