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Sample GSM2344225

Query DataSets for GSM2344225

Status

Public on Nov 08, 2016

Title

total RNA-seq from upper lobe of left lung (ENCLB692XZA)

Sample type

SRA

Source name

Homo sapiens upper lobe of left lung tissue male adult (54 years)

Organism

Homo sapiens

Characteristics

tissue_type: upper lobe of left lung
biomaterial_type: tissue
description: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS271JIM (SAMN05897040)
age: 54 year
dev stage: adult
donor_id: ENCDO451RUA
Sex: male
lab: Thomas Gingeras, CSHL
link: ENCBS271JIM at ENCODE; https://www.encodeproject.org/ENCBS271JIM/
link: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/d921255f-4038-4d8e-b5b9-180fb3270361/@@download/attachment/296291.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR839ZDH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's lung tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR839ZDH
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB692XZA
size range: >200
spikeins used: /references/ENCSR156CIL/

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Oct 13, 2016

Last update date

May 15, 2019

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

GPL16791

Series (1)

GSE88579

total RNA-seq from upper lobe of left lung (ENCSR839ZDH)

Relations

BioSample

SAMN05897040

SRA

SRX2244624

Named Annotation

GSM2344225_ENCFF404VBN_minus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2344225_ENCFF365YIZ_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344225_ENCFF116QMF_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344225_ENCFF570ZJA_plus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2344225_ENCFF016AUE_minus_strand_signal_of_unique_reads_hg19.bigWig	51.7 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF059RIW_plus_strand_signal_of_unique_reads_hg19.bigWig	53.6 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF116QMF_minus_strand_signal_of_unique_reads_GRCh38.bigWig	52.0 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF249QYL_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2344225_ENCFF324ESX_transcript_quantifications_GRCh38.tsv.gz	7.6 Mb	(ftp)(http)	TSV
GSM2344225_ENCFF345UZD_plus_strand_signal_of_all_reads_hg19.bigWig	58.4 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF365YIZ_plus_strand_signal_of_unique_reads_GRCh38.bigWig	53.8 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF404VBN_minus_strand_signal_of_all_reads_GRCh38.bigWig	57.5 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF570ZJA_plus_strand_signal_of_all_reads_GRCh38.bigWig	59.1 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF595DKP_minus_strand_signal_of_all_reads_hg19.bigWig	56.9 Mb	(ftp)(http)	BIGWIG
GSM2344225_ENCFF678UAV_transcript_quantifications_hg19.tsv.gz	7.5 Mb	(ftp)(http)	TSV
GSM2344225_ENCFF808NEL_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2344225_ENCLB692XZA_README.txt.gz	1.1 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file