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Sample GSM2072423

Query DataSets for GSM2072423

Status

Public on Mar 18, 2016

Title

polyA mRNA RNA-seq from endothelial cell of umbilical vein (ENCLB555AVK)

Sample type

SRA

Source name

Homo sapiens endothelial of umbilical vein primary cell male newborn

Organism

Homo sapiens

Characteristics

cell_type: endothelial cell of umbilical vein
biomaterial_type: primary cell
description: umbilical vein endothelial cells
biosample encode accession: ENCBS529ENC (SAMN04284426)
age: unknown
donor_id: ENCDO341AAA
dev stage: newborn
Sex: male
health state: unknown
lab: Thomas Gingeras, CSHL
link: ENCBS529ENC at ENCODE; https://www.encodeproject.org/ENCBS529ENC/
link: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/
link: ENCODE dbxrefs HUVEC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HUVEC
link: Lonza sample source; http://www.lonza.com/products-services/bio-research/primary-and-stem-cells/human-cells-and-media/endothelial-cells-and-media/huvec-human-umbilical-vein-endothelial-cells.aspx

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/fb66948b-8b40-4c13-8542-bd527137ad80/@@download/attachment/LID8464.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

Description

https://www.encodeproject.org/experiments/ENCSR000COZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human HUVEC whole cell long polyA+ RNA
experiment encode accession: ENCSR000COZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVK
size range: >200
spikeins used: /references/ENCSR402QNO/

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Feb 25, 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

GPL10999

Series (1)

GSE78588

polyA mRNA RNA-seq from endothelial cell of umbilical vein (ENCSR000COZ)

Relations

SRA

SRX1603459

BioSample

SAMN04284426

Named Annotation

GSM2072423_ENCFF890BTZ_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2072423_ENCFF723FTP_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2072423_ENCFF189BUI_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2072423_ENCFF563FKQ_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2072423_ENCFF170QMM_minus_strand_signal_of_unique_reads_hg19.bigWig	140.8 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF189BUI_minus_strand_signal_of_unique_reads_GRCh38.bigWig	149.0 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF209NMC_minus_strand_signal_of_unique_reads_hg19.bigWig	148.4 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF278MHA_plus_strand_signal_of_unique_reads_hg19.bigWig	152.5 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF322QPX_minus_strand_signal_of_all_reads_hg19.bigWig	154.4 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF530HNB_gene_quantifications_hg19.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2072423_ENCFF560ZLH_plus_strand_signal_of_all_reads_hg19.bigWig	157.4 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF563FKQ_minus_strand_signal_of_all_reads_GRCh38.bigWig	164.1 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF650CVW_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2072423_ENCFF690JZR_minus_strand_signal_of_all_reads_hg19.bigWig	162.8 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF723FTP_plus_strand_signal_of_unique_reads_GRCh38.bigWig	152.6 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF860IST_plus_strand_signal_of_all_reads_hg19.bigWig	165.8 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF867URU_transcript_quantifications_hg19.tsv.gz	7.8 Mb	(ftp)(http)	TSV
GSM2072423_ENCFF873DKO_plus_strand_signal_of_unique_reads_hg19.bigWig	144.8 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCFF887FYR_transcript_quantifications_GRCh38.tsv.gz	7.8 Mb	(ftp)(http)	TSV
GSM2072423_ENCFF890BTZ_plus_strand_signal_of_all_reads_GRCh38.bigWig	166.9 Mb	(ftp)(http)	BIGWIG
GSM2072423_ENCLB555AVK_README.txt.gz	2.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record