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Sample GSM2400232 Query DataSets for GSM2400232
Status Public on Dec 07, 2016
Title polyA mRNA RNA-seq from B cell (ENCLB555APR)
Sample type SRA
 
Source name Homo sapiens B primary cell female adult (43 years)
Organism Homo sapiens
Characteristics cell_type: B cell
biomaterial_type: primary cell
description: CD20+ B cells, caucasian, draw number 1
biosample encode accession: ENCBS483ENC (SAMN06044617)
dev stage: adult
Sex: female
donor_id: ENCDO114AAA
age: 43 year
health state: normal
passage number: 2
lab: John Stamatoyannopoulos, UW
link: ENCBS483ENC at ENCODE; https://www.encodeproject.org/ENCBS483ENC/
link: Derived from ENCODE donor ENCDO114AAA; https://www.encodeproject.org/ENCDO114AAA/
link: cell isolation protocol; https://www.encodeproject.org/documents/8f459e88-6344-434f-8f9f-6375a9ff1880/@@download/attachment/CD20%2B_Stam_protocol.pdf
link: ENCODE dbxrefs CD20+_RO01778; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CD20+_RO01778
link: ENCODE dbxrefs CD20+; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=CD20+
link: Sample source; http://depts.washington.edu/medgen/faculty/Rajinder_Kaul.shtml
Extracted molecule total RNA
Extraction protocol extraction method: see document
general protocol: https://www.encodeproject.org/documents/8f00d99f-26c6-4c37-af3d-787432fa467b/@@download/attachment/LID44499.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description https://www.encodeproject.org/experiments/ENCSR000CTV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent isolates of CD20+ B cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTV
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APR
size range: >200
spikeins used: /references/ENCSR402QNO/
Data processing See GSM*_README.txt supplementary file linked below
 
Submission date Nov 22, 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 CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL10999
Series (1)
GSE90268 polyA mRNA RNA-seq from B cell (ENCSR000CTV)
Relations
BioSample SAMN06044617
SRA SRX2370548
Named Annotation GSM2400232_ENCFF302QNI_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2400232_ENCFF903XZF_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2400232_ENCFF844YRB_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2400232_ENCFF819VCB_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2400232_ENCFF111CWV_minus_strand_signal_of_unique_reads_hg19.bigWig 137.3 Mb (ftp)(http) BIGWIG
GSM2400232_ENCFF230HGP_minus_strand_signal_of_all_reads_hg19.bigWig 151.1 Mb (ftp)(http) BIGWIG
GSM2400232_ENCFF231GYC_gene_quantifications_GRCh38.tsv.gz 2.6 Mb (ftp)(http) TSV
GSM2400232_ENCFF302QNI_plus_strand_signal_of_unique_reads_GRCh38.bigWig 143.0 Mb (ftp)(http) BIGWIG
GSM2400232_ENCFF308ZJB_plus_strand_signal_of_all_reads_hg19.bigWig 155.3 Mb (ftp)(http) BIGWIG
GSM2400232_ENCFF410IPV_transcript_quantifications_hg19.tsv.gz 7.7 Mb (ftp)(http) TSV
GSM2400232_ENCFF422SXS_gene_quantifications_hg19.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM2400232_ENCFF541AEO_transcript_quantifications_GRCh38.tsv.gz 7.8 Mb (ftp)(http) TSV
GSM2400232_ENCFF819VCB_minus_strand_signal_of_all_reads_GRCh38.bigWig 152.5 Mb (ftp)(http) BIGWIG
GSM2400232_ENCFF844YRB_minus_strand_signal_of_unique_reads_GRCh38.bigWig 138.1 Mb (ftp)(http) BIGWIG
GSM2400232_ENCFF903XZF_plus_strand_signal_of_all_reads_GRCh38.bigWig 156.9 Mb (ftp)(http) BIGWIG
GSM2400232_ENCFF955JCA_plus_strand_signal_of_unique_reads_hg19.bigWig 142.4 Mb (ftp)(http) BIGWIG
GSM2400232_ENCLB555APR_README.txt.gz 1.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record
Processed data provided as supplementary file

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