|
| Status |
Public on Dec 07, 2016 |
| Title |
polyA mRNA RNA-seq from CD14-positive monocyte (ENCLB555AWY) |
| Sample type |
SRA |
| |
|
| Source name |
Homo sapiens CD14-positive monocyte primary cell female
|
| Organism |
Homo sapiens |
| Characteristics |
cell_type: CD14-positive monocyte
biomaterial_type: primary cell
description: Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis
biosample encode accession: ENCBS626ENC (SAMN06044634)
dev stage: unknown
Sex: female
donor_id: ENCDO265AAA
age: unknown
health state: unknown
lab: Thomas Gingeras, CSHL
link: ENCBS626ENC at ENCODE; https://www.encodeproject.org/ENCBS626ENC/
link: Derived from ENCODE donor ENCDO265AAA; https://www.encodeproject.org/ENCDO265AAA/
link: ENCODE dbxrefs Monocytes-CD14+_RO01746; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Monocytes-CD14+_RO01746
link: Heimfeld sample source; http://labs.fhcrc.org/heimfeld/contact.html
|
| Extracted molecule |
total RNA |
| Extraction protocol |
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7870b6db-c081-4c62-9090-380640bd60f1/@@download/attachment/LID44497.pdf
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
https://www.encodeproject.org/experiments/ENCSR000CUC/
***************
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 mobilized CD14+ monocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUC
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWY
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) |
| GSE90272 |
polyA mRNA RNA-seq from CD14-positive monocyte (ENCSR000CUC) |
|
| Relations |
| BioSample |
SAMN06044634 |
| SRA |
SRX2370556 |
| Named Annotation |
GSM2400240_ENCFF724GUM_minus_strand_signal_of_all_reads_GRCh38.bigWig |
| Named Annotation |
GSM2400240_ENCFF676HVY_plus_strand_signal_of_unique_reads_GRCh38.bigWig |
| Named Annotation |
GSM2400240_ENCFF336UAC_minus_strand_signal_of_unique_reads_GRCh38.bigWig |
| Named Annotation |
GSM2400240_ENCFF902LWD_plus_strand_signal_of_all_reads_GRCh38.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2400240_ENCFF005IVU_plus_strand_signal_of_unique_reads_hg19.bigWig |
100.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCFF256KUG_minus_strand_signal_of_all_reads_hg19.bigWig |
104.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCFF336UAC_minus_strand_signal_of_unique_reads_GRCh38.bigWig |
96.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCFF397DFK_gene_quantifications_GRCh38.tsv.gz |
2.6 Mb |
(ftp)(http) |
TSV |
| GSM2400240_ENCFF400ACO_minus_strand_signal_of_unique_reads_hg19.bigWig |
95.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCFF669GZO_gene_quantifications_hg19.tsv.gz |
2.4 Mb |
(ftp)(http) |
TSV |
| GSM2400240_ENCFF676HVY_plus_strand_signal_of_unique_reads_GRCh38.bigWig |
100.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCFF697ZVB_transcript_quantifications_hg19.tsv.gz |
7.5 Mb |
(ftp)(http) |
TSV |
| GSM2400240_ENCFF724GUM_minus_strand_signal_of_all_reads_GRCh38.bigWig |
105.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCFF780XKG_transcript_quantifications_GRCh38.tsv.gz |
7.6 Mb |
(ftp)(http) |
TSV |
| GSM2400240_ENCFF790QBJ_plus_strand_signal_of_all_reads_hg19.bigWig |
108.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCFF902LWD_plus_strand_signal_of_all_reads_GRCh38.bigWig |
109.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM2400240_ENCLB555AWY_README.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
