GEO Publications
Handout
NAR 2024 (latest)
NAR 2002 (original)
All publications
FAQ
MIAME
Email GEO
NCBI
>
GEO
>
Accession Display
Not logged in |
Login
GEO help:
Mouse over screen elements for information.
Scope:
Self
Platform
Samples
Series
Family
Format:
HTML
SOFT
MINiML
Amount:
Brief
Quick
GEO accession:
Sample GSM6782812
Query DataSets for GSM6782812
Status
Public on Dec 04, 2022
Title
microRNA-seq from Caco-2 (ENCLB693HZV)
Sample type
SRA
Source name
Homo sapiens Caco-2 cell line
Organism
Homo sapiens
Characteristics
line: Caco-2
biomaterial_type: cell line
biosample encode accession: ENCBS020DQC (SAMN31997689)
organism: Homo sapiens
Sex: male
health state: colorectal adenocarcinoma
dev stage: adult
age: 72 year
donor_id: ENCDO000ACR
lab: Mats Ljungman, UMichigan
source: ATCC
link: ENCBS020DQC at ENCODE;
https://www.encodeproject.org/ENCBS020DQC/
link: Derived from ENCODE donor ENCDO000ACR;
https://www.encodeproject.org/ENCDO000ACR/
Extracted molecule
total RNA
Extraction protocol
general protocol:
https://www.encodeproject.org/documents/49f43842-5ab4-4aa1-a6f4-2b1234955d93/@@download/attachment/Multiplexed%20miRNA%20Sequencing%20Library%20Generation%20Protocol-3.4.pdf
Library strategy
miRNA-Seq
Library source
transcriptomic
Library selection
size fractionation
Instrument model
NextSeq 2000
Description
https://www.encodeproject.org/experiments/ENCSR638OIX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation human Caco-2 cell line microRNA-seq from Mortazavi
experiment encode accession: ENCSR638OIX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2022-02-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB693HZV
size range: <30
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Dec 02, 2022
Last update date
Jan 20, 2023
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
GPL30173
Series (1)
GSE219558
microRNA-seq from Caco-2 (ENCSR638OIX)
Relations
BioSample
SAMN31997689
SRA
SRX18485672
Named Annotation
GSM6782812_ENCFF889ACL_minus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation
GSM6782812_ENCFF711DDS_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation
GSM6782812_ENCFF041CSP_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation
GSM6782812_ENCFF102ZDP_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Supplementary file
Size
Download
File type/resource
GSM6782812_ENCFF041CSP_plus_strand_signal_of_all_reads_GRCh38.bigWig
13.9 Mb
(ftp)
(http)
BIGWIG
GSM6782812_ENCFF102ZDP_minus_strand_signal_of_unique_reads_GRCh38.bigWig
6.2 Mb
(ftp)
(http)
BIGWIG
GSM6782812_ENCFF419EMB_microRNA_quantifications_GRCh38.tsv.gz
9.5 Kb
(ftp)
(http)
TSV
GSM6782812_ENCFF711DDS_plus_strand_signal_of_unique_reads_GRCh38.bigWig
6.2 Mb
(ftp)
(http)
BIGWIG
GSM6782812_ENCFF889ACL_minus_strand_signal_of_all_reads_GRCh38.bigWig
13.4 Mb
(ftp)
(http)
BIGWIG
GSM6782812_ENCLB693HZV_README.txt.gz
661 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
|
NLM
|
NIH
|
GEO Help
|
Disclaimer
|
Accessibility
|
