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 GSM6782473
Query DataSets for GSM6782473
Status
Public on Dec 04, 2022
Title
long read RNA-seq from HL-60 (ENCLB045HKM)
Sample type
SRA
Source name
Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours
Organism
Homo sapiens
Characteristics
line: HL-60
biomaterial_type: cell line
description: HL-60 derived M0 macrophages
biosample encode accession: ENCBS848YJL (SAMN31998630)
organism: Homo sapiens
Sex: female
health state: acute promyelocytic leukemia
dev stage: adult
age: 36 year
donor_id: ENCDO000AAM
lab: Ali Mortazavi, UCI
source: ATCC
treatments: treatment_term_id: CHEBI:37537; treatment_term_name: phorbol 13-acetate 12-myristate; treatment_type: chemical; duration: 120; duration_units: hour;
link: ENCBS848YJL at ENCODE;
https://www.encodeproject.org/ENCBS848YJL/
link: Derived from ENCODE donor ENCDO000AAM;
https://www.encodeproject.org/ENCDO000AAM/
Extracted molecule
total RNA
Extraction protocol
general protocol:
https://www.encodeproject.org/documents/6d583a1d-d692-4511-b13b-c051822d861c/@@download/attachment/ENCODE%20Long%20Read%20RNA-Seq%20Analysis%20Pipeline%20v3.2%20%28Human%29.pdf,
general protocol:
https://www.encodeproject.org/documents/3baa46d2-cb88-4608-8877-70596d200489/@@download/attachment/ENCODE_longread_wetlab_protocolv3.pdf
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Sequel II
Description
https://www.encodeproject.org/experiments/ENCSR546DFO/
***************
biological replicate number: 1
technical replicate number: 1
description: HL-60 derived M0 macrophages
experiment encode accession: ENCSR546DFO
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB045HKM
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Dec 02, 2022
Last update date
Dec 06, 2022
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
GPL28352
Series (1)
GSE219379
long read RNA-seq from HL-60 (ENCSR546DFO)
Relations
BioSample
SAMN31998630
SRA
SRX18485333
Supplementary file
Size
Download
File type/resource
GSM6782473_ENCFF090EAM_transcriptome_annotations_GRCh38.gtf.gz
69.9 Mb
(ftp)
(http)
GTF
GSM6782473_ENCFF566QZV_transcript_quantifications_GRCh38.tsv.gz
5.6 Mb
(ftp)
(http)
TSV
GSM6782473_ENCLB045HKM_README.txt.gz
539 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
|
