|
| Status |
Public on Dec 04, 2022 |
| Title |
long read RNA-seq from HL-60 (ENCLB605OTC) |
| Sample type |
SRA |
| |
|
| Source name |
Homo sapiens HL-60 cell line treated with 10 uM phorbol 13-acetate 12-myristate for 120 hours, 10 ng/mL interleukin-13 for 12 hours, 10 ng/mL interleukin-4 for 12 hours
|
| Organism |
Homo sapiens |
| Characteristics |
line: HL-60
biomaterial_type: cell line
description: HL-60 derived M2A macrophages (12hr)
biosample encode accession: ENCBS756IEB (SAMN31998516)
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; treatment_term_id: UniProtKB:P35225; treatment_term_name: interleukin-13; treatment_type: protein; duration: 12; duration_units: hour; treatment_term_id: UniProtKB:P05112; treatment_term_name: interleukin-4; treatment_type: protein; duration: 12; duration_units: hour;
link: ENCBS756IEB at ENCODE; https://www.encodeproject.org/ENCBS756IEB/
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/ENCSR278ZPI/
***************
biological replicate number: 2
technical replicate number: 1
description: HL-60 derived M2A macrophages (12hr)
experiment encode accession: ENCSR278ZPI
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB605OTC
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., 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 03, 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) |
| GSE219989 |
long read RNA-seq from HL-60 (ENCSR278ZPI) |
|
| Relations |
| BioSample |
SAMN31998516 |
| SRA |
SRX18486434 |
