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GEO accession:
Sample GSM5330800
Query DataSets for GSM5330800
Status
Public on May 23, 2021
Title
long read RNA-seq from Panc1 (ENCLB962HZB)
Sample type
SRA
Source name
Homo sapiens Panc1 cell line
Organism
Homo sapiens
Characteristics
line: Panc1
biomaterial_type: cell line
biosample encode accession: ENCBS777OZT (SAMN19193443)
Sex: male
dev stage: adult
age: 56 year
donor_id: ENCDO000ABB
lab: Mats Ljungman, UMichigan
source: ATCC
health state: pancreatic carcinoma
link: ENCBS777OZT at ENCODE;
https://www.encodeproject.org/ENCBS777OZT/
link: Derived from ENCODE donor ENCDO000ABB;
https://www.encodeproject.org/ENCDO000ABB/
Extracted molecule
total RNA
Extraction protocol
pipeline protocol:
https://www.encodeproject.org/documents/0a54a6da-ddb4-44bd-af95-2cd02754aa93/@@download/attachment/ENCODE%20Long%20Read%20RNA-Seq%20Analysis%20Pipeline%20v3.1%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/ENCSR181CES/
***************
biological replicate number: 1
technical replicate number: 1
description: Panc1 cell line
experiment encode accession: ENCSR181CES
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-02-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB962HZB
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 5
nucleic acid starting quantity units: µg
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
May 22, 2021
Last update date
May 28, 2021
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)
GSE175064
long read RNA-seq from Panc1 (ENCSR181CES)
Relations
BioSample
SAMN19193443
SRA
SRX10976676
Supplementary file
Size
Download
File type/resource
GSM5330800_ENCFF218FJR_transcript_quantifications_GRCh38.tsv.gz
3.7 Mb
(ftp)
(http)
TSV
GSM5330800_ENCFF830DIW_transcriptome_annotations_GRCh38.gtf.gz
64.9 Mb
(ftp)
(http)
GTF
GSM5330800_ENCLB962HZB_README.txt.gz
546 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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