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GEO accession:
Sample GSM5330320
Query DataSets for GSM5330320
Status
Public on May 23, 2021
Title
long read RNA-seq from progenitor cell of endocrine pancreas (ENCLB671SMF)
Sample type
SRA
Source name
Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells
Organism
Homo sapiens
Characteristics
cell_type: progenitor cell of endocrine pancreas
biomaterial_type: in vitro differentiated cells
description: WA09 derived pancreatic progenitor cells
biosample encode accession: ENCBS832MSN (SAMN19193461)
Sex: female
dev stage: embryonic
age: 5 day
donor_id: ENCDO222AAA
lab: Bradley Bernstein, Broad
source: SESCC
health state: healthy
link: ENCBS832MSN at ENCODE;
https://www.encodeproject.org/ENCBS832MSN/
link: Derived from ENCODE donor ENCDO222AAA;
https://www.encodeproject.org/ENCDO222AAA/
Extracted molecule
total RNA
Extraction protocol
general protocol:
https://www.encodeproject.org/documents/77db752f-abf7-4c93-a460-510464134f52/@@download/attachment/ENCODE_protocol_2020pacbio_Final.pdf,
general protocol:
https://www.encodeproject.org/documents/81af563b-5134-4f78-9bc4-41cb42cc6a48/@@download/attachment/ENCODE%20Long%20Read%20RNA-Seq%20Analysis%20Pipeline%20v3%20%28Human%29.pdf
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Sequel II
Description
https://www.encodeproject.org/experiments/ENCSR530BOC/
***************
biological replicate number: 1
technical replicate number: 1
description: H9-derived pancreatic progenitors
experiment encode accession: ENCSR530BOC
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB671SMF
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
May 21, 2021
Last update date
May 25, 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)
GSE174883
long read RNA-seq from progenitor cell of endocrine pancreas (ENCSR530BOC)
Relations
BioSample
SAMN19193461
SRA
SRX10976128
Supplementary file
Size
Download
File type/resource
GSM5330320_ENCFF057RHY_transcript_quantifications_GRCh38.tsv.gz
3.4 Mb
(ftp)
(http)
TSV
GSM5330320_ENCFF161YNH_transcriptome_annotations_GRCh38.gtf.gz
64.4 Mb
(ftp)
(http)
GTF
GSM5330320_ENCLB671SMF_README.txt.gz
551 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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