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GEO accession:
Sample GSM6783460
Query DataSets for GSM6783460
Status
Public on Dec 04, 2022
Title
PRO-cap from Calu3 (ENCLB785FAS)
Sample type
SRA
Source name
Homo sapiens Calu3 cell line
Organism
Homo sapiens
Characteristics
line: Calu3
biomaterial_type: cell line
biosample encode accession: ENCBS974LON (SAMN31998780)
organism: Homo sapiens
Sex: male
health state: Lung adenocarcinoma
dev stage: adult
age: 25 year
donor_id: ENCDO109DGE
lab: Mats Ljungman, UMichigan
source: ATCC
link: ENCBS974LON at ENCODE;
https://www.encodeproject.org/ENCBS974LON/
link: Derived from ENCODE donor ENCDO109DGE;
https://www.encodeproject.org/ENCDO109DGE/
Extracted molecule
total RNA
Extraction protocol
pipeline protocol:
https://www.encodeproject.org/documents/d21a2b5b-11c2-4967-adcf-937ec0ee7d03/@@download/attachment/20220128_PROcap_Experimental_Protocol.pdf
general protocol:
https://www.encodeproject.org/documents/8a82200a-023f-439d-ae91-a1a1bf80eaa0/@@download/attachment/20220128_PROcap_Experimental_Protocol.pdf
Library strategy
OTHER
Library source
transcriptomic
Library selection
other
Instrument model
HiSeq X Ten
Description
https://www.encodeproject.org/experiments/ENCSR935RNW/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in CALU3.
experiment encode accession: ENCSR935RNW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2022-07-07
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB785FAS
spikeins used: The drosophila spike-in reference used for alignment
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Dec 03, 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
GPL20795
Series (1)
GSE219926
PRO-cap from Calu3 (ENCSR935RNW)
Relations
BioSample
SAMN31998780
SRA
SRX18486320
Named Annotation
GSM6783460_ENCFF585UOU_minus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation
GSM6783460_ENCFF671MMN_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Supplementary file
Size
Download
File type/resource
GSM6783460_ENCFF585UOU_minus_strand_signal_of_unique_reads_GRCh38.bigWig
13.7 Mb
(ftp)
(http)
BIGWIG
GSM6783460_ENCFF671MMN_plus_strand_signal_of_unique_reads_GRCh38.bigWig
13.8 Mb
(ftp)
(http)
BIGWIG
GSM6783460_ENCLB785FAS_README.txt.gz
701 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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