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GEO accession:
Sample GSM5378709
Query DataSets for GSM5378709
Status
Public on Jun 15, 2021
Title
microRNA-seq from layer of hippocampus (ENCLB356JLO)
Sample type
SRA
Source name
Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax layer of hippocampus tissue
Organism
Mus musculus
Characteristics
tissue_type: layer of hippocampus
biomaterial_type: tissue
description: 5xFAD hippo het Female
biosample encode accession: ENCBS251XQY (SAMN19597526)
Sex: not collected
dev stage: unknown
age: not collected
donor_id: ENCDO835CXP
lab: Ali Mortazavi, UCI
source: MODEL-AD
link: ENCBS251XQY at ENCODE;
https://www.encodeproject.org/ENCBS251XQY/
link: Derived from ENCODE donor ENCDO835CXP;
https://www.encodeproject.org/ENCDO835CXP/
Extracted molecule
total RNA
Extraction protocol
general protocol:
https://www.encodeproject.org/documents/49f43842-5ab4-4aa1-a6f4-2b1234955d93/@@download/attachment/Multiplexed%20miRNA%20Sequencing%20Library%20Generation%20Protocol-3.4.pdf
pipeline protocol:
https://www.encodeproject.org/documents/e3eb2a94-9842-40d6-8153-fdf21e748e24/@@download/attachment/adapter_trimming_2.pdf
Library strategy
miRNA-Seq
Library source
transcriptomic
Library selection
size fractionation
Instrument model
Illumina NextSeq 500
Description
https://www.encodeproject.org/experiments/ENCSR659HKO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation 5xFAD female mouse layer of hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR659HKO
assay title: microRNA-seq
assembly: mm10
encode release date: 2020-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB356JLO
size range: <30
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Jun 12, 2021
Last update date
Jul 02, 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
GPL19057
Series (1)
GSE177698
microRNA-seq from layer of hippocampus (ENCSR659HKO)
Relations
BioSample
SAMN19597526
SRA
SRX11167665
Named Annotation
GSM5378709_ENCFF407VSD_minus_strand_signal_of_all_reads_mm10.bigWig
Named Annotation
GSM5378709_ENCFF995FMK_minus_strand_signal_of_unique_reads_mm10.bigWig
Named Annotation
GSM5378709_ENCFF174HAN_plus_strand_signal_of_all_reads_mm10.bigWig
Named Annotation
GSM5378709_ENCFF583PIZ_plus_strand_signal_of_unique_reads_mm10.bigWig
Supplementary file
Size
Download
File type/resource
GSM5378709_ENCFF174HAN_plus_strand_signal_of_all_reads_mm10.bigWig
8.6 Mb
(ftp)
(http)
BIGWIG
GSM5378709_ENCFF407VSD_minus_strand_signal_of_all_reads_mm10.bigWig
8.6 Mb
(ftp)
(http)
BIGWIG
GSM5378709_ENCFF583PIZ_plus_strand_signal_of_unique_reads_mm10.bigWig
4.9 Mb
(ftp)
(http)
BIGWIG
GSM5378709_ENCFF952HQO_microRNA_quantifications_mm10.tsv.gz
10.3 Kb
(ftp)
(http)
TSV
GSM5378709_ENCFF995FMK_minus_strand_signal_of_unique_reads_mm10.bigWig
4.9 Mb
(ftp)
(http)
BIGWIG
GSM5378709_ENCLB356JLO_README.txt.gz
665 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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