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GEO accession:
Sample GSM2071348
Query DataSets for GSM2071348
Status
Public on Mar 18, 2016
Title
single cell RNA-seq from pyramidal neuron (ENCLB542OIM)
Sample type
SRA
Source name
Mus musculus strain B6NCrl pyramidal neuron primary cell adult (8 months)
Organism
Mus musculus
Characteristics
cell_type: pyramidal neuron
biomaterial_type: primary cell
description: Mm_C57Bl6_8mo_M_WT_layerV_pyramid_single_cell
biosample encode accession: ENCBS918UDX (SAMN04284182)
age: 8 month
donor_id: ENCDO956IXV
dev stage: adult
Sex: not collected
lab: Barbara Wold, Caltech
link: ENCBS918UDX at ENCODE;
https://www.encodeproject.org/ENCBS918UDX/
link: Derived from ENCODE donor ENCDO956IXV;
https://www.encodeproject.org/ENCDO956IXV/
link: general protocol;
https://www.encodeproject.org/documents/a6e06058-5019-488f-9195-8bcd2e9229c1/@@download/attachment/Laser%20capture%20dissection%20procedure%20general%20protocol_Wold_group.pdf
Extracted molecule
total RNA
Extraction protocol
extraction method: n/a
extraction protocol:
https://www.encodeproject.org/documents/49fd5b3b-9878-4ec8-92bf-ef6dce9116e3/@@download/attachment/SMARTer%20Ultra%20Low%20RNA%20Kit%20for%20Illumina%20Sequencing%20User%20Manual%20%28PT5163-1%29_120213.pdf
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Illumina HiSeq 2500
Description
https://www.encodeproject.org/experiments/ENCSR195BCE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC772)
experiment encode accession: ENCSR195BCE
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB542OIM
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Feb 24, 2016
Last update date
May 15, 2019
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
GPL17021
Series (1)
GSE78342
single cell RNA-seq from pyramidal neuron (ENCSR195BCE)
Relations
SRA
SRX1603043
BioSample
SAMN04284182
Named Annotation
GSM2071348_ENCFF186LFI_signal_of_all_reads_mm10.bigWig
Named Annotation
GSM2071348_ENCFF086DYB_signal_of_unique_reads_mm10.bigWig
Supplementary file
Size
Download
File type/resource
GSM2071348_ENCFF086DYB_signal_of_unique_reads_mm10.bigWig
24.1 Mb
(ftp)
(http)
BIGWIG
GSM2071348_ENCFF186LFI_signal_of_all_reads_mm10.bigWig
33.3 Mb
(ftp)
(http)
BIGWIG
GSM2071348_ENCFF247PXV_transcript_quantifications_mm10.tsv.gz
4.0 Mb
(ftp)
(http)
TSV
GSM2071348_ENCFF377OUV_gene_quantifications_mm10.tsv.gz
1.9 Mb
(ftp)
(http)
TSV
GSM2071348_ENCLB542OIM_README.txt.gz
646 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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