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| Status |
Public on Aug 25, 2016 |
| Title |
Vsx2_2a_G2_S170_R1_001 |
| Sample type |
SRA |
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| Source name |
Mus musculus retina, P17
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| Organism |
Mus musculus |
| Characteristics |
tissue: retina
genotype: Vsx2-GFP
developmental stage: P17
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| Extracted molecule |
total RNA |
| Extraction protocol |
Dissociated retina were FACS sorted into 96-well plates (single cells) and tubes (bulk libraries) containing lysis buffer
Smart-seq2 (Picelli et al., Nature Methods, 2014)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
single cell
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| Data processing |
Base calls performed using bcl2fastq2.15
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values)
Genome_build: mm10
Supplementary_files_format_and_content: text files with tab delimiters containing inferred counts and tpm values.
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| Submission date |
Apr 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Karthik Shekhar |
| E-mail(s) |
karthik@broadinstitute.org
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| Phone |
217-979-9852
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| Organization name |
Broad Institute
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| Street address |
415 Main St.
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE80232 |
Smart-seq2 analysis of P17 FACS sorted retinal cells from the Tg(Chx10-EGFP/cre,-ALPP)2Clc or Vsx2-GFP transgenic line |
| GSE81905 |
Single cell RNA-sequencing of retinal bipolar cells |
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| Relations |
| BioSample |
SAMN04849477 |
| SRA |
SRX1702280 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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