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| Status |
Public on Dec 09, 2019 |
| Title |
Mouse_Probe-Seq_Cell_Grik1+_2 |
| Sample type |
SRA |
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| Source name |
Mouse Retina
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
tissue: retina
age: Adult (>P30)
rna marker: Grik1+
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| Extracted molecule |
total RNA |
| Extraction protocol |
The tissue was dissociated fresh or the tissue was frozen. Cells or nuclei were extracted, fixed, and labeled with appropriate SABER FISH probes. Specific cellular or nuclear populations were FACS isolated and the RNA was extracted from the cells or nuclei using the RecoverAll Kit. For live cells, Grik1-GFP plasmid was electroporated at P2 into the developing mouse retina. The retina was harvested at P40, and the cells were dissociated. GFP+ cells were FACS isolated into Trizol. The RNA was extracted based upon Trizol manual.
cDNA was generated using the SMART-Seq v.4 kit. The indices were added using the Nextera XT Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Cellular RNA
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| Data processing |
Quality control of RNA-seq reads were performed using fastqc version 0.10.1
RNA-seq reads were clipped and mapped onto onto the either the mouse genome (Ensembl GRCm38.90), chick genome (Ensembl GRCg6a.96), or Drosophila genome (BDGP6.22) using STAR version 2.5.2b. Parameters used were as follows: --runThreadN 6 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --clip3pAdapterSeq --quantMode TranscriptomeSAM GeneCounts
Read counts were generated by HT-seq version 0.9.1. Sample parameters used were as follows: -i gene_name -s no
Genome_build: Ensembl GRCm38.90, Ensembl GRCg6a.96, BDGP6.22
Supplementary_files_format_and_content: Text files with the read counts for every gene for each sample.
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| Submission date |
Aug 08, 2019 |
| Last update date |
Dec 09, 2019 |
| Contact name |
Ryoji Amamoto |
| E-mail(s) |
[email protected]
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| Phone |
6177498955
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
Cepko
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE135572 |
Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation |
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| Relations |
| BioSample |
SAMN12534699 |
| SRA |
SRX6678759 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4018741_Mouse_Probe-Seq_Cell_Grik1+_2.txt.gz |
172.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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