|
| Status |
Public on Oct 10, 2022 |
| Title |
Mouse retina cell layers, Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Retina
cell type: Mixed retinal layer cells
genotype: WT
genome build: mm39
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Light-Seq
Nextera tagmentation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
LS8B
ReorderedLightSeq_RetinaLayers.csv
RGC_2/BP_2/ONL_2 in ReorderedLightSeq_RetinaLayers.csv
Barcodes for each cell population are: TATGGA = ONL; GTTAGG = BCL; AGGGTA = GCL
|
| Data processing |
Assembly: mm39
'Merged_R1.fastq.gz' files were merged for lanes 1 and 2 based on the i7 index sequence
Extracted Light-Seq DNA barcodes (corresponding to different cell populations) using UMI-tools 1.1.1
Aligned to genome with STAR aligner 2.7.9a
Used featureCounts (subread) 2.0.1 to assign mapped reads to genes
Deduplicated reads based on UMIs + mapped gene pairs (samtools 1.9, 1.12)
Supplementary files format and content: CSV file containing Light-Seq read counts per gene. Rows are genes, columns are replicates for each cell population
|
| |
|
| Submission date |
Jul 20, 2022 |
| Last update date |
Oct 10, 2022 |
| Contact name |
Emma West |
| E-mail(s) |
[email protected]
|
| Phone |
7742396537
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Constance Cepko, Peng Yin
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE208650 |
Light-Seq: Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing |
|
| Relations |
| BioSample |
SAMN29844880 |
| SRA |
SRX16359036 |
