|
| Status |
Public on Apr 05, 2019 |
| Title |
CN80_D1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-Seq of Mus musculus: p30 female spinal cord
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spinal cord
mouse id: 1057
genotype: B6SJLSOD1-G93A
age: p30
Sex: female
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Spatial Transcriptomics
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
1000L6_barcodes.txt
|
| Data processing |
ST Pipeline v0.8.5
Image alignment in ImageJ
ST aligner v0.1
ST Annotator v0.2
Genome_build: GRCm38.v79
Supplementary_files_format_and_content: counts: tab-delimited text files include raw UMI filtered counts for each ST spot; processed using ST Pipeline v0.8.5
Tissue jpg image: Aligned and processed HE stainesd image in a coordinate system; colnames in the counts files; processed using ST aligner v0.1
Annotation file: columns for the counts file are associate with an anatomical region tab used ST Annotator v0.2
Barcode file: Barcode file needed for spatial demultiplexing of each sample; used in ST Pipeline v0.8.5. Column1 corresponds to the first 18 bp in the R1.fastq.gz; Column2 corresponds to x and Columns3 to y in a (x.y) Cartesian system on an ST array. In processed files 1, 2 and 4 the x_y values can be rouned and will correspond to Columns 2 and 3 (x,y) in the respective barcode files.
|
| |
|
| Submission date |
Sep 24, 2018 |
| Last update date |
Apr 05, 2019 |
| Contact name |
Sanja Vickovic |
| E-mail(s) |
vickovic@broadinsitute.org
|
| Organization name |
Broad Institute of MIT and Harvard
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE120374 |
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis |
|
| Relations |
| BioSample |
SAMN10113771 |
| SRA |
SRX4733030 |
