 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 28, 2021 |
| Title |
B06 |
| Sample type |
SRA |
| |
|
| Source name |
Foot skin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
subject id: Subject 3
ulcer location: plantar left foot
roi location: Ulcer
Sex: F
age: 59
healing status: Non-Healer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures (CD45, aSMA, panCK). Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).
Each collection of oligo tags from one well (representing an area of illumination-AOI- from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio. Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Library strategy: GeoMX-Seq
Adapter trimming with trim galore, trimGaloreOpts = " --hardtrim5 26 --dont_gzip" If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27" Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN" Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc" Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes), see attached Alpha_CTA_v2.0.pkc file
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode). Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.
|
| |
|
| Submission date |
Feb 03, 2021 |
| Last update date |
Oct 28, 2021 |
| Contact name |
Aristidis Veves |
| E-mail(s) |
[email protected]
|
| Phone |
6176627075
|
| Organization name |
Beth Israel Deaconess Medical Center
|
| Lab |
Rongxiang Xu, MD, Center for Regenerative Therapeutics
|
| Street address |
330 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE166120 |
Spatial transcriptomics of healing and non-healing diabetic foot ulcers |
|
| Relations |
| BioSample |
SAMN17771905 |
| SRA |
SRX10015199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5061985_DSP-1003680000819-B06.dcc.gz |
28.2 Kb |
(ftp)(http) |
DCC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
