|
| Status |
Public on Nov 10, 2023 |
| Title |
tdKO, bio1, tech2 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
replicate: Rep 1
technical replicate: 2
genotype: Zfp148 fl/fl; Zfp281 fl/fl; Cd4-Cre+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Probe hybridization and all subsequent steps were performed as per 10X User guide for Visium CytAssist Spatial Gene Expression (CG000495).
Subsequently, probe extension was carried out and the ligation product was eluted, and a pre-amplification step performed. A subset of the pre-amplification product was used for library construction.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling was performed using RTA 3.4.4, demultiplexing was performed using spaceranger v2.0.0 (Bcl2fastq 2.20.0), and alignment was performed using spaceranger v2.0.0 (STAR2.7.2a). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A) and probe set (Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A).
Assembly: mm10
Supplementary files format and content: jpg; aligned tissue images
Supplementary files format and content: jpg; aligned fiducials
Supplementary files format and content: tiff; cytassist image
Supplementary files format and content: jpg; detected tissue images
Supplementary files format and content: png; tissue images
Supplementary files format and content: csv; spatial enrichment
Supplementary files format and content: csv; tissue positions
Supplementary files format and content: h5; matrix file
Supplementary files format and content: json; scalefactors
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Mar 14, 2023 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Remy Bosselut |
| E-mail(s) |
bosselur@helix.nih.gov
|
| Phone |
240-760-6866
|
| Organization name |
National Cancer Institute, National Institute of Health
|
| Department |
Laboratory of Immune Cell Biology
|
| Lab |
Bosselut
|
| Street address |
9000 Rockville Pike, Building 37
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE207572 |
Zfp281 and Zfp148 control CD4+ T cell thymic development and Th2 functions |
| GSE227332 |
The transcription factor Zfp281 serves redundantly with Zfp148 to support CD4+ T cell development and functions [Thymus Visium] |
|
| Relations |
| BioSample |
SAMN33760094 |
| SRA |
SRX19676893 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7097916_tdKO_bio1_tech2_aligned_fiducials.jpg.gz |
2.1 Mb |
(ftp)(http) |
JPG |
| GSM7097916_tdKO_bio1_tech2_aligned_tissue_image.jpg.gz |
1.1 Mb |
(ftp)(http) |
JPG |
| GSM7097916_tdKO_bio1_tech2_cytassist_image.tiff.gz |
19.6 Mb |
(ftp)(http) |
TIFF |
| GSM7097916_tdKO_bio1_tech2_detected_tissue_image.jpg.gz |
967.1 Kb |
(ftp)(http) |
JPG |
| GSM7097916_tdKO_bio1_tech2_filtered_feature_bc_matrix.h5 |
10.3 Mb |
(ftp)(http) |
H5 |
| GSM7097916_tdKO_bio1_tech2_raw_feature_bc_matrix.h5 |
14.2 Mb |
(ftp)(http) |
H5 |
| GSM7097916_tdKO_bio1_tech2_scalefactors_json.json.gz |
199 b |
(ftp)(http) |
JSON |
| GSM7097916_tdKO_bio1_tech2_spatial_enrichment.csv.gz |
910.5 Kb |
(ftp)(http) |
CSV |
| GSM7097916_tdKO_bio1_tech2_tissue_hires_image.png.gz |
3.3 Mb |
(ftp)(http) |
PNG |
| GSM7097916_tdKO_bio1_tech2_tissue_lowres_image.png.gz |
241.8 Kb |
(ftp)(http) |
PNG |
| GSM7097916_tdKO_bio1_tech2_tissue_positions_list.csv.gz |
61.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
