|
| Status |
Public on Jan 08, 2021 |
| Title |
spleen_slice_S20C2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse spleen injected with MC38 and with HEK293t spike in
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
mouse strain: C57BL/6
mouse organ: Spleen
injection: MC38
human cell line: HEK293T
|
| Treatment protocol |
MC38 tumor cells (5x10^5 cells) were injected directly into liver or spleen of a C57BL/6 mouse. 10 days post tumor inoculation, mice were sacrificed and harvested. Organs were fixed in dithiobis (succinimidyl propionate) (DSP) and cryopreserved.
|
| Growth protocol |
MC38 cell line was cultured in complete cell culture medium (RPMI 1640 with GlutaMAX, penicillin, streptomycin, sodium pyruvate, HEPES, NEAA, and 10% fetal bovine serum).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell lysis and amplification.
In-situ reverse transcription on spatially barcoded microwell array. Pooling cells off array and FACS sorting for secondary indexing. Cell lysis, reverse transcription template switching and barcoded cDNA amplification. cDNA tagmentation amplification with primers containing short-read sequencing adapters (Illumina).
Combinatorial indexing for single cell barcoding. Initial barcoding step provides 2-dimensional spatial index.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
S20C2
Combinatorially-indexed transcriptome
spleen_all_raw_labeled.h5ad
|
| Data processing |
Fastq files generated from raw Illumina base calls using bcl2fastq v2.0, demultiplexed along the second combinatorial barcode.
Reads trimmed using Trim Galore v0.6.5 with parameters: -a AAAAAAAA --three_prime_clip_R1 1
Reads aligned using STAR v2.7.0a with parameters: --outFilterMatchNminOverLread 0.3 --outSAMstrandField intronMotif
Reads quality filtered using samtools v1.10 with parameters: view -bh -q 30 -F 4
Reads UMI deduplicated and split along the first combinatorial barcode using a custom python script.
Cell by gene matrix generated using a custom python script.
Genome_build: Merged GRCm38 GRCh38 genome
Supplementary_files_format_and_content: 10X_raw_feature_bc_matrix.h5: 10x-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: 10X_mouse_down_processed.h5ad: AnnData-formatted h5 file containing a matrix with downsampled, transformed counts from mouse cells of a liver slice.
Supplementary_files_format_and_content: L10C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L30C8.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L30C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L20C1.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L20T.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: cell_line_raw_labeled.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a cell line mixture.
Supplementary_files_format_and_content: S10C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S20C2.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S20C1.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S15C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: liver_all_raw_labeled.loom: Loom file containing a matrix with raw counts and cell labels from multiple liver slices.
Supplementary_files_format_and_content: spleen_all_raw_labeled.h5ad: AnnData-formatted h5 file containing a matrix with raw counts and cell labels from multiple spleen slices.
|
| |
|
| Submission date |
Jan 07, 2021 |
| Last update date |
Jan 09, 2021 |
| Contact name |
George Christopher Hartoularos |
| E-mail(s) |
george.hartoularos@ucsf.edu
|
| Organization name |
University of California, San Francisco
|
| Department |
Graduate Division
|
| Lab |
Ye
|
| Street address |
513 Parnassus Ave S965F
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE164430 |
Spatially resolved single-cell RNA-sequencing reveals expression heterogeneity in tumor microenvironment |
|
| Relations |
| BioSample |
SAMN17255564 |
| SRA |
SRX9804446 |
