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| Status |
Public on Jul 01, 2020 |
| Title |
NHP_43_Host |
| Sample type |
SRA |
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| Source name |
Host_colon
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| Organism |
Macaca mulatta |
| Characteristics |
sample type: Host sample
tissue: colon
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| Extracted molecule |
total RNA |
| Extraction protocol |
Four colon samples from the allo-HCT cohort and four colon samples from the untransplanted healthy control cohort were aseptically thawed, labeled with the viability dye LIVE/DEAD Violet (Invitrogen), then stained with αCD45 antibodies, conjugated with PerCP-Cy5.5 (BD Biosciences), and PE-conjugated αMAMU-A001 antibodies (NHP Reagent Resource). Viable LIVE/DEAD Violet-negative CD45-positive cells were sorted from two out of four GVHD-derived samples into host and donor fractions, based on MAMU-A001 expression. Sorted samples were also CD45-AF488 (IVas)-negative. Donor- and host-derived cells were defined computationally from two additional GVHD samples (see the corresponding Methods section, below).
Single cell libraries from sorted samples were generated using a UMI-based droplet-partitioning platform with the Chromium single cell 3’ library and gel bead kit v2 and v3 (10X Genomics) and then sequenced using a NovaSeq S2 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
NHP_43_*_S1_L002
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| Data processing |
Align with cellranger count (v3.1.0) to MMul10 with Ensembl98 annotations
Combine samples with cellranger aggregate, set “normalization=none”
Load matrix of UMI counts into Seurat v3.1
Retain cells with at least 800 genes detected and 1,500 transcripts detected.
Normalize data with SCTransform function in Seurat, using Lane as batch variable to correct for batch effects
Genome_build: mmul10
Supplementary_files_format_and_content: matrix.mtx.gz contains raw reads after aggregate command in cellranger. Normalized_Count_Matrix.mtx contains normalized counts after SCTransform
barcodes.tsv.gz: Barcodes file output by cellranger count
features.tsv.gz: Features file output by cellranger count
Supplementary_files_format_and_content: matrix.mtx.gz: Count matrix output by cellranger count
Normalized_Count_Matrix.mtx.gz: MatrixMarket formatted matrix of Normalized UMI counts for each gene in each cell, after QC and filtering
Normalized_Count_Matrix__ColumnNames.txt: Cell IDs for Normalized Count Matrix
Normalized_Count_Matrix__RowNames.txt: Genes for Normalized Count Matrix
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| Submission date |
Dec 21, 2019 |
| Last update date |
Jul 01, 2020 |
| Contact name |
James John Kaminski |
| E-mail(s) |
james.kaminski@childrens.harvard.edu
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| Organization name |
Boston Children's Hospital
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| Department |
Hematology / Oncology
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| Lab |
Kean/Shalek
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE142483 |
Deconvoluting alloimmunity in time and space through Serial Intravascular Staining: Evidence for rapid donor tissue-resident memory T cell resident memory formation during gastrointestinal GVHD. |
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| Relations |
| BioSample |
SAMN13663912 |
| SRA |
SRX7427903 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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