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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 12, 2022 |
| Title |
Myeloid cells from MDA-MB-231 tumor bearing humanized mice, hashtag library |
| Sample type |
SRA |
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| Source name |
BM, PB, Lung, Tumor
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: BM, PB, Lung, Tumor
Sex: Female
cell type: Human CD33+ myeloid cells
genotype: Homozygous
strain: NSG-SGM3
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Human CD33+ myeloid cells were sorted from different tissues of humanized mice, and then labeled with cell hashing antibodies. Cells were loaded into one lane of a 10X Chromium microfluidic chip. Cells capture, lysis and RNA extraction were performed using the 10X V3 Chromium technology following the manufacturer’s protocol.
Single cell capture, barcoding and library preparation were performed with the 10x Chromium system using version 3 chemistry, following the manufacturer’s protocol. cDNA was synthesized and amplified as per manufacturer’s protocol and amplified to construct an Illumina sequencing library. cDNA and libraries were checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Hashtag-derived oligonucleotide (HTO)
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| Data processing |
The raw data (FASTQ file) of each library were produced and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For all libraries, R1 contains a 16bp cell barcode + 12bp UMI barcode and R2 contains the biological reads. If present, I1 and I2 contains the index which is needed for 10X CellRanger pipelines.
An unfiltered digital gene expression matrix was generated for each gene expression library against the 10X Genomics reference genome (GRCh38-2020-A) build using CellRanger v6.1.1
A digital counts matrix was generated for each hashtag library using CITE-Seq-Count. This produces a matrix of counts with hashtag labels for rows and cell barcodes for columns.
Assembly: GRCh38-2020-A
Supplementary files format and content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market sparse CSC matrix format. Rows correspond to genes in the order provided in features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.
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| Submission date |
Nov 07, 2022 |
| Last update date |
Dec 12, 2022 |
| Contact name |
Guangwen Ren |
| E-mail(s) |
Gary.Ren@jax.org
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| Organization name |
The Jackson Laboratory
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| Street address |
600 Main Street
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| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platform ID |
GPL25526 |
| Series (1) |
| GSE217499 |
Single-cell transcriptional profiles of different tissue-derived myeloid cells from naïve and MDA-MB-231 tumor-bearing humanized mice |
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| Relations |
| BioSample |
SAMN31648206 |
| SRA |
SRX18200975 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6720648_SC2100113-HTO_barcodes.tsv.gz |
1.3 Mb |
(ftp)(http) |
TSV |
| GSM6720648_SC2100113-HTO_features.tsv.gz |
129 b |
(ftp)(http) |
TSV |
| GSM6720648_SC2100113-HTO_matrix.mtx.gz |
1.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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