Fred Hutch Innovation Lab

Reliable DSP cell storage is a game-changer for single-cell experiment planning, as shown by Attar et al. 2018 and Jimenez-Garcia et al. 2024. We just demonstrated another practical alternative to fix and freeze samples, such as infectious cells, before sorting for scRNAseq.

02.09.2025 20:05 — 👍 0    🔁 0    💬 0    📌 0

Tips: After staining and washing, swap out the wash buffer for the dehydration buffer and proceed with DSP methanol fix and freeze cells. At rehydration, the final resuspension buffer is switched to 2X PBS to maintain cell osmolarity while flow sorting. Sort into a tube with 2X PBS. (6/7)

02.09.2025 20:05 — 👍 0    🔁 0    💬 1    📌 0

One might expect paired chain proportions to differ, but the SFFS sample had a 69% paired chain recovery, similar to its fresh F1 counterpart, and a slightly higher proportion of TRA and TRβ chains. (5/7)

02.09.2025 20:05 — 👍 0    🔁 0    💬 1    📌 0

T-cell composition was similar for the SSFS and fresh F1 samples, including T-regs. Some unresolved cells were seen in each. (4/7)

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Saturation curve comparison

The SFFS sample had a 7% decrease in the median genes at 20k reads/cell (blue) compared to fresh samples (red), which tracked with example data from the demonstrated protocol. (3/7)

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Percent cell recovery

Our goals were twofold: Test sorting DSP fixed cells in sheath fluid & compare the performance of SFFS cells to fresh samples. Using a standard donor PBMC (F1), we made GEM-X 5’ and VDJ libraries from DSP fixed and sorted T cells to compare with previous data and saw similar cell recovery. (2/7)

02.09.2025 20:05 — 👍 0    🔁 0    💬 1    📌 0

Banking fixed samples before sorting improves experiment planning & instrument scheduling. 10x GEM-X DSP-based fixation recommends sorting before fixing cells. We attempted to stain, fix, and freeze cells before sorting & generating GEMs for 5' libraries. SFFS = STAIN FIX FREEZE SORT (1/7)

02.09.2025 20:05 — 👍 4    🔁 1    💬 1    📌 0

Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility, a...

We offer the latest evaluation of 7 single-cell RNAseq technologies comparing recently updated chemistries to previous versions and across platforms in two separate experiments. Workflow, sensitivity, cost, sequencing efficiency, annotation, and DGE included. www.biorxiv.org/cgi/content/...

28.05.2025 00:39 — 👍 0    🔁 0    💬 0    📌 1

Cell simulation as cell segmentation - Nature Methods Proseg is a segmentation approach for single-cell spatially resolved transcriptomics data that uses unsupervised probabilistic modeling of the spatial distribution of transcripts to accurately segment...

Excited to share work from our team, released today. Check out how it compares to other methods on multiple platform's datasets. Would love to hear how it performs on your data.
www.nature.com/articles/s41...

23.05.2025 00:40 — 👍 3    🔁 1    💬 0    📌 0

FHIL loves working with the Srivastava Lab! Their work explores factors enabling CAR-T response to checkpoint blockade in solid tumors. Infiltration of CAR-Ts was assessed spatially with a Xenium custom panel including probes targeting the construct and lung tumor. www.biorxiv.org/content/10.1...

24.04.2025 17:56 — 👍 3    🔁 2    💬 1    📌 1