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Series GSE109535 Query DataSets for GSE109535
Status Public on Nov 02, 2018
Title scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3’ mRNA profiling
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We present sc-FTDseq, a microchip platform for single-cell freeze-thaw lysis directly toward 3’ mRNA sequencing. It offers format flexibility with a much simplified, widely adoptable workflow that reduces the number of preparation steps and hands-on time, with the quality of data and the cost per sample matching that of the state-of-the-art scRNA-seq platforms. Freeze-thaw, known as an unfavorable lysis method resulting in RNA fragmentation, turns out to be fully compatible with single-cell 3’ mRNA sequencing, which detects only ~50 bases at the 3’ end. We applied it to the profiling of mixed populations including whole tumors for distinguishing all major cell types and to the profiling of circulating follicular helper T cells implicated in systemic lupus erythematosus pathogenesis. Our results delineate the heterogeneity in the transcriptional programs and effector functions of these rare pathogenic T cells.
Overall design mRNA sequencing libraries are prepared after lysing the cells using three cycles of freeze-thaw. Open-surface and closed-environment formats refer to how a microwell array is used for co-loading cells and uniquely barcoded beads for mRNA capture. In closed-environment format, the microwell array is bonded with a channel on top of the array, and the cells and beads are introduced into the microwells through the channel. In open-surface format, microwell arrays are used without a channel on top, and cells and beads are introduced onto the array using a pipette.
Contributor(s) Dura B, Fan R
Citation(s) 30462277
Submission date Jan 23, 2018
Last update date Mar 27, 2019
Contact name Burak Dura
Phone 6173350782
Organization name Yale University
Department Biomedical Engineering
Lab Rong Fan Lab
Street address 55 Prospect St
City New Haven
State/province Connecticut
ZIP/Postal code 06511
Country USA
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (9)
GSM2945918 Species_mix_open-surface_format
GSM2945919 Species_mix_closed-environment_format
GSM2945920 Species_mix_5000_single_cells
BioProject PRJNA431313
SRA SRP131173

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE109535_RAW.tar 322.4 Mb (http)(custom) TAR (of TXT, XLSX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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