Date: March 21st, 2024

Dataset Title: Seq-Scope Protocol Dataset : Deep Sequencing of Liver Section Library.

Dataset Creators: Yongsung Kim, Weiqiu Cheng, Chun-Seok Cho, Hyun Min Kang, Jun Hee Lee

Dataset Contact: Hyun Min Kang hmkang@umich.edu

Funding: R01-AG-079163 (NIH)

Dataset Overview:
This dataset contains a typical example of Seq-Scope dataset that investigators would generate after examining the initial sequence data. If the quality of the initial Seq-Scope dataset looks great, one may decide to sequence the library much more deeply to maximize the information content. (see NovaScope tutorial at https://seqscope.github.io/NovaScope/ for more details). The spatial barcode sequences and the initial version of the sequenced cDNA library are deposited in a separate repository, which is described in the NovaScope documentation (https://seqscope.github.io/NovaScope/). This data repository contains a deeper sequencing of the same library. 

Methodology:
This dataset contains the sequence of cDNA libraries, attached with spatial barcodes, of mouse liver tissue section prepared by the Seq-Scope methodology (https://doi.org/10.1016/j.cell.2021.05.010). Adult mouse liver tissue was previously collected from 8-week-old male C57BL/6 wild-type mice immediately after CO2 euthanasia. The tissue was embedded in an optical cutting temperature (OCT) compound on cooled isopentane (2-methylbutane) in a liquid nitrogen bath and stored at –80 °C. The tissue was placed on a section of NovaSeq 6000 flowcell, which was sequenced according to the Seq-Scope protocol. After mRNA release and reverse transcription, the cDNA library was deeply sequenced using Illumina NovaSeq X System.

Files contained here:
Paired-end FASTQ files for deeply sequenced Seq-Scope library of liver section. There are 7 pairs of FASTQ files. This should be added to the shallow liver dataset deposited in the separate library (https://doi.org/10.5281/zenodo.10835761). MD5sums for each FASTQ file are also available. 
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v3a/N3_B08C_v3a.R1.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v3a/N3_B08C_v3a.R2.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2c/N3_B08C_v2c.R1.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2c/N3_B08C_v2c.R2.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v3b/N3_B08C_v3b.R1.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v3b/N3_B08C_v3b.R2.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2a/N3_B08C_v2a.R2.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2a/N3_B08C_v2a.R1.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2bu/N3_B08C_v2bu.R1.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2bu/N3_B08C_v2bu.R2.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2cu/N3_B08C_v2cu.R2.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2cu/N3_B08C_v2cu.R1.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2b/N3_B08C_v2b.R1.fastq.gz
- N3_B08C_deep_xtra/seq2nd/N3_B08C_v2b/N3_B08C_v2b.R2.fastq.gz

Use and Access:
This data set is made available under a Creative Commons license CC BY 4.0

To Cite Data:
Yongsung Kim, Weiqiu Cheng, Chun-Seok Cho, Yongha Hwang, Yichen Si, Anna Park, Mitchell Schrank, Jer-En Hsu, Jingyue Xi, Myungjin Kim, Ellen Pedersen, Olivia I. Koues, Thomas Wilson, Goo Jun, Hyun Min Kang, Jun Hee Lee, “Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics” (submitted)