So, what is the difference between Parse and Scale Bio scRNA-seq kits?
At a recent meeting, two researchers asked me this great question after Parse Biosciences (Parse) and Scale Bioscience (Scale Bio) presented their technologies. I have to admit, I didn't have a robust answer then, but I shared what I knew and promised to dig deeper. In this blog post, I'll share with you what I have found out about. And hey, if you've got more insights, please share them!
Common Ground
Let's start with what these kits have in common.
Goal: Parse and Scale Bio scRNA-seq kits were designed to study the transcriptome without bias towards the 3' or 5' end of coding RNA molecules.
Equipment: Neither Parse nor Scale Bio need specialized (aka. expensive) equipment. Everything happens on plate wells and tubes.
Logistics Flexibility: Both start with the fixation of the cells or nuclei suspensions before the experiment, enabling samples to be stored for months. This provides significant logistical flexibility, allowing us, for example, to batch our samples and process them simultaneously or to ship them to the lab where the experiment will be done.
General Approach: Parse and Scale Bio kits employ a method known as “split and pool”. Imagine we have two groups of cells in separate wells. These wells contain a unique tag that will be linked to the RNA of each individual cell. Then, we combine (pool) these two groups in a new well without any tags. After that, we split the cells into three other wells, each with its own unique tag. The cells' RNA will also be linked to these new tags. If we keep doing this process multiple times, there's a high chance that each cell's RNA will end up with a unique combination of tags. So, by the end of the experiment, we will be able to separate each individual cell and know which RNA belongs to them. However, the “split and pool” method is the base of both kits; the strategy of tagging the cell is different. Something I will explain after.
Scalability: Parse and Scale Bio kits helped us study more cells in a shorter period of time if needed. How? By adjusting the number of tags we use during our experiments. Adding more tags lets us study more cells. So, instead of only being able to analyze tens of thousands of cells, we can now study hundreds of thousands of cells at once. But let’s keep in mind that studying so many cells costs a lot, mainly because of the sequencing. Also, remember that both the Parse and Scale Bio kits can only be used once. So, if we buy a kit for 96 samples, we need to have all 96 samples ready to go. Otherwise, we'll end up wasting half of the kit.
Distinguishing Factors
Now, let's delve into the main differences that set these kits apart.
Strategy: Parse uses the split-pool method together with combinatorial barcoding (Figure 1), while Scale Bio uses it with combinatorial indexing (Figure 2). At first, I thought they were the same, but they're actually different. The main difference is the type of “tags” that are used. Parse uses barcodes, whereas Scale Bio employs indexes. Both are oligos, but indexes are longer and contain more information. Let me explain with an analogy. Imagine organizing a library. Barcodes are similar to the stickers on a book's spine, each representing a different book and used to quickly locate it on the shelf. Indexes, on the other hand, are like cards with detailed information about a book, such as the title, author, and publication year. Indexes can include barcodes, but barcodes cannot include indexes. In case you would like more details on this topic, I advise you to read the original papers that are behind both scRNA-seq kits: SPLit-seq for Parse and sci-RNA-seq3 for Scale Bio.
Figure 1: Parse combinatorial barcoding strategy. Figure from Gokhan Demirkan 
Figure 2: Scale Bio combinatorial indexing strategy. Image from https://scale.bio scRNA-seq kits: Parse scRNA-seq kits are called Evercode™. There are kits for studying the entire transcriptome (WT) or T-cell receptors (TCR). They can have different sizes depending on how many cells we need to analyze or how many samples we have. The "mini" kit can analyze up to 10 thousand cells and 12 samples; the "normal" kit can analyze up to 100 thousand cells and 48 samples; and the "mega" kit can analyze up to 1 million cells and 96 samples. Scale Bio offers a the Single-cell RNA sequencing kit that can analyze up to 125 thousand cells and 96 samples. The number of cells can be increased up to 500 thousand using the Extended Throughput Kit1.
Workflow time: When comparing the workflow time from the Parse Evercode ™ WT Mega kit v22 with the Scale Bio Single-cell RNA sequencing kit, the second is faster.
Plate Configuration: Parse protocol uses three 96-well plates, while Scale Bio uses two 96-well plates and one 384-well plate.
Pooling Method: Parse relies on pipetting for pooling samples, whereas Scale Bio employs a funnel-based approach.
Libraries Flexibility: Parse has a strategy of sublibraries, giving us flexibility to choose the number of cells to be sequenced. On the other hand, Scale Bio allow us to sequence individual wells, which can also give us flexibility concerning our experimental design.
Sequencing Compatibility3: Parse provides sequencing compatibility with a variety of platforms, including PacBio, Ultima Genomics, Singular Genomics, Illumina, Oxford Nanopore, Compete Genomics, and Element Biosciences. In contrast, Scale Bio is optimized for Illumina sequencing.
In conclusion, I hope it's more clear now that the Parse and Scale Bio scRNA-seq kits are different. I hope this blog post empowers you to make informed decisions to advance your projects.
Thanks for reading it ❤️. If you think it was interesting, please share it.
I couldn’t find a online information about this kit.
First, let me say that I couldn’t have access to the Evercode™ Mega Kit v3 protocol. Second, I compared these kits since they are both for 96 samples.
Official information on companies websites