Data / Libraries

Library & Species Data Inventory

Every library, every species, side by side with its QC status

The BrainStorm atlas integrates 165 single-nucleus RNA-seq libraries spanning 100 vertebrate species, 4,414,988 cells in the full matrix. This page lists every library recorded in Supplementary Table 1, including one library that delivered no usable data and is absent from the integrated dataset, so that the composition, platform and integration status of the resource can be inspected directly. A per-species rollup below gives full-matrix and analysis-layer cell counts together with curation flags.

166
Libraries Listed
every batch recorded in ST1
165
In Integrated Matrix
one empty delivery excluded
100
Species
50 newly profiled + 50 public
4,414,988
Cells, Full Matrix
492,121 in the analysis layer
Library Inventory

All 166 Libraries at a Glance

Each row is one sequencing library (sample batch). Platform is shown at the species level; where a species combines multiple platforms, the platform-to-library mapping is documented in Supplementary Tables ST1 and ST6.

#Library IDSpeciesClass SourcePlatform (species level)Status
Species Rollup

Cell Counts and Curation Flags per Species

Full-matrix cells are the post-QC nuclei contributed by each species to the integrated resource; the analysis layer samples at most 5,000 cells per species for balanced cross-species comparison. Curation flags are descriptive annotations from ST1 (for example region-restricted sampling or multiple technologies) and do not indicate exclusion.

SpeciesCommon NameClassSource LibrariesIntegrated Platform(s)Full-Matrix Cells Analysis-Layer CellsCuration Flags

Inclusion & Exclusion Notes

  • Pelodiscus_sinensis_40367951_batch1 delivered no usable data files (empty delivery directory) and is absent from the integrated dataset; the species is represented by its other 3 libraries.
  • An additional in-house library for Plectropomus leopardus (Plectropomus_leopardus_present_study_2024_batch3, PLLE-S001-BRA-10SN, 10x Chromium) was excluded after QC: only 14.4% of reads mapped to the genome and 7.6% confidently to the transcriptome (versus about 94% genome mapping for the two retained SeekOne libraries), with a median of 179 genes per nucleus and 2,440 post-QC nuclei. Its raw fastq is deposited in GSA but the library is not used in the analysis layer, so it does not appear among the 166 listed batches.
  • Two species profiled in-house, Misgurnus anguillicaudatus and Salarias fasciatus (two libraries each), were excluded before the analysis layer because of low genome-mapping rates (23.3 to 51.3%, versus at least 85.1% for all retained in-house libraries) and the resulting low gene complexity, attributable to incomplete reference annotation.
  • QC for the newly generated libraries retained cells with 200 to 6,000 detected genes, removed doublets with Scrublet, and applied no mitochondrial-percentage filter.

From Inventory to Exploration

Download the matrices and metadata behind every library, or open the interactive browser to inspect clusters and annotations directly.

Datasets Species Catalog Cell Browser