Datasets

Here we provide a single table with some links, size and md5 checksums for the files provided in the following tutorials.

Tip

All raw reads for the datasets showcased in our paper are available at SRA, and all processed objects (H&E images and spatial transcriptomes) are available at GEO

Tip

When downloading any of the files below, using Linux or macOS, we recommend wget.

Adult mouse hippocampus

File	Link	md5 checksum
adult_hippocampus_tiles.tar.xz	http	3788d6774212d8eb50ffb17fc970c1c3
adult_mouse_hippocampus.h5ad.tar.gz	http	833bd94d8901b6605fd41c22e5755e1c
adult_mouse_hippocampus_by_cell.h5ad.tar.gz	http	c837f3184d25fb4842a0e27bde1b3941
adult_mouse_hippocampus_R1_001.fastq.gz	http	cff74ca79bfa645de31cee80f035b6fe
adult_mouse_hippocampus_R2_001.fastq.gz	http	4f3af67c09967ca6bdd9575a02692a4f
adult_mouse_hippocampus.tif	http	d23dba7f2eeb88c3de9fa869099b30dd

E13 mouse head

File	Link	md5 checksum
e13_mouse_head_tiles.tar.xz	http	a7f63b5049a8e06d9c3a37cab7af8205
e13_mouse_head.h5ad.tar.gz	http	c727ec6d7b34bffd79919570ae5b4b6d
e13_mouse_head_R1_001.fastq.gz	http	92f291e2033bf71096836a239a49fc1e
e13_mouse_head_R2_001.fastq.gz	http	841e5a8fe667f247e6dc4bd9641a3cc8
e13_mouse_head_reseq_R1_001.fastq.gz	http	43c8a107652022f6f675bbd761dc330d
e13_mouse_head_reseq_R2_001.fastq.gz	http	a6a7c0cb3c6626977444b43a9ba07450
e13_mouse_head.tif	http	c7703951d2602d487d0336c7c50f49c6

Barcode spatial coordinates and coordinate systems

File	Link	md5 checksum
fc_1_coordinate_system.csv	http	83016d6d9179b68dbfe07d1da01aa0c0
fc_2_coordinate_system.csv	http	6da374f1d4b07b2d3c8c424e76fa8567
fc_1_L3.fastq.gz	http	7ee4cc818708caa87401744ac9366732
fc_2_L3.fastq.gz	http	67e2d95e9b17bc8ebdf9f315f9a09952

Genomes and annotations

File	Link	md5 checksum
GRCm39vM30.genome.fa	http	f7e956ab58169c9b457c93bc7ecca0a2
gencodevM30.annotation.gtf	http	de5e3b939daf633970582756f90c01df
phiX.fa	http	69a6c72e164d1a57c0f8cf375a246b0a
mouse.rRNA.fa	http	cbf1d516d570cf085c9d5a61ac1b97c5