Dynamics of chromatin accessibility during human first-trimester neurodevelopment (Camiel Mannens et al. 2023, in review).
To download the 10X output for individual samples use the command below, replacing {sample} with the sample you need. A list of all the sample names can be found in 10X_output, and the metadata providing region, name, sample ID etc can be found in Extended data 1
wget https://storage.googleapis.com/linnarsson-lab-human/ATAC_dev/10X/{sample}
We use the Chromograph pipeline.
Code for making many of the figures is available as Jupyter notebooks The package versions used to generate these figures are in this environment file
Our gene and transcripts annotation is based on Based on GRCh38.p13 gencode V35 primary sequence assembly as previously described in Emelie Braun et al., 2022, in review.
We discarded genes or transcripts that overlapped or mapped to other genes or non-coding RNAs 3’ UTR.
The GTF file used for read counts: gb_pri_annot_filtered.gtf
The genes and transcripts that were discarded: filtered_transcripts.txt