diff --git a/README.md b/README.md index 1df6c63..c2d4ee9 100644 --- a/README.md +++ b/README.md @@ -16,16 +16,9 @@ The dataset can be browsed from [our collection](https://cellxgene.cziscience.co ### Raw sequence reads -Raw data in fastq and BAM format is available [at NeMO](http://data.nemoarchive.org/biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/). - -Our gene and transcripts annotation is based on Based on GRCh38.p13 gencode V35 primary sequence assembly. - -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](https://storage.googleapis.com/linnarsson-lab-tmp/gb_pri_annot.gtf) - -The genes and transcripts that were discarded: [filtered_transcripts.txt](https://storage.googleapis.com/linnarsson-lab-tmp/filtered_transcripts.txt) +Raw data in fastq and BAM format are available [at NeMO](http://data.nemoarchive.org/biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/). +Our gene and transcript annotation is based on GRCh38.p13 gencode V35 primary sequence assembly. We discarded genes or transcripts that overlapped or mapped to other genes' or non-coding RNAs' 3’ UTRs. Here we provide [the GTF file used to count reads](https://storage.googleapis.com/linnarsson-lab-tmp/gb_pri_annot.gtf), and [the genes and transcripts that were discarded](https://storage.googleapis.com/linnarsson-lab-tmp/filtered_transcripts.txt). ### Expression matrices @@ -43,7 +36,7 @@ Note that [adult_human_20221007.loom](https://storage.cloud.google.com/linnarsso The files with the molecule coordinates (as .parquet) and gene x cell counts (as .loom) are available in the EEL_adult folder at: https://storage.cloud.google.com/linnarsson-lab-human -Data in the [.parquet](https://parquet.apache.org/) format and can be opened by [FISHscale](https://github.com/linnarsson-lab/FISHscale), Python [Pandas](https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html) or any other Parquet reader. +Data in the [.parquet](https://parquet.apache.org/) format can be opened by [FISHscale](https://github.com/linnarsson-lab/FISHscale), Python [Pandas](https://pandas.pydata.org/docs/reference/api/pandas.read_parquet.html) or any other Parquet reader. `r_px_microscope_stitched` and `c_px_microscope_stitched` contain the RNA molecule coordinates in pixels (pixel size of 0.18um). `r_transformed` and `c_transformed` contain the RNA molecule coordinates in pixels (pixel size of 0.27um). @@ -51,7 +44,7 @@ Data in the [.parquet](https://parquet.apache.org/) format and can be opened by Clustering was performed using `cytograph`. Installation and usage are described [here](https://github.com/linnarsson-lab/adult-human-brain/tree/main/cytograph). Other materials include: - `scripts`: other scripts named in the Methods section -- `notebooks`: some of the code used to make figures -- `tables`: the sample-metadata and cluster-annotation tables (Tables S1 and S2). Note that Tables S3 and S4 correspond to "de_oligos.csv" and "de_opcs.csv" in the "notebooks" folder. +- `notebooks`: the code used to make figures +- `tables`: the manuscript's supplementary tables Auto-annotations are available in a separate [repository](https://github.com/linnarsson-lab/auto-annotation-ah). diff --git a/tables/annotation.xlsx b/tables/annotation.xlsx deleted file mode 100644 index ed8d7f4..0000000 Binary files a/tables/annotation.xlsx and /dev/null differ diff --git a/tables/cluster_annotation.xlsx b/tables/cluster_annotation.xlsx new file mode 100644 index 0000000..1521854 Binary files /dev/null and b/tables/cluster_annotation.xlsx differ diff --git a/notebooks/Preprint/de_oligo.csv b/tables/de_oligo.csv similarity index 100% rename from notebooks/Preprint/de_oligo.csv rename to tables/de_oligo.csv diff --git a/notebooks/Preprint/de_opc.csv b/tables/de_opc.csv similarity index 100% rename from notebooks/Preprint/de_opc.csv rename to tables/de_opc.csv diff --git a/tables/dissections.xlsx b/tables/dissections.xlsx new file mode 100644 index 0000000..7a9cf6c Binary files /dev/null and b/tables/dissections.xlsx differ diff --git a/tables/donors.xlsx b/tables/donors.xlsx new file mode 100644 index 0000000..2fe260b Binary files /dev/null and b/tables/donors.xlsx differ diff --git a/tables/samples.xlsx b/tables/samples.xlsx index 8a1c02b..403a4a4 100644 Binary files a/tables/samples.xlsx and b/tables/samples.xlsx differ