isoMiGA: Isoform and gene-level counts and TPM in short-read human microglia

https://github.com/RajLabMSSM/isoMiGA  

Isoform quantification performed with Salmon on 4 datasets from human microglia. 

Files are in the naming format {cohort}_{quantification}_{reference}.tsv.gz - 4 cohort, 4, quantifications, 2 references = 32 files.

Cohorts:

1. Raj

350 samples from multiple brain regions. Publication PMID: 34992268

Raw data: https://dss.niagads.org/datasets/ng00105/

2. Roussos

192 samples.

Publication PMID: 35931864.

Raw data: https://doi.org/10.7303/syn26207321  https://www.synapse.org/#!Synapse:syn52052829  

3. Gaffney

118 samples.

Raw data: https://ega-archive.org/datasets/EGAD00001005736

4. ipsc 

IPS-derived human microglia-like cells (iMGLs)

27 samples from 3 stimulation conditions.

Citation: Navarro et al, LRRK2 G2019S variant triggers transcriptional changes in Parkinson’s disease human myeloid cells under pro-inflammatory environment, in preparation

Raw data: Gene Expression Omnibus GSE240907

Quantification types:

transcript_tpm: transcript-level quantification, TPM normalization

transcript_counts: transcript-level quantification, estimated counts

gene_tpm: gene-level quantification, TPM normalization

gene_counts: gene_level quantification, estimated counts

References:

See https://zenodo.org/record/8290956 for details

gencode: all transcripts in GENCODE v38: https://www.gencodegenes.org/human/release_38.html

union: combination of all GENCODE v38 transcripts with 35,879 novel transcripts found in PacBio long-read RNA-seq