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"Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq" Replogle et al. 2022 SRA and GEO file manifest

dataset
posted on 22.06.2022, 18:24 authored by Joseph ReplogleJoseph Replogle, Jonathan Weissman

These tables list the raw fastq files (found on SRA under BioProject PRJNA831566 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA831566) and associated BAM/MTX files for each lane/gemgroup of single-cell RNA-sequencing. 


In these manifest files, all FASTQ files associated with a single lane/gemgroup of 10X Genomics single-cell RNA-sequencing are listed in a single row. These files can be used as input for an aligner like celllranger count, starsolo, or kallisto-bustools.


The "gemgroup" field indicates the integer value which is assigned to this gemgroup for aggregation of single-cell RNA-sequencing data in the finalized h5ad dataset.

Funding

Cancer Center Support Grant

National Cancer Institute

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Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human Disease

National Human Genome Research Institute

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The role of TMA7 in mitochondrial dysfunction

National Institute of Neurological Disorders and Stroke

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Predictive engineering of cellular transcriptional state

National Institute of General Medical Sciences

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DARPA HR0011-19-2-0007

History

Research Institution(s)

University of California, San Francisco; Whitehead Institute

Contact email

joseph@wi.mit.edu

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