Single-cell RNA-seq of human endometrium organoids under EM, EM+E2 and DM conditions

Single-cell RNA-seq of human endometrium organoids=================================================== Data accompanying: Human Embryo Implantation involves Fusion with theEndometrial Epithelium (Noordzij, Celotti et al.) Analysis code: https://github.com/RubenVanEsch/code_endometrium_analysis CONTENTS-------- TX1192.tar.gz Expansion medium (EM)TX1193.tar.gz Expansion medium + oestradiol (EM+E2)TX1194.tar.gz Differentiation medium (DM), replicate 1TX1195.tar.gz Differentiation medium (DM), replicate 2checksums.md5 MD5 checksums for the archives above Each archive expands to a directory named after the sample, containing theCell Ranger filtered feature-barcode matrix: TX119x/ barcodes.tsv.gz features.tsv.gz matrix.mtx.gz SAMPLES------- Sample Condition DescriptionTX1192 EM Expansion mediumTX1193 EM+E2 Expansion medium supplemented with oestradiolTX1194 DM Differentiation mediumTX1195 DM Differentiation medium TX1194 and TX1195 are replicates of the same condition. LIBRARY PREPARATION AND SEQUENCING---------------------------------- 30,000 cells were used for library preparation with the 10x Chromium GEM-XUniversal 3' Gene Expression v4 4-plex on-chip multiplexing kit (10x Genomics,CG000768). Libraries were sequenced on a NovaSeq X. PROCESSING---------- Cell Ranger v9.0.0 (cellranger multi) was used to demultiplex samples on theiron-chip multiplexing barcodes, align reads to the GRCh38-2020-A humanreference, and generate per-sample filtered feature-barcode matrices. The matrices in this deposit are the Cell Ranger output as generated; nofurther filtering has been applied. Quality control, doublet removal andnormalisation are performed in the analysis notebooks