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Laura Kalliokoski
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This DAC controls 6 datasets

Dataset ID	Description	Technology	Samples
EGAD50000000227	This dataset contains single-end fastq files for human oocytes (n=12), zygotes (n=5), and early embryos (n=10) sequenced with Illumina NextSeq500. The sequencing libraries were prepared from single oocytes, zygotes, and embryos in two batches.	NextSeq 500	27
EGAD50000001443	Histone modification ChIP-seq for chromatin state annotations of myometrium and UL subclasses. Altogether 5 analyses and 210 runs. Includes fastq files; both ChIP and Input for each sample. Some Inputs are used for multiple ChIP experiments. ChIP-seq alignment files for trimmed, mapping q20 and nonredundant reads; both ChIP and Input for each sample. Software: Trim Galore v0.6.7; Bowtie 2 v2.5.0; samtools v1.6	Illumina HiSeq 2500 Illumina NovaSeq 6000	82
EGAD50000001933	Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.	Illumina NovaSeq 6000	2
EGAD50000001934	Single cell RNA sequencing and coupled TCR sequencing data generated following immunological treatments in patient-derived ex vivo tumor models. Dataset consist of 46 sequencing samples originating from eight individual patient-derived ex vivo models. Single cell RNA and TCR sequencing data is generated using 10X Genomics platform with 5´ sequencing. The submission contains 46 Fastq files where each patient-derived ex vivo model and it's transcriptomic response to specified treatment is a unique sequencing run. TCR sequencing runs are submitted as one file per individual model, gathering all the treatment conditions.	Illumina NovaSeq 6000	46
EGAD50000002724	This dataset contains .FASTQ files of targeted genotyping by single-cell amplicon sequencing (scAmp-seq) data of human bone marrow samples across ERCC6L2 disease (33 amplicon libraries from 15 samples from 9 patients) and Shwachman-Diamond syndrome (6 amplicon libraries from 4 samples from 3 patients). TP53 locus-specific scAmp-seq libraries were generated using a double-nested PCR approach resulting in four PCR rounds. Locus-specific reverse primers preserving the mutation site together with generic forward primers preserving the single-cell barcoding structure were designed. The resulting files were processed using CellRanger 6.0.2 pipelines with default parameters to generate FASTQ files.	Illumina NovaSeq 6000	19
EGAD50000002725	This dataset contains .FASTQ and .BAM files of scRNA-seq data of human bone marrow samples across ERCC6L2 disease (16 samples from 10 patients) and Shwachman-Diamond syndrome (6 samples from 5 patients). We applied single-cell RNA sequencing (scRNA-seq, 3’ 10X Genomics, Chromium Next GEM Single Cell 3' Gene Expression version 3.1 Dual Index chemistry) following manufacturer’s instructions. Libraries were sequenced on Illumina NovaSeq 6000 platform using read lengths: 28bp (Read 1), 10bp (i7 Index), 10bp (i5 Index) and 90bp (Read 2). The resulting files were processed using CellRanger 6.0.2 pipelines with default parameters to generate FASTQ files and count matrices, and the Illumina bcl2fastq v2.2.0 was used to run the mkfastq pipeline and alignment was done using GRCh38.	Illumina NovaSeq 6000	22