Bulk RNA sequencing of bone marrow cells from MDS-RS patients and healthy donors

This dataset consists of bulk RNA sequencing data of MACS-separated bone marrow cells (CD34+ stem cells, GPA+ erythroblasts, CD71+ reticulocytes, ring sideroblasts and siderocytes) obtained from multiple healthy bone marrow donors and MDS-RS patients. A second minibulk dataset is included, where CD34+ and GPA+ cells were treated with cycloheximide or left untreated. The objective of this data collection was to assess several parameters on how the bone marrow of MDS-RS patients differs from that of healthy donors.

This dataset includes raw sequencing data in .fastq format, processed count matrices and associated pseudonymized metadata.

Processing:
Bulk:
CD34+ HSPC samples, mixed GPA+ erythroblast samples and CD71+ PB reticulocyte samples (RetPB) were isolated through MACS. RS and siderocytes were obtained through MACS+FACS. Cells were lysed in RLT (Qiagen) + 40 mM dithiothreitol (Sigma-Aldrich) and RNA extraction was performed with RNeasy Micro Kit (Qiagen) with RNase-free DNase treatment according to the manufacturer’s protocol. RNA integrity numbers (RIN) were estimated using Agilent RNA 6000 Pico Kits (Agilent Technologies, CA, USA). A minimum RIN value of 6.5 was considered adequate.

Minibulk:
Minibulk RNAseq was performed for assessment of cycloheximide treatment effects in CD34+ and GPA+ cell populations. The library preparation procedure was performed using the Xpress Genomics bulk RNA-seq kit v1, automated on a SP960 liquid handler (MGI Tech). In short, the library preparation procedure denatures RNA samples in presence of oligo-dT primer, which is followed by reverse transcription of RNA with a template-switching procedure and pre-amplification of full-length cDNA for 10 PCR cycles. cDNA was subsequently tagmented using Tn5 (TDE1 Tagment DNA Enzyme; Illumina) and reactions quenched after 10 min at 55 °C by addition of 0.2 % SDS (Sigma-Aldrich). Tagmented DNA was indexed using custom dual-unique Nextera index primers in a 12 cycle PCR reaction. Indexed libraries were cleaned up using SPRI beads in 22% PEG8000 buffer and eluted in 12 µL H2O.

The dataset consists of 2 folders:
- Bulk_Main
- Minibulk_Cycloheximide

The folder Bulk_Main contains 67 GNU zipped fastq files, 1 tsv file, and 1 txt file.
The folder Minibulk_Cycloheximide contains 2 GNU zipped fastq files, and 4 txt files.

The documentation file File_list_BulkMinibulk.txt contains a full list of the files in the dataset.

The total size of the dataset is approximately 360 GB.