scRNA This dataset contains 50 scRNA-seq samples from bone marrow aspirates of 11 multiple myeloma patients experiencing long-term survival and 3 healthy donors. For each donor, total bone marrow and CD3+ T cells were sequenced. For multiple myeloma patients, paired samples were collected at initial diagnosis and between 7-17 years after first-line therapy. Bone marrow mononuclear cells were isolated by Ficoll density gradient centrifugation. For sorting of total bone marrow cells singlet, live cells were gated and sorted, for sorting of T cells CD45+, CD3+ cells were gated and sorted on either FACSAria Fusion or FACSAria II. Single-cell RNA sequencing were generated using 10x Genomics single-cell RNAseq technology (Chromium Single Cell 3’ Solution v2) according to the manufacturer’s protocol and sequenced on an Illumina HiSeq4000 (paired end, 26 and 74 bp). Bulk RNA Singlet, live CD3+CD4- CXCR3+CD8+ and CD3+CD4- CXCR3-CD8+ cells were sorted from 7 bone marrow and 3 peripheral blood samples of 7 multiple myeloma patients using a FACSAria Fusion machine. Bulk-RNA sequencing libraries were generated using the SMART Seq Stranded Total RNA-Seq kit (Takara) and sequenced using the Illumina NovaSeq 6000 platform (2 x 100 bp).
GENCORD2 RNA-seq BAM files using BWA
Single Cell RNA-Seq of Primary GBM. Gender Female, Age, 57.
Bulk RNA-seq for cALL patient-derived PDX samples
Paired-end RNA-seq of follicular T cell lymphoma for the discovery of fusion transcripts
INSPIRE whole transcriptome sequencing of tumors
Purpose: To further understand the molecular pathogenesis of desmoplastic small round cell tumor (DSRCT), a rare but often fatal malignancy occurring primarily in young males, we used next-generation RNA sequencing to investigate the gene expression profiles intrinsic to this disease.Experimental Design: RNA from DSRCT tumor samples were obtained from the Cooperative Human Tissue Network biorepository. RNA sequencing was completed using the Illumina HiSeq 2000 system. Presence of the EWSR1-WT1 fusion was verified using both RNA-sequencing and PCR. Validation studies, including WT1 ChIP-seq, RNA sequencing, and EWS-WT1 knockdown experiments, were performed on an established DSRCT cell line, JN-DSRCT-1. Protein expression of clinically relevant genes determined by RNA sequencing was confirmed using immunohistochemistry. A panel of immune signature genes was also evaluated to identify possible immune therapeutic targets. Results: We analyzed the RNA from 14 tumor samples, of which two were confirmed negative for the diagnostic EWSR1-WT1 translocation. Principal component analysis of the sequencing data indicated that fusion-negative and fusion-positive tumors are transcriptionally distinct entities. Overlapping the significant ChIP-seq peaks with genes found to be highly expressed in the RNA sequencing data revealed that IGF2 and FGFR4 were both highly expressed, and targets of the EWS-WT1 fusion gene. This finding has potential clinical relevance for targeted therapeutic intervention. In addition, we identified the immune checkpoints CD200 and CD276 as potentially targetable genes whose expression is independent of the EWS-WT1 fusion gene in vitro.Conclusions: Despite the transcriptional complexity of this disease, we were able to identify IGF2, FGFR4, CD200, and CD276 as potential therapeutic targets for patients suffering from DSRCT.
DEEP (German Epigenome Project) sequence data of following samples (Sequencing Types: Chip-Seq, WGBS-Seq, RNA-Seq, sncRNA-Seq, NOMe-Se, DNase-Seq): 41_Hf01_LiHe_Ct, 41_Hf02_LiHe_Ct, 41_Hf03_LiHe_Ct, 01_HepG2_LiHG_Ct1, 01_HepG2_LiHG_Ct2, 01_HepaRG_LiHR_D31, 01_HepaRG_LiHR_D32, 01_HepaRG_LiHR_D33, 43_Hm01_BlMo_Ct, 43_Hm03_BlMo_Ct, 43_Hm05_BlMo_Ct, 43_Hm03_BlMa_Ct, 43_Hm05_BlMa_Ct, 43_Hm03_BlMa_TO, 43_Hm05_BlMa_TO, 43_Hm03_BlMa_TE, 43_Hm05_BlMa_TE, 51_Hf01_BlCM_Ct, 51_Hf03_BlCM_Ct, 51_Hf04_BlCM_Ct, 51_Hf02_BlCM_Ct, 51_Hf05_BlCM_Ct, 51_Hf06_BlCM_Ct, 51_Hf06_BlCM_T1, 51_Hf06_BlCM_T2, 51_Hf03_BlEM_Ct, 51_Hf04_BlEM_Ct, 51_Hf02_BlEM_Ct, 51_Hf05_BlEM_Ct, 51_Hf06_BlEM_Ct, 51_Hf06_BlEM_T1, 51_Hf06_BlEM_T2, 51_Hf03_BlTN_Ct, 51_Hf04_BlTN_Ct, 51_Hf02_BlTN_Ct, 51_Hf05_BlTN_Ct, 51_Hf06_BlTN_Ct, 51_Hf06_BlTN_T1, 51_Hf06_BlTN_T2, 51_Hf07_BmTM4_Ct, 51_Hf08_BlTM4_Ct, 51_Hf08_BmTM4_SP1, 51_Hf08_BmTM4_SP2, 51_Hf05_BlTA_Ct, 44_Mm01_WEAd_C2, 44_Mm03_WEAd_C2, 44_Mm02_WEAd_C2, 44_Mm07_WEAd_C2, 44_Mm04_WEAd_C1, 44_Mm05_WEAd_C1
Single-cell multi-omic profiling of healthy controls, asymptomatic and hosptial-admitted COVID19 patients recruited from Newcastle University hospitals. These data also include healthy control volunteers treated with IV-LPS as inflammatory controls. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors.
Single Cell-RNA Seq of Wildtype Primary GBM for Female, Age 50.
