Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell analysis of human fetal bone marrow

ABSTRACT: Toal 13 patient samples (Iliac or pyramidal cancellous) were collected with lung cancer who were pathologically diagnosed in Dazhou Central Hospital from June 2020 to January 2021. Patients were monitored by a professional orthopaedic surgeon in the interventional room prior to collecting the samples. This study was approved by the ethics committee and informed consent of patients (IRB2020023). The obtained samples are quickly placed into an Eppendorf tube with PBS buffer for flushing the blood. Then, the samples were cleaned in a cell preservation solution. Finally, the cleaned samples were placed into a sterile EP tube with 2 mL cell preservation solution before being stored in a refrigerator at 4 ° C. Further, the samples with two replicates were sequenced in a 10x genomic chromium platform with a chemistry library (Single Cell 3; v3). The samples were sequenced at BGI (https://www.bgi.com).

INSTRUMENT(S): BGISEQ-500

ORGANISM(S): Homo sapiens

SUBMITTER: Amit Singh

PROVIDER: E-MTAB-11560 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA and CITE sequencing of cells from synovial tissue biopsies of healthy donors, and Rheumatoid Arthritis (RA) patients with active disease or sustained clinical remission

Project description:Synovial biopsies were taken using 14G Precisa Needle (HS Hospital Service, Italy) in ultrasound-guided protocol, and digested as described previously (Alivernini et al, 2020). Live CD45+ cells from the synovial tissue (ST) of healthy donors (n=3), patients with active RA (n=5) and patients in sustained remission (n=2) were sorted for single cell RNA (scRNA) or CITE (scCITE) sequencing using the 10x Genomics platform. Maximum 20,000 immune cells from tissue were sorted into Protein LoBind 1.5 ml Eppendorf tube containing 300 μl of RPMI media with 10% of FSC. Cells were loaded onto a Chromium Controller (10X Genomics) for single-cell partitioning, followed by library preparation using Single-Cell 3’ Reagent Kits v3.1. For 3 healthy ST and 4 ST from active RA (Figure S1), Totalseq Hashtag were used (Biolegend #394601, #394603, #394605, #394607, #394609) to combine 2 samples per run, and TotalSeq™-A Human Universal Cocktail (V1.0) was used to collect protein expression (CITEseq) data together with transcriptome data. Single-cell libraries were sequenced on the Illumina HiSeq 4000 system to a minimum depth of 50k reads/cell.

2024-12-06 | E-MTAB-14213 | biostudies-arrayexpress

Single-cell RNA-sequencing of cardiac cells isolated from infant mouse at postnatal 3 weeks

Project description:To study the gene profiling of different cardiac adipogenic progenitor populations, we isolated individual cells from postnatal 3-week heart and performed single-cell RNA-sequencing. Single cell suspensions from isolated mouse heart were prepared by retrograde Langendorff perfusion. Briefly, mouse at P3W was administered with 0.2 mL heparin sodium salt solution (1000 IU/mL) via intraperitoneal injection and then euthanized by CO2 asphyxiation. The heart was harvested and hung onto the Langendorff apparatus, followed by perfusing with modified Tyrode’s solution (MTS) for 2 min. The heart was next perfused with MTS containing 0.4 mg/ mL collagenase II and 25 µg/ mL DNase I for 10 min. After removed from cannula, atria and valves were removed and ventricles were minced with fine forceps. Cells were filtered through a 70 µm cell strainer and centrifuged at 30x g for 5 minutes at 4°C to remove most cardiomyocytes. The cell suspension was carefully transferred into a new 15 mL centrifuge tube and centrifuged at 300x g for 5 minutes at 4°C. Cell pellet was washed and suspended in DMEM containing 10% FBS for single-cell sequencing. Single cell library was generated using 10x Genomic Chromium system with the v3 single cell reagent kit. Sequencing of library was performed on Illumina NovoSeq 6000 platform.

2020-07-16 | E-MTAB-9366 | biostudies-arrayexpress

Single-nucleus RNA-seq of liver tissue of 3 months old mice to investigate crosstalk between ploidy and zonation

Project description:Single-nucleus RNA-seq-2 method that allows deep characterization of nuclei isolated from frozen archived tissues. We have used this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy. This method has the potential to explore archived samples, for instance to study the development and progression of disease in complex tissues. To illustrate the potential of this method, we have deeply characterized the cellular heterogeneity driven by spatial distribution and different levels of ploidy in the young adult mouse liver.

2021-05-06 | E-MTAB-10223 | biostudies-arrayexpress

Transcriptomes of novel human genomic safe harbor sites for gene and cell therapies

Project description:Bulk RNA-sequencing experiments were performed to analyze the transcriptomic effects of such integrations into two newly established genomic safe harbor sites. Jurkat and HEK293T cells were edited to integrate CMV-mRuby expressing cassette into Rogi2 genomic safe harbor site using Cas9 RNP

2022-02-11 | E-MTAB-11289 | biostudies-arrayexpress

Single cell sequencing for B cell repertoire of multi-year serial blood samples from a healthy donors.

Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from a single healthy donor with an interval of 4 years.

2022-05-14 | E-MTAB-11697 | biostudies-arrayexpress

Single cell sequencing for B cell repertoire of multi-year serial blood samples from two healthy donors.

Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from two healthy donors with an interval of 10 or 6 years.

2022-04-26 | E-MTAB-11174 | biostudies-arrayexpress

Single-cell RNA-seq of tumor-infiltrating lymphocytes in metastatic uveal melanoma

Project description:Metastatic uveal melanoma generally responds poorly to immunotherapy. The aim here was to sequence tumor-infiltrating lymphocytes from uveal melanoma metastases to study their phenotypes and T-cell receptor (TCR) clonotypes. We performed paired single-cell transcriptome and TCR sequencing using the 10x Genomics platform of IL2-expanded tumor-infiltrating lymphocytes from 7 liver and 1 subcutaneous metastasis.

2020-03-16 | E-MTAB-8846 | biostudies-arrayexpress

Spatial transcriptomics of 3-month-old and 18-month-old mouse ovarian and uterine tissues

Project description:We used Visium technology (10X Genomics) to infer cell-to-cell communication in ovarian and uterine tissue based on spatial proximity. Organs from 3-month mice in diestrus and 18-month old mice were collected and frozen in OCT. 10 µm thick tissue slices were placed on Visium Spatial Gene Expression Slides (10X Genomics) and stained with Hematoxylin and Eosin (H&E). Libraries were prepared by manufacturer’s recommendations and sequenced on NovaSeq6000. For samples that were sequenced in two runs, both sequencing runs were merged when running spaceranger (10X Genomics). Original nd2 microscopy images and results of scRNA-seq (linked datasets) and spatial transcriptomics analysis are available at Biostudies (S-BIAD482 and S-BSST852).

2024-07-23 | E-MTAB-12105 | biostudies-arrayexpress

scRNAseq of gastric tumors and adjacent mucosa from Twist2Cre;Lkb1fl/+;Rosa26RTdtomato/+ mice

Project description:5000 target cells per sample where sequenced from 2 gastric tumor samples and 1 sample of adjacent gastric mucosa Twist2Cre;Lkb1fl/+;RosaRTdtomato+/- mice. Drop-seq 10X Genomics (10X v3 library kit) was used for single cell barcoding and library preparation. Samples were sequenced with Novaseq6000.

2024-07-24 | E-MTAB-13624 | biostudies-arrayexpress

Single cell RNA-seq profiles of patient derived organoids

Project description:Three patient-derived organoids from liver metastasis of CRC samples were profiled by scRNA-seq.

2024-02-29 | E-MTAB-13123 | biostudies-arrayexpress