|
| Status |
Public on Sep 26, 2018 |
| Title |
J |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
age: 43
cell type: mononuclear cells
|
| Treatment protocol |
Ficoll density gradient separation
|
| Growth protocol |
Human bone marrow aspirate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN AllPrep Kit
Illumina TruSeq Stranded Total RNA Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Fastq files were mapped using kallisto 0.43.1. kallisto quant -i ../transcripts.idx -o output --bias LD3047-name_L006_R1_001.fastq.gz LD3047-name_L006_R2_001.fastq.gz
Gene counts were tabulated using tximport.
Deconvolution was performed using Xcell v1.1 (xcell.ucsf.edu) or Cibersort using LM22 gene signature and 100 permutations (cibersort.stanford.edu).
Genome_build: GRCh38
Supplementary_files_format_and_content: "h5" is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length (can be read in by sleuth); "tsv" is a plaintext file of the abundance estimates without bootstrap estimates; "json" is a json file containing information about the run.
|
| |
|
| Submission date |
Sep 25, 2018 |
| Last update date |
Sep 27, 2018 |
| Contact name |
Laura Dillon |
| E-mail(s) |
laura.dillon2@nih.gov
|
| Organization name |
National Heart Lung and Blood Institute, NIH
|
| Department |
Hematology Branch
|
| Lab |
Myeloid Malignancies
|
| Street address |
Room 10CRC 6-5142, 10 Center Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE120444 |
Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry [bulk] |
| GSE120446 |
Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry |
|
| Relations |
| BioSample |
SAMN10127750 |
| SRA |
SRX4737523 |
