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Sample GSM3400916 Query DataSets for GSM3400916
Status Public on Sep 26, 2018
Title H
Sample type SRA
 
Source name Bone marrow
Organism Homo sapiens
Characteristics tissue: Bone marrow
age: 50
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 Christopher Hourigan
E-mail(s) christopher.hourigan@nih.gov
Phone 3014510257
Organization name National Heart Lung and Blood Institute, NIH
Department Hematology Branch
Lab Myeloid Malignancies
Street address Room 10CRC 5-5130, 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 SAMN10127751
SRA SRX4737522

Supplementary file Size Download File type/resource
GSM3400916_abundance_H.h5 2.9 Mb (ftp)(http) H5
GSM3400916_abundance_H.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM3400916_run_info_H.json.gz 248 b (ftp)(http) JSON
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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