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| Status |
Public on Feb 03, 2020 |
| Title |
HD_1_S60 |
| Sample type |
SRA |
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| Source name |
Bone marrow
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| Organism |
Homo sapiens |
| Characteristics |
age: 50
gender: F
disease status: Healthy
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| Treatment protocol |
No treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from PAXgeneTM BM RNA tubes using the PAXgene BM RNA kit (PreAnalytiX). RNA quantity was measured using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA quality was assessed using the TapeStation system (Agilent Technologies, Santa Clara, CA). All samples had RNA Integrity Numbers (RIN) of seven or higher.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina Inc., San Diego, CA) using 1 μg of total RNA input and paired-end 75-bp sequencing on a HiSeq 3000 (Illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
S60
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| Data processing |
Reads were aligned to human genome assembly GRCh37/hg19 by HISAT2 (version 2.1.0) with default setting for paired-end reads. The aligned reads were converted to BAM files and sorted by SAMtools 1.9 with index files created. The sorted BAM files were processed in R (version 3.5; R Foundation for Statistical Computing, Vienna, Austria) with Bioconductor packages. The count matrix on gene level was generated by featureCounts in Rsubread function.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Gene raw count matrix in csv
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| Submission date |
Oct 10, 2019 |
| Last update date |
Jul 20, 2020 |
| Contact name |
Laura Dillon |
| E-mail(s) |
laura.dillon2@nih.gov
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| Organization name |
National Heart Lung and Blood Institute, NIH
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| Department |
Hematology Branch
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| Lab |
Myeloid Malignancies
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| Street address |
Room 10CRC 6-5142, 10 Center Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE138702 |
Highly multiplexed proteomic assessment of the human bone marrow microenvironment reveals elevated levels of CCL23 in acute myeloid leukemia |
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| Relations |
| BioSample |
SAMN13011899 |
| SRA |
SRX6975515 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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