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Sample GSM6541583 Query DataSets for GSM6541583
Status Public on Jan 30, 2023
Title bone marrow, R3, 2nd
Sample type SRA
 
Source name bone marrow
Organism Homo sapiens
Characteristics Sex: M
tissue: bone marrow
age: 68
treatment response: Responder
time: 2nd
Extracted molecule total RNA
Extraction protocol RNA was isolated from patient FFPE core bone marrow biopsies using the Qiagen's Rneasy FFPE Kit (Catalog# 73504)
Library preparation, Illumina, RNA with rRNA depletion
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description PDFFPERNA50
Data processing Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files show raw hit counts for each Sample
 
Submission date Sep 02, 2022
Last update date Jan 30, 2023
Contact name Patrycja M Dubielecka
E-mail(s) patrycja_dubielecka-szczerba@brown.edu
Organization name Warren Alpert Medical School of Brown University and Rhode Island Hospital
Department Division of Hematology/Oncology, Department of Medicine
Lab Dubielecka Lab
Street address 1 Hoppin St., Coro West, 5th Fl., Suite 5.36
City Providence
State/province RI
ZIP/Postal code 02903
Country USA
 
Platform ID GPL20301
Series (2)
GSE212615 Transcriptomics of AML core bone marrow biopsies reveals distinct therapy response-specific osteo-mesenchymal profiles
GSE213210 Transcriptomics of AML core bone marrow biopsies reveals distinct therapy response-specific osteo-mesenchymal profiles by RNA-seq and microarray analysis
Relations
BioSample SAMN30649095
SRA SRX17409065

Supplementary file Size Download File type/resource
GSM6541583_PDFFPERNA50.txt.gz 245.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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