|
| Status |
Public on Jan 30, 2023 |
| Title |
bone marrow, R5, 1st |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: F
tissue: bone marrow
age: 66
treatment response: Responder
time: 1st
|
| 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 |
PDFFPERNA52
|
| 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 |
SAMN30649094 |
| SRA |
SRX17409066 |
