|
| Status |
Public on Oct 02, 2023 |
| Title |
trial number 07, Responder at baseline |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Myeloproliferative neoplasms
treatment response: responder
timepoint: baseline
tissue: Peripheral blood
cell type: CD34+ HSPCs
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After ficoll centrifugation of blood, mononuclear cells were subjected to red blood cell lysis and CD34+ HSPCs were immunomagnetically isolated using the Ultrapure CD34 microbead kit suing AUTOMACS. RNA was extracted using Trizol.
Briefly, the Smart-seq2 protocol was implemented with improved reverse transcription, template switching and preamplification to increase both yield and length of cDNA libraries generated from individual cells. The Illumina-compatible cDNA sequencing library was prepared with Nextera XT DNA Library Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
07_00
|
| Data processing |
Sequencing fastq files were demultiplexed using Casava v1.8.2 pipeline.
Reads with adapter contaminations were trimmed using cutadapt.
The alignment of reads to the reference genome was performed using TopHat version v2.1.0; the quantification of expression was performed using RSEM v1.17
Only genes with more than 2 counts per million in at least 2 samples were considered for statistical analysis.
Normalisation and differential expression analysis was performed using DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: normalised expression matrix
|
| |
|
| Submission date |
Apr 13, 2021 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Wellcome-MRC Cambridge Stem Cell Institute
|
| Street address |
Puddicombe Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE172022 |
Bulk RNAseq of primary CD34+ HSPCs in Myeloproliferative neoplasms patients receiving tamoxifen |
| GSE172025 |
RNA-seq of Myeloproliferative neoplasms primary CD34+ HSPCs and cell lines after tamoxifen treatment |
|
| Relations |
| BioSample |
SAMN18736932 |
| SRA |
SRX10596387 |
