|
| Status |
Public on Feb 28, 2019 |
| Title |
AML707B-nanopore |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow aspirate from AML patient
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
age: 26
|
| Treatment protocol |
Not applicable, material from human subjects
|
| Growth protocol |
Not applicable, material from human subjects
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bone marrow aspirates were viably frozen after using density gradient centrifugation to isolate mononuclear cells.
Single-cell transcriptome analysis was performed using the Seq-Well method.
Bone marrow aspirates were viably frozen after using density gradient centrifugation to isolate mononuclear cells.
Single-cell transcriptome analysis was performed using the Seq-Well method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
Single cell nanopore data for AML707B
|
| Data processing |
Data procesing was performed in three main steps:
1) Cell barcodes were extracted from sequencing reads prior to alignment.
2) Reads were aligned to the human genome using STAR guided by RefSeq gene annoations, producing both genome and pseudo-transcriptome alignments.
3) For each cell barcode, reads mapping uniquely to a gene were collapsed by their unique molecular identifier (UMI).
4) For each gene and cell barcode the number of UMIs was used to generate a digital expression matrix (DEM).
Genome_build: Hg38
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files. There are two files per sample. The first file contains a number of annotations (columns) for each cell (rows). The second file contains a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns).
|
| |
|
| Submission date |
Feb 01, 2019 |
| Last update date |
Mar 02, 2019 |
| Contact name |
Peter van Galen |
| E-mail(s) |
petervangalen@gmail.com, pvangalen@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital / Broad Institute of MIT and Harvard
|
| Department |
Hematology
|
| Lab |
Van Galen Lab
|
| Street address |
4 Blackfan Circle
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE116256 |
Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity |
|
| Relations |
| BioSample |
SAMN10861630 |
| SRA |
SRX5324551 |
