|
| Status |
Public on Jun 19, 2022 |
| Title |
BM sample pre/post allo-SCT |
| Sample type |
SRA |
| |
|
| Source name |
BM aspiration from UPN57 and UPN36
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: BM aspiration from UPN57 and UPN36
cell type: CD34-purified bone marrow cells
indice: illumina index 1 (i7) sequence: Library reverse primer 2(CGAGGCTG)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We prepared BM samples at three time points from identical patients: non-hCR before SCT, CR at engraftment after allo-SCT, and non-hCR at relapse. We purified CD34+ cells from each sample using an indirect CD34 MicroBead Kit (Miltenyi Biotec). Cells (4,000) from each sample were used for single-cell isolation using BD Rhapsody Single-Cell Analysis System (BD Biosciences). Before single-cell isolation, all cells were labeled using a BD Single-Cell Multiplexing Kit and BD AbSeq antibody against TIM-3; six samples derived from two patients were loaded onto a single cartridge
cDNA library preparation was performed according to the manufacturer’s instructions. For cDNA amplification, we used costumed 435 primer pairs (46 genes associated with stem cell signature on BD Onco-BC Panel Hs, which contains 389 genes). An aliquot of the PCR products was used for assessing concentration and for the quality check of size and integrity using a Qubit (High Sensitivity dsDNA kit, Thermo Fisher Scientific) and the Agilent 4200 TapeStation system (High Sensitivity D1000 screen tape, Agilent), respectively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
This file were multiplexed using BD Single-cell Multiplexing Kit Sample Tag - Human
Sample name | Title | Sample Tag
Sample7 | UPN57: diagnosis| BD Single-cell Multiplexing Kit Sample Tag 7
Sample8 | UPN57: hCR at day 28 post SCT | BD Single-cell Multiplexing Kit Sample Tag 8
Sample9 | UPN57: Relapse at day 84 post-SCT | BD Single-cell Multiplexing Kit Sample Tag 9
Sample10 | UPN36: diagnosis| BD Single-cell Multiplexing Kit Sample Tag 10
Sample11 | UPN36: hCR at day17 post SCT| BD Single-cell Multiplexing Kit Sample Tag 11
Sample12 | UPN36: Relapse at day 224 post SCT| BD Single-cell Multiplexing Kit Sample Tag 12
|
| Data processing |
Basecalls performed using bcl2fastq version 2.20.0.422.
FASTQ files obtained from sequencing were provided to the BD Targeted Multplex Rhapsody Analysis Pypeline Version 1.8 (BD Biosciences) with the default settings.
Molecule count data were adjusted using the distribution-based error correction (DBEC) algorithm.
Assembly: Hg19
Supplementary files format and content: Matrix table with counted mols per cells for every gene and every sample
|
| |
|
| Submission date |
Jun 16, 2022 |
| Last update date |
Jun 19, 2022 |
| Contact name |
Teppei Sakoda |
| E-mail(s) |
s_teppei@mti.biglobe.ne.jp
|
| Organization name |
Kyushu University
|
| Street address |
3-1-1, Maidashi, Higashi-ku
|
| City |
Fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE206251 |
targeted single-cell RNA sequencing data of residual TIM-3+ leukemic stem cells post-SCT_2 |
|
| Relations |
| BioSample |
SAMN29135714 |
| SRA |
SRX15720290 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6248703_984_Kyushu_University_Faculty_of_Medicine2_amplicons.fasta.gz |
52.3 Kb |
(ftp)(http) |
FASTA |
| GSM6248703_BDAbSeq_Tim3.fasta.gz |
98 b |
(ftp)(http) |
FASTA |
| GSM6248703_Sample2_SampleTag07_hs_DBEC_MolsPerCell.csv.gz |
147.3 Kb |
(ftp)(http) |
CSV |
| GSM6248703_Sample2_SampleTag08_hs_DBEC_MolsPerCell.csv.gz |
129.7 Kb |
(ftp)(http) |
CSV |
| GSM6248703_Sample2_SampleTag09_hs_DBEC_MolsPerCell.csv.gz |
129.8 Kb |
(ftp)(http) |
CSV |
| GSM6248703_Sample2_SampleTag10_hs_DBEC_MolsPerCell.csv.gz |
197.5 Kb |
(ftp)(http) |
CSV |
| GSM6248703_Sample2_SampleTag11_hs_DBEC_MolsPerCell.csv.gz |
103.9 Kb |
(ftp)(http) |
CSV |
| GSM6248703_Sample2_SampleTag12_hs_DBEC_MolsPerCell.csv.gz |
68.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
