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| Status |
Public on Mar 15, 2024 |
| Title |
cKO_t-1 |
| Sample type |
SRA |
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| Source name |
Bone marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell type: Lin-cKit+
genotype: Atf4 KO
treatment: 2nd transplantation
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly sorted Lin-cKit+ and CMP cells from the BM of WT or KO mice.
For 10x Genomics scRNA-seq, samples with cell viability >80%, a cell concentration ranging from 700 cells/ml to 1,200 cells/ml (based on trypan blue staining), and cell diameters ranging from 5 mm to 40 mm were collected and analyzed. A Chromium Single cell 30 Library and Gel Bead Kit V2 (10x Genomics) were used to generate single-cell gel beads in emulsion for reverse transcription and library preparation. Sequencing was performed on an Illumina HiSeq PE150 platform with 50,000 to 100,000 reads per cell and a 70–80% saturation level, as recommended by the manufacturer (10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 fl/fl mice in homeostasis.
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 fl/fl mice after secon transplantation.
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 KO mice in homeostasis.
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 KO mice after secon transplantation.
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| Submission date |
Jun 26, 2023 |
| Last update date |
Mar 15, 2024 |
| Contact name |
chao tang |
| E-mail(s) |
tangchao@ihcams.ac.cn
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| Organization name |
Institute of Hematology and Blood Diseases Hospital
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| Street address |
288 Nanjing Road
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| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE235798 |
Atf4 promotes erythroid differentiation by regulating ribosome biogenesis via RPS19BP1 |
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| Relations |
| BioSample |
SAMN36008393 |
| SRA |
SRX20800377 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7509777_cKO_t.tar.gz |
133.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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