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| Status |
Public on Jun 06, 2024 |
| Title |
RNAseq36low.6 |
| Sample type |
SRA |
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| Source name |
Bone marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell type: hematopoietic stem cells
fus level: low
strain: C57BL/6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fus low and Fus high HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice using fus gtp; Young(2 months) and Aged(30 months) HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice
RNA-seq: First, 100 HSCs (Lineage- Sca-1+ c-kit+ CD34- GFPlow/high) from Fus-gfp mice were sorted into lysis buffer directly. The transcriptome libraries were prepared using Smart-seq2 method. Then, Agilent Bioanalyzer 2100 system (Agilent Technologies) was used to assess the insertion size, and HiSeq PE Cluster Kit v4-cBot-HS (Illumina) was used to perform the clustering of the index-coded samples according the manufacturer’s instructions. Finally, the libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Hi-C: Hi-C data analysis was performed with HiC-Pro(https://github.com/nservant/HiC-Pro).
CUT&RUN: CTCF CUT&RUN data was performed with CUT&RUNTools piplines(https://bitbucket.org/qzhudfci/cutruntools/src/master/).
RNA-seq:Reads were mapped to reference genome mm10 by Hisat2(version 2.2.1), and then counted for each gene by htseq-count(version 0.11.1). Next, DEseq2(version 1.26.0) was used to get differentially expressed genes
Assembly: mm10
Supplementary files format and content: hic(Hi-C data valid pairs)
Supplementary files format and content: bigWig(CTCF signal), bed(seacr peaks)
Supplementary files format and content: tab-delimited text (RNA-seq counts), matrix table (gene TPM counts for every gene and every sample)
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| Submission date |
Jul 25, 2022 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Jianwei Wang |
| E-mail(s) |
wangjianwei@ihcams.ac.cn
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| Organization name |
HAIHE LABORATORY OF CELL ECOSYSTEM
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| Street address |
10 Yuexin Street, Binhai New Area
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| City |
Tianjin |
| ZIP/Postal code |
300301 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE209715 |
Chromatin structure and gene expression signatures in FUS low and high expressed hematopoietic stem cells |
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| Relations |
| BioSample |
SAMN29946694 |
| SRA |
SRX16660377 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6387262_M_36low-6_htseq_counts.txt.gz |
92.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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