|
| Status |
Public on Apr 30, 2023 |
| Title |
sgLuc rpl4 |
| Sample type |
SRA |
| |
|
| Source name |
Murine whole bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Whole bone marrow
strain: C57BL/6
treatment: sgLuc
|
| Growth protocol |
1-4x10^4 LSK cells from Cas9 knockin mice were transduced with the given sgRNA combinations and transplanted after 24 h into irradiated (7 Gy) C57Bl/6J mice. Complete BM was harvested after presenting with signs of leukemia or after 6 months.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zymo RNA Micro Kit (Zymo Research No. R1050).
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Luc_4
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx
|
| Data processing |
Base calling was performed using standard Illumina software.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Sequencing reads were aligned to the mouse genome using the HISAT2 tool.
Gene expression was measured by transcript abundance, normalized by the FPKM method, utilizing HTSeq software.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA_Seq_genes.readcount.annot.xlsx: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: RNA_Seq_genes.FPKM.annot.xlsx: Matrix table with FPKM values for every gene and every sample.
|
| |
|
| Submission date |
Apr 28, 2021 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Dorit Borchert |
| E-mail(s) |
Borchert.Dorit@mh-hannover.de
|
| Organization name |
Hannover Medical School
|
| Department |
Pediatric Hematology and Oncology
|
| Street address |
Carl-Neuberg-Str. 1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE173496 |
RNA-Seq data for murine BM Tx transduced with different sgRNA combinations [RNA-seq] |
| GSE173497 |
Oncofetal gene reactivation drives EZH2-mutant myeloid leukemia pathogenesis |
|
| Relations |
| BioSample |
SAMN18906427 |
| SRA |
SRX10697819 |
