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| Status |
Public on Feb 26, 2020 |
| Title |
BM3W_R1 |
| Sample type |
SRA |
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| Source name |
B cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
donor: 1
harvest time: 3 weeks
genotype: IgHEL transgenic
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® UltraII RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
feature_counts.csv
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| Data processing |
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample
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| Submission date |
Aug 09, 2019 |
| Last update date |
Feb 26, 2020 |
| Contact name |
Adam Cribbs |
| E-mail(s) |
[email protected]
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| Organization name |
University of Oxford
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| Department |
NDORMS
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| Street address |
Windmill Road
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| City |
Oxford |
| ZIP/Postal code |
OX37LD |
| Country |
United Kingdom |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE135648 |
An ontogenetic switch in the positive and negative selection of B cells [IgHEL] |
| GSE135650 |
An ontogenetic switch in the positive and negative selection of B cells |
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| Relations |
| BioSample |
SAMN12546239 |
| SRA |
SRX6691072 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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