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| Status |
Public on Nov 30, 2018 |
| Title |
RNA-seq follicular B cell [22431] |
| Sample type |
SRA |
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| Source name |
Follicular B cell
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wildtype
cell preparation: Ex-vivo, FACS-sorted
cell sorting strategy: (CD19+ B220+ CD23hi CD21int)
chip antibody: n.a.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
RNA-seq follicular B cell [22431] wildtype
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| Data processing |
The database generation of RefSeq-annotated genes was performed as previously described (Wöhner et al., 2016). To refine the annotation of immunoglobulin genes, the immunoglobulin l light-chain segments were replaced with their corresponding converted GRCm38.p3 annotations (Ensembl version 79) (Yates et al., 2016). The resulting number of genes was 24,732.
In case of RNA-seq experiments, reads corresponding to mouse ribosomal RNAs (BK000964.1 and NR046144.1) were removed. The remaining reads were cut down to a read length of 44 nucleotides and aligned to the mouse transcriptome (genome assembly version of July 2007 NCBI37/mm9) using TopHat version 1.4.1 (Trapnell et al, 2009).
In case of ChIP-seq, GRO-Seq and ATAC-seq experiments, all sequence reads that passed the Illumina quality filtering were considered for alignment after adapter trimming. The remaining reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program versions 0.12.1, 1.0.0 and 2.1.0, respectively [Langmead et al, 2009; 2014]. For GRO-Seq, additional four bases were trimmed after adapter trimming and filtered against the rDNA with Bowtie version 2.1.0 before mouse genome alignment. For ATAC-seq, additional alignment parameters were ‘-sensitive -X 5000’
The number of reads per gene was counted using featureCounts version 1.5.0 with default settings. TPM values were calculated as described in Liao et al., Bioinformatic (2014).
Peak calling: Peaks were called using the MACS program version 2.1.0 (ref. (Zhang et al., 2008)) with default parameters, appropriate input for Pro-B and Mature B cell (Pro -B: GSM1145867, Schwickert et al., 2014; Mature B: GSM2058441, Wöhner et al., 2016) and a genome size of 2.654.911.517 bp (mm9). 889 peaks (Pro-B) and 14512 peaks (Mature B) had a signficant p-value (< 1e-05). Peaks were further filtered for P values of < 10-10, which resulted in 762 (Pro-B) and 9320 (Mature B), respectively.
Read coverage bigwig files were created using bedtools version 2.26.0 with MACS2 predicted fragment sizes.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base (.cov.all.rpm.bw) or bigWig Track format of read density coverage in reads per million after extension to 150 base pairs (.density_150.rpm.bw); text tab delim = TPM values in ASCII text format tab delimited
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| Submission date |
Mar 12, 2018 |
| Last update date |
Dec 03, 2018 |
| Contact name |
Meinrad Busslinger |
| E-mail(s) |
meinrad.busslinger@imp.ac.at
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| Organization name |
IMP
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| Lab |
Busslinger
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
A-1030 |
| Country |
Austria |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE111692 |
Precocious expression of Blimp1 in the B cell lineage causes autoimmunity |
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| Relations |
| BioSample |
SAMN08687054 |
| SRA |
SRX3781849 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3037408_TPM_22431.txt.gz |
229.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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