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| Status |
Public on Jul 30, 2019 |
| Title |
70136: Control track for Bhlhe40 ChIP-seq (mock’ precipitation sample without antibody) |
| Sample type |
SRA |
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| Source name |
Alveolar macrophages
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| Organism |
Mus musculus |
| Characteristics |
tissue: Alveolar macrophages
genotype: Bhlhe40+/+Bhlhe41+/+
strain background: C57BL/6
cell isolation: Ex vivo, isolated from bronchoalveolar lavage fluid by adherence to plastic
cell-sorting strategy: N/A
chip antibody: N/A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
No extraction
ChIP tagmentation protocol (Gustafsson et al, 2018)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP-seq: For Bhlhe40 ChIP-seq, the reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie program version 1.0.0; for H3K27ac ChIP-seq samples reads were aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9), using the Bowtie2 program (usegalaxy.eu; version 2.3.4.2). Resulting BAM files were processed with BAM to Wiggle (usegalaxy.eu; version Version 2.6.4) and Wig/BedGraph-to-bigWig (usegalaxy.eu; version Version 1.1.1) converters.
RNA-seq: 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). 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. For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (Anders et al, 2014) with the overlap resolution mode set to 'union'. The data sets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 2014). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).
Genome_build: MM9
Supplementary_files_format_and_content: RNA-seq: Excel table with 4 tabs: TPM values for all samples and output of DEseq2 for three pairwise comparisons, see ‘data processing step’ for details. ChIP-seq: Bigwig files provided for all samples, see ‘data processing step’ for details.
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| Submission date |
Jul 29, 2019 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Taras Kreslavsky |
| E-mail(s) |
taras.kreslavskiy@ki.se
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| Phone |
+46761124813
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| Organization name |
Karolinska Institutet
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| Department |
Department of Medicine, Solna (MedS)
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| Lab |
Taras Kreslavsky
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| Street address |
Nks Bioclinicum, J7:30, Visionsgatan 4
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| City |
Solna |
| ZIP/Postal code |
171 64 |
| Country |
Sweden |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE135018 |
Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity |
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| Relations |
| BioSample |
SAMN12390264 |
| SRA |
SRX6608074 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3983823_70137.bigwig |
1.5 Gb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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