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| Status |
Public on May 11, 2019 |
| Title |
23C_ILC2 |
| Sample type |
SRA |
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| Source name |
ILC2 sorted from lung
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| Organism |
Homo sapiens |
| Characteristics |
disease: Tuberculosis
tissue: Lung
cell population: ILC2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from cell lysate (RLT +1% BME) using RNAClean XP SPRI beads. Messenger RNA was primed for reverse transcription and PCR using an oligodT RT primer.
Libraries were constructed using a modified version of the Smart-Seq2 protocol described in Trombetta et al., Curr Protoc Mol Biol, (2014). Libraries were sequenced twice on a NextSeq 500 using the 75-cycle High Throughput kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
hTB_counts.txt
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| Data processing |
Demultiplexing was performed using bcl2fastq2-2.17.1.14 (Illumina).
TopHat (2.0.10) and RSEM (1.2.8) were used to perform genome and transcriptome alignment, respectively, against the hg38 reference (Gencode v21).
Picard Tools were used to determine sample quality metrics. Samples with fewer than 10^6 reads or fewer than 10,000 aligned genes were removed from this study.
Gene expression matrices were generated using RSEM.
Differential Expression analysis was performed using DESeq2 (1.14.1).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt file containing counts for each sample.
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| Submission date |
May 10, 2019 |
| Last update date |
May 12, 2019 |
| Contact name |
Alasdair Leslie |
| E-mail(s) |
al.leslie@ahri.org
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| Organization name |
African Health Research Institute
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| Lab |
Leslie Lab
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| Street address |
719 Umbilo Road
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| City |
Durban |
| ZIP/Postal code |
4001 |
| Country |
South Africa |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE131031 |
Group 3 innate lymphoid cells mediate early protective immunity against Mycobacterium tuberculosis |
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| Relations |
| BioSample |
SAMN11618977 |
| SRA |
SRX5818164 |
| 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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