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| Status |
Public on Aug 21, 2021 |
| Title |
H596 |
| Sample type |
SRA |
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| Source name |
H596 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H596
cell type: Lung adenocarcinoma
treatment: Untreated
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| Treatment protocol |
Untreated
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| Growth protocol |
H2087 and H596 cells were cultured at 37˚C in a humidified atmosphere with 5% CO2 in Corning® RPMI medium (Corning Inc., Corning, NY, USA) supplemented with 10% Corning® Fetal Bovine Serum (Corning Inc., Corning, NY, USA), and 100 U/ml penicillin and 100 mg/ml streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from cells were isolated using TRIzol® (Invitrogen, Carlsbad, CA, USA). TruSeq Stranded mRNA LT Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide(Part #15031047 Rev. E) protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina bcl2fastq v1.8.4 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh37 whole genome by using HISAT2 version 2.0.5 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Aug 18, 2021 |
| Last update date |
Aug 21, 2021 |
| Contact name |
Hyo-Gyoung Kang |
| E-mail(s) |
pearlblue0@gmail.com
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| Organization name |
Kyungpook National University
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| Department |
Cell and Matrix Research Institute, School of Medicine
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| Street address |
Hoguk-ro, Buk-gu
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| City |
Daegu |
| ZIP/Postal code |
41404 |
| Country |
South Korea |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE182383 |
Transcriptomic analyses of lung adenocarcinoma cells |
| GSE182385 |
Transcriptomic analyses of lung adenocarcinoma cells and genome-wide maps of chromatin state in lung adenocarcinoma cells |
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| Relations |
| BioSample |
SAMN20850952 |
| SRA |
SRX11813190 |
| 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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