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| Status |
Public on Oct 12, 2017 |
| Title |
48C |
| Sample type |
SRA |
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| Source name |
colon
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| Organism |
Homo sapiens |
| Characteristics |
pair id: 48
tissue: colon cancer tissue
Sex: female
Stage: T4N0M0
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were immediately frozen in liquid nitrogen and stored at -80℃ until further use.RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
rRNAs were removed from Total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA) and fragmented to approximately 200bp. Subsequently, the purified RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
bcl2fastq-2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 –r 70 --library-type fr-unstranded
Transcripts per million (TPM) were calculated using a protocol from Günter P. Wagner, Koryu Kin, Vincent J. Lynch. Theory Biosci. (2012) 131:281285.
Genome_build: hg19
Supplementary_files_format_and_content: gene_exp.txt: Tab-delimited text file includes COUNT and TPM values for each Sample.
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| Submission date |
Oct 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Meng |
| E-mail(s) |
shiyicissy@126.com
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| Phone |
17732812697
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| Organization name |
colon tissues
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| Street address |
12# Jiankang road
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| City |
Shijiazhuang |
| ZIP/Postal code |
050011 |
| Country |
China |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE104836 |
Differentially expressed LncRNAs and mRNA identified by SEQ analysis in colorectal cancer patients |
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| Relations |
| BioSample |
SAMN07775096 |
| SRA |
SRX3301672 |
| 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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