20210129

Contents

1. Working directories
2. Move documents in BaiduNetDisk
3. SRA Analysis
1. 3.1. SRP262513 (SRA Study)
  1. 3.1.1. Procedures
  2. 3.1.2. Characterisation of Ovarian Cancer Cell Line NIH-OVCAR3 and Implications of Genomic, Transcriptomic, Proteomic and Functional DNA Damage Response Biomarkers for Therapeutic Targeting
    1. 3.1.2.1. RNA-Seq
4. SRA (Sequence Read Archive)

Working directories

i=/media/ht/ht_5T/Work/肿瘤室工作/日常管理/组会/周一科室会/20201221
pcmanfm -n ${i}; cd ${i} # Backup of Powerpoint document
#
i=/media/ht/ht_5T/Work/References/Computer_Tips/Office_Tips/Excel/Agenda
pcmanfm -n ${i}; cd ${i} # Agenda in Excel format
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA
pcmanfm -n ${i}; cd ${i} # HLA-G analysis
#
i=/media/ht/ht_5T/eBooks/网络小说
pcmanfm -n ${i}; cd ${i} # [藏地密码.7z](/media/ht/ht_5T/eBooks/网络小说/藏地密码.7z)
#
i=/media/ht/ht_5T/Work/Funding/2017_重大专项/Management/Administration/09_02_63_HEV/HEV_Notes_20210129_1610.docx
setsid wps ${i} # Revised document for Yin Wenjiao
#
#########################################################
########### E-MTAB-1733 ###################################
#########################################################
#
i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/E-MTAB-1733_Note.Rmd
subl ${i}
#
i=/media/ht/ht_5T_5/HLA-G/SRA/E-MTAB-1733/
pcmanfm -n ${i}; cd ${i} # HLA-G in adults
#
i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/
pcmanfm -n ${i}; cd ${i} # SRA analysis
#
subl /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/README.sh
#
setsid wps /media/ht/ht_5T_5/HLA-G/SRA/Summary/HLA-G_Note_20210128_0818.docx

Send HLA-G_Sum.pdf to GYF. Good review from p169.
藏地密码.7z
Remote Desktop Software for Linux – AnyDesk, AnyDesk update

1
2
3

axel https://download.anydesk.com/linux/anydesk_6.1.0-1_amd64.deb
#
wget -rnp https://download.anydesk.com/linux/

Move documents in BaiduNetDisk

1 2	i=/media/ht/ht_5T/Work/References/Computer_Tips/Office_Tips/Excel/Agenda pcmanfm -n ${i}; cd ${i} # Agenda in Excel format

Direcotry, resources

1日程表【微信公众号：Word联盟】.xltx
2日程表【微信公众号：Word联盟】.xltx
3日程表【微信公众号：Word联盟】.xltm
4日程表【微信公众号：Word联盟】.xltx
5日程表【微信公众号：Word联盟】.xltx
6日程表【微信公众号：Word联盟】.xltx

Cahnge to as below

1日程表.xltx
2日程表.xltx
3日程表.xltm
4日程表.xltx
5日程表.xltx
6日程表.xltx

SRA Analysis

1 2	i=/media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA pcmanfm -n ${i}; cd ${i} # HLA-G analysis

Error

Error: NCBI C++ Exception:
    T0 "/media/ht/ht_2T/Work/Bioinformatics/Bioinfo-Softs/NCBI/magicblast/ncbi-magicblast-1.2.0-src/c++/src/sra/readers/sra/vdbread.cpp", line 996: Error: ncbi::objects::CVDBColumn::Init() - Cannot get VDB column: /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/SRR11296728.sra.READ (0x31c5044a: file invalid while opening directory within file system module)

[bam_sort_core] merging from 1 files and 1 in-memory blocks...
^[[FError: NCBI C++ Exception:
    T0 "/media/ht/ht_2T/Work/Bioinformatics/Bioinfo-Softs/NCBI/magicblast/ncbi-magicblast-1.2.0-src/c++/src/sra/readers/sra/vdbread.cpp", line 996: Error: ncbi::objects::CVDBColumn::Init() - Cannot get VDB column: /media/ht/ht_5T_5/HLA-G/SRA/Endometrial_Cancer/SRA/SRR11296841.sra.READ (0x31c5044a: file invalid while opening directory within file system module)

SRP262513 (SRA Study)

SRR11819915.sra
SRR11819919.sra
SRR11819923.sra

SRR11819915_vs_HLA为空文件。

SRR13281020.sra, Run Browser : Browse : Sequence Read Archive : NCBI/NLM/NIH in Studies : Browse : Sequence Read Archive : NCBI/NLM/NIH. (Ref. Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest - PubMed)

SRP262513.xlsx established. SRP262513.xlsx

**Current viewer**

Tab delimited format
Run Selector :: NCBI

**Old version viewer**

CSV (comma-separated values)
NCBI :: SRA Run Selector

Procedures

Visit Run Selector :: NCBI and search with SRP262513.
Run Selector :: NCBI. Click Metadata to download SraRunTable.txt (Current viewer).
Select “SRR11819915” and browse Run Browser : Browse : Sequence Read Archive : NCBI/NLM/NIH.
Click “SRP262513” from “SRA Study” and browse Studies : Browse : Sequence Read Archive : NCBI/NLM/NIH.
Check “External Link” for reference (Characterisation of Ovarian Cancer Cell Line NIH-OVCAR3 and Implications of Genomic, Transcriptomic, Proteomic and Functional DNA Damage Response Biomarkers for Therapeutic Targeting - PubMed).

Characterisation of Ovarian Cancer Cell Line NIH-OVCAR3 and Implications of Genomic, Transcriptomic, Proteomic and Functional DNA Damage Response Biomarkers for Therapeutic Targeting

In order to be effective models to identify biomarkers of chemotherapy response, cancer cell lines require thorough characterization. In this study, we characterised the widely used high grade serous ovarian cancer (HGSOC) cell line NIH-OVCAR3 using bioinformatics, cytotoxicity assays and molecular/functional analyses of DNA damage response (DDR) pathways in comparison to an ovarian cancer cell line panel. Bioinformatic analysis confirmed the HGSOC-like features of NIH-OVCAR3, including low mutation frequency, TP53 loss and high copy number alteration frequency similar to 201 HGSOCs analysed (TCGA). Cytotoxicity assays were performed for the standard of care chemotherapy, carboplatin, and DDR targeting drugs: rucaparib (a PARP inhibitor) and VE-821 (an ATR inhibitor). Interestingly, NIH-OVCAR3 cells showed sensitivity to carboplatin and rucaparib which was explained by functional loss of homologous recombination repair (HRR) identified by plasmid re-joining assay, despite the ability to form RAD51 foci and absence of mutations in HRR genes. NIH-OVCAR3 cells also showed high non-homologous end joining activity, which may contribute to HRR loss and along with genomic amplification in ATR and TOPBP1, could explain the resistance to VE-821. In summary, NIH-OVCAR3 cells highlight the complexity of HGSOCs and that genomic or functional characterization alone might not be enough to predict/explain chemotherapy response.

Keywords: ATR; PARP; homologous recombination repair; non-homologous end-joining; ovarian cancer; platinum.

RNA-Seq

Cell pellets containing ~40,000 cells were collected of the 13 ovarian cancer cell lines (Table S3) including the NIH-OVCAR3 cells, and cryo-preserved and shipped for targeted RNA-Sequencing analysis by HTG Molecular Diagnostics Inc. (Tucson, AZ, USA). The samples were run on the Illumina NextSeq (Illumina, San Diego, CA, USA) with the HTG EdgeSeq Oncology biomarker panel assay (961–002) containing probes against 2567 genes including 15 housekeeper genes, and four negative and four positive process control genes. The HTG EdgeSeq Parser was used to align FASTQ files to probe list by the company. Following quality control, the raw read counts were estimated followed by estimation of read counts per million after median normalisation. The normalized gene expression for selected DDR genes was calculated by using expression of ACTB gene as the normalization control, which showed the least standard deviation of gene expression across cell lines. The data is accessible through GEO submission GSE150942 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150942).
RNA-Seq data (read counts) for NIH-OVCAR3 cell line was downloaded from the CCLE database
(https://portals.broadinstitute.org/ccle/data).

SRA (Sequence Read Archive)

Studies : Browse : Sequence Read Archive : NCBI/NLM/NIH