---
title: '浜田研リソース'
disqus: hackmd
---

# Guidelines on Access to Restricted Resources for Hamada Lab Members

## The International Cancer Genome Consortium (ICGC)

### Summary

* ICGC has collected data of 86 cancer projects including TCGA
* Data types including somatic mutation, DNA methylation, gene/protein expression
* ICGC homepage: https://dcc.icgc.org/
* Access Expiry Date: ==2024-10-19==

### Application for Access

1. Contact Prof. Hamada and Zeng-san with Slack DM.
2. Get permission from Prof. Hamada.
3. You will receive a Token ID with 1-year granted access via **Collaboratory** and **Data Portal** repository
4. Read [data access policies](https://www.icgc-argo.org/page/132/data-access-and-data-use-policies-and-guidelines)

### Downloading ICGC data using score-client

1. Download [score-client](https://docs.icgc-argo.org/docs/data-access/data-download) and update the configuration file (**OpenJDk 11** is required for running score-client, e.g. `conda install -c conda-forge openjdk=11`)
2. Search and download the manifest file for ICGC controlled data via [ICGC Data Repositories](https://dcc.icgc.org/repositories)
3. An example for downloading data from **Collaboratory repository**: `score-client --profile collab download --manifest manifest.collaboratory.XXX.tsv --output-dir ./`

#### Administrator: `[e-mail]` ([Login](https://daco.icgc-argo.org/))

## NCBI Database of Genotypes and Phenotypes (dbGaP)


### Summary
* dbGap has collected the data from 1240 studies (e.g. GTEx) that have invetisgated the interaction of genotype and phenotype in Humans
* Only access to GTEx dataset has been granted, if you need access to other data please contact Zeng-san ([click here for a full list of studies](https://www.ncbi.nlm.nih.gov/gap/?db=gap&term=1[Is%20Top-Level%20Study]))
* dbGaP homepage: https://www.ncbi.nlm.nih.gov/gap
* Access Expiry Date: ==??==

### Application for Access

1. Contact Prof. Hamada, Uotani-san, and Zeng-san via Slack DM.
3. Get permission from Prof. Hamada.
4. Uotani-san will contact the university administrator to register you for the NIH eRA commons account.
5. Your will get two e-mail notifications for setting the password of your eRA commons account ==in 48 hours==.
6. After changing the password, please contact Zeng-san to approve your access to the dataset.
7. You will receive an email notification of approval being completed.

### Downloading controlled data using fasterq-dump

1. Download a dbGaP repository key (a .ngc file) from https://dbgap.ncbi.nlm.nih.gov/ (log in with your eRA commons account)
2. Download, install and configure sra-tools (see https://github.com/ncbi/sra-tools).
3. Search SRR accessions from https://trace.ncbi.nlm.nih.gov/Traces/study/?dbgap_project=32040&o=acc_s%3Aa
4. An example for downloading a controlled dbGaP data: `fasterq-dump SRR1068687 --ngc prj_32040_D33382.ngc`

#### Administrator: `HAMADALAB` ([Login](https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login&login=NFL)) ※Registered Email: [e-mail]

## Repbase


### Summary

* Repbase is the most commonly used database of repetitive DNA elements
* Repbase homepage: https://www.girinst.org/repbase/
* Access Expiry Date: ==2023-10-31==

### Data Access

The subsciption content can be accessed through Wasada University network, which means that your IP address should be `133.9.*.*`

The version downloaded on 2023-10-19 can be accessed from the following link:
https://waseda.box.com/s/v337je0j4oy6kb5k2ig7qbjmcex20yhx

###### tags: `浜田研`