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Definition

Data derived from the sequencing of miRNA are one of the sources of gene expression data collected by TCGA. 

Data Overview

Platforms Covered in miRNASeq

  • Platform Code - used in archive names.
  • Platform Alias - used to group similar platforms and used in some applications to save space when referring to platforms.
  • Platform Name - full name of platform
  • Available - indicates whether data is available at the DCC for a platform
  • HTTP Display - indicates the directory name data will be deposited in the HTTP directory structure

Platform Code

Platform Alias

Platform Name

Available

Example

FTP Display

IlluminaGA_miRNASeq

IlluminaGA_miRNASeq

Illumina Genome Analyzer miRNA Sequencing

Yes

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
illuminaga_mirnaseq/mirnaseq/

IlluminaHiSeq_miRNASeq

IlluminaHiSeq_miRNASeq

Illumina HiSeq 2000 miRNA Sequencing

Yes

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<domain>/
illuminahiseq_mirnaseq/mirnaseq/

  • Platform Code - used in archive names.
  • Data Level - The TCGA data level (1-3)
  • File Type - The file extension and content type
  • Description - The scientific content of the file

Platform Code

Data Level

File Type

Description

IlluminaGA_miRNASeq

Level 3

Tab-delimited ASCII Text

  1. .isoform.quantification.txt
  2. .mirna.quantification.txt

 

  1. The calculated expression for all reads aligning to a particular miRNA.
  2. The calculated expression for each individual miRNA sequence isoform observed.

IlluminaHiSeq_miRNASeq

Level 3

Tab-delimited ASCII Text

  1. .isoform.quantification.txt
  2. .mirna.quantification.txt

 

  1. The calculated expression for all reads aligning to a particular miRNA.
  2. The calculated expression for each individual miRNA sequence isoform observed.

Specific Validations

Level 3 data

miRNASeq

The table below lists the specific QCLive Java software components (class files) for miRNASeq data file validation.

Component Name

Validates Data File Type

Description

MiRNASeqDataFileValidator

miRNASeq - All

Performs common validation across all miRNASeq data file types

MiRNASeqFileValidator

miRNASeq - miRNASeq

Performs validation of miRNASeq data files

MiRNASeqIsoformFileValidator

miRNASeq - Isoform

Performs validation of miRNASeq Isoform specific data files

The specific miRNASeq data file input types that are validated by the miRNASeq Java software components are listed below.


Note: The MiRNASeqDataFileValidator is omitted from the list, but applies to all miRNASeq data files.

Data Type

Filename Format

File Format

Validators

miRNA

<domain>.<TCGA aliquot barcode/UUID>.<center_token>.<index_integer> .mirna.quantification.txt

Tab delimited ASCII text

MiRNASeqFileValidator

Isoform

<domain>.<TCGA aliquot barcode/UUID>.<center_token>.<index_integer>.isoform.quantification.txt

Tab delimited ASCII text

MiRNASeqIsoformFileValidator

  • <domain> refers to the submitting institutes internet domain. For example, broad.edu or bcgsc.ca
  • <center_token> refers to an identifier that individual institutions may use for internal purposes. In general these are not TCGA identifiers.

miRNA Validation Rules

MiRNASeqDataFileValidator

Name

Location
/Type

Validation
Rules

Example

barcode
(aliquot)

Filename:
barcode

Validates
that the
barcode
part of all
RNASeq data
file names
has a valid
aliquot
barcode
format

  • TCGA-AB-2811-03B-01T-0760-13.isoform.quantification.txt
  • TCGA-AB-2811-03B-01T-0760-13.mirna.quantification.txt

-miRNA_ID
-read_count
-*reads_per_
million_miRNA_
mapped*
-cross-mapped

File
Content:
Column
Header

Validates
the following
for each:

  • column header
    exists and matches
    the expected column
    header name
  • rows have data
    corresponding to
    the column header

Example File

miRNA_ID:
value

File
Content:
Column
Value

Validates
that the value matches
the regular expression:

^[a-zA-Z0-9._-]+$

Example: hsa-let-7a-1

Example File 

read_count:
value

File
Content:
Column
Value

Validates
that the value
represents a
non-negative
integer

Example File 

-*reads_per
million
miRNA_mapped*
:value

File
Content:
Column
Value

Validates
that the value
represents a non-
negative
floating
point number

Example File 

cross-
mapped:value

File
Content:
Column
Value

Validates
that the value
represents
single character
'Y' (yes) or 'N'
(No). Must be
uppercase.

Example File 


MiRNASeqFileValidator

The validation rules for this component are identical to the MiRNASeqDataFileValidator validation rules defined in the previous section.
MiRNASeqIsoformFileValidator

Name

Location/
Type

Validation
Rules

Example

isoform_
coords
miRNA_region

File Content:
Column Header

Performs
the same
validation
as the
MiRNASeqDataFileValidator
for "File Content:Column
Header" types with
the addition of the
"isoform_coords" and
"miRNA_region" columns

Example File

isoform_
coords:
value

File Content:
Column Value

Validates that
value is in the format:

{genome_build}:
{chrom_id}:
{coords}:
{strand}

where:

{genome_build} =
regular expression:
^[a-zA-Z0-9._-]+$
(e.g. "hg19")

{chrom_id} =
regular expression:
^[a-zA-Z0-9._-]+$ (e.g. "9")

{coord} =
set of non-negative
integers separated
by a dash '-' (e.g.
"96938242-96938263")

{strand} =
single character
that is either '+' (plus) or '-'
(minus)

Example File

miRNA_
region:
value

File Content:
Column Value

Validates
that the value
is in the format:

{annotation},
{mimat_acc_number}

where

{annotation} =
regular expression:
^mature | star | stemloop | precursor
| unannotated$ (e.g. "mature")

{mimat_acc_number} =
regular expression: ^MIMAT[0-9]+$
(e.g. "MIMAT0000062")

Example File

Standard Archive Validations

All  miRNASeq data are processed using a standard set of validations. Data from miRNA Sequencing follow the GCC route.

The validation sets run on all miRNASeq data are listed below:

Standard MAGE-TAB File Validations

This data group includes MAGE-TAB archives and documents. All MAGE-TAB archive validations are covered under Standard Archive Validations. All MAGE-TAB documents submitted to the DCC are processed using a standard set of validations.

Standard Result File Validations

MAGE-TAB Data Matrix file

MAGE-TAB Data Matrix format validations are covered in Standard MAGE-TAB File Validations.

Level 2 data 

There will be no Level 2 data associated with miRNASeq

Document Information

Specification for RNASeq Data Format
Version 1.0
March 24, 2011

miRNASeq Data Archives Specification

Synopsis

miRNASeq data contains information about both nucleotide sequence and expression. The CGHUB database Exit Disclaimer logo replaces the NCBI dbGaP database as the official repository for the actual sequence data, produced in the form of BAM files. miRNASeq data archives submitted to the DCC include expression information that is inferred from the sequence data. miRNASeq submissions also include MAGE-TAB Exit Disclaimer logo archives, with some non-standard modification to MAGE-TAB format. These archives contain files that describe the RNASeq experiment and the relationship between the experimental samples and the data files produced by assaying those samples.

This specification covers the validation and disposition of miRNASeq submissions to the DCC. The DCC currently accepts only level 3 (expression and coverage) and MAGE-TAB archives.

 
 

Design

Centers

We expect to receive miRNASeq data from

  • Canada's Michael Smith Genome Sciences Centre (bcgsc.ca)

Data Types and Data Levels

model as described in the text

This image models the data types and data levels we expect to get for RNASeq data. Red rectangles indicate Data Types. Blue rectangles indicate Data Levels. Data Types for RNASeq are on the left and miRNASeq are on the right.

Data Levels

Level 0 (not a real level in the DCC's DB right now) are reserved for Annotation Files. Annotation files are in the Generic Annotation File (GAF) format. The GAF files used for a particular experiment is listed in that experiment's SDRF file under the column "Annotaiton REF". The GAF files and their specification is listed in that column are stored at http://tcga-data.nci.nih.gov/docs/GAF/.

We do not intend on receiving actual Level 1 (BAM) files. In the past, these files are submitted to dbGaP, however starting in March 2012, CGHub Exit Disclaimer logo will be the official repository and we will have telemetry on BAM files based on the metadata available at CGHub.

We are currently receiving Level 3 data.

Data Level monikers do not include the words "file" or "files" as depicted in the image.

Data Types

Annotations

Annotations are a data type reserved for metadata about biospecimens (e.g. annotations available in the Annotations Manager), or genomic mappings (i.e. coordinates of a probe/sequence read map to a transcript that maps to a genomic region; e.g. Platform Design Files (ADFs)). For miRNASeq we are concerned with Generic Annotation Files (GAFs).

Alignments

miRNASeq read sequences are aligned to a target (i.e. transcript or miRNA) database. The alignments take the form of a BAM files (Level 1).

Expression-miRNA

The calculated expression for all reads aligning to a particular miRNA. The calculations are described in the DESCRIPTION.txt file in the mage-tab archive of an experiment. RNA/miRNA Sequence-based data have a data type alias of Quantification-miRNA.

Expression-miRNA Isoform

The calculated expression for each individual miRNA sequence isoform observed. The calculations are described in the DESCRIPTION.txt file in the mage-tab archive of an experiment. RNA/miRNA Sequence-based data have a data type alias of Quantification-miRNA Isoform.

Archive structure

There are two archives for RNA-seq submissions: the data archive and the MAGE-TAB (metadata) archive. Naming conventions are similar to typical archives.

<domain>_<disease_abbrev>.<platform>.Level_3.<index>.<revision>.<series>
<domain>_<disease_abbrev>.<platform>.mage-tab.1.<revision>.<series>

bcgsc.ca_COAD.IlluminaGA_miRNASeq.Level_3.1.0.0
bcgsc.ca_COAD.IlluminaGA_miRNASeq.mage-tab.1.0.0
  • Archives are gzipped tars
  • Archives are flat, below a directory named after the archive
  • Archives contain a MANIFEST.txt file; each file in the archive (will the optional exception of the MANIFEST.txt file) will be represented in the MANIFEST.txt as the output of md5sum run against the file.

Archive files

Data archives

In addition to the MANIFEST.txt file, a complete RNASeq data archive contains

  • exon, gene, and splice junction data files for each aliquot(required)
  • a single DESCRIPTION.txt file (optional)

Expression in miRNASeq archives is considered Level 3 data.

miRNASeq submissions also include separate MAGE-TAB archives, which contain files that describe the miRNASeq experiment and the relationship between the experimental samples and the data files produced by assaying those samples.

Data files

Data file names

Data file names within the Level 3 archives contain the TCGA barcode for the aliquot associated with the data. Names may also include center-specific id tokens, separated by periods. Center tokens are not required, they may consist of the following characters : [a-zA-Z0-9_-]. Extensions indicate the RNASeq data type:

Data type

File name

Validation

miRNA

<center_token>.<TCGA barcode/UUID>.<center_token>.<index_integer>.mirna.quantification.txt

Filename must end with "mirna.quantification.txt"

Isoform

<center_token>.<TCGA barcode/UUID>.<center_token>.<index_integer>.isoform.quantification.txt

Filename must end with "isoform.quantification.txt"

Data file formats

All files are tab-delimited text, header line plus one record per line.

miRNA file records have the following fields in this order: miRNA_ID, read_count, reads_per_million_miRNA_mapped, cross-mapped.
Isoform file records have the following fields in this order: miRNA_ID, isoform_coords, read_count, reads_per_million_miRNA_mapped, cross-mapped, miRNA_region.

Note: RPKM stands for Reads Per Kilobase exon Model per million mapped reads (Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Nature Methods, 2008 Jul;5(7):621-8. Epub 2008 May 30 Exit Disclaimer logo )

Data field formats:

The following table describes the content of data fields:

Field

Description

miRNA_ID

valid miRBASE ID Exit Disclaimer logo

read_count

raw read count

reads_per_million_miRNA_mapped

reads per million miRNA reads

cross-mapped

cross-mapped to other miRNA forms (Y or N)

isoform_coords

alignment coordinates as <version>:<Chromosome>:<Start position>-<End position>:<Strand>

miRNA_region

region within miRNA

Examples

miRNA file:

TCGA-A1-A0SE-01A-11R-A085-13.mirna.quantification.txt

miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
hsa-let-7a-1	19969	6540.858831	N
hsa-let-7a-2	39866	13058.134016	Y
hsa-let-7a-3	19954	6535.945572	N
hsa-let-7b	154622	50646.535841	N
hsa-let-7c	14300	4683.974224	Y
hsa-let-7d	1239	405.835249	N
hsa-let-7e	2684	879.145931	N
hsa-let-7f-1	28	9.171418	N
hsa-let-7f-2	11774	3856.581295	N
hsa-let-7g	1171	383.561805	N
hsa-let-7i	2091	684.908399	N
hsa-mir-1-1	0	0.000000	N
hsa-mir-1-2	26	8.516317	N

Isoform file:

TCGA-A1-A0SE-01A-11R-A085-13.isoform.quantification.txt

miRNA_ID	isoform_coords	read_count	reads_per_million_miRNA_mapped	cross-mapped	miRNA_region
hsa-let-7a-1	hg19:9:96938242-96938263:+	4	1.310203	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938242-96938265:+	4	1.310203	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938243-96938261:+	1	0.327551	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938243-96938263:+	8	2.620405	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938243-96938264:+	7	2.292855	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938243-96938265:+	6	1.965304	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938243-96938266:+	1	0.327551	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938244-96938263:+	5293	1733.725564	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938244-96938264:+	5903	1933.531458	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938244-96938265:+	7602	2490.040004	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938244-96938266:+	961	314.776170	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938244-96938267:+	7	2.292855	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938245-96938263:+	11	3.603057	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938245-96938264:+	16	5.240810	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938245-96938265:+	35	11.464273	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938245-96938266:+	4	1.310203	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938247-96938264:+	2	0.655101	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938247-96938265:+	17	5.568361	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938247-96938266:+	3	0.982652	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938248-96938265:+	2	0.655101	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938248-96938266:+	2	0.655101	N	mature,MIMAT0000062
hsa-let-7a-1	hg19:9:96938249-96938270:+	1	0.327551	N	mature,MIMAT0000062

MAGE-TAB archives

In addition to the MANIFEST.txt file, RNASeq MAGE-TAG archives contain

  • a DESCRIPTION.txt file
  • an IDF
  • an SDRF

MAGE-TAB files

MAGE-TAB file names

<domain>_<disease_abbrev>.<platform>_miRNASeq.<index>.<revision>.<series>.idf.txt
<domain>_<disease_abbrev>.<platform>_miRNASeq.<index>.<revision>.<series>.sdrf.txt

MAGE-TAB file formats

All files are tab-delimited text.

Investigation Description File (IDF)

The IDF can be considered as a set of tables that can have variable numbers of rows and columns. The first field in a IDF line is a row header, while subsequent fields are data items corresponding to the row header. Adjacent row lines represent a table. Data items falling in the same column with in tables are related (i.e., columns can be considered records).

Valid row headers in order are as follows (field values are explained in the next section):

Row Headers

Investigation Title

Experimental Design

Experimental Design Term Source REF

Experimental Factor Type

Experimental Factor Type Term Source REF

Person Last Name

Person First Name

Person Mid Initials

Person Email

Person Phone

Person Address

Person Affiliation

Person Roles

Date of Experiment

Public Release Date

Experiment Description

Protocol Name

Protocol Type

Protocol Term Source REF

Protocol Description

Protocol Parameters

SDRF Files

Term Source Name

Term Source File

Term Source Version

Sample-Data Relationship File (SDRF)

SDRFs have a single header line, followed by records, one record per line.

Valid headers in order are as follows (field values are explained in the next section):

Headers

Extract Name

Comment [TCGA Barcode]

Material Type

Protocol REF

Assay Name

Protocol REF

Assay Name

Protocol REF

Assay Name

Comment [NCBI SRA Experiment Accession]

Annotation REF

Protocol REF

Data Transformation Name

Derived Data File REF

Comment [Genome reference]

Comment [NCBI dbGAP Experiment Accession]

Comment [TCGA Include for Analysis]

Comment [TCGA Data Type]

Comment [TCGA Data Level]

Protocol REF

Data Transformation Name

Derived Data File

Comment [TCGA Include for Analysis]

Comment [TCGA Data Type]

Comment [TCGA Data Level]

Comment [TCGA Archive Name]

Admissible values for the corresponding fields (in the record lines) are given in the next section.

Metadata (MAGE-TAB) field formats

Investigation Description File (IDF)

IDF field description:

Field (row header)

Description

Investigation Title

free text title of study

Experimental Design

standard design terms

Experimental Design Term Source REF

ontological source of terms on previous line

Experimental Factor Type

standard experimental factor terms

Experimental Factor Type Term Source REF

ontological source of terms on previous line

Contact Info 

Person Last Name

list of surnames

Person First Name

list of first names

Person Mid Initials

list of MIs

Person Email

list of emails

Person Phone

list of phone numbers

Person Address

list of mailing addresses

Person Affiliation

list of affiliations

Person Roles

list of roles

Experiment Description 

Date of Experiment

date in YYYYMMDD format

Public Release Date

date in YYYYMMDD format

Experiment Description

free text description (no tabs or linebreaks)

Protocol Name

tokens serving as references in the SDRF

Protocol Type

list of standard protocol types

Protocol Term Source REF

list of ontological sources of protocol types

Protocol Description

list of free text descriptions (no tabs or linebreaks)

Protocol Parameters

list of <tag>=<value> pairs describing experimental parameters

SDRF Files

The SDRF filename, present in the submitted mage-tab archive

Term Source Name

list of ontological sources in above REF fields

Term Source File

list of urls describing the location of ontological source files

Term Source Version

list of version numbers for ontological sources

IDF example:

Investigation Title	miRNA Analysis of TCGA BRCA Samples using Illumina GAIIx
Experimental Design	transcript_identification_design	is_expressed_design
Experimental Design Term Source REF	MGED Ontology	MGED Ontology
Experimental Factor Name	tumor type
Experimental Factor Type	disease_state_design
Experimental Factor Type Term Source REF	MGED Ontology

Person Last Name	Marra	Mungall	Chu
Person First Name	Marco	Andrew	Andy
Person Mid Initials
Person Email	mmarra@bcgsc.ca	amungall@bcgsc.ca	achu@bcgsc.ca
Person Phone	604-707-5900 extn 67-6082	604-675-8000 extn 66-7937
Person Address	"100-570 W 7th Ave, Vancouver, BC, V5Z 4S6, Canada"	"675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada"	"100-570 W 7th Ave, Vancouver, BC, V5Z 4S6, Canada"
Person Affiliation	"Genome Sciences Centre, BCCA"	"Genome Sciences Centre, BCCA"	"Genome Sciences Centre, BCCA"
Person Roles	investigator	investigator	submitter

Date of Experiment	2011-06-21
Public Release Date	2011-07-31

Experiment Description	miRNA Analysis of TCGA BRCA Samples using Illumina GAIIx
Protocol Name	bcgsc.ca:reverse_transcription:IlluminaGA_miRNASeq:01	bcgsc.ca:library_preparation:IlluminaGA_miRNASeq:01	bcgsc.ca:DNA_Sequencing:IlluminaGA_miRNASeq:01	bcgsc.ca:alignment:IlluminaGA_miRNASeq:01	bcgsc.ca:gene_expression:IlluminaGA_miRNASeq:01	bcgsc.ca:gene_expression:IlluminaGA_miRNASeq:01
Protocol Type	reverse_transcription	library_preparation	DNA sequencing	consensus_mRNA	gene_expression	gene_expression
Protocol Type	Term Source REF	MGED Ontology	NCI EVS	NCI EVS	MGED Ontology	MGED Ontology	MGED Ontology
Protocol Description	Ligation of linkers and reverse transcription of small RNAs	"PCR with sequencing primers, size fractionation"	Sequencing on Illumina GAIIx	Alignment of reads to reference genome	Read counts per mirna isoform	Normalized expression per mirna gene

SDRF Files	bcgsc.ca_BRCA.IlluminaGA_miRNASeq.sdrf.txt

Term Source Name	MGED Ontology	NCI EVS
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://evs.nci.nih.gov/
Term Source Version	1.3.1.1	2010-09
Sample-Data Relationship File (SDRF)

Each line in an SDRF describes an aliquot, the processes performed on the aliquot to obtain data, and the files created which contain data related to the aliquot. Columns named Protocol REF contain values referring to content in the IDF. Columns names Derived Data File contain file name values; the files referenced are present in the accompanying data archive.

SDRF field description:

Field

Description

Extract Name

TCGA UUID

Comment [TCGA Barcode]

TCGA Barcode

Material Type

always "Total RNA"

 

Protocol REF

token referring to IDF description

Assay Name

unique identifier that included aliquot barcode or uuid

Comment [NCBI SRA Experiment Accession]

null ( -> ) or SRX accession number

Annotation REF

url pointing to an annotation table file (e.g., GAF)

Data Transformation Name

token referring to an IDF description of a data transformation

Derived Data File REF

file in the data archive that is the product of the adjacent data transformation

Comment [Genome reference]

common name of the reference genome employed

Comment [NCBI dbGAP Experiment Accession]

null ( -> ) or dbGaP accession, e.g. phs000178.v3.p3

Comment [TCGA Include for Analysis]

yes|no QC indicator

 

Comment [TCGA Data Type]

DCC data type identifier

Comment [TCGA Data Level]

Level 1 or Level 3 as appropriate

Comment [TCGA Archive Name]

valid DCC archive name (without .tar.gz extension)

SDRF example:

Extract Name	Comment [TCGA Barcode]	Material Type	Protocol REF	Assay Name	Protocol REF	Assay Name	Protocol REF	Assay Name	Comment [NCBI SRA Experiment Accession]	Annotation REF	Protocol REF	Data Transformation Name	Derived Data File REF	Comment [Genome reference]	Comment [NCBI dbGAP Experiment Accession]	Comment [TCGA Include for Analysis]	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Protocol REF	Data Transformation Name	Derived Data File	Comment [TCGA Include for Analysis]	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA Archive Name]
E9E5B206-5F22-43C5-8D26-E5D53FBE20A3	TCGA-BJ-A28S-01A-11R-A19N-13	Total RNA	bcgsc.ca:reverse_transcription:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_reverse_transcription	bcgsc.ca:library_preparation:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_library_preparation	bcgsc.ca:miRNA_Sequencing:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_miRNA_Sequencing	->	http://tcga-data.nci.nih.gov/docs/integration/adfs/tcga/tcga_mirna_bcgsc_hg19.adf.gz	bcgsc.ca:alignment:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_alignment	TCGA-BJ-A28S-01A-11R-A19N-13_mirna.bam	GRCh37-lite	->	yes	RNA Sequence-Alignment	Level 1	bcgsc.ca:miR_isoform_expression:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_miR_isoform_expression	TCGA-BJ-A28S-01A-11R-A19N-13.isoform.quantification.txt	yes	Expression-miRNA Isoform	Level 3	bcgsc.ca_THCA.IlluminaHiSeq_miRNASeq.Level_3.1.3.0
E9E5B206-5F22-43C5-8D26-E5D53FBE20A3	TCGA-BJ-A28S-01A-11R-A19N-13	Total RNA	bcgsc.ca:reverse_transcription:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_reverse_transcription	bcgsc.ca:library_preparation:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_library_preparation	bcgsc.ca:miRNA_Sequencing:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_miRNA_Sequencing	->	http://tcga-data.nci.nih.gov/docs/integration/adfs/tcga/tcga_mirna_bcgsc_hg19.adf.gz	bcgsc.ca:alignment:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_alignment	TCGA-BJ-A28S-01A-11R-A19N-13_mirna.bam	GRCh37-lite	->	yes	RNA Sequence-Alignment	Level 1	bcgsc.ca:miR_gene_expression:IlluminaHiSeq_miRNASeq:01	E9E5B206-5F22-43C5-8D26-E5D53FBE20A3_miR_gene_expression	TCGA-BJ-A28S-01A-11R-A19N-13.mirna.quantification.txt	yes	Expression-miRNA	Level 3	bcgsc.ca_THCA.IlluminaHiSeq_miRNASeq.Level_3.1.3.0
6F5E5543-829B-4FFA-B133-26DB6117699C	TCGA-BJ-A28V-01A-11R-A19N-13	Total RNA	bcgsc.ca:reverse_transcription:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_reverse_transcription	bcgsc.ca:library_preparation:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_library_preparation	bcgsc.ca:miRNA_Sequencing:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_miRNA_Sequencing	->	http://tcga-data.nci.nih.gov/docs/integration/adfs/tcga/tcga_mirna_bcgsc_hg19.adf.gz	bcgsc.ca:alignment:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_alignment	TCGA-BJ-A28V-01A-11R-A19N-13_mirna.bam	GRCh37-lite	->	yes	RNA Sequence-Alignment	Level 1	bcgsc.ca:miR_isoform_expression:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_miR_isoform_expression	TCGA-BJ-A28V-01A-11R-A19N-13.isoform.quantification.txt	yes	Expression-miRNA Isoform	Level 3	bcgsc.ca_THCA.IlluminaHiSeq_miRNASeq.Level_3.1.3.0
6F5E5543-829B-4FFA-B133-26DB6117699C	TCGA-BJ-A28V-01A-11R-A19N-13	Total RNA	bcgsc.ca:reverse_transcription:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_reverse_transcription	bcgsc.ca:library_preparation:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_library_preparation	bcgsc.ca:miRNA_Sequencing:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_miRNA_Sequencing	->	http://tcga-data.nci.nih.gov/docs/integration/adfs/tcga/tcga_mirna_bcgsc_hg19.adf.gz	bcgsc.ca:alignment:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_alignment	TCGA-BJ-A28V-01A-11R-A19N-13_mirna.bam	GRCh37-lite	->	yes	RNA Sequence-Alignment	Level 1	bcgsc.ca:miR_gene_expression:IlluminaHiSeq_miRNASeq:01	6F5E5543-829B-4FFA-B133-26DB6117699C_miR_gene_expression	TCGA-BJ-A28V-01A-11R-A19N-13.mirna.quantification.txt	yes	Expression-miRNA	Level 3	bcgsc.ca_THCA.IlluminaHiSeq_miRNASeq.Level_3.1.3.0
7E6CC5EC-69CD-441D-8961-7C87FE766BB9	TCGA-BJ-A290-01A-11R-A17X-13	Total RNA	bcgsc.ca:reverse_transcription:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_reverse_transcription	bcgsc.ca:library_preparation:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_library_preparation	bcgsc.ca:miRNA_Sequencing:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_miRNA_Sequencing	->	http://tcga-data.nci.nih.gov/docs/integration/adfs/tcga/tcga_mirna_bcgsc_hg19.adf.gz	bcgsc.ca:alignment:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_alignment	TCGA-BJ-A290-01A-11R-A17X-13_mirna.bam	GRCh37-lite	->	yes	RNA Sequence-Alignment	Level 1	bcgsc.ca:miR_isoform_expression:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_miR_isoform_expression	TCGA-BJ-A290-01A-11R-A17X-13.isoform.quantification.txt	yes	Expression-miRNA Isoform	Level 3	bcgsc.ca_THCA.IlluminaHiSeq_miRNASeq.Level_3.1.3.0
7E6CC5EC-69CD-441D-8961-7C87FE766BB9	TCGA-BJ-A290-01A-11R-A17X-13	Total RNA	bcgsc.ca:reverse_transcription:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_reverse_transcription	bcgsc.ca:library_preparation:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_library_preparation	bcgsc.ca:miRNA_Sequencing:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_miRNA_Sequencing	->	http://tcga-data.nci.nih.gov/docs/integration/adfs/tcga/tcga_mirna_bcgsc_hg19.adf.gz	bcgsc.ca:alignment:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_alignment	TCGA-BJ-A290-01A-11R-A17X-13_mirna.bam	GRCh37-lite	->	yes	RNA Sequence-Alignment	Level 1	bcgsc.ca:miR_gene_expression:IlluminaHiSeq_miRNASeq:01	7E6CC5EC-69CD-441D-8961-7C87FE766BB9_miR_gene_expression	TCGA-BJ-A290-01A-11R-A17X-13.mirna.quantification.txt	yes	Expression-miRNA	Level 3	bcgsc.ca_THCA.IlluminaHiSeq_miRNASeq.Level_3.1.3.0
21E9567D-4DF4-4A04-994A-40222147F28C	TCGA-BJ-A290-11A-11R-A17X-13	Total RNA	bcgsc.ca:reverse_transcription:IlluminaHiSeq_miRNASeq:01	21E9567D-4DF4-4A04-994A-40222147F28C_reverse_transcription	bcgsc.ca:library_preparation:IlluminaHiSeq_miRNASeq:01	21E9567D-4DF4-4A04-994A-40222147F28C_library_preparation	bcgsc.ca:miRNA_Sequencing:IlluminaHiSeq_miRNASeq:01	21E9567D-4DF4-4A04-994A-40222147F28C_miRNA_Sequencing	->	http://tcga-data.nci.nih.gov/docs/integration/adfs/tcga/tcga_mirna_bcgsc_hg19.adf.gz	bcgsc.ca:alignment:IlluminaHiSeq_miRNASeq:01	21E9567D-4DF4-4A04-994A-40222147F28C_alignment	TCGA-BJ-A290-11A-11R-A17X-13_mirna.bam	GRCh37-lite	->	yes	RNA Sequence-Alignment	Level 1	bcgsc.ca:miR_isoform_expression:IlluminaHiSeq_miRNASeq:01	21E9567D-4DF4-4A04-994A-40222147F28C_miR_isoform_expression	TCGA-BJ-A290-11A-11R-A17X-13.isoform.quantification.txt	yes	Expression-miRNA Isoform	Level 3	bcgsc.ca_THCA.IlluminaHiSeq_miRNASeq.Level_3.1.3.0
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