05. RNASeq and miRNASeq Data

There are three tables in tranSMART for NGS data, two for RNA Sequencing data and one for miRNA Sequencing data. One of the RNASeq Data Tables is intended for loading raw read count observation data which can be used with Group Test for RNASeq Advanced Workflow. R package behind this workflow (EdgeR) includes normalization step. I believe this RNASeq special case data loading is not part of the original set of HDD data developed by Sanofi. Perhaps this was developed for a customer and then contributed by Hyve. At this time, tMDataLoader does not have a specific procedure to load RNASeq data in a raw read count observation format. All other Analysis Workflows require pre-normalized RNASeq data (RPKM, FPKM, TPM, etc.) which is loaded similar to Expression data. Even though there is a special table for miRNA sequencing data, it can also be loaded as RNASeq. This is mostly a matter of preference for standard IDs. For RNASeq data “probes” which in this case are transcript IDs are mapped to Standard Gene Symbols. For miRNA sequencing data miRBase symbols are used as standard IDs.

Normalized RNASeq Data Loading Instruction

RNASeq Data (sample)

RNASeq Data is loaded from the RNASeqDataToUpload Directory similar to the Expression Data. For more details see “Expression Data”

RNASeq Data File

TranscriptID	S57023	S57024
NM_001011874	0	0.0093
NM_001195662	0.0384	0.051

Data Types

The last symbol in data file name (before extension) is one of following letters:
R - raw data. Values are loaded into Value column. Raw values are transformed to calculate log2 value and z-score. log2 values are loaded into Log values column
L - log2 data. Values are loaded into Log value column, raw values are restored and loaded into Value column. z-score is calculated.
T and Z - z-score data. Has same meaning, value will be written to z-score without modifications if it in range of (-2.5; 2.5). It will be truncated to this range otherwise.

NOTE: if data is loaded as R, 0.001 is added to all values before log2 transformation to avoid dropping 0 values (0 can't be log transformed). Normalized Raw RNA Seq data are not expected to have any negative values.

RNASeq Platform File

#PLATFORM_ID: RNASeq999 #PLATFORM_TITLE: Test RNASeq Platform #SPECIES: Homo Sapiens

Transcript ID	Gene Symbol	Organism
NM_001011874	MEF2C	Homo sapiens
NM_001195662	ALDH8A1	Homo sapiens
NM_011283	MEF2A	Homo sapiens
NM_011441	MEF2C	Homo sapiens

RNASeq Subject Sample Mapping File

STUDY_ID	SITE_ID	SUBJECT_ID	SAMPLE_ID	PLATFORM	TISSUETYPE	ATTR1	ATTR2	CATEGORY_CD	SOURCE_CD
GSE_A_37424	0	1	S57023	RNASeq999	Intestine			Biomarker_Data+PLATFORM+TISSUETYPE	STD

#Normalized miRNASeq Data Loading Instruction

RNASeq Data is loaded from the MIRNA_SEQDataToUpload Directory similar to Expression Data. For more details see “Expression Data”.

miRNASeq Data (sample)

miRNASeq Data File

ID_REF	GSM918942	GSM918943	GSM918944	GSM918945	GSM918946	GSM918947	GSM918948	GSM918949
1	0.002908561	0.004549935	0.021626957	0.015697885	0.005178485	0.00498247	0.005311656	0.010319512
2	0.01039278	0.010017933	0.038167632	0.040012373	0.010484615	0.010744884	0.011629359	0.023468306
3	0.006034899	0.010552801	0.035375773	0.027333613	0.007408354	0.00969822	0.0095548	0.015315651

Data Types

The last symbol in data file name (before extension) is one of following letters:
R - raw data. Values are loaded into Value column. Raw values are transformed to calculate log2 value and z-score. log2 values are loaded into Log values column
L - log2 data. Values are loaded into Log value column, raw values are restored and loaded into Value column. z-score is calculated.
T and Z - z-score data. Has same meaning, value will be written to z-score without modifications if it in range of (-2.5; 2.5). It will be truncated to this range otherwise.

NOTE: if data is loaded as R, 0.001 is added to all values before log2 transformation to avoid dropping 0 values (0 can't be log transformed). Normalized miRNA Seq Raw data are not expected to have any negative values.

miRNASeq Platform File

#PLATFORM_ID: GPL15467seqbased #PLATFORM_TITLE: Test MIRNAseq Platform #SPECIES: Homo Sapiens

ID_REF	MIRNA_ID	SN_ID	PLT_NAME	ORGANISM
1	hsa-miR-1		GPL15467seqbased	Homo Sapiens
2	hsa-miR-9		GPL15467seqbased	Homo Sapiens
3	hsa-miR-10a		GPL15467seqbased	Homo Sapiens

miRNASeq Subject Sample Mapping File

STUDY_ID	SITE_ID	SUBJECT_ID	SAMPLE_CD	PLATFORM	TISSUETYPE	ATTRITBUTE_1	ATTRITBUTE_2	CATEGORY_CD	SOURCE_CD
mirnaseqbased		GSM918942	GSM918942	GPL15467seqbased	Human	Synovium		Biomarker_Data+PLATFORM+ATTR1	STD