Rice MPSS: Data Download

Rice MPSS data files may be obtained by clicking on the links below to download the respective files.

mRNA Summary Data Tables

These two tables contain the normalized expression levels in "TPM" (transcripts per million), for either the 17 or 20 base MPSS signatures. The normalization procedure is described in more detail in a paper published in Genome Research (Meyers et al., 2004) When these signatures have been matched uniquely (hits = 1) to the genome, the location is indicated, based on the TIGR annotation (version 4.0). The summary table is described in more detail in a paper published in Plant Physiology (Meyers et al., 2004). These data will be the most useful for whole-genome analyses that require the processed MPSS data. All of the data are described in Nature Biotechnology (Nobuta et al., 2007). Additional libraries are in preparation.

17bp signature data: 17bp_summary.txt (gzip)
20bp signature data: 20bp_summary.txt (gzip)

Library-Specific Summary Files

NYR Library	17bp_NYR.txt	20bp_NYR.txt
NR2 Library	17bp_NR2.txt	20bp_NR2.txt
NGD Library	17bp_NGD.txt	20bp_NGD.txt
NST Library	17bp_NST.txt	20bp_NST.txt
NYL Library	17bp_NYL.txt	20bp_NYL.txt
NL4 Library	17bp_NL4.txt	20bp_NL4.txt
NME Library	17bp_NME.txt	20bp_NME.txt
NPO Library	17bp_NPO.txt	20bp_NPO.txt
NOS Library	17bp_NOS.txt	20bp_NOS.txt
NIP Library	17bp_NIP.txt	20bp_NIP.txt
NGS Library	17bp_NGS.txt	20bp_NGS.txt
NCA Library	17bp_NCA.txt	20bp_NCA.txt
NSR Library	17bp_NSR.txt	20bp_NSR.txt
NSL Library	17bp_NSL.txt	20bp_NSL.txt
NDR Library	17bp_NDR.txt	20bp_NDR.txt
NDL Library	17bp_NDL.txt	20bp_NDL.txt
NCR Library	17bp_NCR.txt	20bp_NCR.txt
NCL Library	17bp_NCL.txt	20bp_NCL.txt

Note: "NRA" and "NRB" are combined as "NR2", and "NLA","NLB, "NLC" and "NLD" are combined as "NL4".

mRNA Raw MPSS Sequencing Runs - Data Tables

The first two files contain the raw abundance levels for each distinct signature and for either the 17- or 20-base MPSS data. The files consist of only the sequence and the abundance. These values are NOT normalized, and so the sum of the abundances is equal to the total number of successfully sequenced beads in each "flowcell". For more information, you may want to read the original MPSS paper by Brenner et al., 2000 (Nature Biotechnolgy). For the average user, this information will not be of much use.

17bp signatures - all runs (zip)
20bp signatures - all runs (zip)

Library-Specific Raw Run Files

NYR Library	NYR_raw17bp.txt	NYR_raw20bp.txt
NRA Library	NRA_raw17bp.txt	NRA_raw20bp.txt
NRB Library	NRB_raw17bp.txt	NRB_raw20bp.txt
NR2 Library	NR2_raw17bp.txt	NR2_raw20bp.txt
NGD Library	NGD_raw17bp.txt	NGD_raw20bp.txt
NST Library	NST_raw17bp.txt	NST_raw20bp.txt
NYL Library	NYL_raw17bp.txt	NYL_raw20bp.txt
NLA Library	NLA_raw17bp.txt	NLA_raw20bp.txt
NLB Library	NLB_raw17bp.txt	NLB_raw20bp.txt
NLC Library	NLC_raw17bp.txt	NLC_raw20bp.txt
NLD Library	NLD_raw17bp.txt	NLD_raw20bp.txt
NL4 Library	NL4_raw17bp.txt	NL4_raw20bp.txt
NME Library	NME_raw17bp.txt	NME_raw20bp.txt
NPO Library	NPO_raw17bp.txt	NPO_raw20bp.txt
NOS Library	NOS_raw17bp.txt	NOS_raw20bp.txt
NIP Library	NIP_raw17bp.txt	NIP_raw20bp.txt
NGS Library	NGS_raw17bp.txt	NGS_raw20bp.txt
NCA Library	NCA_raw17bp.txt	NCA_raw20bp.txt
NSR Library	NSR_raw17bp.txt	NSR_raw20bp.txt
NSL Library	NSL_raw17bp.txt	NSL_raw20bp.txt
NDR Library	NDR_raw17bp.txt	NDR_raw20bp.txt
NDL Library	NDL_raw17bp.txt	NDL_raw20bp.txt
NCR Library	NCR_raw17bp.txt	NCR_raw20bp.txt
NCL Library	NCL_raw17bp.txt	NCL_raw20bp.txt

Small RNA Summary Data Tables

These files contain the normalized expression levels in "TPQ" (transcripts per quarter million) for the 17 base MPSS signatures. The normalization procedure is identical to that described in Genome Research (Meyers et al., 2004), except that the smaller total numbers of signatures are better normalized to 250,000. The files include genomic information based on the TIGR annotation (version 4.0).

MPSS data: smallRNA_summary.txt (gzip)
MPSS data - only signatures matching to t/r/sno/snRNAs (those signatures are excluded from the file above): smallRNA_trsnosn_summary.txt (gzip)

Library-Specific Summary Files

STM Library	STM.txt
SNU Library	SNU.txt
FLR Library	FLR.txt
SNM Library	SNM.txt
ABA Library	ABA.txt
UNT Library	UNT.txt

Small RNA Raw Data Tables

The first file contains the raw abundance levels for each distinct signature and for the 17-base MPSS data. The file consists of only the sequence and the abundance. These values are NOT normalized, and so the sum of the abundances is equal to the total number of successfully sequenced "flowcell". For more information, please see our papers in Science (Lu et. al., 2005) and Nature Biotechnology (Nobuta et al., 2007).

MPSS all runs (zip)

Library-Specific Raw Run Files

STM Library	STM_raw.txt
SNU Library	SNU_raw.txt
FLR Library	FLR_raw.txt
SNM Library	SNM_raw.txt
ABA Library	ABA_raw.txt
UNT Library	UNT_raw.txt